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  1. Assessing Autism Knowledge Across the Global Landscape Using the ASK-Q
    Harrison AJ, Naqvi NC, Smit AK, Kumar PN, Muhammad NA, Saade S, et al.
    J Autism Dev Disord, 2023 Mar 09.
    PMID: 36892718 DOI: 10.1007/s10803-023-05936-5
    Substantial variability exists with regard to autism service provision around the world. Service disparities observed in many low- and middle-income countries may be driven, in part, by limited autism knowledge; however, measurement limitations have made it difficult to quantify autism knowledge across countries. The current study uses the autism stigma and knowledge questionnaire (ASK-Q) to quantify autism knowledge and stigma between different countries and demographics. The current study compiled data from 6830 participants collected using adapted versions of the ASK-Q administered in 13 different countries, representing four different continents. Structural equation modeling was used to examine how autism knowledge varied across country and individual factors. Results reveal cross country variability with a large, 17-point difference between the countries with the highest knowledge (Canada) and the lowest knowledge (Lebanon). As expected, countries with higher economies had higher levels of knowledge. We also documented differences based on country worldview, participant occupation, gender, age, and education level. These results help to identify specific regions and populations that might most need greater information about autism.
  2. Mucosal and systemic responses of immunogenic vaccines candidates against enteric Escherichia coli infections in ruminants: A review
    Lawan A, Jesse FFA, Idris UH, Odhah MN, Arsalan M, Muhammad NA, et al.
    Microb Pathog, 2018 Apr;117:175-183.
    PMID: 29471137 DOI: 10.1016/j.micpath.2018.02.039
    Innumerable Escherichia coli of animal origin are identified, which are of economic significance, likewise, cattle, sheep and goats are the carrier of enterohaemorrhagic E. coli, which are less pathogenic, and can spread to people by way of direct contact and through the contamination of foodstuff or portable drinking water, causing serious illness. The immunization of ruminants has been carried out for ages and is largely acknowledged as the most economical and maintainable process of monitoring E. coli infection in ruminants. Yet, only a limited number of E. coli vaccines are obtainable. Mucosal surfaces are the most important ingress for E. coli and thus mucosal immune responses function as the primary means of fortification. Largely contemporary vaccination processes are done by parenteral administration and merely limited number of E. coli vaccines are inoculated via mucosal itinerary, due to its decreased efficacy. Nevertheless, aiming at maximal mucosal partitions to stimulate defensive immunity at both mucosal compartments and systemic site epitomises a prodigious task. Enormous determinations are involved in order to improve on novel mucosal E. coli vaccines candidate by choosing apposite antigens with potent immunogenicity, manipulating novel mucosal itineraries of inoculation and choosing immune-inducing adjuvants. The target of E. coli mucosal vaccines is to stimulate a comprehensive, effective and defensive immunity by specifically counteracting the antibodies at mucosal linings and by the stimulation of cellular immunity. Furthermore, effective E. coli mucosal vaccine would make vaccination measures stress-free and appropriate for large number of inoculation. On account of contemporary advancement in proteomics, metagenomics, metabolomics and transcriptomics research, a comprehensive appraisal of the immeasurable genes and proteins that were divulged by a bacterium is now in easy reach. Moreover, there exist marvellous prospects in this bourgeoning technologies in comprehending the host bacteria affiliation. Accordingly, the flourishing knowledge could massively guarantee to the progression of immunogenic vaccines against E. coli infections in both humans and animals. This review highlight and expounds on the current prominence of mucosal and systemic immunogenic vaccines for the prevention of E. coli infections in ruminants.
  3. Dissecting the Biology of Rafflesia Species: Current Progress and Future Directions Made Possible with High-Throughput Sequencing Data
    Mursyidah AK, Hafizzudin-Fedeli M, Nor Muhammad NA, Latiff A, Firdaus-Raih M, Wan KL
    Plant Cell Physiol, 2023 Apr 17;64(4):368-377.
    PMID: 36611267 DOI: 10.1093/pcp/pcad004
    The angiosperm Rafflesia exhibits a unique biology, including a growth strategy that involves endophytic parasitism of a specific host, with only the gigantic flower externally visible. The Rafflesia possesses many unique evolutionary, developmental and morphological features that are rooted in yet-to-be-explained physiological processes. Although studies on the molecular biology of Rafflesia are limited by sampling difficulties due to its rarity in the wild and the short life span of its flower, current advances in high-throughput sequencing technology have allowed for the genome- and transcriptome-level dissection of the molecular mechanisms behind the unique characteristics of this parasitic plant. In this review, we summarize major findings on the cryptic biology of Rafflesia and provide insights into future research directions. The wealth of data obtained can improve our understanding of Rafflesia species and contribute toward the conservation strategy of this endangered plant.
  4. Fulltext Questionnaire development and validity to measure sexual intention among youth in Malaysia
    Muhammad NA, Shamsuddin K, Mohd Amin R, Omar K, Thurasamy R
    BMC Public Health, 2017 02 02;17(1):157.
    PMID: 28152993 DOI: 10.1186/s12889-016-3949-1
    BACKGROUND: From the Theory of Planned Behaviour perspective, sexual intention is determined by a permissive attitude, perception of social norms and perceived self-efficacy in performing sexual activity. The aim of this study was to develop and validate the Youth Sexual Intention Questionnaire (YSI-Q), which was designed to measure sexual intention among youths in Malaysia.

