Displaying publications 1 - 20 of 59 in total

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  1. Abu Bakar N, Lefeber DJ, van Scherpenzeel M
    J Inherit Metab Dis, 2018 May;41(3):499-513.
    PMID: 29497882 DOI: 10.1007/s10545-018-0144-9
    Clinical glycomics comprises a spectrum of different analytical methodologies to analyze glycan structures, which provides insights into the mechanisms of glycosylation. Within clinical diagnostics, glycomics serves as a functional readout of genetic variants, and can form a basis for therapy development, as was described for PGM1-CDG. Integration of glycomics with genomics has resulted in the elucidation of previously unknown disorders of glycosylation, namely CCDC115-CDG, TMEM199-CDG, ATP6AP1-CDG, MAN1B1-CDG, and PGM1-CDG. This review provides an introduction into protein glycosylation and presents the different glycomics methodologies ranging from gel electrophoresis to mass spectrometry (MS) and from free glycans to intact glycoproteins. The role of glycomics in the diagnosis of congenital disorders of glycosylation (CDG) is presented, including a diagnostic flow chart and an overview of glycomics data of known CDG subtypes. The review ends with some future perspectives, showing upcoming technologies as system wide mapping of the N- and O-glycoproteome, intact glycoprotein profiling and analysis of sugar metabolism. These new advances will provide additional insights and opportunities to develop personalized therapy. This is especially true for inborn errors of metabolism, which are amenable to causal therapy, because interventions through supplementation therapy can directly target the pathogenesis at the molecular level.
  2. Siew WY, Abu Bakar NHH, Abu Bakar M, Zainal Abidin A
    J Hazard Mater, 2021 Aug 15;416:125846.
    PMID: 34492799 DOI: 10.1016/j.jhazmat.2021.125846
    The incorporation of different percentages of Fe2+ into copper benzene-1,3,5-tricarboxylate (CuBTC) was successfully carried out at room-temperature synthesis with water as the only solvent. The XRD and XPS analysis shows that the Fe2+ were substituted into the paddlewheel structure. The incorporation of 18% Fe2+ into CuBTC can increase the surface area and porosity of the framework. The BET surface area of Cu82Fe18BTC (1240 m2/g) was significantly higher than CuBTC (708 m2/g). Further increase in the Fe2+ percentage will reduce the surface area of the compound. The presence of Fe2+ in the framework successfully disturbs the pore formation and widens the pore size on the surface of these compounds. This as well as the pHpzc, which is related to the surface acidity of the resulting bimetallic organic framework (BMOF), play an important role in the adsorption process. Cu53Fe47BTC with an adsorption capacity of 94.42 mg/g shows approximately 6 times greater adsorption capacity against MB compared to CuBTC. This shows that by utilizing a different ratio of Cu and a second metal, it is possible to effectively design the surface morphology of BMOF for specific applications.
  3. Ramli AS, Daher AM, Nor-Ashikin MN, Mat-Nasir N, Ng KK, Miskan M, et al.
    Biomed Res Int, 2013;2013:760963.
    PMID: 24175300 DOI: 10.1155/2013/760963
    Metabolic syndrome (MetS) is a steering force for the cardiovascular diseases epidemic in Asia. This study aimed to compare the prevalence of MetS in Malaysian adults using NCEP-ATP III, IDF, and JIS definitions, identify the demographic factors associated with MetS, and determine the level of agreement between these definitions. The analytic sample consisted of 8,836 adults aged ≥30 years recruited at baseline in 2007-2011 from the Cardiovascular Risk Prevention Study (CRisPS), an ongoing, prospective cohort study involving 18 urban and 22 rural communities in Malaysia. JIS definition gave the highest overall prevalence (43.4%) compared to NCEP-ATP III (26.5%) and IDF (37.4%), P < 0.001. Indians had significantly higher age-adjusted prevalence compared to other ethnic groups across all MetS definitions (30.1% by NCEP-ATP III, 50.8% by IDF, and 56.5% by JIS). The likelihood of having MetS amongst the rural and urban populations was similar across all definitions. A high level of agreement between the IDF and JIS was observed (Kappa index = 0.867), while there was a lower level of agreement between the IDF and NCEP-ATP III (Kappa index = 0.580). JIS definition identified more Malaysian adults with MetS and therefore should be recommended as the preferred diagnostic criterion.
  4. Mohamed-Yassin MS, Baharudin N, Daher AM, Abu Bakar N, Ramli AS, Abdul-Razak S, et al.
    BMC Cardiovasc Disord, 2021 03 23;21(1):149.
    PMID: 33757445 DOI: 10.1186/s12872-021-01956-0
    BACKGROUND: Dyslipidaemia refers to lipid abnormalities consisting of either one or any combination of the following: elevated total cholesterol (TC), elevated low-density lipoprotein cholesterol (LDL-c), elevated triglycerides (TG), and low high-density lipoprotein cholesterol (HDL-c). The prevalence of hypercholesterolaemia is steadily increasing in Malaysia. However, data on the prevalence of dyslipidaemia subtypes among Malaysians are lacking. This is important as it may have implications for preventive and management strategies for this increasing public health challenge. This study is aimed at determining the prevalence of dyslipidaemia subtypes and their associated personal and clinical attributes in Malaysians.

