Browse publications by year: 2017

  1. Kamarudin KH, Hattori M, Sumita YI, Taniguchi H
    J Prosthet Dent, 2017 Sep 06.
    PMID: 28888415 DOI: 10.1016/j.prosdent.2017.06.005
    A surgical obturator may need to be modified during the healing process after tissue resection. Apart from relining the fitting surfaces to accommodate the healing wound and changes in the surrounding tissues, other modifications such as adding teeth are sometimes required to improve esthetics and speech. This article describes a chairside technique to add customized acrylic resin teeth to an existing surgical obturator.
  2. Al Maghaireh DF, Abdullah KL, Chong MC, Chua YP, Al Kawafha MM
    J Pediatr Nurs, 2017 06 19;36:132-140.
    PMID: 28888494 DOI: 10.1016/j.pedn.2017.06.007
    PURPOSE: To investigate the stressors and stress levels among Jordanian parents of infants in the NICU and their relationship to three factors: anxiety, depression and sleep disturbance.

    DESIGN AND METHODS: A cross-sectional survey was conducted in two hospitals in Jordan among 310 parents of infants in the NICU by using PSS: NICU and PROMIS.

    RESULTS: Both parents experienced high levels of stress, anxiety, depression and sleep disturbance. There was a significant difference in stress level between mothers and fathers [t (308)=3.471, p=0.001], with the mothers experiencing higher stress than the fathers [mean: mothers=108.58; fathers=101.68]. The highest and lowest sources of stress were infant behavior and appearance (M=4.09) and sights and sounds in the NICU (M=3.54), respectively. The correlation between stress levels with anxiety (r=0.79) and depression (r=0.75) was strong and positive while sleep disturbance was significant and moderate (r=0.43).

    CONCLUSIONS: The mothers experienced higher levels of stress compared to fathers, with positive correlations between stress and anxiety, depression and sleep disturbance.

    PRACTICAL IMPLICATIONS: The findings of this study create nursing awareness of parent stress and its impact, which will help them to improve nursing care for parents.

    MeSH terms: Adult; Anxiety/etiology; Anxiety/epidemiology; Cross-Sectional Studies; Depression/diagnosis; Depression/epidemiology*; Fathers/psychology; Female; Humans; Infant; Infant, Newborn; Intensive Care Units, Neonatal*; Jordan; Male; Mothers/psychology; Parent-Child Relations; Parents/psychology*; Sleep Wake Disorders/etiology; Sleep Wake Disorders/epidemiology*; Stress, Psychological/etiology; Stress, Psychological/epidemiology; Incidence; Risk Assessment
  3. Nudin NFH, Ali AM, Ngah N, Mazlan NZ, Mat N, Ghani MNA, et al.
    C. R. Biol., 2017 Aug;340(8):359-366.
    PMID: 28888550 DOI: 10.1016/j.crvi.2017.08.003
    Plant breeding is a way of selection of a particular individual for the production of the progeny by separating or combining desired characteristics. The objective of this study was to justify different characteristics of Dioscorea hispida (Ubi gadong) varieties using molecular techniques to select the best variety for sustainable production at the farmer's level. A total of 160 germplasms of Ubi gadong were collected from different locations at the Terengganu and Kelantan states of Malaysia. Forty eight (48) out of 160 germplasms were selected as "primary" selection based on yield and other qualitative characters. Selected collections were then grown and maintained for ISSR marker-assisted genetic diversity analysis. Overall plant growth and yield of tubers were also determined. A total of 12 ISSR markers were tested to justify the characteristics of Ubi gadong varieties among which three markers showed polymorphic bands and on average 57.3% polymorphism were observed representing the highest variation among germplasms. The ISSR marker based on UPGMA cluster analysis grouped all 48 D. hispida into 10 vital groups that proved a vast genetic variation among germplasm collections. Therefore, hybridization should be made between two distant populations. The D. hispida is already proved as the highest starch content tuber crops and very rich in vitamins with both micro and macro minerals. Considering all these criteria and results from marker-assisted diversity analysis, accessions that are far apart based on their genetic coefficient (like DH27 and DH71; DH30 and DH70; DH43 and DH62; DH45 and DH61; DH77 and DH61; DH78 and DH57) could be selected as parents for further breeding programs. This will bring about greater diversity, which will lead to high productive index in terms of increase in yield and overall quality and for the ultimate target of sustainable Ubi gadong production.
    MeSH terms: Plant Breeding*; Genetic Markers; Hybridization, Genetic; Malaysia; Phylogeny; Polymorphism, Genetic; Genetic Variation*; Cluster Analysis; Crops, Agricultural; Dioscorea/genetics*
  4. Gan SY, Saedon NI, Sukanya S, Fairuz NHA, Sakinah SMN, Fatin NIAH, et al.
    Med J Malaysia, 2017 08;72(4):203-208.
    PMID: 28889130 MyJurnal
    No abstract available.
    MeSH terms: Aged; Aged, 80 and over; Emergency Service, Hospital/organization & administration; Emergency Service, Hospital/statistics & numerical data; Female; Health Services Accessibility/organization & administration; Humans; Malaysia; Male; Syncope/diagnosis; Syncope/therapy*
  5. Koh KC, Islam M, Chan WK, Lee WY, Ho YW, Alsagoff SAH, et al.
    Med J Malaysia, 2017 08;72(4):209-214.
    PMID: 28889131
    INTRODUCTION: In Malaysia, the prevalence of missed opportunities for HIV-testing is unknown. Missed opportunities have been linked to late diagnosis of HIV and poorer outcome for patients. We describe missed opportunities for earlier HIV-testing in newly-HIV-diagnosed patients.

