Displaying publications 1 - 20 of 266 in total

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  1. Inherent differential propensity of dental pulp stem cells derived from human deciduous and permanent teeth
    Govindasamy V, Abdullah AN, Ronald VS, Musa S, Ab Aziz ZA, Zain RB, et al.
    J Endod, 2010 Sep;36(9):1504-15.
    PMID: 20728718 DOI: 10.1016/j.joen.2010.05.006
    Lately, several new stem cell sources and their effective isolation have been reported that claim to have potential for therapeutic applications. However, it is not yet clear which type of stem cell sources are most potent and best for targeted therapy. Lack of understanding of nature of these cells and their lineage-specific propensity might hinder their full potential. Therefore, understanding the gene expression profile that indicates their lineage-specific proclivity is fundamental to the development of successful cell-based therapies.
    Matched MeSH terms: Principal Component Analysis
  2. Fulltext Identification of Pathways Mediating Growth Differentiation Factor5-Induced Tenogenic Differentiation in Human Bone Marrow Stromal Cells
    Tan SL, Ahmad TS, Ng WM, Azlina AA, Azhar MM, Selvaratnam L, et al.
    PLoS One, 2015;10(11):e0140869.
    PMID: 26528540 DOI: 10.1371/journal.pone.0140869
    To date, the molecular signalling mechanisms which regulate growth factors-induced MSCs tenogenic differentiation remain largely unknown. Therefore, a study to determine the global gene expression profile of tenogenic differentiation in human bone marrow stromal cells (hMSCs) using growth differentiation factor 5 (GDF5) was conducted. Microarray analyses were conducted on hMSCs cultures supplemented with 100 ng/ml of GDF5 and compared to undifferentiated hMSCs and adult tenocytes. Results of QuantiGene® Plex assay support the use and interpretation of the inferred gene expression profiles and pathways information. From the 27,216 genes assessed, 873 genes (3.21% of the overall human transcriptome) were significantly altered during the tenogenic differentiation process (corrected p<0.05). The genes identified as potentially associated with tenogenic differentiation were ARHGAP29, CCL2, integrin alpha 8 and neurofilament medium polypeptides. These genes, were mainly associated with cytoskeleton reorganization (stress fibers formation) signaling. Pathway analysis demonstrated the potential molecular pathways involved in tenogenic differentiation were: cytoskeleton reorganization related i.e. keratin filament signaling and activin A signaling; cell adhesion related i.e. chemokine and adhesion signaling; and extracellular matrix related i.e. arachidonic acid production signaling. Further investigation using atomic force microscopy and confocal laser scanning microscopy demonstrated apparent cytoskeleton reorganization in GDF5-induced hMSCs suggesting that cytoskeleton reorganization signaling is an important event involved in tenogenic differentiation. Besides, a reduced nucleostemin expression observed suggested a lower cell proliferation rate in hMSCs undergoing tenogenic differentiation. Understanding and elucidating the tenogenic differentiation signalling pathways are important for future optimization of tenogenic hMSCs for functional tendon cell-based therapy and tissue engineering.
    Matched MeSH terms: Principal Component Analysis
  3. Fulltext Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa
    Loke MF, Chua EG, Gan HM, Thulasi K, Wanyiri JW, Thevambiga I, et al.
    PLoS One, 2018;13(12):e0208584.
    PMID: 30576312 DOI: 10.1371/journal.pone.0208584
    Colorectal cancer (CRC) is ranked the third most common cancer in human worldwide. However, the exact mechanisms of CRC are not well established. Furthermore, there may be differences between mechanisms of CRC in the Asian and in the Western populations. In the present study, we utilized a liquid chromatography-mass spectrometry (LC-MS) metabolomic approach supported by the 16S rRNA next-generation sequencing to investigate the functional and taxonomical differences between paired tumor and unaffected (normal) surgical biopsy tissues from 17 Malaysian patients. Metabolomic differences associated with steroid biosynthesis, terpenoid biosynthesis and bile metabolism could be attributed to microbiome differences between normal and tumor sites. The relative abundances of Anaerotruncus, Intestinimonas and Oscillibacter displayed significant relationships with both steroid biosynthesis and terpenoid and triterpenoid biosynthesis pathways. Metabolites involved in serotonergic synapse/ tryptophan metabolism (Serotonin and 5-Hydroxy-3-indoleacetic acid [5-HIAA]) were only detected in normal tissue samples. On the other hand, S-Adenosyl-L-homocysteine (SAH), a metabolite involves in methionine metabolism and methylation, was frequently increased in tumor relative to normal tissues. In conclusion, this study suggests that local microbiome dysbiosis may contribute to functional changes at the cancer sites. Results from the current study also contributed to the list of metabolites that are found to differ between normal and tumor sites in CRC and supported our quest for understanding the mechanisms of carcinogenesis.