    METHODS: A total of 25 items were developed based on literature reviews encompassing four main constructs: sexual intention, attitude, social norms and self-efficacy. The YSI-Q then underwent a validation process that included content and face validity, exploratory factor analysis (EFA), reliability analysis, and confirmatory factor analysis (CFA). This study was conducted on unmarried youths aged 18 to 22 years who were studying in colleges around Klang Valley, Malaysia.

    RESULTS: EFA supported the four factor structure, but five items were removed due to incorrect placement or low factor loading (<0.60). Internal reliability using Cronbach's alpha ranged between 0.89 and 0.94. The CFA further confirmed the construct, convergent and discriminant validity of the YSI-Q with χ 2 = 392.43, df = 164, p 

  5. Reply letter to: Is there any importance of Migraine with Aura amongst medical students?
    Thiagarajan A, Muhammad NA, Tan CE
    Malays Fam Physician, 2022 Nov 30;17(3):156-157.
    PMID: 36606181 DOI: 10.51866/lte.249r
  6. Fulltext Protocol of a Single-Blind Two-Arm (Waitlist Control) Parallel-Group Randomised Controlled Pilot Feasibility Study for mHealth App among Incontinent Pregnant Women
    Jaffar A, Mohd Sidik S, Foo CN, Muhammad NA, Abdul Manaf R, Fadhilah Ismail SI, et al.
    Int J Environ Res Public Health, 2021 04 30;18(9).
    PMID: 33946203 DOI: 10.3390/ijerph18094792
    BACKGROUND: The delivery of pelvic floor muscle training (PFMT) through mHealth apps has been shown to produce promising results in improving pelvic floor muscle strength and urinary incontinence (UI). However, there is limited evidence on mHealth apps designed for pregnant women who are at high risk of developing UI. This pilot study aims to evaluate the feasibility of conducting an effectiveness trial for a newly developed PFMT app among pregnant women in Malaysia.

    METHODS: This is a prospective, single-centre, single-blind, randomised controlled pilot feasibility study: The Kegel Exercise Pregnancy Training app (KEPT-app) Trial. Sixty-four incontinent pregnant women who attended one primary care clinic for the antenatal follow-up will be recruited and randomly assigned to either intervention or waitlist control group. The intervention group will receive the intervention, the KEPT-app developed from the Capability, Opportunity, Motivation-Behaviour (COM-B) theory with Persuasive Technology and Technology Acceptance Model.

    DISCUSSION: This study will provide a fine-tuning for our future randomised control study on the recruitment feasibility methods, acceptability, feasibility, and usability of the KEPT-app, and the methods to reduce the retention rates among pregnant women with UI.

    TRIAL REGISTRATION: This study was registered on ClinicalTrials.gov on 19 February 2021 (NCT04762433) and is not yet recruiting.

