Displaying publications 81 - 100 of 114 in total

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  1. Characterization of TiO(2)-chitosan/glass photocatalyst for the removal of a monoazo dye via photodegradation-adsorption process
    Zainal Z, Hui LK, Hussein MZ, Abdullah AH, Hamadneh IM
    J Hazard Mater, 2009 May 15;164(1):138-45.
    PMID: 18809254 DOI: 10.1016/j.jhazmat.2008.07.154
    In this paper, the newly explored TiO(2)-Chitosan/Glass was suggested as a promising alternative material to conventional means of wastewater treatment. Characterization of TiO(2)-Chitosan/Glass photocatalyst was studied with SEM-EDX, XRD, and Fourier transform infrared spectroscopy (FTIR) analysis. The combination effect of photodegradation-adsorption process for the removal of methyl orange (MO), an acid dye of the monoazo series occur promisingly when four layers of TiO(2)-Chitosan/Glass photocatalyst was used for MO removal. Approximately, 87.0% of total MO removal was achieved. The reactive -NH(2), -OH, and metal oxide contents in the prepared photocatalyst responsible for the photodegradation-adsorption effect were confirmed by FTIR study. Similarly, MO removal behavior was well supported by SEM-EDX and XRD analysis. Significant dependence of MO removal on the TiO(2)-Chitosan loading can be explained in terms of relationship between quantum yield of photocatalytic reactions and photocatalyst structure/activity. Hence, the research work done thus far suggests a new method, having both the advantages of photodegradation-adsorption process in the abatement of various wastewater pollutants.
  2. Optical fibre chemical sensor for trace vanadium(V) determination based on newly synthesized palm based fatty hydroxamic acid immobilized in polyvinyl chloride membrane
    Isha A, Yusof NA, Ahmad M, Suhendra D, Yunus WM, Zainal Z
    Spectrochim Acta A Mol Biomol Spectrosc, 2007 Aug;67(5):1398-402.
    PMID: 17141557
    Fatty hydroxamic acid (FHA) immobilized in polyvinyl chloride (PVC) has been studied as a sensor element of an optical fibre chemical sensor for V(V). By using this instrument, V(V) in solution has been determined in the log concentration range of 0-2.5 (i.e. 1.0-300 mg/L). The detection limit was 1.0 mg/L. The relative standard deviation (R.S.D.) of the method for the reproducibility study at V(V) concentration of 200 mg/L and 300 mg/L were calculated to be 2.9% and 2.0%, respectively. Interference from foreign ions was also studied at 1:1 mole ratio of V(V):foreign ions. It was found that, Fe(III) ion interfered most in the determination of vanadium(V). Excellent agreement with ICP-AES method was achieved when the proposed method was applied towards determination of V(V).
  3. Molecular cloning and immunoglobulin E reactivity of a natural rubber latex lecithinase homologue, the major allergenic component of Hev b 4
    Sunderasan E, Bahari A, Arif SA, Zainal Z, Hamilton RG, Yeang HY
    Clin Exp Allergy, 2005 Nov;35(11):1490-5.
    PMID: 16297147 DOI: 10.1111/j.1365-2222.2005.02371.x
    BACKGROUND:
    Hev b 4 is an allergenic natural rubber latex (NRL) protein complex that is reactive in skin prick tests and in vitro immunoassays. On SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Hev b 4 is discerned predominantly at 53-55 kDa together with a 57 kDa minor component previously identified as a cyanogenic glucosidase. Of the 13 NRL allergens recognized by the International Union of Immunological Societies, the 53-55 kDa Hev b 4 major protein is the only candidate that lacks complete cDNA and protein sequence information.

    OBJECTIVE:
    We sought to clone the transcript encoding the Hev b 4 major protein, and characterize the native protein and its recombinant form in relation to IgE binding.