    METHODS: REDISCOVER, a prospective study, enrolled 11,288 adults where sociodemographic data, anthropometric and blood pressure measurements, fasting lipid profile and glucose, and history of diabetes, hypertension, and smoking were obtained. The cross-sectional analytic sample presented in this article comprised 10,482 participants from baseline recruitment. The data was analysed by descriptive statistics and multivariable logistic regression.

    RESULTS: The overall prevalence of elevated TC, elevated LDL-c, elevated TG, low HDL-c, and elevated non-HDL-c were 64.0% (95% CI 63.0-65.0), 56.7% (CI 55.7-57.7), 37.4% (CI 36.5-38.4), 36.2% (CI 35.2-37.1), and 56.2% (CI 55.3-57.2), respectively. Overweight, obesity, and central obesity were highly prevalent and significantly associated with elevated TC and all dyslipidaemia subtypes. Older age was associated with elevated TC, elevated LDL-c and elevated non-HDL-c. Hypertension was associated with elevated TC, elevated TG, and elevated non-HDL-c, while diabetes was associated with elevated TG and low HDL-c.

    CONCLUSIONS: Elevated TC and all dyslipidaemia subtypes are highly prevalent in Malaysia where increased body mass seems the main driver. Differences in the prevalence and associated personal and clinical attributes may facilitate specific preventive and management strategies.