    Matched MeSH terms: Principal Component Analysis
  4. 1 H-NMR metabolomics for evaluating the protective effect of Clinacanthus nutans (Burm. f) Lindau water extract against nitric oxide production in LPS-IFN-γ activated RAW 264.7 macrophages
    Khoo LW, Kow ASF, Maulidiani M, Ang MY, Chew WY, Lee MT, et al.
    Phytochem Anal, 2019 Jan;30(1):46-61.
    PMID: 30183131 DOI: 10.1002/pca.2789
    INTRODUCTION: Clinacanthus nutans, a small shrub that is native to Southeast Asia, is commonly used in traditional herbal medicine and as a food source. Its anti-inflammation properties is influenced by the metabolites composition, which can be determined by different binary extraction solvent ratio and extraction methods used during plant post-harvesting stage.

    OBJECTIVE: Evaluate the relationship between the chemical composition of C. nutans and its anti-inflammatory properties using nuclear magnetic resonance (NMR) metabolomics approach.

    METHODOLOGY: The anti-inflammatory effect of C. nutans air-dried leaves extracted using five different binary extraction solvent ratio and two extraction methods was determined based on their nitric oxide (NO) inhibition effect in lipopolysaccharide-interferon-gamma (LPS-IFN-γ) activated RAW 264.7 macrophages. The relationship between extract bioactivity and metabolite profiles and quantifications were established using 1 H-NMR metabolomics and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The possible metabolite biosynthesis pathway was constructed to further strengthen the findings.

    RESULTS: Water and sonication prepared air-dried leaves possessed the highest NO inhibition activity (IC50  = 190.43 ± 12.26 μg/mL, P 

    Matched MeSH terms: Principal Component Analysis
  5. Fulltext The Changes in Endogenous Metabolites in Hyperlipidemic Rats Treated with Herbal Mixture Containing Lemon, Apple Cider, Garlic, Ginger, and Honey
    Abu Bakar Sajak A, Azlan A, Abas F, Hamzah H
    Nutrients, 2021 Oct 12;13(10).
    PMID: 34684574 DOI: 10.3390/nu13103573
    An herbal mixture composed of lemon, apple cider, garlic, ginger and honey as a polyphenol-rich mixture (PRM) has been reported to contain hypolipidemic activity on human subjects and hyperlipidemic rats. However, the therapeutic effects of PRM on metabolites are not clearly understood. Therefore, this study aimed to provide new information on the causal impact of PRM on the endogenous metabolites, pathways and serum biochemistry. Serum samples of hyperlipidemic rats treated with PRM were subjected to biochemistry (lipid and liver profile) and hydroxymethylglutaryl-CoA enzyme reductase (HMG-CoA reductase) analyses. In contrast, the urine samples were subjected to urine metabolomics using 1H NMR. The serum biochemistry revealed that PRM at 500 mg/kg (PRM-H) managed to lower the total cholesterol level and low-density lipoprotein (LDL-C) (p < 0.05) and reduce the HMG-CoA reductase activity. The pathway analysis from urine metabolomics reveals that PRM-H altered 17 pathways, with the TCA cycle having the highest impact (0.26). Results also showed the relationship between the serum biochemistry of LDL-C and HMG-CoA reductase and urine metabolites (trimethylamine-N-oxide, dimethylglycine, allantoin and succinate). The study's findings demonstrated the potential of PRM at 500 mg/kg as an anti-hyperlipidemic by altering the TCA cycle, inhibiting HMG-CoA reductase and lowering the LDL-C in high cholesterol rats.