    METHODS:
    The 5'/3' rapid amplification of cDNA ends method was employed to obtain the complete cDNA of the Hev b 4 major protein. A recombinant form of the protein was over-expressed in Escherichia coli. The native Hev b 4 major protein was deglycosylated by trifluoromethane sulphonic acid. Western immunoblots of the native, deglycosylated and recombinant proteins were performed using both polyclonal antibodies and sera from latex-allergic patients.

    RESULTS:
    The cDNA encoding the Hev b 4 major protein was cloned. Its open reading frame matched lecithinases in the conserved domain database and contained 10 predicted glycosylation sites. Detection of glycans on the Hev b 4 lecithinase homologue confirmed it to be a glycoprotein. The deglycosylated lecithinase homologue was discerned at 40 kDa on SDS-PAGE, this being comparable to the 38.53 kDa mass predicted by its cDNA. Deglycosylation of the lecithinase homologue resulted in the loss of IgE recognition, although reactivity to polyclonal rabbit anti-Hev b 4 was retained. IgE from latex-allergic patients also failed to recognize the non-glycosylated E. coli recombinant lecithinase homologue.

    CONCLUSION:
    The IgE epitopes of the Hev b 4 lecithinase homologue reside mainly in its carbohydrate moiety, which also account for the discrepancy between the observed molecular weight of the protein and the value calculated from its cDNA.
  4. Removal of dyes using immobilized titanium dioxide illuminated by fluorescent lamps
    Zainal Z, Hui LK, Hussein MZ, Taufiq-Yap YH, Abdullah AH, Ramli I
    J Hazard Mater, 2005 Oct 17;125(1-3):113-20.
    PMID: 15996813
    The photodegradation of various dyes in aqueous solution was studied. Experiments were carried out using glass coated titanium dioxide thin film as photocatalyst. Photodegradation processes of methylene blue (MB), methyl orange (MO), indigo carmine (IC), chicago sky blue 6B (CSB), and mixed dye (MD, mixture of the four mentioned single dye) were reported. As each photodegradation system is pH dependent, the photodegradation experiment was carried out in each dye photodegradation reactive pH range at approximately 28 degrees C. The dyes removal efficiency was studied and compared using UV-vis spectrophotometer analysis. The total removal of each dye was: methylene blue (90.3%), methyl orange (98.5%), indigo carmine (92.4%), chicago sky blue 6B (60.3%), and mixed dyes (70.1%), respectively. The characteristic of the photocatalyst was investigated using X-ray diffractometer (XRD). The amount of each dye intermediate produced in the photodegradation process was also determined with the help of total organic carbon (TOC) analysis.
  5. Electrochemical-assisted photodegradation of dye on TiO2 thin films: investigation on the effect of operational parameters
    Zainal Z, Lee CY, Hussein MZ, Kassim A, Yusof NA
    J Hazard Mater, 2005 Feb 14;118(1-3):197-203.
    PMID: 15721544
    Electrochemical-assisted photodegradation of methyl orange has been investigated using TiO2 thin films. The films were prepared by sol-gel dip-coating method. Several operational parameters to achieve optimum efficiency of this electrochemical-assisted photodegradation system have been tested. Photoelectrochemical degradation was studied using different light sources and light intensity. The light sources chosen ranged from ultraviolet to visible light. The effect of agitation of the solution at different speeds has also been studied. Slight improvement of photodegradation rate was observed by applying higher agitation speed. Investigation on the electrode after repeated usages show the electrode can be reused up to 20 times with percentage of deficiency less than 15%. The study on the effect of solution temperature indicated that the activation energy of the methyl orange degradation is 18.63 kJ mol(-1).
  6. Electrochemical-assisted photodegradation of mixed dye and textile effluents using TiO2 thin films
    Zainal Z, Lee CY, Hussein MZ, Kassim A, Yusof NA
    J Hazard Mater, 2007 Jul 19;146(1-2):73-80.
    PMID: 17196740
