Displaying publications 1 - 20 of 60 in total

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  1. UV-blocking and photocatalytic properties of Ag-coated cotton fabrics with Si binders for photo-degradation of recalcitrant dyes in aqueous solutions under sunlight
    Amjad M, Mohyuddin A, Ulfat W, Goh HH, Dzarfan Othman MH, Kurniawan TA
    J Environ Manage, 2024 Feb 27;353:120287.
    PMID: 38335595 DOI: 10.1016/j.jenvman.2024.120287
    Textile wastewater laden with dyes has emerged as a source of water pollution. This possesses a challenge in its effective treatment using a single functional material. In respond to this technological constraint, this work presents multifunctional cotton fabrics (CFs) within a single, streamlined preparation process. This approach utilizes the adherence of Ag NPs (nanoparticles) using Si binder on the surface of CFs, resulting in Ag-coated CFs through a pad dry method. The prepared samples were characterized using scanning electron microscope-energy dispersive X-ray electroscopy (SEM-EDS), thermal gravimetric analysis (TGA), Fourier transformation infrared (FT-IR). It was found that the FT-IR spectra of Ag NPs-coated CFs had peaks appear at 3400, 2900, and 1200 cm-1, implying the stretching vibrations of O-H, C-H, and C-O, respectively. Based on the EDX analysis, the presence of C, O, and Ag related to the coated CFs were detected. After coating the CFs with varying concentrations of Ag NPs (1%, 2% and 3% (w/w)), they were used to remove dyes. Under the same concentration of 10 mg/L and optimized pH 7.5 and 2 h of reaction time, 3% (w/w) Ag-coated CFs exhibited a substantial MB degradation of 98 %, while removing 95% of methyl orange, 85% of rhodamine B, and 96% of Congo red, respectively, following 2 h of Vis exposure. Ag NPs had a strong absorption at 420 nm with 2.51 eV of energy band gap. Under UV irradiation, electrons excited and produced free radicals that promoted dyes photodegradation. The oxidation by-products included p-dihydroxybenzene and succinic acid. Spent Ag-coated CFs attained 98% of regeneration efficiency. The utilization of Ag-coated CFs as a photocatalyst facilitated treated effluents to meet the required discharge standard of lower than 1 mg/L mandated by national legislation. The integration of multifunctional CFs in the treatment system presents a new option for tackling water pollution due to dyes.
  2. Leveraging food waste for electricity: A low-carbon approach in energy sector for mitigating climate change and achieving net zero emission in Hong Kong (China)
    Kurniawan TA, Liang X, Goh HH, Dzarfan Othman MH, Anouzla A, Al-Hazmi HE, et al.
    J Environ Manage, 2024 Feb;351:119879.
    PMID: 38157574 DOI: 10.1016/j.jenvman.2023.119879
    In recent years, food waste has been a global concern that contributes to climate change. To deal with the rising impacts of climate change, in Hong Kong, food waste is converted into electricity in the framework of low-carbon approach. This work provides an overview of the conversion of food waste into electricity to achieve carbon neutrality. The production of methane and electricity from waste-to-energy (WTE) conversion are determined. Potential income from its sale and environmental benefits are also assessed quantitatively and qualitatively. It was found that the electricity generation from the food waste could reach 4.33 × 109 kWh annually, avoiding equivalent electricity charge worth USD 3.46 × 109 annually (based on US' 8/kWh). An equivalent CO2 mitigation of 9.9 × 108 kg annually was attained. The revenue from its electricity sale in market was USD 1.44×109 in the 1st year and USD 4.24 ×109 in the 15th year, respectively, according to the projected CH4 and electricity generation. The modelling study indicated that the electricity production is 0.8 kWh/kg of landfilled waste. The food waste could produce electricity as low as US' 8 per kW ∙ h. In spite of its promising results, there are techno-economic bottlenecks in commercial scale production and its application at comparable costs to conventional fossil fuels. Issues such as high GHG emissions and high production costs have been determined to be resolved later. Overall, this work not only leads to GHG avoidance, but also diversifies energy supply in providing power for homes in the future.
  3. Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress
    Othman SMIS, Mustaffa AF, Mohd Zahid NII, Che-Othman MH, Samad AFA, Goh HH, et al.