  7. Adolescent pregnancy outcomes and risk factors in Malaysia
    Omar K, Hasim S, Muhammad NA, Jaffar A, Hashim SM, Siraj HH
    Int J Gynaecol Obstet, 2010 Dec;111(3):220-3.
    PMID: 20800837 DOI: 10.1016/j.ijgo.2010.06.023
    OBJECTIVE: To assess the outcomes and risk factors of adolescent pregnancies in 2 major hospitals in Malaysia.
    METHODS: We conducted a case-control study of pregnant girls aged 10 through 19 years. The controls were women aged 20 through 35 years who did not become pregnant in their adolescence. Cases and controls were matched for parity and place of delivery. Data were collected from questionnaires and the hospitals' medical records.
    RESULTS: The study included 102 cases and 102 controls. There were significant associations between adolescent pregnancy and low education level, low socioeconomic status, being raised by a single parent, not engaging in extracurricular school activities, engaging in unsupervised activities with peers after school, and substance abuse (P<0.05 for all); being anemic, being unsure of the expected delivery date, and having few antenatal visits and a late delivery booking; and low Apgar scores and perinatal complications.
    CONCLUSION: Adolescent pregnancies are high-risk pregnancies. Better sexual health strategies are required to address the associated complications.
  8. Fulltext Case report: Bipolar disorder in 48,XXYY syndrome
    Razali NA, Mohd Daud TI, Woon LS, Mohamed Saini S, Muhammad NA, Sharip S
    Front Psychiatry, 2022;13:1080698.
    PMID: 36713919 DOI: 10.3389/fpsyt.2022.1080698
    48,XXYY syndrome is a rare condition. The presentations of impulsive and aggressive behavior have been reported in several case reports among patients with 48,XXYY syndrome. The management of the psychological impact and neuropsychiatric sequela of this condition is a significant issue faced by families, carers, and healthcare professionals. We report a patient, 21-year-old Malay male, with underlying 48,XXYY syndrome with attention deficit hyperactivity disorder (ADHD) and intellectual disability, diagnosed later in adulthood with a bipolar mood disorder and benefited after being started on lithium. We describe the key clinical features and diagnostic workouts that allowed the arrival of the correct psychiatric diagnosis. Challenges in psychopharmacotherapy, including the risks of metabolic syndrome and deep vein thrombosis associated with 48,XXYY syndrome, are also considered. We suggest that for patients with 48,XXYY syndrome, routine psychological screening for mood symptoms such as mania and depression should be done by healthcare professionals with early involvement of psychiatrist in the multidisciplinary team due to the challenges in the management of these patients.
  9. Fulltext Correlation between nutritional status and comprehensive physical performance measures among older adults with undernourishment in residential institutions
    Singh DK, Manaf ZA, Yusoff NA, Muhammad NA, Phan MF, Shahar S
    Clin Interv Aging, 2014;9:1415-23.
    PMID: 25187701 DOI: 10.2147/CIA.S64997
    The consequences of combined undernourishment and decreased physical performance in older adults are debilitating and increases cost of care. To date, the information regarding the association between nutritional status and physical performance does not provide a complete picture. Most studies used limited or self-reported measures to evaluate physical performance. The objective of this study was to examine the correlation between nutritional status and comprehensive physical performance measures among undernourished older adults who reside in residential institutions.
  10. The cost and quality of life of Malaysian type 2 diabetes mellitus patients with chronic kidney disease and anemia
    Azmi S, Goh A, Muhammad NA, Tohid H, Rashid MRA
    Value Health Reg Issues, 2018 May;15:42-49.
    PMID: 29474177 DOI: 10.1016/j.vhri.2017.06.002
    BACKGROUND: Anemia is common among patients with type 2 diabetes mellitus (T2DM) and chronic kidney disease (CKD) and an independent risk factor for renal disease progression. Health economic evidence is important in Malaysia and yet cost and quality-of-life (QOL) data are scarce.

    OBJECTIVES: To investigate prevalence, factors associated with anemia, and cost and QOL among T2DM patients with CKD. Here, we present the estimated 1-year cost and QOL related to anemia in this group.