    Mixed dye consists of six commercial dyes and textile effluents from cotton dyeing process were treated by electrochemical-assisted photodegradation under halogen lamp illumination. Two types of effluents were collected which are samples before and after undergone pre-treatment at the factory wastewater treatment plant. The photodegradation process was studied by evaluating the changes in concentration employing UV-vis spectrophotometer (UV-vis) and total organic carbon (TOC) analysis. The photoelectrochemical degradation of mixed dye was found to follow the Langmuir Hinshelwood pseudo-first order kinetic while pseudo-second order kinetic model for effluents by using TOC analyses. The chemical oxygen demand (COD) and biochemical oxygen demand (BOD) values of mixed dye and raw effluents were reported. Photoelectrochemical characteristic of pollutants was studied using the cyclic voltammetry technique. Raw effluent was found to exhibit stronger reduction behaviour at cathodic bias potential but slightly less photoresponse at anodic bias than mixed dye.
  7. Fulltext Formation and yield of multi-walled carbon nanotubes synthesized via chemical vapour deposition routes using different metal-based catalysts of FeCoNiAl, CoNiAl and FeNiAl-LDH
    Hussein MZ, Jaafar AM, Yahaya AH, Masarudin MJ, Zainal Z
    Int J Mol Sci, 2014;15(11):20254-65.
    PMID: 25380526 DOI: 10.3390/ijms151120254
    Multi-walled carbon nanotubes (MWCNTs) were prepared via chemical vapor deposition (CVD) using a series of different catalysts, derived from FeCoNiAl, CoNiAl and FeNiAl layered double hydroxides (LDHs). Catalyst-active particles were obtained by calcination of LDHs at 800 °C for 5 h. Nitrogen and hexane were used as the carrier gas and carbon source respectively, for preparation of MWCNTs using CVD methods at 800 °C. MWCNTs were allowed to grow for 30 min on the catalyst spread on an alumina boat in a quartz tube. The materials were subsequently characterized through X-ray diffraction, Fourier transform infrared spectroscopy, surface area analysis, field emission scanning electron microscopy and transmission electron microscopy. It was determined that size and yield of MWCNTs varied depending on the type of LDH catalyst precursor that is used during synthesis. MWCNTs obtained using CoNiAl-LDH as the catalyst precursor showed smaller diameter and higher yield compared to FeCoNiAl and FeNiAl LDHs.
  8. Fulltext Induction and analysis of the alkaloid mitragynine content of a Mitragyna speciosa suspension culture system upon elicitation and precursor feeding
    Mohamad Zuldin NN, Said IM, Mohd Noor N, Zainal Z, Jin Kiat C, Ismail I
    ScientificWorldJournal, 2013;2013:209434.
    PMID: 24065873 DOI: 10.1155/2013/209434
    This study aimed to determine the effects of different concentrations and combinations of the phytohormones 2,4-dichlorophenoxy acetic acid (2,4-D), kinetin, 6-benzylaminopurine (BAP), and 1-naphthaleneacetic acid (NAA) on callus induction and to demonstrate the role of elicitors and exogenous precursors on the production of mitragynine in a Mitragyna speciosa suspension culture. The best callus induction was achieved from petiole explants cultured on WPM that was supplemented with 4 mg L⁻¹ 2,4-D (70.83%). Calli were transferred to liquid media and agitated on rotary shakers to establish Mitragyna speciosa cell suspension cultures. The optimum settled cell volume was achieved in the presence of WPM that contained 3 mg L⁻¹ 2,4-D and 3% sucrose (9.47 ± 0.4667 mL). The treatment of cultures with different concentrations of yeast extract and salicylic acid for different inoculation periods revealed that the highest mitragynine content as determined by HPLC was achieved from the culture treated with 250 mg L⁻¹ yeast extract (9.275 ± 0.082 mg L⁻¹) that was harvested on day 6 of culturing; salicylic acid showed low mitragynine content in all concentrations used. Tryptophan and loganin were used as exogenous precursors; the highest level of mitragynine production was achieved in cultures treated with 3  μM tryptophan and harvested at 6 days (13.226 ± 1.98 mg L⁻¹).
