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Fulltext Diversity and Evolutionary Histories of Human Coronaviruses NL63 and 229E Associated with Acute Upper Respiratory Tract Symptoms in Kuala Lumpur, Malaysia

Al-Khannaq MN, Ng KT, Oong XY, Pang YK, Takebe Y, Chook JB, et al.

Am J Trop Med Hyg, 2016 05 04;94(5):1058-64.
PMID: 26928836 DOI: 10.4269/ajtmh.15-0810

The human alphacoronaviruses HCoV-NL63 and HCoV-229E are commonly associated with upper respiratory tract infections (URTI). Information on their molecular epidemiology and evolutionary dynamics in the tropical region of southeast Asia however is limited. Here, we analyzed the phylogenetic, temporal distribution, population history, and clinical manifestations among patients infected with HCoV-NL63 and HCoV-229E. Nasopharyngeal swabs were collected from 2,060 consenting adults presented with acute URTI symptoms in Kuala Lumpur, Malaysia, between 2012 and 2013. The presence of HCoV-NL63 and HCoV-229E was detected using multiplex polymerase chain reaction (PCR). The spike glycoprotein, nucleocapsid, and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference. A total of 68/2,060 (3.3%) subjects were positive for human alphacoronavirus; HCoV-NL63 and HCoV-229E were detected in 45 (2.2%) and 23 (1.1%) patients, respectively. A peak in the number of HCoV-NL63 infections was recorded between June and October 2012. Phylogenetic inference revealed that 62.8% of HCoV-NL63 infections belonged to genotype B, 37.2% was genotype C, while all HCoV-229E sequences were clustered within group 4. Molecular dating analysis indicated that the origin of HCoV-NL63 was dated to 1921, before it diverged into genotype A (1975), genotype B (1996), and genotype C (2003). The root of the HCoV-229E tree was dated to 1955, before it diverged into groups 1-4 between the 1970s and 1990s. The study described the seasonality, molecular diversity, and evolutionary dynamics of human alphacoronavirus infections in a tropical region.
Fulltext Differential Gene Expression Reflects Morphological Characteristics and Physiological Processes in Rice Immunity against Blast Pathogen Magnaporthe oryzae

Azizi P, Rafii MY, Mahmood M, Abdullah SN, Hanafi MM, Nejat N, et al.

PLoS One, 2015;10(5):e0126188.
PMID: 26001124 DOI: 10.1371/journal.pone.0126188

The rice blast fungus Magnaporthe oryzae is a serious pathogen that jeopardises the world's most important food-security crop. Ten common Malaysian rice varieties were examined for their morphological, physiological and genomic responses to this rice blast pathogen. qPCR quantification was used to assess the growth of the pathogen population in resistant and susceptible rice varieties. The chlorophyll content and photosynthesis were also measured to further understand the disruptive effects that M. oryzae has on infected plants of these varieties. Real-time PCR was used to explore the differential expression of eight blast resistance genes among the ten local varieties. Blast disease has destructive effects on the growth of rice, and the findings of our study provide evidence that the Pikh, Pi9, Pi21, and Osw45 genes are involved in defence responses in the leaves of Malaysian rice at 31 h after inoculation with M. oryzae pathotype P7.2. Both the chlorophyll content and photosynthesis were reduced, but the levels of Pikh gene expression remained constant in susceptible varieties, with a developed pathogen population and mild or severe symptoms. The Pi9, Pi21, and Osw45 genes, however, were simultaneously upregulated in infected rice plants. Therefore, the presence of the Pikh, Pi9, Pi21, and Osw45 genes in the germplasm is useful for improving the resistance of rice varieties.
Molecular insights into the regulation of rice kernel elongation

Azizi P, Osman M, Hanafi MM, Sahebi M, Rafii MY, Taheri S, et al.