  5. Abu Bakar N', Hakim Abdullah MN, Lim V, Yong YK
    PMID: 35069762 DOI: 10.1155/2022/6098929
    Peptic ulcer disease is a multifactorial disorder and is the most significant public health concern nowadays. Previous study showed that essential oil extracted from Momordica charantia's seed exhibited gastroprotective effect. However, the evidence for the gastroprotective effect of its active compound, polypeptide K (PPK), remains unclear. This study aimed to examine the preventive effect of PPK against different experimental gastric lesions models in rats. The possible gastroprotective effect of PPK was assessed in hydrochloride ethanol- and indomethacin-induced gastric ulcer models in Sprague Dawley rats and was further evaluated macroscopically and microscopically. Pyloric ligation experiments were used to investigate gastric secretion. Oral administration of PPK at all concentrations (10, 25, and 50 mg/kg) showed significant (p < 0.05) reduction in total area of lesion in both hydrochloride ethanol- and indomethacin-induced gastric ulcer models. The highest inhibition rate was seen in PPK dose of 50 mg/kg with 64.9% and 72.2% on hydrochloride ethanol and indomethacin models, respectively. Microscopically, PPK preserved the normal architectures of the gastric tissues from being damaged by hydrochloride ethanol and indomethacin. Further, in the pyloric ligation studies, PPK significantly (p < 0.05) decreased the ulcer area where the highest protection was exhibited by 50 mg/kg with 70% inhibition rate. Moreover, all concentrations of PPK also significantly (p < 0.05) enhanced the gastric wall mucus secretion. Collectively, this study demonstrated the gastroprotective effect of PPK on hydrochloride ethanol- and indomethacin-induced gastric ulcer models. The possible mechanism might be associated with enhanced mucus secretion and thus lowering the total acidity.
  6. Abu Bakar N', Hakim Abdullah MN, Lim V, Yong YK
    PMID: 33976701 DOI: 10.1155/2021/5525584
    Momordica charantia (MC) is popular for its medicinal uses especially for treating diabetic-related complications. However, the antiulcer activity of essential oil derived from the seeds has not been systematically studied. This study aims to evaluate the gastroprotective activities of essential oil derived from the seed of MC induced by hydrochloride acid/ethanol (HCl/EtOH) and indomethacin and pylorus-ligation model. Gastric ulceration was induced by oral administration of HCl/EtOH solution or indomethacin on day 7 after animals have been pretreated with testing compounds. The first group received just distilled water and the second group received ranitidine (100 mg/kg). Groups 3, 4, and 5 received 10, 50, and 100 mg/kg of essential oil based on their body weight (10 mL/kg), respectively. Macroscopically, pretreatment of essential oil extracted from MC significantly decreased ulceration induced by HCl/EtOH and indomethacin in vivo. Microscopically, essential oil also significantly suppressed the formation of edema, epithelial disruption, and mucosa erosions. Moreover, essential oil significantly elevated the pH without decreasing the total acidity of the gastric juice and was able to increase the amount of adherent mucus compared to control. Current results provide scientific basis to the ethno-pharmacological usage of the MC in preventing ulcer formation induced by HCl/EtOH and indomethacin.
  7. Muid S, Abu Bakar NA, Abdul Rahman T, Tengku Ismail TS, Kholin SF, Suvorov AV, et al.
    Malays J Pathol, 2019 Dec;41(3):283-292.
    PMID: 31901913
    INTRODUCTION: Apart from inflammation and endothelial dysfunction, other key components in the development of atherogenesis include prothrombogenesis and oxidative stress. The effects of long-term confinement and isolation, exposure to radiation and different gravity forces during space travel could potentially increase the long-term risk of atherosclerosis. To the best of our knowledge, this is the first study determining the status of prothrombogenesis and oxidative stress in six cosmonauts subjected to the longest duration of confined isolation period of 520 days in preparation for prospective undetermined manned space travel to Mars.

    MATERIALS AND METHODS: This collaborative research between the National Space Agency (ANGKASA), Universiti Teknologi MARA, Malaysia and Institute of Biomedical Problems (IBMP), Russia was conducted at the Russian Academy of Sciences IBMP, Moscow, Russia. Six multi-national cosmonauts were assigned to live in a ground-based confined module for 520 days. Standard exercise and diet regime were instituted throughout the isolation phase. Six age, ethnic and gender-matched healthy, free-living ground controls were recruited in parallel. Serial serum and whole blood were analysed for biomarkers of prothrombogenesis [plasminogen activator inhibitor-1 (PAI-1) and homocysteine] and oxidative stress [oxidised low-density lipoprotein (ox-LDL) and malondialdehyde (MDA)].

    RESULTS: There were significantly lower concentrations of PAI-1 and homocysteine in cosmonauts during confinement compared to the controls. There were no significant differences seen in the concentrations of biomarkers of oxidative stress during confinement but there was a significant percentage change increment for serum MDA in cosmonauts.

    CONCLUSION: Long-term confinement decreased the risk of prothrombogenesis and this could be attributed to the exercise and diet regime which includes omega-3 fatty acids supplementation given to the crew members during their confinement period. However, oxidative damage could not be excluded and may be attributed to the influence of psychological stress during this prolonged confinement.