    METHODS: Cross sectional study. Adult patients diagnosed with HIV infection and had at least one medical encounter in a primary healthcare setting during three years prior to diagnosis were included. We collected data on sociodemographic characteristics, patient characteristics at diagnosis, HIV-related conditions and whether they were subjected to risk assessment and offered HIV testing during the three years prior to HIV diagnosis.

    RESULTS: 65 newly HIV-diagnosed patients (male: 92.3%; Malays: 52.4%; single: 66.7%; heterosexual: 41%; homosexual 24.6%; CD4 <350 at diagnosis: 63%). 93.8% were unaware of their HIV status at diagnosis. Up to 56.9% had presented with HIV-related conditions at a primary healthcare facility during the three years prior to diagnosis. Slightly more than half were had risk assessment done and only 33.8% were offered HIV-testing.

    CONCLUSIONS: Missed opportunities for HIV-testing was unacceptably high with insufficient risk assessment and offering of HIV-testing. Risk assessment must be promoted and primary care physicians must be trained to recognize HIV-related conditions that will prompt them to offer HIVtesting.

    MeSH terms: Adult; Cross-Sectional Studies; Female; Humans; Malaysia; Male; Middle Aged; Referral and Consultation/statistics & numerical data; HIV Infections/diagnosis*; Early Diagnosis; Young Adult; Tertiary Care Centers/statistics & numerical data*
  6. Pang KA, Pang KP, Pang EB, Tan YN, Chan YH, Siow JK
    Med J Malaysia, 2017 08;72(4):215-220.
    PMID: 28889132
    OBJECTIVE: To describe the prevalence of food allergy in Asian patients with allergic rhinitis.

    STUDY DESIGN: A non-randomized prospectively collected patients over a three year period, with complaints of nose congestion, rhinorrhea and/or nasal discharge.

    RESULTS: There were 435 patients enrolled, 213 children and 222 adults. The children group had a high prevalence of allergen specific IgE to Dermatophagoides pteryonysinus (70%), Dermatophagoides farina (69%), and Blomia tropicalis (55%); followed by dogs (32%), cats (19%) and cockroaches (19%). In the children food allergy category, the top three allergens were egg white (54%), milk (31%) and soya bean (13%). The adult group had results of Dermatophagoides pteryonysinus (71%), Dermatophagoides farina (72%), and Blomia tropicalis (59%); the adult food allergy category, the top 3 allergens were egg white (13%), milk (6%) and soya bean (5%). There was a statistically significant difference in the child and adult group for Dust, D. pteryonysinus, D. farina, B.tropicalis, egg white, wheat, gluten and soya bean. In the age specific child groups, there was an increased in egg food allergy levels, with a peak at the age of five-nine years old and decreasing thereafter (p=0.04). In the children group, the mean Total Nasal Symptom Score (TNSS) was 10.3 (range of 7 to 13); the adult group was similar, with a mean TNSS of 9.8 (range 5 to 12).