Crit Rev Biotechnol, 2019 Nov;39(7):904-923.
PMID: 31303070 DOI: 10.1080/07388551.2019.1632257

A large number of rice agronomic traits are complex, multi factorial and polygenic. As the mechanisms and genes determining grain size and yield are largely unknown, the identification of regulatory genes related to grain development remains a preeminent approach in rice genetic studies and breeding programs. Genes regulating cell proliferation and expansion in spikelet hulls and participating in endosperm development are the main controllers of rice kernel elongation and grain size. We review here and discuss recent findings on genes controlling rice grain size and the mechanisms, epialleles, epigenomic variation, and assessment of controlling genes using genome-editing tools relating to kernel elongation.
Fulltext An overview of fractional anisotropy as a reliable quantitative measurement for the corticospinal tract (CST) integrity in correlation with a Fugl-Meyer assessment in stroke rehabilitation

Zolkefley MKI, Firwana YMS, Hatta HZM, Rowbin C, Nassir CMNCM, Hanafi MH, et al.

J Phys Ther Sci, 2021 Jan;33(1):75-83.
PMID: 33519079 DOI: 10.1589/jpts.33.75

[Purpose] Understanding the essential mechanisms in post-stroke recovery not only provides important basic insights into brain function and plasticity but can also guide the development of new therapeutic approaches for stroke patients. This review aims to give an overview of how various variables of Magnetic Resonance-Diffusion Tensor Imaging (MR-DTI) metrics of fractional anisotropy (FA) can be used as a reliable quantitative measurement and indicator of corticospinal tract (CST) changes, particularly in relation to functional motor outcome correlation with a Fugl-Meyer assessment in stroke rehabilitation. [Methods] PubMed electronic database was searched for the relevant literature, using key words of diffusion tensor imaging (dti), corticospinal tract, and stroke. [Results] We reviewed the role of FA in monitoring CST remodeling and its role of predicting motor recovery after stroke. We also discussed the mechanism of CST remodeling and its modulation from the value of FA and FMA-UE. [Conclusion] Heterogeneity of post-stroke brain disorganization and motor impairment is a recognized challenge in the development of accurate indicators of CST integrity. DTI-based FA measurements offer a reliable and evidence-based indicator for CST integrity that would aid in predicting motor recovery within the context of stroke rehabilitation.
Fulltext Over-Expression of the Pikh Gene with a CaMV 35S Promoter Leads to Improved Blast Disease (Magnaporthe oryzae) Tolerance in Rice

Azizi P, Rafii MY, Abdullah SN, Hanafi MM, Maziah M, Sahebi M, et al.

Front Plant Sci, 2016;7:773.
PMID: 27379107 DOI: 10.3389/fpls.2016.00773

Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is susceptible to the blast fungus pathotype P7.2. Thus, a full DNA and coding DNA sequence (CDS) of the Pikh gene, 3172 bp, and 1206 bp in length, were obtained through amplifying the gDNA and cDNA template from a PH9-resistant rice variety using a specific primer. Agrobacterium-mediated transformation technology was also used to introduce the Pikh gene into the MR219 callus. Subsequently, transgenic plants were evaluated from the DNA to protein stages using polymerase chain reaction (PCR), semi-quantitative RT-PCR, real-time quantitative PCR and high performance liquid chromatography (HPLC). Transgenic plants were also compared with a control using a real-time quantification technique (to quantify the pathogen population), and transgenic and control plants were challenged with the local most virulent M. oryzae pathotype, P7.2. Based on the results, the Pikh gene encodes a hydrophilic protein with 18 sheets, 4 helixes, and 21 coils. This protein contains 401 amino acids, among which the amino acid sequence from 1 to 376 is a non-cytoplasmic region, that from 377 to 397 is a transmembrane region, and that from 398 to 401 is a cytoplasmic region with no identified disordered regions. The Pikh gene was up-regulated in the transgenic plants compared with the control plants. The quantity of the amino acid leucine in the transgenic rice plants increased significantly from 17.131 in the wild-type to 47.865 mg g(-1) in transgenic plants. The M. oryzae population was constant at 31, 48, and 72 h after inoculation in transgenic plants, while it was increased in the inoculated control plants. This study successfully clarified that over-expression of the Pikh gene in transgenic plants can improve their blast resistance against the M. oryzae pathotype P7.2.
Ursodeoxycholic acid protects cardiomyocytes against cobalt chloride induced hypoxia by regulating transcriptional mediator of cells stress hypoxia inducible factor 1α and p53 protein

Mohamed AS, Hanafi NI, Sheikh Abdul Kadir SH, Md Noor J, Abdul Hamid Hasani N, Ab Rahim S, et al.