  9. Fulltext Preparation and controlled-release studies of a protocatechuic acid-magnesium/aluminum-layered double hydroxide nanocomposite
    Barahuie F, Hussein MZ, Hussein-Al-Ali SH, Arulselvan P, Fakurazi S, Zainal Z
    Int J Nanomedicine, 2013;8:1975-87.
    PMID: 23737666 DOI: 10.2147/IJN.S42718
    In the study reported here, magnesium/aluminum (Mg/Al)-layered double hydroxide (LDH) was intercalated with an anticancer drug, protocatechuic acid, using ion-exchange and direct coprecipitation methods, with the resultant products labeled according to the method used to produce them: "PANE" (ie, protocatechuic acid-Mg/Al nanocomposite synthesized using the ion-exchange method) and "PAND" (ie, protocatechuic acid-Mg/Al nanocomposite synthesized using the direct method), respectively. Powder X-ray diffraction and Fourier transform infrared spectroscopy confirmed the intercalation of protocatechuic acid into the inter-galleries of Mg/Al-LDH. The protocatechuic acid between the interlayers of PANE and PAND was found to be a monolayer, with an angle from the z-axis of 8° for PANE and 15° for PAND. Thermogravimetric and differential thermogravimetric analysis results revealed that the thermal stability of protocatechuic acid was markedly enhanced upon intercalation. The loading of protocatechuic acid in PANE and PAND was estimated to be about 24.5% and 27.5% (w/w), respectively. The in vitro release study of protocatechuic acid from PANE and PAND in phosphate-buffered saline at pH 7.4, 5.3, and 4.8 revealed that the nanocomposites had a sustained release property. After 72 hours incubation of PANE and PAND with MCF-7 human breast cancer and HeLa human cervical cancer cell lines, it was found that the nanocomposites had suppressed the growth of these cancer cells, with a half maximal inhibitory concentration of 35.6 μg/mL for PANE and 36.0 μg/mL for PAND for MCF-7 cells, and 19.8 μg/mL for PANE and 30.3 μg/mL for PAND for HeLa cells. No half maximal inhibitory concentration for either nanocomposite was found for 3T3 cells.
  10. Fulltext High Coke-Resistance Pt/Mg1-xNixO Catalyst for Dry Reforming of Methane
    Al-Doghachi FA, Islam A, Zainal Z, Saiman MI, Embong Z, Taufiq-Yap YH
    PLoS One, 2016;11(1):e0145862.
    PMID: 26745623 DOI: 10.1371/journal.pone.0145862
    A highly active and stable nano structured Pt/Mg1-xNixO catalysts was developed by a simple co-precipitation method. The obtained Pt/Mg1-xNixO catalyst exhibited cubic structure nanocatalyst with a size of 50-80 nm and realized CH4 and CO2 conversions as high as 98% at 900°C with excellent stability in the dry reforming of methane. The characterization of catalyst was performed using various kinds of analytical techniques including XRD, BET, XRF, TPR-H2, TGA, TEM, FESEM, FT-IR, and XPS analyses. Characterization of spent catalyst further confirms that Pt/Mg1-xNixO catalyst has high coke-resistance for dry reforming. Thus, the catalyst demonstrated in this study, offers a promising catalyst for resolving the dilemma between dispersion and reducibility of supported metal, as well as activity and stability during high temperature reactions.
  11. Fulltext Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom
    Abdullah-Zawawi MR, Govender N, Harun S, Muhammad NAN, Zainal Z, Mohamed-Hussein ZA
    Plants (Basel), 2022 Oct 05;11(19).
    PMID: 36235479 DOI: 10.3390/plants11192614
    In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
  12. Overexpression of rice High-affinity Potassium Transporter gene OsHKT1;5 improves salinity and drought tolerance in Arabidopsis
    Ullah MA, Abdullah-Zawawi MR, Razalli II, Sukiran NL, Uddin MI, Zainal Z
    Mol Biol Rep, 2024 Dec 07;52(1):40.
    PMID: 39644345 DOI: 10.1007/s11033-024-10130-6
    BACKGROUND: Rice is subjected to various environmental stresses, resulting in significant production losses. Abiotic stresses, particularly drought and salinity, are the leading causes of plant damage worldwide. The High-affinity Potassium Transporter (HKT) gene family plays an important role in enhancing crop stress tolerance by regulating physiological and enzymatic functions.