    Matched MeSH terms: Principal Component Analysis
  6. Fulltext Biochemical and anatomical changes and yield reduction in rice (Oryza sativa L.) under varied salinity regimes
    Hakim MA, Juraimi AS, Hanafi MM, Ismail MR, Selamat A, Rafii MY, et al.
    Biomed Res Int, 2014;2014:208584.
    PMID: 24579076 DOI: 10.1155/2014/208584
    Five Malaysian rice (Oryza sativa L.) varieties, MR33, MR52, MR211, MR219, and MR232, were tested in pot culture under different salinity regimes for biochemical response, physiological activity, and grain yield. Three different levels of salt stresses, namely, 4, 8, and 12 dS m(-1), were used in a randomized complete block design with four replications under glass house conditions. The results revealed that the chlorophyll content, proline, sugar content, soluble protein, free amino acid, and yield per plant of all the genotypes were influenced by different salinity levels. The chlorophyll content was observed to decrease with salinity level but the proline increased with salinity levels in all varieties. Reducing sugar and total sugar increased up to 8 dS m(-1) and decreased up to 12 dS m(-1). Nonreducing sugar decreased with increasing the salinity levels in all varieties. Soluble protein and free amino acid also decreased with increasing salinity levels. Cortical cells of MR211 and MR232 did not show cell collapse up to 8 dS m(-1) salinity levels compared to susceptible checks (IR20 and BRRI dhan29). Therefore, considering all parameters, MR211 and MR232 showed better salinity tolerance among the tested varieties. Both cluster and principal component analyses depict the similar results.
    Matched MeSH terms: Principal Component Analysis
  7. A new hybrid intelligent system for accurate detection of Parkinson's disease
    Hariharan M, Polat K, Sindhu R
    Comput Methods Programs Biomed, 2014 Mar;113(3):904-13.
    PMID: 24485390 DOI: 10.1016/j.cmpb.2014.01.004
    Elderly people are commonly affected by Parkinson's disease (PD) which is one of the most common neurodegenerative disorders due to the loss of dopamine-producing brain cells. People with PD's (PWP) may have difficulty in walking, talking or completing other simple tasks. Variety of medications is available to treat PD. Recently, researchers have found that voice signals recorded from the PWP is becoming a useful tool to differentiate them from healthy controls. Several dysphonia features, feature reduction/selection techniques and classification algorithms were proposed by researchers in the literature to detect PD. In this paper, hybrid intelligent system is proposed which includes feature pre-processing using Model-based clustering (Gaussian mixture model), feature reduction/selection using principal component analysis (PCA), linear discriminant analysis (LDA), sequential forward selection (SFS) and sequential backward selection (SBS), and classification using three supervised classifiers such as least-square support vector machine (LS-SVM), probabilistic neural network (PNN) and general regression neural network (GRNN). PD dataset was used from University of California-Irvine (UCI) machine learning database. The strength of the proposed method has been evaluated through several performance measures. The experimental results show that the combination of feature pre-processing, feature reduction/selection methods and classification gives a maximum classification accuracy of 100% for the Parkinson's dataset.
    Matched MeSH terms: Principal Component Analysis
  8. Fulltext Differential protein expression between chondrogenic differentiated MSCs, undifferentiated MSCs and adult chondrocytes derived from Oryctolagus cuniculus in vitro
    Tay LX, Lim CK, Mansor A, Kamarul T
    Int J Med Sci, 2014;11(1):24-33.
    PMID: 24396283 DOI: 10.7150/ijms.7244
    This preliminary study aims to determine the differentially expressed proteins from chondrogenic differentiated multipotent stromal cells (cMSCs) in comparison to undifferentiated multipotent stromal cells (MSCs) and adult chondrocytes (ACs).
    Matched MeSH terms: Principal Component Analysis
  9. Multivariate statistical techniques for the assessment of seasonal variations in surface water quality of pasture ecosystems
    Ajorlo M, Abdullah RB, Yusoff MK, Halim RA, Hanif AH, Willms WD, et al.
    Environ Monit Assess, 2013 Oct;185(10):8649-58.