Cell Biochem Funct, 2017 Oct;35(7):453-463.
PMID: 29027248 DOI: 10.1002/cbf.3303

In hepatocytes, ursodeoxycholic acid (UDCA) activates cell signalling pathways such as p53, intracellular calcium ([Ca2+ ]i ), and sphingosine-1-phosphate (S1P)-receptor via Gαi -coupled-receptor. Recently, UDCA has been shown to protect the heart against hypoxia-reoxygenation injury. However, it is not clear whether UDCA cardioprotection against hypoxia acts through a transcriptional mediator of cells stress, HIF-1α and p53. Therefore, in here, we aimed to investigate whether UDCA could protect cardiomyocytes (CMs) against hypoxia by regulating expression of HIF-1α, p53, [Ca2+ ]i , and S1P-Gαi -coupled-receptor. Cardiomyocytes were isolated from newborn rats (0-2 days), and hypoxia was induced by using cobalt chloride (CoCl2 ). Cardiomyocytes were treated with UDCA and cotreated with either FTY720 (S1P-receptor agonist) or pertussis toxin (PTX; Gαi inhibitor). Cells were subjected for proliferation assay, beating frequency, QuantiGene Plex assay, western blot, immunofluorescence, and calcium imaging. Our findings showed that UDCA counteracted the effects of CoCl2 on cell viability, beating frequency, HIF-1α, and p53 protein expression. We found that these cardioprotection effects of UDCA were similar to FTY720, S1P agonist. Furthermore, we observed that UDCA protects CMs against CoCl2 -induced [Ca2+ ]i dynamic alteration. Pharmacological inhibition of the Gαi -sensitive receptor did not abolish the cardioprotection of UDCA against CoCl2 detrimental effects, except for cell viability and [Ca2+ ]i . Pertussis toxin is partially effective in inhibiting UDCA protection against CoCl2 effects on CM cell viability. Interestingly, PTX fully inhibits UDCA cardioprotection on CoCl2 -induced [Ca2+ ]i dynamic changes. We conclude that UDCA cardioprotection against CoCl2 -induced hypoxia is similar to FTY720, and its actions are not fully mediated by the Gαi -coupled protein sensitive pathways. Ursodeoxycholic acid is the most hydrophilic bile acid and is currently used to treat liver diseases. Recently, UDCA is shown to have a cardioprotection effects; however, the mechanism of UDCA cardioprotection is still poorly understood. The current data generated were the first to show that UDCA is able to inhibit the activation of HIF-1α and p53 protein during CoCl2 -induced hypoxia in cardiomyocytes. This study provides an insight of UDCA mechanism in protecting cardiomyocytes against hypoxia.
Fulltext The effects of dietary edible bird nest supplementation on learning and memory functions of multigenerational mice

Mahaq O, P Rameli MA, Jaoi Edward M, Mohd Hanafi N, Abdul Aziz S, Abu Hassim H, et al.

Brain Behav, 2020 11;10(11):e01817.
PMID: 32886435 DOI: 10.1002/brb3.1817

INTRODUCTION: Edible bird nest (EBN) is a natural food product produced from edible nest swiftlet's saliva which consists of glycoproteins as one of its main components; these glycoproteins contain an abundant of sialic acid. The dietary EBN supplementation has been reported to enhance brain functions in mammals and that the bioactivities and nutritional value of EBN are important during periods of rapid brain growth particularly for preterm infant. However, the effects of EBN in maternal on multigeneration learning and memory function still remain unclear. Thus, the present study aimed to determine the effects of maternal EBN supplementation on learning and memory function of their first (F1)- and second (F2)-generation mice.
METHODS: CJ57BL/6 breeder F0 mice were fed with EBN (10 mg/kg) from different sources. After 6 weeks of diet supplementations, the F0 animals were bred to produce F1 and F2 animals. At 6 weeks of age, the F1 and F2 animals were tested for spatial recognition memory using a Y-maze test. The sialic acid content from EBN and brain gene expression were analyzed using HPLC and PCR, respectively.
RESULTS: All EBN samples contained glycoprotein with high level of sialic acid. Dietary EBN supplementation also showed an upregulation of GNE, ST8SiaIV, SLC17A5, and BDNF mRNA associated with an improvement in Y-maze cognitive performance in both generations of animal. Qualitatively, the densities of synaptic vesicles in the presynaptic terminal were higher in the F1 and F2 animals which might derive from maternal EBN supplementation.
CONCLUSION: This study provided a solid foundation toward the growing research on nutritional intervention from dietary EBN supplementation on cognitive and neurological development in the generation of mammals.
Fulltext Antioxidant Enzyme Activities and Secondary Metabolite Profiling of Oil Palm Seedlings Treated with Combination of NPK Fertilizers Infected with Ganoderma boninense

Sahebi M, Hanafi MM, Mohidin H, Rafii MY, Azizi P, Idris AS, et al.