    Plant Physiol Biochem, 2024 Feb;207:108387.
    PMID: 38266565 DOI: 10.1016/j.plaphy.2024.108387
    Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.
  4. Decarbonization in waste recycling industry using digitalization to promote net-zero emissions and its implications on sustainability
    Kurniawan TA, Othman MHD, Liang X, Goh HH, Gikas P, Kusworo TD, et al.
    J Environ Manage, 2023 Jul 15;338:117765.
    PMID: 36965421 DOI: 10.1016/j.jenvman.2023.117765
    Digitalization and sustainability have been considered as critical elements in tackling a growing problem of solid waste in the framework of circular economy (CE). Although digitalization can enhance time-efficiency and/or cost-efficiency, their end-results do not always lead to sustainability. So far, the literatures still lack of a holistic view in understanding the development trends and key roles of digitalization in waste recycling industry to benefit stakeholders and to protect the environment. To bridge this knowledge gap, this work systematically investigates how leveraging digitalization in waste recycling industry could address these research questions: (1) What are the key problems of solid waste recycling? (2) How the trends of digitalization in waste management could benefit a CE? (3) How digitalization could strengthen waste recycling industry in a post-pandemic era? While digitalization boosts material flows in a CE, it is evident that utilizing digital solutions to strengthen waste recycling business could reinforce a resource-efficient, low-carbon, and a CE. In the Industry 4.0 era, digitalization can add 15% (about USD 15.7 trillion) to global economy by 2030. As digitalization grows, making the waste sector shift to a CE could save between 30% and 35% of municipalities' waste management budget. With digitalization, a cost reduction of 3.6% and a revenue increase of 4.1% are projected annually. This would contribute to USD 493 billion in an increasing revenue yearly in the next decade. As digitalization enables tasks to be completed shortly with less manpower, this could save USD 421 billion annually for the next decade. With respect to environmental impacts, digitalization in the waste sector could reduce global CO2 emissions by 15% by 2030 through technological solutions. Overall, this work suggests that digitalization in the waste sector contributes net-zero emission to a digital economy, while transitioning to a sustainable world as its social impacts.
  5. Source, occurrence, distribution, fate, and implications of microplastic pollutants in freshwater on environment: A critical review and way forward
    Kurniawan TA, Haider A, Ahmad HM, Mohyuddin A, Umer Aslam HM, Nadeem S, et al.
    Chemosphere, 2023 Jun;325:138367.
    PMID: 36907482 DOI: 10.1016/j.chemosphere.2023.138367
    The generation of microplastics (MPs) has increased recently and become an emerging issue globally. Due to their long-term durability and capability of traveling between different habitats in air, water, and soil, MPs presence in freshwater ecosystem threatens the environment with respect to its quality, biotic life, and sustainability. Although many previous works have been undertaken on the MPs pollution in the marine system recently, none of the study has covered the scope of MPs pollution in the freshwater. To consolidate scattered knowledge in the literature body into one place, this work identifies the sources, fate, occurrence, transport pathways, and distribution of MPs pollution in the aquatic system with respect to their impacts on biotic life, degradation, and detection techniques. This article also discusses the environmental implications of MPs pollution in the freshwater ecosystems. Certain techniques for identifying MPs and their limitations in applications are presented. Through a literature survey of over 276 published articles (2000-2023), this study presents an overview of solutions to the MP pollution, while identifying research gaps in the body of knowledge for further work. It is conclusive from this review that the MPs exist in the freshwater due to an improper littering of plastic waste and its degradation into smaller particles. Approximately 15-51 trillion MP particles have accumulated in the oceans with their weight ranging between 93,000 and 236,000 metric ton (Mt), while about 19-23 Mt of plastic waste was released into rivers in 2016, which was projected to increase up to 53 Mt by 2030. A subsequent degradation of MPs in the aquatic environment results in the generation of NPs with size ranging from 1 to 1000 nm. It is expected that this work facilitates stakeholders to understand the multi-aspects of MPs pollution in the freshwater and recommends policy actions to implement sustainable solutions to this environmental problem.
  6. Molecular cloning and in silico analysis of chalcone isomerase from Polygonum minus
    Shah FLA, Baharum SN, Goh HH, Leow TC, Ramzi AB, Oslan SN, et al.