    METHODS AND RESULTS: This study investigates the effect of overexpressing the rice HKT1;5 gene in Arabidopsis thaliana on its tolerance to salinity and drought. The OsHKT1;5 gene was introduced into Arabidopsis under the control of 35 S promoter of CaMV via floral dip transformation method. PCR confirmed the integration of the transgene into the Arabidopsis genome, while qPCR analysis showed its expression. Three transgenic lines of OsHKT1;5 were used for stress treatment and phenotypic studies. The overexpressed lines showed considerably higher germination rates, increased leaf counts, greater fresh and dry weights of the roots and shoots, higher chlorophyll contents, longer root lengths, and reduced Na+ levels together with increased K+ ions levels after salt and drought treatments, in comparison to wild-type plants. Furthermore, overexpressed lines exhibited higher antioxidant levels than wild-type plants under salinity and drought conditions. In addition, transgenic lines showed higher expression levels of the OsHKT1;5 gene in both roots and shoots compared to wild-type plants.

    CONCLUSIONS: In conclusion, this study revealed OsHKT1;5 as a promising candidate for enhancing tolerance to salinity and drought stresses in rice, marking a significant step toward developing a new rice variety with improved abiotic stress tolerance.

  13. Reduction of disease activity in rheumatoid arthritis by tocotrienol-rich fraction supplementation: a randomized, double-blind, placebo-controlled trial
    Zainal Z, Othman AZ, Rahim AA, Meganathan P, Radhakrishnan AK
    Eur J Nutr, 2025 Jun 24;64(5):227.
    PMID: 40553171 DOI: 10.1007/s00394-025-03742-6
    PURPOSE: Tocotrienol-rich fraction (TRF), an antioxidant, can treat rheumatoid arthritis (RA) which is an autoimmune inflammatory illness that causes severe joint pain. Preclinical studies on rats reveal that TRF reduces RA. The clinical study on RA patients has not been extensively investigated. A six month, randomized, double-blind, placebo-controlled trial was conducted to evaluate the efficacy of Tocotrienol-Rich Fraction supplementation in reducing disease activity in patients with moderate-to-severe RA as measured by the Disease Activity Score-28 (DAS 28).

    METHODS: TRF supplementation was investigated in RA patients with an MDA-CRP score of 28 joints (DAS 28). In this RCT, 50 active RA patients were randomly assigned to receive 400 mg of TRF (TocovidTM) or placebo (palm olein) daily (1:1). Both groups had the same dose of conventional disease-modifying anti-rheumatic drugs (cDMARDS) throughout the intervention. Questionnaires, pain intensity measurements, and laboratory analysis were done at baseline and trial conclusion. Patients' data were collected after one, three, six months of supplementation and three months post-intervention. DAS28 joints, CRP, ESR, SJC, TJC, and total health scale (VAS) were measured.

    RESULTS: Daily supplementation with 400 mg of TRF for six months significantly improved clinical outcomes in patients with moderate-to-severe RA. TRF supplementation effectively reduced joint stiffness, edema, and discomfort, while also significantly lowering the DAS 28. Furthermore, TRF supplementation alleviated knee pain, improved physical function, and was well-tolerated with no reported side effects.