Biomed Res Int, 2018;2018:1494157.
PMID: 29721500 DOI: 10.1155/2018/1494157

Oil palm (Elaeis guineensis Jacq) is one of the major sources of edible oil. Reducing the effect of Ganoderma, main cause of basal stem rot (BSR) on oil palm, is the main propose of this study. Understanding the oil palm defense mechanism against Ganoderma infection through monitoring changes in the secondary metabolite compounds levels before/after infection by Ganoderma under different fertilizing treatment is required. Oil palm requires macro- and microelements for growth and yield. Manipulating the nutrient for oil palm is a method to control the disease. The 3-4-month-old oil palm seedlings were given different macronutrient treatments to evaluate induction of defense related enzymes and production of secondary metabolite compounds in response to G. boninense inoculation. The observed trend of changes in the infected and uninfected seedlings was a slightly higher activity for β-1,3-glucanases, chitinase, peroxidase, and phenylalanine ammonia-lyase during the process of pathogenesis. It was found that PR proteins gave positive response to the interaction between oil palm seedlings and Ganoderma infection. Although the responses were activated systematically, they were short-lasting as the changes in enzymes activities appeared before the occurrence of visible symptoms. Effect of different nutrients doses was obviously observed among the results of the secondary metabolite compounds. Many identified/unidentified metabolite compounds were presented, of which some were involved in plant cell defense mechanism against pathogens, mostly belonging to alkaloids with bitter-tasting nitrogenous-compounds, and some had the potential to be used as new markers to detect basal stem rot at the initial step of disease.
Pharmaceuticals residues in selected tropical surface water bodies from Selangor (Malaysia): Occurrence and potential risk assessments

Praveena SM, Shaifuddin SNM, Sukiman S, Nasir FAM, Hanafi Z, Kamarudin N, et al.

Sci Total Environ, 2018 Nov 15;642:230-240.
PMID: 29902621 DOI: 10.1016/j.scitotenv.2018.06.058

This study investigated the occurrence of nine pharmaceuticals (amoxicillin, caffeine, chloramphenicol, ciprofloxacin, dexamethasone, diclofenac, nitrofurazone, sulfamethoxazole, and triclosan) and to evaluate potential risks (human health and ecotoxicological) in Lui, Gombak and Selangor (Malaysia) rivers using commercial competitive Enzyme-Linked Immunosorbent Assay (ELISA) kit assays. Physicochemical properties of these rivers showed the surface samples belong to Class II of Malaysian National Water Quality Standards which requires conventional treatment before consumption. All the pharmaceuticals were detected in all three rivers except for triclosan, dexamethasone and diclofenac which were not detected in few of sampling locations in these three rivers. Highest pharmaceutical concentrations were detected in Gombak river in line of being as one of the most polluted rivers in Malaysia. Ciprofloxacin concentrations were detected in all the sampling locations with the highest at 299.88 ng/L. While triclosan, dexamethasone and diclofenac concentrations were not detected in a few of sampling locations in these three rivers. All these nine pharmaceuticals were within the levels reported previously in literature. Pharmaceutical production, wastewater treatment technologies and treated sewage effluent were found as the potential sources which can be related with pharmaceuticals occurrence in surface water samples. Potential human risk assessment showed low health risk except for ciprofloxacin and dexamethasone. Instead, ecotoxicological risk assessment indicated moderate risks were present for these rivers. Nevertheless, results confirmation using instrumental techniques is needed for higher degree of specificity. It is crucial to continuously monitor the surface water bodies for pharmaceuticals using a cost-effective prioritisation approach to assess sensitive sub-populations risk.
Fulltext Performance of a Taqman Assay for Improved Detection and Quantification of Human Rhinovirus Viral Load

Ng KT, Chook JB, Oong XY, Chan YF, Chan KG, Hanafi NS, et al.