    PMID: 23604787 DOI: 10.1007/s10661-013-3201-8
    This study investigates the applicability of multivariate statistical techniques including cluster analysis (CA), discriminant analysis (DA), and factor analysis (FA) for the assessment of seasonal variations in the surface water quality of tropical pastures. The study was carried out in the TPU catchment, Kuala Lumpur, Malaysia. The dataset consisted of 1-year monitoring of 14 parameters at six sampling sites. The CA yielded two groups of similarity between the sampling sites, i.e., less polluted (LP) and moderately polluted (MP) at temporal scale. Fecal coliform (FC), NO3, DO, and pH were significantly related to the stream grouping in the dry season, whereas NH3, BOD, Escherichia coli, and FC were significantly related to the stream grouping in the rainy season. The best predictors for distinguishing clusters in temporal scale were FC, NH3, and E. coli, respectively. FC, E. coli, and BOD with strong positive loadings were introduced as the first varifactors in the dry season which indicates the biological source of variability. EC with a strong positive loading and DO with a strong negative loading were introduced as the first varifactors in the rainy season, which represents the physiochemical source of variability. Multivariate statistical techniques were effective analytical techniques for classification and processing of large datasets of water quality and the identification of major sources of water pollution in tropical pastures.
    Matched MeSH terms: Principal Component Analysis
  10. Fulltext Metabolic profiling of Lactococcus lactis under different culture conditions
    Azizan KA, Baharum SN, Mohd Noor N
    Molecules, 2012 Jul 03;17(7):8022-36.
    PMID: 22759915 DOI: 10.3390/molecules17078022
    Gas chromatography mass spectrometry (GC-MS) and headspace gas chromatography mass spectrometry (HS/GC-MS) were used to study metabolites produced by Lactococcus lactis subsp. cremoris MG1363 grown at a temperature of 30 °C with and without agitation at 150 rpm, and at 37 °C without agitation. It was observed that L. lactis produced more organic acids under agitation. Primary alcohols, aldehydes, ketones and polyols were identified as the corresponding trimethylsilyl (TMS) derivatives, whereas amino acids and organic acids, including fatty acids, were detected through methyl chloroformate derivatization. HS analysis indicated that branched-chain methyl aldehydes, including 2-methylbutanal, 3-methylbutanal, and 2-methylpropanal are degdradation products of isoleucine, leucine or valine. Multivariate analysis (MVA) using partial least squares discriminant analysis (PLS-DA) revealed the major differences between treatments were due to changes of amino acids and fermentation products.
    Matched MeSH terms: Principal Component Analysis
  11. Microarray profiling of secretory-phase endometrium from patients with recurrent miscarriage
    Othman R, Omar MH, Shan LP, Shafiee MN, Jamal R, Mokhtar NM
    Reprod Biol, 2012 Jul;12(2):183-99.
    PMID: 22850470
    The aim of the present study was to identify differentially expressed genes and their related biological pathways in the secretory phase endometrium from patients with recurrent miscarriage (RM) and fertile subjects. Endometrial samples from RM and fertile patients were analyzed using the Affymetrix GeneChip® ST Array. The bioinformatic analysis using the Partek Genomic Suite revealed 346 genes (175 up-regulated and 171 down-regulated) that were differentially expressed in the endometrium of RM patients compared to the fertile subjects (fold change ≥1.5, p<0.005). Validation step using quantitative real-time polymerase chain reaction (qPCR) confirmed a similar expression pattern of four exemplary genes: one up-regulated gene (fibroblast growth factor 9, FGF9) and three down-regulated genes: integrin β3 (ITGB3), colony stimulating factor 1 (CSF1) and matrix-metalloproteinases 19 (MMP19). The Gene Set Enrichment Analysis (GSEA) and the Pathway Studio software have found 101 signaling pathways (p<0.05) associated with the affected genes including the FGFR3 /signal transducer and activator of transcription (STAT) pathway and the CSF1R/STAT pathway. Cell adhesion, cell differentiation and angiogenesis were among biological processes indicated by this system. In conclusion, microarray technique is a useful tool to study gene expression in the secretory phase-endometrium of RM patients. The differences in endometrial gene expressions between healthy and RM subjects contribute to an increase in our knowledge on molecular mechanisms of RM development and may improve the outcome of pregnancies in high-risk women with RM.