    Mol Biol Rep, 2023 Jun;50(6):5283-5294.
    PMID: 37148413 DOI: 10.1007/s11033-023-08417-1
    BACKGROUND: Chalcone isomerase (CHI; EC 5.5.1.6) is one of the key enzymes in the flavonoid biosynthetic pathway that is responsible for the intramolecular cyclization of chalcones into specific 2S-flavanones.

    METHODS AND RESULTS: In this study, the open reading frame (ORF) of CHI was successfully isolated from the cDNA of Polygonum minus at 711-bp long, encoding for 236 amino acid residues, with a predicted molecular weight of 25.4 kDa. Multiple sequence alignment and phylogenetic analysis revealed that the conserved residues (Thr50, Tyr108, Asn115, and Ser192) in the cleft of CHI enzyme group active site are present in PmCHI protein sequence and classified as type I. PmCHI comprises more hydrophobic residues without a signal peptide and transmembrane helices. The three-dimensional (3D) structure of PmCHI predicted through homology modeling was validated by Ramachandran plot and Verify3D, with values within the acceptable range of a good model. PmCHI was cloned into pET-28b(+) plasmid, expressed in Escherichia coli BL21(DE3) at 16 °C and partially purified.

    CONCLUSION: These findings contribute to a deeper understanding of the PmCHI protein and its potential for further characterization of its functional properties in the flavonoid biosynthetic pathway.

  7. Challenges and opportunities for biochar to promote circular economy and carbon neutrality
    Kurniawan TA, Othman MHD, Liang X, Goh HH, Gikas P, Chong KK, et al.
    J Environ Manage, 2023 Apr 15;332:117429.
    PMID: 36773474 DOI: 10.1016/j.jenvman.2023.117429
    Biochar, derived from unused biomass, is widely considered for its potential to deal with climate change problems. Global interest in biochar is attributed to its ability to sequester carbon in soil and to remediate aquatic environment from water pollution. As soil conditioner and/or adsorbent, biochar offers opportunity through a circular economy (CE) paradigm. While energy transition continues, progress toward low-emissions materials accelerates their advance towards net-zero emissions. However, none of existing works addresses CE-based biochar management to achieve carbon neutrality. To reflect its novelty, this work provides a critical overview of challenges and opportunities for biochar to promote CE and carbon neutrality. This article also offers seminal perspectives about strengthening biomass management through CE and resource recovery paradigms, while exploring how the unused biomass can promote net zero emissions in its applications. By consolidating scattered knowledge in the body of literature into one place, this work uncovers new research directions to close the loops by implementing the circularity of biomass resources in various fields. It is conclusive from a literature survey of 113 articles (2003-2023) that biomass conversion into biochar can promote net zero emissions and CE in the framework of the UN Sustainable Development Goals (SDGs). Depending on their physico-chemical properties, biochar can become a suitable feedstock for CE. Biochar application as soil enrichment offsets 12% of CO2 emissions by land use annually. Adding biochar to soil can improve its health and agricultural productivity, while minimizing about 1/8 of CO2 emissions. Biochar can also sequester CO2 in the long-term and prevent the release of carbon back into the atmosphere after its decomposition. This practice could sequester 2.5 gigatons (Gt) of CO2 annually. With the global biochar market reaching USD 368.85 million by 2028, this work facilitates biochar with its versatile characteristics to promote carbon neutrality and CE applications.
  8. Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae
    Ting TY, Li Y, Bunawan H, Ramzi AB, Goh HH
    J Biosci Bioeng, 2023 Apr;135(4):259-265.
    PMID: 36803862 DOI: 10.1016/j.jbiosc.2023.01.010
    Saccharomyces cerevisiae has a long-standing history of biotechnological applications even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches. In this review, we highlight the recent findings in the field with a focus on omics studies of S. cerevisiae to investigate its stress tolerance in different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries as well as metabolic engineering. Omics data analysis is key to the identification of exploitable native genes/proteins/pathways in S. cerevisiae with the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.