    CONCLUSION: The prevalence of food allergy in paediatric patients with allergic rhinitis is fairly high and should be considered when treating these children.

    MeSH terms: Adolescent; Adult; Age Factors; Asia, Southeastern/epidemiology; Asia, Western/epidemiology; Child; Child, Preschool; Far East/epidemiology; Food Hypersensitivity/etiology; Food Hypersensitivity/epidemiology*; Humans; Middle Aged; Prospective Studies; Prevalence; Young Adult; Rhinitis, Allergic/etiology; Rhinitis, Allergic/epidemiology*
  7. Ibrahim N, Sherina MS, Phang CK, Mukhtar F, Awang H, Ang JK, et al.
    Med J Malaysia, 2017 08;72(4):221-227.
    PMID: 28889133 MyJurnal
    No abstract available.
    MeSH terms: Adolescent; Age Factors; Anxiety/etiology; Anxiety/epidemiology; Cross-Sectional Studies; Depression/etiology; Depression/epidemiology*; Female; Humans; Malaysia/epidemiology; Male; Psychiatric Status Rating Scales; Psychological Tests; Risk Factors; Schools/statistics & numerical data*; Self Concept; Sex Factors; Socioeconomic Factors; Stress, Psychological/etiology; Stress, Psychological/epidemiology; Prevalence; Bullying/statistics & numerical data; Suicidal Ideation*
  8. Manakandan SK, Rosnah I, Mohd Ridhuan J, Priya R
    Med J Malaysia, 2017 08;72(4):228-235.
    PMID: 28889134 MyJurnal
    BACKGROUND: The most crucial step in forming a set of survey questionnaire is deciding the appropriate items in a construct. Retaining irrelevant items and removing important items will certainly mislead the direction of a particular study. This article demonstrates Fuzzy Delphi method as one of the scientific analysis technique to consolidate consensus agreement within a panel of experts pertaining to each item's appropriateness. This method reduces the ambiguity, diversity, and discrepancy of the opinions among the experts hence enhances the quality of the selected items. The main purpose of this study was to obtain experts' consensus on the suitability of the preselected items on the questionnaire.

    METHODS: The panel consists of sixteen experts from the Occupational and Environmental Health Unit of Ministry of Health, Vector-borne Disease Control Unit of Ministry of Health and Occupational and Safety Health Unit of both public and private universities. A set of questionnaires related to noise and chemical exposure were compiled based on the literature search. There was a total of six constructs with 60 items in which three constructs for knowledge, attitude, and practice of noise exposure and three constructs for knowledge, attitude, and practice of chemical exposure. The validation process replicated recent Fuzzy Delphi method that using a concept of Triangular Fuzzy Numbers and Defuzzification process.

    RESULTS: A 100% response rate was obtained from all the sixteen experts with an average Likert scoring of four to five. Post FDM analysis, the first prerequisite was fulfilled with a threshold value (d) ≤ 0.2, hence all the six constructs were accepted. For the second prerequisite, three items (21%) from noise-attitude construct and four items (40%) from chemical-practice construct had expert consensus lesser than 75%, which giving rise to about 12% from the total items in the questionnaire. The third prerequisite was used to rank the items within the constructs by calculating the average fuzzy numbers. The seven items which did not fulfill the second prerequisite similarly had lower ranks during the analysis, therefore those items were discarded from the final draft.

    CONCLUSION: Post FDM analysis, the experts' consensus on the suitability of the pre-selected items on the questionnaire set were obtained, hence it is now ready for further construct validation process.

    MeSH terms: Delphi Technique; Humans; Health Knowledge, Attitudes, Practice; Noise, Occupational/adverse effects; Surveys and Questionnaires/standards; Reproducibility of Results; Occupational Exposure/adverse effects; Fuzzy Logic
  9. Guelker JE, Rock T, Ott R, Katoh M, Kroeger K, Guelker R, et al.
    Med J Malaysia, 2017 08;72(4):236-240.
    PMID: 28889135
    OBJECTIVES: Percutaneous coronary intervention (PCI) of total chronic total occlusion (CTO) still remains a major challenge in interventional cardiology. There is only insignificant knowledge reported in the literature about age differences in CTO recanalization. We analyzed in this study the issue of the impact of age on procedural characteristics, complications and short-term outcome.