    Matched MeSH terms: Principal Component Analysis
  12. Spatial aspects of surface water quality in the Jakara Basin, Nigeria using chemometric analysis
    Mustapha A, Aris AZ
    J Environ Sci Health A Tox Hazard Subst Environ Eng, 2012;47(10):1455-65.
    PMID: 22571534 DOI: 10.1080/10934529.2012.673305
    Multivariate statistical techniques such as hierarchical Agglomerated cluster analysis (HACA), discriminant analysis (DA), principal component analysis (PCA), and factor analysis (FA) were applied to identify the spatial variation and pollution sources of Jakara River, Kano, Nigeria. Thirty surface water samples were collected: 23 along Getsi River and 7 along the main channel of River Jakara. Twenty-three water quality parameters, namely pH, temperature, turbidity, electrical conductivity (EC), dissolved oxygen (DO), 5-day biochemical oxygen demand (BOD(5)), Faecal coliform, total solids (TS), nitrates (NO(3)(-)), phosphates (PO(4)(3-)), cobalt (Co), iron (Fe), nickel (Ni), manganese (Mn), copper (Cu), sodium (Na), potassium (K), mercury (Hg), chromium (Cr), cadmium (Cd), lead (Pb), magnesium (Mg), and calcium(Ca) were analysed. HACA grouped the sampling points into three clusters based on the similarities of river water quality characteristics: industrial, domestic, and agricultural water pollution sources. Forward and backward DA effectively discriminated 5 and 15 water quality variables, respectively, each assigned with 100% correctness from the original 23 variables. PCA and FA were used to investigate the origin of each water quality parameter due to various land use activities, 7 principal components were obtained with 77.5% total variance, and in addition PCA identified 3 latent pollution sources to support HACA. From this study, one can conclude that the application of multivariate techniques derives meaningful information from water quality data.
    Matched MeSH terms: Principal Component Analysis
  13. A comparison of Malaysian and Australian speech-language pathologists' practices with children with developmental disabilities who are pre-symbolic
    Joginder Singh S, Iacono T, Gray KM
    Int J Speech Lang Pathol, 2011 Oct;13(5):389-98.
    PMID: 21888557 DOI: 10.3109/17549507.2011.603429
    The aim of this study was to explore the assessment, intervention, and family-centred practices of Malaysian and Australian speech-language pathologists (SLPs) when working with children with developmental disabilities who are pre-symbolic. A questionnaire was developed for the study, which was completed by 65 SLPs from Malaysia and 157 SLPs from Australia. Data reduction techniques were used prior to comparison of responses across questionnaire items. Results indicated that SLPs relied mostly on informal assessments. Malaysian and Australian SLPs differed significantly in terms of obtaining information from outside the clinic to inform assessment. When providing intervention, SLPs focused mostly on improving children's pre-verbal skills. A third of Australian SLPs listed the introduction of some form of symbolic communication as an early intervention goal, compared to only a small percentage of Malaysian SLPs. Regarding family involvement, SLPs most often involved mothers, with fathers and siblings being involved to a lesser extent. Overall, it appeared that practices of Malaysian SLPs had been influenced by developments in research, although there were some areas of service delivery that continued to rely on traditional models. Factors leading to similarities and differences in practice of SLPs from both countries as well as clinical and research implications of the study are discussed.
    Matched MeSH terms: Principal Component Analysis
  14. Genomic copy number variations in three Southeast Asian populations
    Ku CS, Pawitan Y, Sim X, Ong RT, Seielstad M, Lee EJ, et al.
    Hum Mutat, 2010 Jul;31(7):851-7.
    PMID: 20506136 DOI: 10.1002/humu.21287
    Research on the role of copy number variations (CNVs) in the genetic risk of diseases in Asian populations has been hampered by a relative lack of reference CNV maps for Asian populations outside the East Asians. In this article, we report the population characteristics of CNVs in Chinese, Malay, and Asian Indian populations in Singapore. Using the Illumina Human 1M Beadchip array, we identify 1,174 CNV loci in these populations that corroborated with findings when the same samples were typed on the Affymetrix 6.0 platform. We identify 441 novel loci not previously reported in the Database of Genomic Variations (DGV). We observe a considerable number of loci that span all three populations and were previously unreported, as well as population-specific loci that are quite common in the respective populations. From this we observe the distribution of CNVs in the Asian Indian population to be considerably different from the Chinese and Malay populations. About half of the deletion loci and three-quarters of duplication loci overlap UCSC genes. Tens of loci show population differentiation and overlap with genes previously known to be associated with genetic risk of diseases. One of these loci is the CYP2A6 deletion, previously linked to reduced susceptibility to lung cancer.