    METHODS: A cross-sectional, observational study was performed at 20 government clinics. Treatment cost was calculated on the basis of resource utilization ascertained through data extracted from medical records and patient recall. QOL was elicited using the short form 36 health survey version 2 questionnaire. Propensity score matching was performed and costs and QOL were analyzed by anemia status and CKD stage.

    RESULTS: Data for 816 patients were obtained. The propensity score matching enabled a comparison of 257 patients with and without anemia. Annual treatment costs were significantly higher for patients with anemia (Ringgit Malaysia [RM] 4219 [US $983] vs. RM2705 [US $630]; P = 0.01). QOL scores were lower for patients with anemia but not statistically significant (physical component summary score: 44.8 vs. 46.2; P = 0.052; mental component summary score: 51.3 vs. 51.7; P = 0.562). Costs were higher and QOL lower among CKD stage 5 patients.

    CONCLUSIONS: This study was the first to examine anemia in this group of patients. Costs were significantly higher among anemic patients compared with nonanemic patients; patients with higher CKD stage 5 fared less well than did those in lower stages. This information suggests the need to increase detection, prevention, and early treatment of anemia when managing T2DM patients, particularly those with CKD.
  11. Towards consolidated bioprocessing of biomass and plastic substrates for semi-synthetic production of bio-poly(ethylene furanoate) (PEF) polymer using omics-guided construction of artificial microbial consortia
    Omar MN, Minggu MM, Nor Muhammad NA, Abdul PM, Zhang Y, Ramzi AB
    Enzyme Microb Technol, 2024 Mar 15;177:110429.
    PMID: 38537325 DOI: 10.1016/j.enzmictec.2024.110429
    Poly(ethylene furanoate) (PEF) plastic is a 100% renewable polyester that is currently being pursued for commercialization as the next-generation bio-based plastic. This is in line with growing demand for circular bioeconomy and new plastics economy that is aimed at minimizing plastic waste mismanagement and lowering carbon footprint of plastics. However, the current catalytic route for the synthesis of PEF is impeded with technical challenges including high cost of pretreatment and catalyst refurbishment. On the other hand, the semi-biosynthetic route of PEF plastic production is of increased biotechnological interest. In particular, the PEF monomers (Furan dicarboxylic acid and ethylene glycol) can be synthesized via microbial-based biorefinery and purified for subsequent catalyst-mediated polycondensation into PEF. Several bioengineering and bioprocessing issues such as efficient substrate utilization and pathway optimization need to be addressed prior to establishing industrial-scale production of the monomers. This review highlights current advances in semi-biosynthetic production of PEF monomers using consolidated waste biorefinery strategies, with an emphasis on the employment of omics-driven systems biology approaches in enzyme discovery and pathway construction. The roles of microbial protein transporters will be discussed, especially in terms of improving substrate uptake and utilization from lignocellulosic biomass, as well as from depolymerized plastic waste as potential bio-feedstock. The employment of artificial bioengineered microbial consortia will also be highlighted to provide streamlined systems and synthetic biology strategies for bio-based PEF monomer production using both plant biomass and plastic-derived substrates, which are important for circular and new plastics economy advances.
  12. Modeling and computational characterization of a Xanthomonas sp. Hypothetical protein identifies a remote ortholog of Burkholderia lethal factor 1
    Muhamad Ismail NAS, Yap SH, Mohamad Yussoff MA, Nor Muhammad NA, Firdaus-Raih M, Quay DHX
    J Biomol Struct Dyn, 2023;41(13):6027-6039.
    PMID: 35862639 DOI: 10.1080/07391102.2022.2100827
    Burkholderia Lethal Factor 1 (BLF1) is a deamidase first characterized in Burkholderia pseudomallei. This enzyme inhibits cellular protein synthesis by deamidating a glutamine residue to a glutamic acid in its target protein, the eukaryotic translation initiation factor 4 A (eIF4A). In this work, we present the characterization of a hypothetical protein from Xanthomonas sp. Leaf131 as the first report of a BLF1 family ortholog outside of the Burkholderia genus. Although standard sequence similarity searches such as BLAST were not able to detect the homology between the Xanthomonas sp. Leaf131 hypothetical protein sequence and BLF1, our computed structure model for the Xanthomonas sp. hypothetical protein revealed structural similarities with an RMSD of 2.7 Å/164 Cα atoms and a TM-score of 0.72 when superposed. Structural comparisons of the Xanthomonas model structure against BLF1 and Escherichia coli cytotoxic necrotizing factor 1 (CNF1) revealed that the conserved signature LXGC motif and putative catalytic residues are structurally aligned thus signifying a level of functional or mechanistic similarity. Protein-protein docking analysis and molecular dynamics simulations also demonstrated that eIF4A could still be a possible target substrate for deamidation by XLF1 as it is for BLF1. We therefore propose that this Xanthomonas hypothetical protein be renamed as Xanthomonas Lethal Factor 1 (XLF1). Our work also provides further evidence of the utility of programs such as AlphaFold in bridging the computational function annotation transfer gap despite very low sequence identities of under 20%.Communicated by Ramaswamy H. Sarma.