Sci Rep, 2016 10 10;6:34855.
PMID: 27721388 DOI: 10.1038/srep34855

Human rhinovirus (HRV) is the major aetiology of respiratory tract infections. HRV viral load assays are available but limitations that affect accurate quantification exist. We developed a one-step Taqman assay using oligonucleotides designed based on a comprehensive list of global HRV sequences. The new oligonucleotides targeting the 5'-UTR region showed high PCR efficiency (E = 99.6%, R2 = 0.996), with quantifiable viral load as low as 2 viral copies/μl. Assay evaluation using an External Quality Assessment (EQA) panel yielded a detection rate of 90%. When tested on 315 human enterovirus-positive specimens comprising at least 84 genetically distinct HRV types/serotypes (determined by the VP4/VP2 gene phylogenetic analysis), the assay detected all HRV species and types, as well as other non-polio enteroviruses. A commercial quantification kit, which failed to detect any of the EQA specimens, produced a detection rate of 13.3% (42/315) among the clinical specimens. Using the improved assay, we showed that HRV sheds in the upper respiratory tract for more than a week following acute infection. We also showed that HRV-C had a significantly higher viral load at 2-7 days after the onset of symptoms (p = 0.001). The availability of such assay is important to facilitate disease management, antiviral development, and infection control.
Fulltext The effects of age on clinical characteristics, hospitalization and mortality of patients with influenza-related illness at a tertiary care centre in Malaysia

Wong PL, Sii HL, P'ng CK, Ee SS, Yong Oong X, Ng KT, et al.

Influenza Other Respir Viruses, 2020 05;14(3):286-293.
PMID: 32022411 DOI: 10.1111/irv.12691

BACKGROUND: Age is an established risk factor for poor outcomes in individuals with influenza-related illness, and data on its influence on clinical presentations and outcomes in the South-East Asian settings are scarce. The aim of this study was to determine the above among adults with influenza-related upper respiratory tract infection at a teaching hospital in Malaysia.
METHODS: A retrospective case-note analysis was conducted on a cohort of 3935 patients attending primary care at the University Malaya Medical Centre, Malaysia from February 2012 till May 2014 with URTI symptoms. Demographics, clinical characteristics, medical and vaccination history were obtained from electronic medical records, and mortality data from the National Registration Department. Comparisons were made between those aged <25, ≥25 to <65 and ≥65 years.
RESULTS: 470 (11.9%) had PCR-confirmed influenza virus infection. Six (1.3%) received prior influenza vaccination. Those aged ≥65 years were more likely to have ≥2 comorbidities (P
Fulltext Potential Effects of Non-Surgical Periodontal Therapy on Periodontal Parameters, Inflammatory Markers, and Kidney Function Indicators in Chronic Kidney Disease Patients with Chronic Periodontitis

Chaudhry A, Kassim NK, Zainuddin SLA, Taib H, Ibrahim HA, Ahmad B, et al.

Biomedicines, 2022 Oct 29;10(11).
PMID: 36359271 DOI: 10.3390/biomedicines10112752

Chronic kidney disease (CKD) and chronic periodontitis (CP) contribute to the increased level of inflammatory biomarkers in the blood. This study hypothesized that successful periodontal treatment would reduce the level of inflammatory biomarkers in CKD patients. This prospective study recruited two groups of CP patients: 33 pre-dialysis CKD patients and 33 non-CKD patients. All patients underwent non-surgical periodontal therapy (NSPT). Their blood samples and periodontal parameters were taken before and after six weeks of NSPT. The serum level of high-sensitivity C-reactive protein (hs-CRP), interleukin 6 (IL-6), and periodontal parameters were compared between groups. On the other hand, kidney function indicators such as serum urea and estimated glomerular filtration rate (eGFR) were only measured in CKD patients. Clinical periodontal parameters and inflammatory markers levels at baseline were significantly higher (p < 0.05) in the CKD group than in the non-CKD group and showed significant reduction (p < 0.05) after six weeks of NSPT. CKD patients demonstrated a greater periodontitis severity and higher inflammatory burden than non-CKD patients. Additionally, CKD patients with CP showed a good response to NSPT. Therefore, CKD patients’ periodontal health needs to be screened for early dental interventions and monitored accordingly.
Fulltext Are doctors assessing patients with hypertension appropriately at their initial presentation?