  9. Influence of Fe2O3 and bacterial biofilms on Cu(II) distribution in a simulated aqueous solution: A feasibility study to sediments in the Pearl River Estuary (PR China)
    Kurniawan TA, Lo W, Othman MHD, Liang X, Goh HH, Chew KW
    J Environ Manage, 2023 Mar 01;329:117047.
    PMID: 36563449 DOI: 10.1016/j.jenvman.2022.117047
    This study investigated physico-chemical interactions among Cu(II), biogenic materials, and Fe2O3 in a continuous-flow biofilm reactor system under a well-controlled environment. The effects of Fe2O3 and bacterial biofilms on the distribution of Cu(II) in a simulated aquatic environment were studied. To control biological and abiotic elements in the marine environment, a biofilm reactor was designed to understand the metal speciation of Cu(II) and its distribution. The reactor consisted of a biofilm chamber equipped with glass slides for biofilms attachment. Due to its ability to grow as biofilm in the medium, Pseudomonas atlantica was cultivated to adsorb trace Cu(II) to attached and suspended cells. It was found that biofilms with 170-285 mequiv chemical oxygen demand (COD) concentration/m2 of total oxidizable materials accelerated the Cu(II) adsorption to the surface of the reactor significantly by a factor of five. A significant inhibition to the bacterial growth took place (p ≤ 0.05; t-test) when Cu(II) concentration was higher than 0.5 mg/L. In the absence of Cu(II), bacterial cells grew normally to 0.075 of optical density (OD). However, at the Cu(II) concentration of 0.2 mg/L, the cells grew to a lower OD of 0.58. The presence of glycine and EDTA substantially reduced the toxicity of Cu(II) on bacterial growth (p ≤ 0.05; paired t-test). Their complexation with Cu(II) rendered the metal ions less available to bacterial cells. This implies that the Fe2O3 and bacterial biofilm affected Cu(II) distribution and speciation in the aquatic environment.
  10. Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology
    Othman SMIS, Mustaffa AF, Che-Othman MH, Samad AFA, Goh HH, Zainal Z, et al.
    Plants (Basel), 2023 Feb 03;12(3).
    PMID: 36771753 DOI: 10.3390/plants12030669
    The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial-temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.
  11. Fulltext Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory
    Baharin A, Ting TY, Goh HH
    Plants (Basel), 2023 Jan 15;12(2).
    PMID: 36679121 DOI: 10.3390/plants12020408
    Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.
  12. Fulltext Comparative metabolomics analysis reveals alkaloid repertoires in young and mature Mitragyna speciosa (Korth.) Havil. Leaves
    Veeramohan R, Zamani AI, Azizan KA, Goh HH, Aizat WM, Razak MFA, et al.
    PLoS One, 2023;18(3):e0283147.
    PMID: 36943850 DOI: 10.1371/journal.pone.0283147
    The fresh leaves of Mitragyna speciosa (Korth.) Havil. have been traditionally consumed for centuries in Southeast Asia for its healing properties. Although the alkaloids of M. speciosa have been studied since the 1920s, comparative and systematic studies of metabolite composition based on different leaf maturity levels are still lacking. This study assessed the secondary metabolite composition in two different leaf stages (young and mature) of M. speciosa, using an untargeted liquid chromatography-electrospray ionisation-time-of-flight-mass spectrometry (LC-ESI-TOF-MS) metabolite profiling. The results revealed 86 putatively annotated metabolite features (RT:m/z value) comprising 63 alkaloids, 10 flavonoids, 6 terpenoids, 3 phenylpropanoids, and 1 of each carboxylic acid, glucoside, phenol, and phenolic aldehyde. The alkaloid features were further categorised into 14 subclasses, i.e., the most abundant class of secondary metabolites identified. As per previous reports, indole alkaloids are the most abundant alkaloid subclass in M. speciosa. The result of multivariate analysis (MVA) using principal component analysis (PCA) showed a clear separation of 92.8% between the young and mature leaf samples, indicating a high variance in metabolite levels between them. Akuammidine, alstonine, tryptamine, and yohimbine were tentatively identified among the many new alkaloids reported in this study, depicting the diverse biological activities of M. speciosa. Besides delving into the knowledge of metabolite distribution in different leaf stages, these findings have extended the current alkaloid repository of M. speciosa for a better understanding of its pharmaceutical potential.