    CONCLUSION: This RCT shows that daily supplementation of 400 mg of TRF for six months lowers RA disease activity by reducing stiffness, edema, and joint discomfort.

  14. Fulltext RNA-seq data from whole rice grains of pigmented and non-pigmented Malaysian rice varieties
    Zainal-Abidin RA, Zainal Z, Mohamed-Hussein ZA, Abu-Bakar N, Ab Razak MSF, Simoh S, et al.
    Data Brief, 2020 Jun;30:105432.
    PMID: 32280737 DOI: 10.1016/j.dib.2020.105432
    Pigmented rice is enriched with antioxidants, macro- and micronutrients. A comprehensive investigation of the gene expression patterns among the pigmented rice varieties would help to understand the cellular mechanism and biological processes of rice grain pigmentation. Hence, we performed RNA sequencing and analysis on the whole grain of dehusked mature seeds of selected six Malaysian rice varieties with varying grain pigmentations. These varieties were black rice (BALI and Pulut Hitam 9), red rice (MRM16 and MRQ100) and white rice (MR297 and MRQ76). Illumina HiSeq™ 4000 sequencer was used to generate total raw nucleotides of approximately 53 Gb in size. From 353,937,212 total paired-end raw reads, 340,131,496 total clean reads were obtained. The raw reads were deposited into European Nucleotide Archive (ENA) database and can be accessed via accession number PRJEB34340. This dataset allows us to identify and profile all expressed genes with functions related to nutritional traits (i.e. antioxidants, folate and amylose content) and quality trait (i.e. aroma) across both pigmented and non-pigmented rice varieties. In addition, the transcriptome data obtained will be valuable for discovery of potential gene markers and functional SNPs related to functional traits to assist in rice breeding programme.
  15. Fulltext Physical and Physiological Monitoring on Red Palm Weevil-Infested Oil Palms
    Harith-Fadzilah N, Haris-Hussain M, Abd Ghani I, Zakaria A, Amit S, Zainal Z, et al.
    Insects, 2020 Jun 30;11(7).
    PMID: 32630104 DOI: 10.3390/insects11070407
    The red palm weevil (RPW) is a stem boring Coleoptera that decimates host palm trees from within. The challenge of managing this pest is due to a lack of physical symptoms during the early stages of infestation. Investigating the physiological changes that occur within RPW-infested palm trees may be useful in establishing a new approach in RPW detection. In this study, the effects of RPW infestation were investigated in Elaeis guineensis by observing changes in physical and physiological parameters during the progress of infestation by visual inspection and the comparison of growth, gas exchange, stomatal conductance, and chlorophyll content between the non-infested control, physically wounded, and RPW-infested E. guineensis groups. During the study period, four distinct levels of physical infestation were observed and recorded. The RPW-infested group displayed significantly lower maximum photosynthesis activity (Amax) starting from the third week post-infestation. However, growth in terms of change in plant height and stem circumference, leaves' stomatal conductance, and chlorophyll content were not significantly different between the three groups during the duration of the study. The significant drop in photosynthesis was observed one week before physical changes appeared. This suggests the promising utilisation of photosynthesis activity as a signal for detecting RPW infestation at the early stage of attacks, which could be useful for integration in integrated pest management (IPM).
  16. Fulltext Data on genome resequencing of pigmented and non-pigmented Malaysian rice varieties
    Zainal-Abidin RA, Zainal Z, Mohamed-Hussein ZA, Sew YS, Simoh S, Ab Razak S, et al.
    Data Brief, 2020 Aug;31:105806.
    PMID: 32566707 DOI: 10.1016/j.dib.2020.105806
    The genomics and genetic data of pigmented and non-pigmented Malaysian rice varieties are still limited. Hence, we performed the genome resequencing of two black rice varieties (Bali, Pulut Hitam 9), two red rice varieties (MRM16, MRQ100) and two white rice varieties (MR297 and MRQ76) using Illumina HiSeq 4000 platform with 30x sequencing coverage. We aimed to identify and annotate single nucleotide polymorphisms (SNPs) from the genome of these four pigmented and two non-pigmented rice varieties. The potential SNPs will be used in developing the functional SNP markers related to nutritional (i.e. antioxidant, folate, amylose) and quality (i.e. aromatic) traits. Raw data of the pigmented and non-pigmented rice varieties have been deposited into the European Nucleotide Archive (ENA) database with accession number PRJEB29070 and PRJEB32344, respectively.
  17. Fulltext Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids
    Loke KK, Rahnamaie-Tajadod R, Yeoh CC, Goh HH, Mohamed-Hussein ZA, Zainal Z, et al.
    PeerJ, 2017;5:e2938.
    PMID: 28265493 DOI: 10.7717/peerj.2938
    BACKGROUND: Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production.