Wong SL, Lee PY, Ng CJ, Hanafi NS, Chia YC, Lai PS, et al.

Singapore Med J, 2015 Sep;56(9):518-22.
PMID: 26451055 DOI: 10.11622/smedj.2015137

INTRODUCTION: The aim of this study was to determine the extent to which primary care doctors assessed patients newly diagnosed with hypertension for the risk factors of cardiovascular disease (CVD) during the patients' first clinic visit for hypertension. The study also aimed to examine the trend of assessment for CVD risk factors over a 15-year period.
METHODS: This retrospective study was conducted between January and May 2012. Data was extracted from the paper-based medical records of patients with hypertension using a 1:4 systematic random sampling method. Data collected included CVD risk factors and a history of target organ damage (TOD), which were identified during the patient's first visit to the primary care doctor for hypertension, as well as the results of the physical examinations and investigations performed during the same visit.
RESULTS: A total of 1,060 medical records were reviewed. We found that assessment of CVD risk factors during the first clinic visit for hypertension was poor (5.4%-40.8%). Assessments for a history of TOD were found in only 5.8%-11.8% of the records, and documented physical examinations and investigations for the assessment of TOD and secondary hypertension ranged from 0.1%-63.3%. Over time, there was a decreasing trend in the percentage of documented physical examinations performed, but an increasing trend in the percentage of investigations ordered.
CONCLUSION: There was poor assessment of the patients' CVD risk factors, secondary causes of hypertension and TOD at their first clinic visit for hypertension. The trends observed in the assessment suggest an over-reliance on investigations over clinical examinations.
Promoting cardioprotection with fenugreek: Insights from CoCl2-induced hypoxia in neonatal rat cardiomyocytes

Hanafi NI, Mohamed M, Sirajudeen KNMS, Hafizoh Saidan N, Siew Hua G, Pahirulzaman KAK, et al.

Iran J Basic Med Sci, 2023;26(11):1360-1369.
PMID: 37885997 DOI: 10.22038/IJBMS.2023.71521.15547

OBJECTIVES: This study aimed to investigate the protective effects of fenugreek on CoCl2-induced hypoxia in neonatal rat cardiomyocytes.
MATERIALS AND METHODS: Primary cardiomyocytes were isolated from Sprague Dawley rats aged 0-2 days and incubated with various concentrations of fenugreek (10-320 µg/ml) and CoCl2-induced hypoxia for different durations (24, 48, and 72 hr). Cell viability, calcium signaling, beating rate, and gene expression were evaluated.
RESULTS: Fenugreek treatments did not cause any toxicity in cardiomyocytes. At a concentration of 160 µg/ml for 24 hr, fenugreek protected the heart against CoCl2-induced hypoxia, as evidenced by reduced expression of caspases (-3, -6, -8, and -9) and other functional genes markers, such as HIF-1α, Bcl-2, IP3R, ERK5, and GLP-1r. Calcium signaling and beating rate were also improved in fenugreek-treated cardiomyocytes. In contrast, CoCl2 treatment resulted in up-regulation of the hypoxia gene HIF-1α and apoptotic caspases gene (-3, -9, -8, -12), and down-regulation of Bcl-2 activity.
CONCLUSION: Fenugreek treatment at a concentration of 160 µg/ml was not toxic to neonatal rat cardiomyocytes and protected against CoCl2-induced hypoxia. Furthermore, fenugreek improved calcium signaling and beating rate and altered gene expression. Fenugreek may be a potential therapeutic agent for promoting cardioprotection against hypoxia-induced injuries.
Fulltext Heavy Metal in Paddy Soil and its Bioavailability in Rice Using In Vitro Digestion Model for Health Risk Assessment

Zulkafflee NS, Mohd Redzuan NA, Hanafi Z, Selamat J, Ismail MR, Praveena SM, et al.