    METHODS: Between 2012-2016 we included 440 patients. They underwent PCI for at least one CTO. Antegrade and retrograde CTO techniques were applied. The retrograde approach was used only after failed antegrade intervention. Continuous data are presented as the mean ± standard deviation; categorical data are presented as numbers and percentages unless otherwise specified. We used Twosamplet- t-test with equal variance to test the significant differences of the variables between the two cohorts.

    RESULTS: Procedural success proved independently of age. There was no significant interaction between age and procedural success (p=0.5). Complication rates were low in both groups (2.7% vs. 4%; p=0,4) with no difference in statistical significance.

    CONCLUSIONS: Our study suggests that in an aging society patients with severe coronary artery disease and chronical total occlusions an interventional therapy should be used more intensively. It can be performed safe and feasible.

    MeSH terms: Age Factors; Aged; Female; Humans; Male; Middle Aged; Retrospective Studies; Treatment Outcome; Coronary Occlusion/surgery*
  10. Faisal AH, Sopian AW, Tidi H
    Med J Malaysia, 2017 08;72(4):241-243.
    PMID: 28889136 MyJurnal
    Electromagnetic navigational bronchoscopy (ENB), one of the methods of navigational bronchoscopy is an advanced diagnostic tool allowing tissue sampling at the lung peripheries which were previously accessible only by computed tomography (CT) guidance or video-assisted thoracoscopic surgery (VATS). We report a 53-year-old man who presented with a cough and dyspnea with constitutional symptoms for one month. CT thorax revealed multiple bilateral peripheral lung nodules and there were no endobronchial lesions on flexible bronchoscopy. ENB was performed using a loan machine from Veran navigational technology. Biopsy successfully revealed small cell carcinoma of the lung thus preventing him from undergoing a more invasive diagnostic procedure. This case highlights the utility of ENB in the evaluation of peripheral lung nodules that were inaccessible by conventional bronchoscopy. This is one of the first few successful applications of Veran ENB in Asia.
    MeSH terms: Bronchoscopy/methods; Humans; Lung Neoplasms/diagnosis*; Male; Middle Aged; Radiography, Thoracic; Tomography, X-Ray Computed; Small Cell Lung Carcinoma/diagnosis*
  11. Ng CY, Lee SL, Foo SL
    Med J Malaysia, 2017 08;72(4):244-245.
    PMID: 28889137 MyJurnal
    Abdominal pain is one of the common presentations in severe dengue infection. We report a rare case of perforated gastric ulcer in a young man diagnosed with severe dengue infection and the challenges we faced in managing this patient. Perforated gastric ulcer need to be considered if there are signs of peritonitis and persistent abdominal pain that does not conform to the natural history of dengue. Proper imaging and early surgical intervention in perforated gastric ulcer is vital in preventing further complication and reducing the risk of mortality.
    MeSH terms: Adult; Dengue/complications*; Humans; Male; Peptic Ulcer Perforation/etiology*; Peptic Ulcer Perforation/surgery; Peptic Ulcer Perforation/virology; Tomography, X-Ray Computed
  12. Boo YL, How KN, Pereira DS, Chin PW, Foong KK, Lim SY
    Med J Malaysia, 2017 08;72(4):246-247.
    PMID: 28889138 MyJurnal
    Pulmonary actinomycosis is a rare yet important and challenging diagnosis to make. It is commonly confused with other lung diseases, such as tuberculosis and bronchogenic carcinoma, leading to delay diagnosis or misdiagnosis. A 49-year-old man presented with a chronic cough, hemoptysis, and pleuritic chest pain. His initial imaging studies including computed tomography (CT) was suggestive of bronchogenic carcinoma. A subsequent CTguided biopsy was consistent with pulmonary actinomycosis and excluded the possibility of bronchogenic carcinoma. He was treated with antibiotic therapy and achieved remission with complete radiological resolution upon follow-up.
    MeSH terms: Actinomycosis/diagnosis*; Diagnosis, Differential; Humans; Lung/microbiology; Lung Diseases/diagnosis*; Lung Diseases/microbiology; Lung Neoplasms/diagnosis*; Male; Middle Aged; Radiography, Thoracic; Tomography, X-Ray Computed
  13. Visayaragawan N, Selvarajah N, Apparau H, Kamaru Ambu V
    Med J Malaysia, 2017 08;72(4):248-249.
    PMID: 28889139 MyJurnal
    The diagnostic challenge of Bohring-Opitz Syndrome, a rare genetic disorder has haunted clinicians for ages. Our patient was born at term via caesarean-section with a birth weight of 1.95 kilograms. She had mild laryngomalacia, gastroesophageal reflux disease and seizures. Physical signs included microcephaly, hemangioma, low set ears, cleft palate, micrognatia and the typical BOS posture. Chromosomal analysis showed 46 xx -Bohring-Opitz Syndrome overlapped with C- syndrome. Goal-directed holistic care with integration of parent/carer training was started very early. She succumbed to a Respiratory- Syncitial-Virus and Pseudomonas pneumonia complicated with sepsis at the age of two years and 11 months.