    Matched MeSH terms: Principal Component Analysis
  15. Assessment of 3-D nasal airway morphology in Southeast Asian adults with obstructive sleep apnea using acoustic rhinometry
    Banabilh SM, Suzina AH, Mohamad H, Dinsuhaimi S, Samsudin AR, Singh GD
    Clin Oral Investig, 2010 Oct;14(5):491-8.
    PMID: 19806371 DOI: 10.1007/s00784-009-0342-9
    The aim of the present study is to investigate nasal airway morphology in Asian adults with and without obstructive sleep apnea (OSA) using acoustic rhinometry (AR), principal components analysis (PCA), and 3-D finite-element analysis (FEA). One hundred eight adult Malays aged 18-65 years (mean ± SD, 33.2 ± 13.31) underwent clinical examination and limited channel polysomnography, providing 54 patients with OSA and 54 non-OSA controls. The mean minimal cross section area 1 (MCA1) and the mean minimal cross sectional area 2 (MCA2) were obtained from AR for all subjects and subjected to t tests. The OSA and control nasal airways were reconstructed in 3-D and subjected to PCA and FEA. The mean MCA1 and MCA2 using AR were found to be significantly smaller in the OSA group than in the control group (p < 0.001). Comparing the 3-D OSA and control nasal airways using PCA, the first two eigenvalues accounted for 94% of the total shape change, and statistical differences were found (p < 0.05). Similarly, comparing the nasal airways using FEA, the 3-D mean OSA nasal airway was significantly narrower in the OSA group compared to the control group. Specifically, decreases in size of approx. 10-22% were found in the nasal valve/head of inferior turbinate area. In conclusion, differences in nasal airway morphology are present when comparing patients with OSA to controls. These differences need to be recognized as they can improve our understanding of the etiological basis of obstructive sleep apnea and facilitate its subsequent management.
    Matched MeSH terms: Principal Component Analysis
  16. Fulltext Isolation, Characterization, Crystal Structure Elucidation of Two Flavanones and Simultaneous RP-HPLC Determination of Five Major Compounds from Syzygium campanulatum Korth
    Memon AH, Ismail Z, Al-Suede FS, Aisha AF, Hamil MS, Saeed MA, et al.
    Molecules, 2015;20(8):14212-33.
    PMID: 26248073 DOI: 10.3390/molecules200814212
    Two flavanones named (2S)-7-Hydroxy-5-methoxy-6,8-dimethyl flavanone (1), (S)-5,7-dihydroxy-6,8-dimethyl-flavanone (2), along with known chalcone, namely, (E)-2',4'- dihydroxy-6'-methoxy-3',5'-dimethylchalcone (3) and two triterpenoids, namely, betulinic and ursolic acids (4 and 5), were isolated from the leaves of Syzygium campanulatum Korth (Myrtaceae). The structures of compounds (1 and 2) were determined on the basis of UV-visible, FTIR, NMR spectroscopies and LC-EIMS analytical techniques. Furthermore, new, simple, precise, selective, accurate, highly sensitive, efficient and reproducible RP-HPLC method was developed and validated for the quantitative analysis of the compounds (1-5) from S. campanulatum plants of five different age. RP-HPLC method was validated in terms of specificity, linearity (r2 ≤ 0.999), precision (2.0% RSD), and recoveries (94.4%-105%). The LOD and LOQ of these compounds ranged from 0.13-0.38 and 0.10-2.23 μg·mL-1, OPEN ACCESS respectively. Anti-proliferative activity of isolated flavanones (1 and 2) and standardized extract of S. campanulatum was evaluated on human colon cancer (HCT 116) cell line. Compounds (1 and 2) and extract revealed potent and dose-dependent activity with IC50 67.6, 132.9 and 93.4 μg·mL-1, respectively. To the best of our knowledge, this is the first study on isolation, characterization, X-ray crystallographic analysis of compounds (1 and 2) and simultaneous RP-HPLC determination of five major compounds (1-5) from different age of S. campanulatum plants.