  13. Harnessing landfill gas (LFG) for electricity: A strategy to mitigate greenhouse gas (GHG) emissions in Jakarta (Indonesia)
    Kurniawan TA, Liang X, Singh D, Othman MHD, Goh HH, Gikas P, et al.
    J Environ Manage, 2022 Jan 01;301:113882.
    PMID: 34638040 DOI: 10.1016/j.jenvman.2021.113882
    Due to its increasing demands for fossil fuels, Indonesia needs an alternative energy to diversify its energy supply. Landfill gas (LFG), which key component is methane (CH4), has become one of the most attractive options to sustain its continued economic development. This exploratory study seeks to demonstrate the added value of landfilled municipal solid waste (MSW) in generating sustainable energy, resulting from CH4 emissions in the Bantargebang landfill (Jakarta). The power generation capacity of a waste-to-energy (WTE) plant based on a mathematical modeling was investigated. This article critically evaluated the production of electricity and potential income from its sale in the market. The project's environmental impact assessment and its socio-economic and environmental benefits in terms of quantitative and qualitative aspects were discussed. It was found that the emitted CH4 from the landfill could be reduced by 25,000 Mt annually, while its electricity generation could reach one million kW ⋅h annually, savings on equivalent electricity charge worth US$ 112 million/year (based on US' 8/kW ⋅ h). An equivalent CO2 mitigation of 3.4 × 106 Mt/year was obtained. The income from its power sale were US$ 1.2 ×106 in the 1st year and 7.7 ×107US$ in the 15th year, respectively, based on the projected CH4 and power generation. The modeling study on the Bantargebang landfill using the LFG extraction data indicated that the LFG production ranged from 0.05 to 0.40 m3 per kg of the landfilled MSW. The LFG could generate electricity as low as US' 8 per kW ⋅ h. With respect to the implications of this study, the revenue not only defrays the cost of landfill's operations and maintenance (O&M), but also provides an incentive and means to further improve its design and operations. Overall, this work not only leads to a diversification of primary energy, but also improves environmental protection and the living standard of the people surrounding the plant.
  14. Fulltext Transcriptome analysis of Rafflesia cantleyi flower stages reveals insights into the regulation of senescence
    Mohd-Elias NA, Rosli K, Alias H, Juhari MA, Abu-Bakar MF, Md-Isa N, et al.
    Sci Rep, 2021 Dec 08;11(1):23661.
    PMID: 34880337 DOI: 10.1038/s41598-021-03028-x
    Rafflesia is a unique plant species existing as a single flower and produces the largest flower in the world. While Rafflesia buds take up to 21 months to develop, its flowers bloom and wither within about a week. In this study, transcriptome analysis was carried out to shed light on the molecular mechanism of senescence in Rafflesia. A total of 53.3 million high quality reads were obtained from two Rafflesia cantleyi flower developmental stages and assembled to generate 64,152 unigenes. Analysis of this dataset showed that 5,166 unigenes were differentially expressed, in which 1,073 unigenes were identified as genes involved in flower senescence. Results revealed that as the flowers progress to senescence, more genes related to flower senescence were significantly over-represented compared to those related to plant growth and development. Senescence of the R. cantleyi flower activates senescence-associated genes in the transcription activity (members of the transcription factor families MYB, bHLH, NAC, and WRKY), nutrient remobilization (autophagy-related protein and transporter genes), and redox regulation (CATALASE). Most of the senescence-related genes were found to be differentially regulated, perhaps for the fine-tuning of various responses in the senescing R. cantleyi flower. Additionally, pathway analysis showed the activation of genes such as ETHYLENE RECEPTOR, ETHYLENE-INSENSITIVE 2, ETHYLENE-INSENSITIVE 3, and ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR, indicating the possible involvement of the ethylene hormone response pathway in the regulation of R. cantleyi senescence. Our results provide a model of the molecular mechanism underlying R. cantleyi flower senescence, and contribute essential information towards further understanding the biology of the Rafflesiaceae family.
  15. Protease activity is maintained in Nepenthes ampullaria digestive fluids depleted of endogenous proteins with compositional changes
    Ravee R, Baharin A, Cho WT, Ting TY, Goh HH
    Physiol Plant, 2021 Dec;173(4):1967-1978.