  13. Fulltext Translation and Validation of the Malay Version of the Emotion Regulation Questionnaire for Children and Adolescents (ERQ-CA)
    Mohd Ali M, Mohd Hoesni S, Rosharudin NA, Yusoff SR, Razman MOI, Khairuddin KF, et al.
    Int J Environ Res Public Health, 2022 Sep 10;19(18).
    PMID: 36141671 DOI: 10.3390/ijerph191811399
    The Emotion Regulation Questionnaire for Children and Adolescents (ERQ-CA) has been translated and adapted globally. This study aimed to examine the psychometric properties of the Malay version of the ERQ-CA. The ERQ-CA underwent forward and back translation twice and was tested in two separate studies, Study 1 and Study 2, with 296 and 359 students aged between 13 and 14 years old, respectively. Cronbach's alpha values were calculated, and confirmatory factor analysis was conducted. The results from Study 1 demonstrate good internal consistency for cognitive reappraisal and expressive suppression. The results indicate a good factor loading for most of the items, but only one value of the goodness-of-fit met the criteria for a good fit. The results from Study 2 show improvements in the values of the goodness-of-fit that are comparable to previous studies, but there was a decrease in the factor loading scores. Overall, the Malay version of the ERQ-CA possesses acceptable reliability and validity. Further studies are required in the near future to develop a Malay version of the ERQ-CA that reasonably represents Malaysian adolescents.
  14. Role of Religion in Preventing Youth Sexual Activity in Malaysia: A Mixed Methods Study
    Muhammad NA, Shamsuddin K, Sulaiman Z, Amin RM, Omar K
    J Relig Health, 2017 Dec;56(6):1916-1929.
    PMID: 26809242 DOI: 10.1007/s10943-016-0185-z
    One of the popular approaches of preventing youth sexual activity in Malaysia is using religion to promote premarital sexual abstinence. Despite this intervention, youth continue to practise premarital sex. Thus, the purpose of this exploratory mixed methods study was to understand the role of religion on sexual activity among college students in Klang Valley, Malaysia. A self-administered questionnaire survey to determine the relationship between religiosity and youth sexual activity was carried out on 1026 students recruited from 12 randomly selected colleges. Concurrently, face-to-face interviews were conducted on 15 students to explore how religiosity had influenced their decision on sexual activity. The survey data were analysed using logistic regression, while the qualitative data from the interviews were examined using thematic analysis with separate analysis for each gender. Both quantitative and qualitative results were then compared and integrated. Religious activity significantly reduced the risk of continuing sexual activity among female students (AOR = 0.67, CI = 0.47, 0.95, p = 0.02) but not male students. There was no significant relationship of religious affiliation and intrinsic religiosity (inner faith) to sexual activity by gender. Having faith in religion and strong sexual desire were the main themes that explained participants' sexual behaviour. Engaging in religious activity might be effective at preventing female students from being sexually active. However, when sexual urges and desires are beyond control, religiosity might not be effective.
  15. Fulltext Physical and psychosocial impacts of pregnancy on adolescents and their coping strategies: a descriptive study in Kuala Lumpur, Malaysia
    Su XV, Muhammad NA, Tan PS, Tan KTM, Tohid H, Omar K
    Malaysian Journal of Public Health Medicine, 2014;14(3):0-0.
    MyJurnal
    Teenage pregnancy carries serious impacts on adolescent health. This study aimed to examine the effects of pregnancy on adolescents and to explore how they cope with the problems they faced during the pregnancy. It involved 26 adolescents residing in a government shelter home in Kuala Lumpur. A self-administered questionnaire containing a mixture of open- and closed-ended questions was used. Among physical (sleeping problem and self-care problem), psychological (emotional difficulties and low self-efficacy) and social (stigma and discrimination, financial difficulty, friendship problem and school dropout) problems, emotional difficulties were the most common problems, whereas stigma and discrimination was the least common. Young adolescents aged less than 16 years old were significantly associated with poor self-care (p=0.01). To cope with their problems, the adolescents generally used avoidance, withdrawal, and social support, particularly from parents and peers. Doctors were the least popular among all. In conclusion, holistic and individualised care is needed. Strategies to reduce emotional problem experienced by pregnant adolescents should be implemented. The available healthcare services for teenage pregnancy should also be promoted.