    Matched MeSH terms: Principal Component Analysis
  17. Fulltext A blood-based gene expression and signaling pathway analysis to differentiate between high and low grade gliomas
    Ponnampalam SN, Kamaluddin NR, Zakaria Z, Matheneswaran V, Ganesan D, Haspani MS, et al.
    Oncol Rep, 2017 Jan;37(1):10-22.
    PMID: 28004117 DOI: 10.3892/or.2016.5285
    The aims of the present study were to undertake gene expression profiling of the blood of glioma patients to determine key genetic components of signaling pathways and to develop a panel of genes that could be used as a potential blood-based biomarker to differentiate between high and low grade gliomas, non-gliomas and control samples. In this study, blood samples were obtained from glioma patients, non-glioma and control subjects. Ten samples each were obtained from patients with high and low grade tumours, respectively, ten samples from non-glioma patients and twenty samples from control subjects. Total RNA was isolated from each sample after which first and second strand synthesis was performed. The resulting cRNA was then hybridized with the Agilent Whole Human Genome (4x44K) microarray chip according to the manufacturer's instructions. Universal Human Reference RNA and samples were labeled with Cy3 CTP and Cy5 CTP, respectively. Microarray data were analyzed by the Agilent Gene Spring 12.1V software using stringent criteria which included at least a 2-fold difference in gene expression between samples. Statistical analysis was performed using the unpaired Student's t-test with a p<0.01. Pathway enrichment was also performed, with key genes selected for validation using droplet digital polymerase chain reaction (ddPCR). The gene expression profiling indicated that were a substantial number of genes that were differentially expressed with more than a 2-fold change (p<0.01) between each of the four different conditions. We selected key genes within significant pathways that were analyzed through pathway enrichment. These key genes included regulators of cell proliferation, transcription factors, cytokines and tumour suppressor genes. In the present study, we showed that key genes involved in significant and well established pathways, could possibly be used as a potential blood-based biomarker to differentiate between high and low grade gliomas, non-gliomas and control samples.
    Matched MeSH terms: Principal Component Analysis
  18. Fulltext Tocotrienol-Rich Fraction (TRF) Treatment Promotes Proliferation Capacity of Stress-Induced Premature Senescence Myoblasts and Modulates the Renewal of Satellite Cells: Microarray Analysis
    Lim JJ, Wan Zurinah WN, Mouly V, Norwahidah AK
    Oxid Med Cell Longev, 2019;2019:9141343.
    PMID: 30774750 DOI: 10.1155/2019/9141343
    Human skeletal muscle is a vital organ involved in movement and force generation. It suffers from deterioration in mass, strength, and regenerative capacity in sarcopenia. Skeletal muscle satellite cells are involved in the regeneration process in response to muscle loss. Tocotrienol, an isomer of vitamin E, was reported to have a protective effect on cellular aging. This research is aimed at determining the modulation of tocotrienol-rich fraction (TRF) on the gene expressions of stress-induced premature senescence (SIPS) human skeletal muscle myoblasts (CHQ5B). CHQ5B cells were divided into three groups, i.e., untreated young control, SIPS control (treated with 1 mM hydrogen peroxide), and TRF-posttreated groups (24 hours of 50 μg/mL TRF treatment after SIPS induction). The differential gene expressions were assessed using microarray, GSEA, and KEGG pathway analysis. Results showed that TRF treatment significantly regulated the gene expressions, i.e., p53 (RRM2B, SESN1), ErbB (EREG, SHC1, and SHC3), and FoxO (MSTN, SMAD3) signalling pathways in the SIPS myoblasts compared to the SIPS control group (p < 0.05). TRF treatment modulated the proliferation capacity of SIPS myoblasts through regulation of ErbB (upregulation of expression of EREG, SHC1, and SHC3) and FoxO (downregulation of expression of MSTN and SMAD3) and maintaining the renewal of satellite cells through p53 signalling (upregulation of RRM2B and SESN1), MRF, cell cycle, and Wnt signalling pathways.