    MeSH terms: Child, Preschool; Craniosynostoses/complications; Craniosynostoses/diagnosis; Craniosynostoses/genetics*; Craniosynostoses/therapy; Female; Gastroesophageal Reflux/etiology; Humans; Intellectual Disability/complications; Intellectual Disability/diagnosis; Intellectual Disability/genetics*; Intellectual Disability/therapy; Seizures/etiology; Fatal Outcome
  14. Tang RY, Cheong BM
    Med J Malaysia, 2017 08;72(4):250-251.
    PMID: 28889140 MyJurnal
    The incidence of renal abscesses is not common. Patients usually have risk factors like diabetes mellitus or an underlying condition which predisposes to urinary tract infections. We report a case of a previously healthy young girl with multiple bilateral renal abscesses. Ultrasonography revealed multiple renal abscesses with a possible differential diagnosis of polycystic kidney disease with infected cysts. No renal calculi were seen. CT-scan of kidneys confirmed the diagnosis. Blood and urine cultures were repeatedly negative. She was treated with two weeks of intravenous antibiotics followed by another four weeks of oral Ciprofloxacin. No surgical intervention was carried out. Repeated ultrasound at six months showed complete resolution of all the renal abscesses.
    MeSH terms: Abscess/diagnosis*; Abscess/drug therapy; Administration, Oral; Adolescent; Ceftazidime/administration & dosage; Ceftazidime/therapeutic use; Ciprofloxacin/administration & dosage; Ciprofloxacin/therapeutic use; Female; Humans; Infusions, Intravenous; Kidney Diseases/diagnosis*; Kidney Diseases/drug therapy; Tomography, X-Ray Computed
  15. Devaraj NK
    Med J Malaysia, 2017 08;72(4):252-253.
    PMID: 28889141 MyJurnal
    This is a rare but interesting case of Mr. MZ who had a lifethreatening pericardial effusion presenting to the primary care clinic. Through great clinical acumen and prudent targeted investigations, diagnosis of this rare condition was reached and urgent referral made to the cardiology team which performed an emergency pericardiocentesis which proved to be life -saving. However, the hovering poor prognosis of Mr. MZ may prompt for a referral to the palliative care team to provide quality end of life care for this unfortunate patient.
    MeSH terms: Emergencies; Emergency Service, Hospital; Humans; Male; Middle Aged; Pericardial Effusion/diagnosis*; Pericardial Effusion/therapy; Primary Health Care; Referral and Consultation; Pericardiocentesis
  16. Teh YH, Tan YP, Zain MM
    Med J Malaysia, 2017 08;72(4):254-256.
    PMID: 28889142 MyJurnal
    Eyelid reconstruction is complex and challenging since it is not only for structural and functional restoration, but also for an acceptable aesthetic result. In full thickness eyelid injuries, it will involve both anterior and posterior lamella. Therefore, when reconstructing the defect, it requires at least two layers; one will be a flap with blood supply, and the other can be a free graft. In this case, a rotational advancement cheek flap and composite graft were used to reconstruct the lower eyelid.
    MeSH terms: Dengue/complications*; Embolization, Therapeutic/methods*; Female; Hematoma/etiology*; Hematoma/therapy; Humans; Middle Aged; Tomography, X-Ray Computed; Ultrasonography
  17. Othman MA, Ghazali WSW, Hamid WZWA, Wong KK, Yahya NK
    Saudi Med J, 2017 Sep;38(9):934-941.
    PMID: 28889152 DOI: 10.15537/smj.2017.9.20841
    OBJECTIVES: To evaluate levels of anti-carbamylated protein (anti-CarP) antibodies in rheumatoid arthritis (RA) patients and to determine their association with serological parameters and disease activity. Methods: A cross-sectional study involving 105 multiethnic RA patients (48 rheumatoid factor [RF]-positive and 57 RF-negative patients) was conducted at Hospital Universiti Sains Malaysia, Kelantan, Malaysia, from January 2015 to February 2016. Fifty healthy controls (HCs) were included. C-reactive protein (CRP), RF, anti-cyclic citrullinated peptide (anti-CCP) and anti-CarP antibodies were measured. A health assessment questionnaire (HAQ) was administered to the study participants and 28-joint Disease Activity Score (DAS28) were obtained. Results: The level of anti-CarP antibodies was significantly increased in the RA patients compared with HCs (p=0.042). The presence of anti-CarP antibodies was significantly associated with RF (p=0.019) and the HAQ (p=0.010). A significant association between the presence of anti-CarP antibodies and the DAS28 was not found (p=0.632). Conclusion: Our study provides further evidence that the level of anti-CarP antibodies is significantly elevated in RA patients.