  8. Abu Bakar N, Mat Salleh M, Ali Umar A, Shapter JG
    MethodsX, 2017;4:486-491.
    PMID: 29201649 DOI: 10.1016/j.mex.2017.11.008
    Silver nanoparticles deposited on quartz substrates are widely used as SERS substrates. The nanoparticles can be deposited directly from colloidal solution by dipping technique. However, the adhesion of the particles on the quartz surface is very poor. Normally the substrate is pre-treated with hydroxylation or silanisation process. In this paper, we have demonstrated that the application of the sequence pre-treatment hydroxylation and silanisation have improved the density of silver nanoplates desposited on the quartz surface. •Sequence hydroxylation and silanisation pre-treatment assists the deposition of the nanoplate on the surface.•Various immersion times of the quartz surface into the colloidal nanoplates determined size distributions and density surface of the nanoplates on the surface.
  9. Abu Bakar N, Shapter JG
    Heliyon, 2023 Mar;9(3):e14686.
    PMID: 36994401 DOI: 10.1016/j.heliyon.2023.e14686
    Strategies for synthetic control of anisotropic metal nanostructures have grown in recent years in part due to their great potential for application as surface-enhanced Raman scattering (SERS) sensing substrates. It has been shown that SERS using silver substrates is a powerful tool for identification and qualification of trace chemical analysis on the basis of their unique molecular vibrations. In this work, we synthesized star-shaped silver nanostructures and fabricated SERS substrates to use the SERS enhancement of the Raman signal to detect neonicotinoid pesticides. These silver nanostar substrates were prepared by assembling the nanostar particles on a glass substrate surface using a self-assembly technique with various layers of silver nanostars film. The silver nanostar distribution on the solid substrate surface was found to have good reproducibility, reusability and were a stable SERS substrate giving SERS enhancements for pesticide detection at concentrations as low as 10-6 mg/ml. The distribution of these silver nanostars on the surface allowed excellent reproducibility of the detection with a low relative standard derivation (RSD) of SERS intensity of 8%. This work potentially builds a platform for an ultrasensitive detector where samples can be probed with little to no pre-processing and a range of pollutants can be detected at very low levels.
  10. Chan SN, Abu Bakar N, Mahmood M, Ho CL, Shaharuddin NA
    Biomed Res Int, 2014;2014:973790.
    PMID: 25853138 DOI: 10.1155/2014/973790
    Phytocystatin, a type of protease inhibitor (PI), plays major roles in plant defense mechanisms and has been reported to show antipathogenic properties and plant stress tolerance. Recombinant plant PIs are gaining popularity as potential candidates in engineering of crop protection and in synthesizing medicine. It is therefore crucial to identify PI from novel sources like Curcuma longa as it is more effective in combating against pathogens due to its novelty. In this study, a novel cDNA fragment encoding phytocystatin was isolated using degenerate PCR primers, designed from consensus regions of phytocystatin from other plant species. A full-length cDNA of the phytocystatin gene, designated CypCl, was acquired using 5'/3' rapid amplification of cDNA ends method and it has been deposited in NCBI database (accession number KF545954.1). It has a 687 bp long open reading frame (ORF) which encodes 228 amino acids. BLAST result indicated that CypCl is similar to cystatin protease inhibitor from Cucumis sativus with 74% max identity. Sequence analysis showed that CypCl contains most of the motifs found in a cystatin, including a G residue, LARFAV-, QxVxG sequence, PW dipeptide, and SNSL sequence at C-terminal extension. Phylogenetic studies also showed that CypCl is related to phytocystatin from Elaeis guineensis.