  16. Fulltext Perceived effects of the Malaysian National Tobacco Control Programme on adolescent smoking cessation: a qualitative study
    Tohid H, Ishak N, Muhammad NA, Ahmad FN, Aziz AA, Omar K
    Malays J Med Sci, 2012 Apr;19(2):35-47.
    PMID: 22973136 MyJurnal
    BACKGROUND: The prevalence of teenage smoking has decreased over the past decade following the implementation of the national tobacco control programme. However, the effect of the programme on smoking cessation in teenagers has not been determined.
    METHODS: Twenty-eight participants (12 teenagers, 8 teachers, and 8 doctors) were interviewed using 5 in-depth interviews and 3 group discussions. Social cognitive theory (SCT) was applied as the theoretical framework. Semi-structured interview protocols were used, and thematic analysis and analytic generalisation utilising SCT were performed.
    RESULTS: The current national tobacco control programme was found to be ineffective in promoting smoking cessation among teenagers. The participants attributed the ineffective campaign to the followings: inadequacy of message content, lack of exposure to the programme, and poor presentation and execution. In addition, the participants perceived the developed tobacco control policies to be a failure based on poor law enforcement, failure of retailers to comply with the law, social availability of cigarettes to teenagers, and easy availability of cheap, smuggled cigarettes. This study highlighted that the programme-related problems (environmental factors) were not the only factors contributing to its perceived ineffectiveness. The cunning behaviour of the teenagers (personal factor) and poor self-efficacy to overcome nicotine addiction (behavioural factor) were also found to hinder cessation.
    CONCLUSION: Tobacco control programmes should include strategies beyond educating teenagers about smoking and restricting their access to cigarettes. Strategies to manage the cunning behaviour of teenagers and strategies to improve their self-efficacy should also be implemented. These comprehensive programmes should have a foundation in SCT, as this theory demonstrates the complex interactions among the environmental, personal, and behavioural factors that influence teenage smoking.
    KEYWORDS: adolescent; health campaigns; qualitative research; tobacco cessation; tobacco smoking
  17. Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer
    Emrizal R, Nor Muhammad NA
    PeerJ, 2020;8:e9019.
    PMID: 32617187 DOI: 10.7717/peerj.9019
    Porphyromonas gingivalis is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that ultimately leads to tooth loss. Virulence factors that contribute to periodontitis are secreted by Type IX Secretion System (T9SS). There are aspects of T9SS protein components that have yet to be characterised. Thus, the aim of this study is to investigate the phylogenetic relationship between members of 20 T9SS component protein families. The Bayesian Inference (BI) trees for 19 T9SS protein components exhibit monophyletic clades for all major classes under Bacteroidetes with strong support for the monophyletic clades or its subclades that is consistent with phylogeny exhibited by the constructed BI tree of 16S rRNA. The BI tree of PorR is different from the 19 BI trees of T9SS protein components as it does not exhibit monophyletic clades for all major classes under Bacteroidetes. There is strong support for the phylogeny exhibited by the BI tree of PorR which deviates from the phylogeny based on 16S rRNA. Hence, it is possible that the porR gene is subjected to horizontal transfer as it is known that virulence factor genes could be horizontally transferred. Seven genes (porR included) that are involved in the biosynthesis of A-LPS are found to be flanked by insertion sequences (IS5 family transposons). Therefore, the intervening DNA segment that contains the porR gene might be transposed and subjected to conjugative transfer. Thus, the seven genes can be co-transferred via horizontal gene transfer. The BI tree of UgdA does not exhibit monophyletic clades for all major classes under Bacteroidetes which is similar to the BI tree of PorR (both are a part of the seven genes). Both BI trees also exhibit similar topology as the four identified clusters with strong support and have similar relative positions to each other in both BI trees. This reinforces the possibility that porR and the other six genes might be horizontally transferred. Other than the BI tree of PorR, the 19 other BI trees of T9SS protein components also exhibit evidence of horizontal gene transfer. However, their genes might undergo horizontal gene transfer less frequently compared to porR because the intervening DNA segment that contains porR is easily exchanged between bacteria under Bacteroidetes due to the presence of insertion sequences (IS5 family transposons) that flank it. In conclusion, this study can provide a better understanding about the phylogeny of T9SS protein components.
  18. Fulltext Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis
    Ramzi AB, Che Me ML, Ruslan US, Baharum SN, Nor Muhammad NA
    PeerJ, 2019;7:e8065.
    PMID: 31879570 DOI: 10.7717/peerj.8065
    Background: G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels.