Int J Environ Res Public Health, 2019 11 28;16(23).
PMID: 31795132 DOI: 10.3390/ijerph16234769

Rice ingestion is one of the major pathways for heavy metal bioaccumulation in human. This study aimed to measure the heavy metal content of paddy soils and its bioavailability in paddy grain in order to assess the health risk. In total, 10 rice samples (50 g each) of paddy plants were harvested from the Selangor and Terengganu areas of Malaysia to assess the bioavailability of heavy metal (As, Cd, Cu, Cr, and Pb) using the in vitro digestion model of Rijksinstituut voor Volksgezondheid en Milieu. The bioavailability of heavy metal concentrations in rice samples were analyzed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The findings showed the bioavailability of heavy metal concentrations was decreased in the order Cr > Cu > Pb > As > Cd. Chromium was found to be the most abundant bioavailable heavy metal in cooked rice, which was the result of its high content in paddy soil. Hazard Quotient values for the bioavailability of the heavy metal studied were less than one indicating no non-carcinogenic health risks for adults and children. Meanwhile, the total Lifetime Cancer Risk exceeded the acceptable value showing a potential of carcinogenic health risk for both adults and children. The application of in vitro digestion model in assessing bioavailability of heavy metal produces a more realistic estimation of human health risks exposure. However, a regular monitoring of pollution in Selangor and Terengganu areas is crucial since the exposure of heavy metals through rice consumption poses the potential non-carcinogenic and carcinogenic health risk to the local residents.
Fulltext Bacterial communities associated with silage of different forage crops in Malaysian climate analysed using 16S amplicon metagenomics

Hisham MB, Hashim AM, Mohd Hanafi N, Abdul Rahman N, Abdul Mutalib NE, Tan CK, et al.

Sci Rep, 2022 May 02;12(1):7107.
PMID: 35501317 DOI: 10.1038/s41598-022-08819-4

Silage produced in tropical countries is prone to spoilage because of high humidity and temperature. Therefore, determining indigenous bacteria as potential inoculants is important to improve silage quality. This study aimed to determine bacterial community and functional changes associated with ensiling using amplicon metagenomics and to predict potential bacterial additives associated with silage quality in the Malaysian climate. Silages of two forage crops (sweet corn and Napier) were prepared, and their fermentation properties and functional bacterial communities were analysed. After ensiling, both silages were predominated by lactic acid bacteria (LAB), and they exhibited good silage quality with significant increment in lactic acid, reductions in pH and water-soluble carbohydrates, low level of acetic acid and the absence of propionic and butyric acid. LAB consortia consisting of homolactic and heterolactic species were proposed to be the potential bacterial additives for sweet corn and Napier silage fermentation. Tax4fun functional prediction revealed metabolic pathways related to fermentation activities (bacterial division, carbohydrate transport and catabolism, and secondary metabolite production) were enriched in ensiled crops (p
Delineating risk zones and evaluation of shelter centres for flood disaster management along the Pahang River Basin, Malaysia

Isahak A, Reza MIH, Siwar C, Ismail SM, Sulaiman N, Hanafi Z, et al.

Jamba, 2018;10(1):501.
PMID: 29955268 DOI: 10.4102/jamba.v10i1.501

Shelter centres are important locations to safeguard people from helpless situations and are an integral part of disaster risk reduction (DRR), particularly for flood DRR. The establishment of shelter centres, and their design based on scientific assessment, is crucial. Yet, they are very much related to the geographic location, socio-economic conditions and the livelihoods of the affected communities. However, many parts of the developing world are still lagging behind in ensuring such scientific design. Considering the flood disaster in 2014 that affected the residents living along the Pahang River Basin, in this study we delineate the communities at risk and evaluate the existing shelter centres to determine how they reduce people's vulnerability to the risks associated with rural and urban landscapes. We used spatial analysis tools to delineate risk zones and to evaluate existing evacuation systems. A flood disaster risk map was produced to determine which communities are living with risks. Subsequently, the distribution of shelter centres examined whether they are able to support people living at the flood risk zones. These centres were also evaluated using a set of international guidelines for effective disaster shelters. This reveals that the number of shelter centres is not adequate. The designation and designing of shelter centres are not being done scientifically. The maps produced here have a lot of potential to support disaster management decisions, in particular site selection and the prioritisation of centres. The study concludes with a set of guidelines and recommendations for structural and non-structural measures, such as alternative livelihoods and the potential of ecotourism, which may improve the resilience among flood-affected communities; and the decision-making process for the overall flood DRR initiatives.
Fulltext Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014

Oong XY, Ng KT, Lam TT, Pang YK, Chan KG, Hanafi NS, et al.