  11. Zakaria F, Akhtar MT, Wan Ibrahim WN, Abu Bakar N, Muhamad A, Shohaimi S, et al.
    Zebrafish, 2021 02;18(1):42-54.
    PMID: 33538644 DOI: 10.1089/zeb.2020.1895
    Depression is a complex and disabling psychiatric disorder, which is expected to be a leading cause for disability by 2030. According to World Health Organization, about 350 million people are suffering with mental health disorders around the globe, especially depression. However, the mechanisms involved in stress-induced depression have not been fully elucidated. In this study, a stress-like state was pharmacologically induced in zebrafish using reserpine, a drug widely used to mediate depression in experimental animal models. Zebrafish received single intraperitoneal (i.p.) injections of 20, 40, and 80 mg/kg body weight reserpine doses and were subjected to open-field test at 2, 24, 48, 72, and 96 h after the treatment. Along with observed changes in behavior and measurement of cortisol levels, the fish were further examined for perturbations in their brain metabolites by 1H nuclear magnetic resonance (NMR)-based metabolomics. We found a significant increase in freezing duration, whereas total distance travelled was decreased 24 h after single intraperitoneal injection of reserpine. Cortisol level was also found to be higher after 48 h of reserpine treatment. The 1H NMR data showed that the levels of metabolites such as glutamate, glutamine, histamine, valine, leucine and histidine, lactate, l-fucose, betaine and γ-amino butyric acid (GABA), β-hydroxyisovalerate, and glutathione were significantly decreased in the reserpine-treated group. This study provided some insights into the molecular nature of stress that could contribute toward a better understanding of depression disorder.
  12. Zainal-Abidin RA, Zainal Z, Mohamed-Hussein ZA, Abu-Bakar N, Ab Razak MSF, Simoh S, et al.
    Data Brief, 2020 Jun;30:105432.
    PMID: 32280737 DOI: 10.1016/j.dib.2020.105432
    Pigmented rice is enriched with antioxidants, macro- and micronutrients. A comprehensive investigation of the gene expression patterns among the pigmented rice varieties would help to understand the cellular mechanism and biological processes of rice grain pigmentation. Hence, we performed RNA sequencing and analysis on the whole grain of dehusked mature seeds of selected six Malaysian rice varieties with varying grain pigmentations. These varieties were black rice (BALI and Pulut Hitam 9), red rice (MRM16 and MRQ100) and white rice (MR297 and MRQ76). Illumina HiSeq™ 4000 sequencer was used to generate total raw nucleotides of approximately 53 Gb in size. From 353,937,212 total paired-end raw reads, 340,131,496 total clean reads were obtained. The raw reads were deposited into European Nucleotide Archive (ENA) database and can be accessed via accession number PRJEB34340. This dataset allows us to identify and profile all expressed genes with functions related to nutritional traits (i.e. antioxidants, folate and amylose content) and quality trait (i.e. aroma) across both pigmented and non-pigmented rice varieties. In addition, the transcriptome data obtained will be valuable for discovery of potential gene markers and functional SNPs related to functional traits to assist in rice breeding programme.
  13. Chong DW, Jayaraj VJ, Ab Rahim FI, Syed Soffian SS, Azmi MF, Mohd Yusri MY, et al.
    PLoS One, 2024;19(4):e0299659.
    PMID: 38593177 DOI: 10.1371/journal.pone.0299659
    INTRODUCTION: Colorectal cancer is a growing global health concern and the number of reported cases has increased over the years. Early detection through screening is critical to improve outcomes for patients with colorectal cancer. In Malaysia, there is an urgent need to optimize the colorectal cancer screening program as uptake is limited by multiple challenges. This study aims to systematically identify and address gaps in screening service delivery to optimize the Malaysian colorectal cancer screening program.