    Study site: Rheumatology clinic, Hospital Universiti Sains Malaysia
    MeSH terms: Adult; Aged; Arthritis, Rheumatoid/immunology*; Autoantibodies/immunology*; Carbamates/immunology*; China/ethnology; Female; Hospitals, University; Humans; India/ethnology; Malaysia/ethnology; Male; Rheumatoid Factor/immunology*
  18. Sakthiswary R, Rajalingam S, Hussein H, Sridharan R, Asrul AW
    Clin Rheumatol, 2017 Dec;36(12):2683-2688.
    PMID: 28889184 DOI: 10.1007/s10067-017-3817-0
    The aim of the study is to investigate the correlation of serum cartilage oligomeric matrix protein (COMP) levels with articular cartilage damage based on sonographic knee cartilage thickness (KCT) and disease activity in rheumatoid arthritis (RA). A total of 61 RA patients and 27 healthy controls were recruited in this study. Serum samples were obtained from all subjects to determine the serum COMP levels. All subjects had bilateral ultrasound scan of their knees. The KCT was based on the mean of measurements at three sites: the medial condyle, lateral condyle and intercondylar notch. Besides, the RA patients were assessed for their disease activity based on 28-joint-based Disease Activity Score (DAS 28). Serum COMP concentrations were significantly elevated in the RA patients compared to the controls (p = 0.001). The serum COMP levels had an inverse relationship with bilateral KCT in RA subjects and the healthy controls. COMP correlated significantly with disease activity based on DAS 28 (r = 0.299, p = 0.010), disease duration (r = 0.439, p = 
    MeSH terms: Adult; Aged; Arthritis, Rheumatoid/blood*; Blood Sedimentation; C-Reactive Protein/metabolism; Cross-Sectional Studies; Female; Hospitals; Humans; Inflammation/blood; Malaysia; Male; Middle Aged; Severity of Illness Index; Ultrasonography; Biomarkers/blood; Cartilage Oligomeric Matrix Protein/blood*
  19. Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, et al.
    Biol. Direct, 2017 Sep 08;12(1):21.
    PMID: 28886750 DOI: 10.1186/s13062-017-0191-4
    BACKGROUND: Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools.

    RESULTS: Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures.

    CONCLUSIONS: We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database ( http://palmxplore.mpob.gov.my ), will provide important resources for studies on the genomes of oil palm and related crops.

    REVIEWERS: This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.

    MeSH terms: Models, Genetic*; Software; Genes, Plant; Genome, Plant*; Computational Biology/methods; Arecaceae/genetics*; Molecular Sequence Annotation*
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