    PMID: 34455610 DOI: 10.1111/ppl.13540
    Nepenthes ampullaria is a unique carnivorous tropical pitcher plant with the detritivorous capability of sequestering nutrients from leaf litter apart from being insectivorous. The changes in the protein composition and protease activity of its pitcher fluids during the early opening of pitchers (D0 and D3C) were investigated via a proteomics approach and a controlled protein depletion experiment (D3L). A total of 193 proteins were identified. Common proteins such as pathogenesis-related protein, proteases (Nep [EC:3.4.23.12], SCP [EC:3.4.16.-]), peroxidase [EC:1.11.1.7], GDSL esterase/lipase [EC:3.1.1.-], and purple acid phosphatase [EC:3.1.3.2] were found in high abundance in the D0 pitchers and were replenished in D3L samples. This reflects their importance for biological processes upon pitcher opening. Meanwhile, prey-inducible chitinases [EC:3.2.1.14] were found in D0 but not in D3C and D3L samples, which suggests their degradation in the absence of prey. Protease activity assays demonstrated the replenishment of proteases in D3L with similar levels of proteolytic activities to that of D3C samples. This supports a feedback mechanism and signaling in the molecular regulation of endogenous protein secretion, turnover, and activity in Nepenthes pitcher fluids. Furthermore, we also discovered several new enzymes (XTH [EC:2.4.1.207], PAE [EC:3.1.1.98]) with possible functions in cell wall degradation that could contribute to the detritivory habit of N. ampullaria.
  16. Temporal gene expression profiling of maslinic acid-treated Raji cells
    Lau WM, Subramaniam M, Goh HH, Lim YM
    Mol Omics, 2021 04 19;17(2):252-259.
    PMID: 33346776 DOI: 10.1039/d0mo00168f
    Maslinic acid is a novel phytochemical reported to target multiple signaling pathways. A complete gene expression profile was therefore constructed to illustrate the anti-tumourigenesis effects of maslinic acid in Raji cells across five time-points. Microarray analysis was used to identify genes that were differentially expressed in maslinic acid treated Raji cells at 0, 4, 8, 12, 24 and 48 h. Extracted RNA was hybridized using the AffymetrixGeneChip to obtain expression profiles. A total of 109 genes were found to be significantly expressed over a period of 48 hours. By 12 hours, maslinic acid regulates the majority of genes involved in the cell cycle, p53 and NF-κB signaling pathways. At the same time, XAF1, APAF1, SESN3, and TP53BP2 were evidently up-regulated, while oncogenes, FAIM, CD27, and RRM2B, were down-regulated by at least 2-fold. In conclusion, maslinic acid shows an hourly progression of gene expression in Raji cells.
  17. ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses
    Harun S, Rohani ER, Ohme-Takagi M, Goh HH, Mohamed-Hussein ZA
    J Plant Res, 2021 Mar;134(2):327-339.
    PMID: 33558947 DOI: 10.1007/s10265-021-01257-9
    Glucosinolates (GSLs) are plant secondary metabolites consisting of sulfur and nitrogen, commonly found in Brassicaceae crops, such as Arabidopsis thaliana. These compounds are known for their roles in plant defense mechanisms against pests and pathogens. 'Guilt-by-association' (GBA) approach predicts genes encoding proteins with similar function tend to share gene expression pattern generated from high throughput sequencing data. Recent studies have successfully identified GSL genes using GBA approach, followed by targeted verification of gene expression and metabolite data. Therefore, a GSL co-expression network was constructed using known GSL genes obtained from our in-house database, SuCComBase. DPClusO was used to identify subnetworks of the GSL co-expression network followed by Fisher's exact test leading to the discovery of a potential gene that encodes the ARIA-interacting double AP2-domain protein (ADAP) transcription factor (TF). Further functional analysis was performed using an effective gene silencing system known as CRES-T. By applying CRES-T, ADAP TF gene was fused to a plant-specific EAR-motif repressor domain (SRDX), which suppresses the expression of ADAP target genes. In this study, ADAP was proposed as a negative regulator in aliphatic GSL biosynthesis due to the over-expression of downstream aliphatic GSL genes (UGT74C1 and IPMI1) in ADAP-SRDX line. The significant over-expression of ADAP gene in the ADAP-SRDX line also suggests the behavior of the TF that negatively affects the expression of UGT74C1 and IPMI1 via a feedback mechanism in A. thaliana.