PLoS One, 2015;10(8):e0136254.
PMID: 26313754 DOI: 10.1371/journal.pone.0136254

Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and sore throat. This study describes the evolution of influenza B viruses in Malaysia and highlights the importance of continuous surveillance for better vaccination policy in this region.
Fulltext Molecular epidemiology and evolutionary histories of human coronavirus OC43 and HKU1 among patients with upper respiratory tract infections in Kuala Lumpur, Malaysia

Al-Khannaq MN, Ng KT, Oong XY, Pang YK, Takebe Y, Chook JB, et al.

Virol J, 2016 Feb 25;13:33.
PMID: 26916286 DOI: 10.1186/s12985-016-0488-4

BACKGROUND: Despite the worldwide circulation of human coronavirus OC43 (HCoV-OC43) and HKU1 (HCoV-HKU1), data on their molecular epidemiology and evolutionary dynamics in the tropical Southeast Asia region is lacking.
METHODS: The study aimed to investigate the genetic diversity, temporal distribution, population history and clinical symptoms of betacoronavirus infections in Kuala Lumpur, Malaysia between 2012 and 2013. A total of 2,060 adults presented with acute respiratory symptoms were screened for the presence of betacoronaviruses using multiplex PCR. The spike glycoprotein, nucleocapsid and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference.
RESULTS: A total of 48/2060 (2.4 %) specimens were tested positive for HCoV-OC43 (1.3 %) and HCoV-HKU1 (1.1 %). Both HCoV-OC43 and HCoV-HKU1 were co-circulating throughout the year, with the lowest detection rates reported in the October-January period. Phylogenetic analysis of the spike gene showed that the majority of HCoV-OC43 isolates were grouped into two previously undefined genotypes, provisionally assigned as novel lineage 1 and novel lineage 2. Sign of natural recombination was observed in these potentially novel lineages. Location mapping showed that the novel lineage 1 is currently circulating in Malaysia, Thailand, Japan and China, while novel lineage 2 can be found in Malaysia and China. Molecular dating showed the origin of HCoV-OC43 around late 1950s, before it diverged into genotypes A (1960s), B (1990s), and other genotypes (2000s). Phylogenetic analysis revealed that 27.3 % of the HCoV-HKU1 strains belong to genotype A while 72.7 % belongs to genotype B. The tree root of HCoV-HKU1 was similar to that of HCoV-OC43, with the tMRCA of genotypes A and B estimated around the 1990s and 2000s, respectively. Correlation of HCoV-OC43 and HCoV-HKU1 with the severity of respiratory symptoms was not observed.
CONCLUSIONS: The present study reported the molecular complexity and evolutionary dynamics of human betacoronaviruses among adults with acute respiratory symptoms in a tropical country. Two novel HCoV-OC43 genetic lineages were identified, warranting further investigation on their genotypic and phenotypic characteristics.
Study site: Primary Care Clinic, University Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia
Fulltext Importance of silicon and mechanisms of biosilica formation in plants

Sahebi M, Hanafi MM, Siti Nor Akmar A, Rafii MY, Azizi P, Tengoua FF, et al.

Biomed Res Int, 2015;2015:396010.
PMID: 25685787 DOI: 10.1155/2015/396010

Silicon (Si) is one of the most prevalent macroelements, performing an essential function in healing plants in response to environmental stresses. The purpose of using Si is to induce resistance to distinct stresses, diseases, and pathogens. Additionally, Si can improve the condition of soils, which contain toxic levels of heavy metals along with other chemical elements. Silicon minimizes toxicity of Fe, Al, and Mn, increases the availability of P, and enhances drought along with salt tolerance in plants through the formation of silicified tissues in plants. However, the concentration of Si depends on the plants genotype and organisms. Hence, the physiological mechanisms and metabolic activities of plants may be affected by Si application. Peptides as well as amino acids can effectively create polysilicic species through interactions with different species of silicate inside solution. The carboxylic acid and the alcohol groups of serine and asparagine tend not to engage in any significant role in polysilicates formation, but the hydroxyl group side chain can be involved in the formation of hydrogen bond with Si(OH)4. The mechanisms and trend of Si absorption are different between plant species. Furthermore, the transportation of Si requires an energy mechanism; thus, low temperatures and metabolic repressors inhibit Si transportation.

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