    METHODS: This study uses a mixed methods design. It focuses primarily on qualitative data to understand processes and strategies and to identify specific areas that can be improved through stakeholder engagement in the screening program. Quantitative data play a dual role in supporting the selection of participants for the qualitative study based on program monitoring data and assessing inequalities in screening and program implementation in healthcare facilities in Malaysia. Meanwhile, literature review identifies existing strategies to improve colorectal cancer screening. Additionally, the knowledge-to-action framework is integrated to ensure that the research findings lead to practical improvements to the colorectal cancer screening program.

    DISCUSSION: Through this complex mix of qualitative and quantitative methods, this study will explore the complex interplay of population- and systems-level factors that influence screening rates. It involves identifying barriers to effective colorectal cancer screening in Malaysia, comparing current strategies with international best practices, and providing evidence-based recommendations to improve the local screening program.

  14. Zain NN, Abu Bakar NK, Mohamad S, Saleh NM
    PMID: 24161875 DOI: 10.1016/j.saa.2013.09.129
    A greener method based on cloud point extraction was developed for removing phenol species including 2,4-dichlorophenol (2,4-DCP), 2,4,6-trichlorophenol (2,4,6-TCP) and 4-nitrophenol (4-NP) in water samples by using the UV-Vis spectrophotometric method. The non-ionic surfactant DC193C was chosen as an extraction solvent due to its low water content in a surfactant rich phase and it is well-known as an environmentally-friendly solvent. The parameters affecting the extraction efficiency such as pH, temperature and incubation time, concentration of surfactant and salt, amount of surfactant and water content were evaluated and optimized. The proposed method was successfully applied for removing phenol species in real water samples.
  15. Abu Bakar N, Abdul Aziz YF, Singh Sandhu R, Fadzli F, Yaakub NA, Krishnasamy S, et al.
    Heart Lung Circ, 2013 Apr;22(4):305-8.
    PMID: 22921797 DOI: 10.1016/j.hlc.2012.07.016
    Pericardial cysts are uncommon mediastinal lesions that are usually congenital in origin. Patients are usually asymptomatic and the cysts are generally discovered on routine radiography for unrelated purposes. This case illustrates a symptomatic presentation of a haemorrhagic pericardial cyst in which radiographic, echocardiographic and multislice (MRI and CT) imaging were performed. The imaging findings were not typical of pericardial cysts leading to a diagnostic quandary despite the varied imaging techniques. In conclusion, it is important to appreciate that the imaging findings of pericardial cysts can be varied. Radiologists and clinicians alike should be aware of this variability.
  16. Nik-Nasir NM, Md-Yasin M, Ariffin F, Mat-Nasir N, Miskan M, Abu-Bakar N, et al.
    Int J Environ Res Public Health, 2022 Dec 15;19(24).
    PMID: 36554769 DOI: 10.3390/ijerph192416888
    Physical activity (PA) in the form of structured or unstructured exercise is beneficial for health. This paper aims to study PA levels across four domains according to the International Physical Activity Questionnaire (IPAQ) and its associated factors. A total of 7479 Malaysian adult participants between 18 to 90 years old from the REDISCOVER study who completed the IPAQ were analyzed. PA was calculated as MET-min per week and were categorized according to insufficiently active, sufficiently active and very active. Multinomial regression was used to determine the association between sociodemographic, clinical factors and the level of PA. The mean age of the participants was 51.68 (±9.5 SD). The total reported physical activity in median (IQR) was 1584.0 (0-5637.3) MET-min per week. The highest total for PA was in the domestic domain which is 490 (0-2400) MET-min per week. Factors associated with sufficiently active or very active PA include Malay ethnicity, no formal education, elementary occupation, current smokers and high HDL. Whereas low income, male and normal BMI are less likely to participate in sufficiently active or very active PA. Intervention to encourage higher PA levels in all domains is important to achieve recommended PA targets.
  17. Sze TL, Abdul Aziz YF, Abu Bakar N, Mohd Sani F, Oemar H
    Iran J Radiol, 2015 Jan;12(1):e6878.
    PMID: 25793089 DOI: 10.5812/iranjradiol.6878
    Coronary artery fistula (CAF) is a rare anomaly of the coronary artery. Patients with this condition are usually asymptomatic. However, cardiac failure may occur later in life due to progressive enlargement of the fistula. Diagnosis is traditionally made by echocardiogram and conventional angiogram. However with the advantage of new technologies such as computed tomography (CT) coronary angiography, the course and communications of these fistulae can be delineated non-invasively and with greater accuracy. We report a case of a left circumflex artery fistula to the coronary sinus which was suspected on echocardiogram and the diagnosis was clinched on ECG-gated CT.
  18. Low SF, Abu Bakar N, Ngiu CS
    Iran Red Crescent Med J, 2014 Aug;16(8):e9481.
    PMID: 25389497 DOI: 10.5812/ircmj.9481
    INTRODUCTION: Camurati-Engelmann disease (CED) is a rare autosomal dominant disease with various phenotypic expressions. The symptoms usually develop during childhood. The hallmark of the disease is bilateral symmetric diaphyseal hyperostosis of the long bones with progressive involvement of the metaphysis. The epiphysis is strictly spared. The common clinical symptoms are pain of the extremities, muscle wasting, waddling gait, and lethargy. CED is rarely seen in conjunction with hypogonadism. CED-associated hypothyroidism has not been reported yet. Clinical assessment and skeletal survey are important to make the diagnosis.

    CASE PRESENTATION: Hereby we reported a case of CED with concomitant hypogonadism and hypothyroidism. Serial plain radiographs of the patient showed classic and progressive diaphyseal cortical hyperostosis of the long bone.

    CONCLUSIONS: Hyperostosis of the skull was observed in the present case. The characteristic osseous changes of CED were highlighted and the differential diagnoses were discussed.

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