    Matched MeSH terms: Principal Component Analysis
  19. Plasma metabolic biomarkers for discriminating individuals with alcohol use disorders from social drinkers and alcohol-naive subjects
    Mostafa H, Amin AM, Teh CH, Murugaiyah VA, Arif NH, Ibrahim B
    J Subst Abuse Treat, 2017 06;77:1-5.
    PMID: 28476260 DOI: 10.1016/j.jsat.2017.02.015
    BACKGROUND: Alcohol use disorders (AUD) is a phase of alcohol misuse in which the drinker consumes excessive amount of alcohol and have a continuous urge to consume alcohol which may lead to various health complications. The current methods of alcohol use disorders diagnosis such as questionnaires and some biomarkers lack specificity and sensitivity. Metabolomics is a novel scientific field which may provide a novel method for the diagnosis of AUD by using a sensitive and specific technique such as nuclear magnetic resonance (NMR).

    METHODS: A cross sectional study was conducted on three groups: individuals with alcohol use disorders (n=30), social drinkers (n=54) and alcohol-naive controls (n=60). 1H NMR-based metabolomics was used to obtain the metabolic profiles of plasma samples. Data were processed by multivariate principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) followed by univariate and multivariate logistic regressions to produce the best fit-model for discrimination between groups.

    RESULTS: The OPLS-DA model was able to distinguish between the AUD group and the other groups with high sensitivity, specificity and accuracy of 64.29%, 98.17% and 91.24% respectively. The logistic regression model identified two biomarkers in plasma (propionic acid and acetic acid) as being significantly associated with alcohol use disorders. The reproducibility of all biomarkers was excellent (0.81-1.0).

    CONCLUSIONS: The applied plasma metabolomics technique was able to differentiate the metabolites between AUD and the other groups. These metabolites are potential novel biomarkers for diagnosis of alcohol use disorders.

    Matched MeSH terms: Principal Component Analysis
  20. Fulltext Association between dietary patterns and cardiometabolic risks in Malaysian Punjabi adults
    Yik Fah Chee, Satvinder Kaur, Roseline Wai Kuan Yap
    Malaysian Journal of Medicine and Health Sciences, 2020;16(106):106-115.
    MyJurnal
    Introduction: Globally, the prevalence of cardiovascular diseases (CVD) is high in Punjabi population. This could due to the increased cardiometabolic risks associated with diets high in dietary fats and refined grains. However, studies on the relationship between dietary pattern and cardiometabolic risks involving Malaysian Punjabis popu- lation are scarce. Hence, this study aims to determine the associations between dietary patterns and cardiometa- bolic risks in Malaysian Punjabi adults. Methods: Socio-demographic, lifestyle and dietary intake information was collected using self-administered questionnaire. Anthropometric measurements: weight and height for body mass index (BMI) calculation, waist circumference (WC); systolic (SBP) and diastolic blood pressure (DBP); and biomark- ers: blood glucose, glycated haemoglobin A1c (HbA1c), triglycerides, total cholesterol (TC), low-density-lipopro- tein cholesterol (LDL-C), high-density-lipoprotein cholesterol (HDL-C), apolipoprotein A1 and B100 were obtained. Major dietary patterns were derived using principal component analysis. Association between dietary patterns and cardiometabolic risk factors were performed using ANCOVA and Kruskal-Wallis tests. Results: A total of 164 (35.4% males and 64.6% females) Punjabis were included in this study. Four dietary patterns were extracted, namely ‘fruits and vegetables diet’ (FVD), ‘whole grains, condiments and beverages diet’ (WCBD), ‘protein diet’ (PD) and ‘rice, noodles, cereals and meat diet’ (RNCMD). Significant associations were obtained for FVD with BMI (p=0.012), WC (p=0.011), SBP (p=0.020) and DBP (p=0.009); WCBD with TC (p=0.010), LDL-C (p=0.015) and apolipoprotein B100 (p=0.038). Conclusion: Dietary pattern comprised of fruits, vegetables and beverages containing antioxidant-rich spices, ginger, and black tea may lower cardiometabolic risks in Malaysian Punjabis, particularly in obesity, high blood pressure and hyperlipidaemia.
    Matched MeSH terms: Principal Component Analysis
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