    Methods: In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3.

    Results: G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis.

    Discussion: This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.

  19. Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models
    Ting CF, Harun S, Daud KM, Sulaiman S, Nor Muhammad NA
    Prog Biophys Mol Biol, 2024 Apr 09.
    PMID: 38604435 DOI: 10.1016/j.pbiomolbio.2024.04.002
    Gene regulatory network (GRN) comprises complicated yet intertwined gene-regulator relationships. Understanding the GRN dynamics will unravel the complexity behind the observed gene expressions. Insect gene regulation is often complicated due to their complex life cycles and diverse ecological adaptations. The main interest of this review is to have an update on the current mathematical modelling methods of GRNs to explain insect science. Several popular GRN architecture models are discussed, together with examples of applications in insect science. In the last part of this review, each model is compared from different aspects, including network scalability, computation complexity, robustness to noise and biological relevancy.
  20. A comparative study of radiation doses between phantom and patients via CT angiography of the intra-/extra-cranial, pulmonary, and abdominal/pelvic arteries
    Karim MKA, Sabarudin A, Muhammad NA, Ng KH
    Radiol Phys Technol, 2019 Dec;12(4):374-381.
    PMID: 31468370 DOI: 10.1007/s12194-019-00532-8
    This study aimed to evaluate effective dose and size-specific dose estimate (SSDE) of computed tomography angiography (CTA) examination using an anthropomorphic phantom. We included three CTA examination protocols to evaluate the intra- and extra-cranial arteries, pulmonary artery (CTPA), and abdominal vessels. Patient SSDEs were measured retrospectively to estimate patient dose, relative to the bodyweight of the patient and volume CT dose index (CTDIvol). Our findings revealed that the highest dose was absorbed by the left lobe of the thyroid gland during intra-/extra-cranial CTA and CTPA, that is, 14.11 ± 0.24 mGy and 16.20 ± 3.95 mGy, respectively. However, the highest absorbed dose in abdominal/pelvic CTA was the gonads (8.98 ± 0.30 mGy), while other radiosensitive organs in intra- and extra-cranial CTA, CTPA, and abdominal/pelvic CTA did not demonstrate significant differences between organs/structures with p value 0.88, 0.11, and 0.54, respectively. The estimated effective dose in intra-/extra-cranial CTA was lower in patients (0.80 ± 0.60 mSv) than in the phantom (0.83 mSv), but it was the opposite for CTPA, with the effective dose being higher in patients (7.54 ± 3.09 mSv) than in the phantom (6.68 mSv). Similar to the effective dose, only CTPA SSDEs were significantly higher in men than in women (19.74 ± 4.79 mGy versus 7.9 mGy). Effective dose and SSDE are clinically relevant parameters that can help estimate a more accurate patient dose based on a patient's size.
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