    METHODS: In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference.

    RESULTS: A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites.

    DISCUSSION: This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.

  18. Fulltext Flavonoid biosynthesis genes putatively identified in the aromatic plant Polygonum minus via Expressed Sequences Tag (EST) analysis
    Roslan ND, Yusop JM, Baharum SN, Othman R, Mohamed-Hussein ZA, Ismail I, et al.
    Int J Mol Sci, 2012;13(3):2692-706.
    PMID: 22489118 DOI: 10.3390/ijms13032692
    P. minus is an aromatic plant, the leaf of which is widely used as a food additive and in the perfume industry. The leaf also accumulates secondary metabolites that act as active ingredients such as flavonoid. Due to limited genomic and transcriptomic data, the biosynthetic pathway of flavonoids is currently unclear. Identification of candidate genes involved in the flavonoid biosynthetic pathway will significantly contribute to understanding the biosynthesis of active compounds. We have constructed a standard cDNA library from P. minus leaves, and two normalized full-length enriched cDNA libraries were constructed from stem and root organs in order to create a gene resource for the biosynthesis of secondary metabolites, especially flavonoid biosynthesis. Thus, large-scale sequencing of P. minus cDNA libraries identified 4196 expressed sequences tags (ESTs) which were deposited in dbEST in the National Center of Biotechnology Information (NCBI). From the three constructed cDNA libraries, 11 ESTs encoding seven genes were mapped to the flavonoid biosynthetic pathway. Finally, three flavonoid biosynthetic pathway-related ESTs chalcone synthase, CHS (JG745304), flavonol synthase, FLS (JG705819) and leucoanthocyanidin dioxygenase, LDOX (JG745247) were selected for further examination by quantitative RT-PCR (qRT-PCR) in different P. minus organs. Expression was detected in leaf, stem and root. Gene expression studies have been initiated in order to better understand the underlying physiological processes.
  19. Fulltext Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture
    Chan PL, Rose RJ, Abdul Murad AM, Zainal Z, Low ET, Ooi LC, et al.
    PLoS One, 2014;9(6):e99774.
    PMID: 24927412 DOI: 10.1371/journal.pone.0099774
    The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels.
  20. Fulltext Cytotoxic aaptamines from Malaysian Aaptos aaptos
    Shaari K, Ling KC, Rashid ZM, Jean TP, Abas F, Raof SM, et al.
    Mar Drugs, 2009;7(1):1-8.
    PMID: 19370166 DOI: 10.3390/md7010001
    In a preliminary screen, Aaptos aaptos showed significant cytotoxic activity towards a panel of cell lines and was thus subjected to bioassay-guided isolation of the bioactive constituents. In addition to the known aaptamine, two new derivatives of the alkaloid were isolated from the bioactive chloroform fraction of the crude methanolic extract. Detailed analysis by NMR and mass spectroscopy enabled their identification to be 3-(phenethylamino)demethyl(oxy)aaptamine and 3-(isopentylamino)demethyl(oxy) aaptamine. The cytotoxic activities of the three alkaloids were further evaluated against CEM-SS cells.
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