  18. Fulltext UPLC-TOF-MS/MS-Based Metabolomics Analysis Reveals Species-Specific Metabolite Compositions in Pitchers of Nepenthes ampullaria, Nepenthes rafflesiana, and Their Hybrid Nepenthes × hookeriana
    Rosli MAF, Mediani A, Azizan KA, Baharum SN, Goh HH
    Front Plant Sci, 2021;12:655004.
    PMID: 33968110 DOI: 10.3389/fpls.2021.655004
    Hybridization is key to the evolution and diversity of plants in nature. Nepenthaceae comprises a family of diverse tropical carnivorous pitcher plant species with extensive hybridization. However, there is no study to date on the metabolite expression of hybrids in this family. We performed a non-targeted metabolomics analysis of the pitchers of two Nepenthes species with different dietary habits, namely, the semi-detritivorous N. ampullaria and carnivorous N. rafflesiana with their hybrid (N. × hookeriana) for a comparative study. The whole-pitcher samples were extracted in methanol:chloroform:water (3:1:1) via sonication-assisted extraction and analyzed using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) followed by data analysis to profile chemical compositions. A total of 1,441 metabolite features were profiled from the three species in which 43.3% of features in the hybrid samples were not found in either of its parents. The partial least squares discriminant analysis (PLS-DA) found 324 metabolite features with variable in projection (VIP) values greater than one in which 55 features were statistically significant. This showed that the hybrid is closer to N. rafflesiana, which is consistent to the previous study on gene and protein expressions. A total of 105 metabolites were putatively identified with manual searches using public metabolite databases. Phenols were detected to be the most abundant secondary metabolites due to a high flavonoid content, especially in N. rafflesiana. The most abundant feature 476.3s:449.102 was found to be the most significant VIP for distinguishing between the three species as a chemical marker. This is the first study comparing metabolites in the carnivory organs of different Nepenthes species with comprehensive profiling and putative identification. The differential metabolite compositions in the pitchers of different species might have ecological implications with the hybrid showing intermediate phenotype between the parents as well as manifesting unique metabolites. However, there is no clear evidence of metabolites related to the differences in dietary habits between the hybrid and the two parent species.
  19. Fulltext Ten simple rules for writing scientific op-ed articles
    Goh HH, Bourne P
    PLoS Comput Biol, 2020 09;16(9):e1008187.
    PMID: 32941423 DOI: 10.1371/journal.pcbi.1008187
  20. A Comprehensive Gene Inventory for Glucosinolate Biosynthetic Pathway in Arabidopsis thaliana
    Harun S, Abdullah-Zawawi MR, Goh HH, Mohamed-Hussein ZA
    J Agric Food Chem, 2020 Jul 15;68(28):7281-7297.
    PMID: 32551569 DOI: 10.1021/acs.jafc.0c01916
    Glucosinolates (GSLs) are plant secondary metabolites comprising sulfur and nitrogen mainly found in plants from the order of Brassicales, such as broccoli, cabbage, and Arabidopsis thaliana. The activated forms of GSL play important roles in fighting against pathogens and have health benefits to humans. The increasing amount of data on A. thaliana generated from various omics technologies can be investigated more deeply in search of new genes or compounds involved in GSL biosynthesis and metabolism. This review describes a comprehensive inventory of A. thaliana GSLs identified from published literature and databases such as KNApSAcK, KEGG, and AraCyc. A total of 113 GSL genes encoding for 23 transcription components, 85 enzymes, and five protein transporters were experimentally characterized in the past two decades. Continuous efforts are still on going to identify all molecules related to the production of GSLs. A manually curated database known as SuCCombase (http://plant-scc.org) was developed to serve as a comprehensive GSL inventory. Realizing lack of information on the regulation of GSL biosynthesis and degradation mechanisms, this review also includes relevant information and their connections with crosstalk among various factors, such as light, sulfur metabolism, and nitrogen metabolism, not only in A. thaliana but also in other crucifers.
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