Displaying publications 1 - 20 of 60 in total

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  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Fulltext DNA shotgun sequencing analysis of Garcinia mangostana L. variety Mesta
    Abu Bakar S, Kumar S, Loke KK, Goh HH, Mohd Noor N
    Genom Data, 2017 Jun;12:118-119.
    PMID: 28516035 DOI: 10.1016/j.gdata.2017.05.001
    Mangosteen (Garcinia mangostana Linn.) is an ultra-tropical tree characterized by its unique dark purple fruits with white flesh. The xanthone-rich purple pericarp tissue contains valuable compounds with medicinal properties. Following previously reported genome sequencing of a common variety of mangosteen [1], we performed another whole genome sequencing of a commercially popular variety of this fruit species (var. Mesta) for comparative analysis of its genome composition. Raw reads of the DNA sequencing project were deposited to SRA database with the accession number SRX2709728.
  7. Fulltext DNA-seq analysis of Garcinia mangostana
    Abu Bakar S, Sampathrajan S, Loke KK, Goh HH, Mohd Noor N
    Genom Data, 2016 Mar;7:62-3.
    PMID: 26981362 DOI: 10.1016/j.gdata.2015.11.018
    Mangosteen (Garcinia mangostana Linn.) is a tropical tree mainly found in South East Asia and considered as "the queen of fruits". The asexually produced fruit is dark purple or reddish in color, with white flesh which is slightly acidic with sweet flavor and a pleasant aroma. The purple pericarp tissue is rich in xanthones which are useful for medical purposes. We performed the first genome sequencing of this commercially important fruit tree to study its genome composition and attempted draft genome assembly. Raw reads of the DNA sequencing project have been deposited to SRA database with the accession number SRX1426419.
  8. Fulltext Data on RNA-seq analysis of Garcinia mangostana L. seed development
    Mazlan O, Abdul-Rahman A, Goh HH, Aizat WM, Mohd Noor N
    Data Brief, 2018 Feb;16:90-93.
    PMID: 29188226 DOI: 10.1016/j.dib.2017.11.001
    Mangosteen (Garcinia mangostana L.) has exceptional potential for commercial and pharmaceutical applications due to its delicious fruit and medicinal properties. Nevertheless, the molecular mechanism of mangosteen seed development is poorly understood. In this study, we performed transcriptomic analysis of four seed developmental stages; eight, ten, twelve and fourteen weeks after anthesis. Illumina HiSeq™ 4000 sequencer was used to generate raw data of approximately 68 Gb in size. From 451,495,326 raw reads, 406,143,756 clean reads were obtained. The raw data were uploaded to SRA database and the BioProject ID is PRJNA395504. These data provide the basis for further exploration and understanding of the molecular mechanism in mangosteen seed development.
  9. 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.
  10. Fulltext Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation
    Rahnamaie-Tajadod R, Loke KK, Goh HH, Noor NM
    Front Plant Sci, 2017;8:109.
    PMID: 28220135 DOI: 10.3389/fpls.2017.00109
    Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P. minus has not been well-studied due to the limited genetic information. Hence, we performed Illumina paired-end RNA-seq for de novo reconstruction of P. minus leaf transcriptome to identify differentially expressed genes (DEGs) in response to MeJA elicitation. A total of 182,111 unique transcripts (UTs) were obtained by de novo assembly of 191.57 million paired-end clean reads using Trinity analysis pipeline. A total of 2374 UTs were identified to be significantly up-/down-regulated 24 h after MeJA treatment. These UTs comprising many genes related to plant secondary metabolite biosynthesis, defense and stress responses. To validate our sequencing results, we analyzed the expression of 21 selected DEGs by quantitative real-time PCR and found a good correlation between the two analyses. The single time-point analysis in this work not only provides a useful genomic resource for P. minus but also gives insights on molecular mechanisms of stress responses in P. minus.
  11. Fulltext Discovery of digestive enzymes in carnivorous plants with focus on proteases
    Ravee R, Mohd Salleh F', Goh HH
    PeerJ, 2018;6:e4914.
    PMID: 29888132 DOI: 10.7717/peerj.4914
    BACKGROUND: Carnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry.

    METHODS: This review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts).

    RESULTS: Since the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants.

    DISCUSSION: These different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications.

  12. Fulltext Extensive mass spectrometry proteomics data of Persicaria minor herb upon methyl jasmonate treatment
    Aizat WM, Ibrahim S, Rahnamaie-Tajadod R, Loke KK, Goh HH, Noor NM
    Data Brief, 2018 Feb;16:1091-1094.
    PMID: 29854898 DOI: 10.1016/j.dib.2017.09.063
    Proteomics is often hindered by the lack of protein sequence database particularly for non-model species such as Persicaria minor herbs. An integrative approach called proteomics informed by transcriptomics is possible [1], in which translated transcriptome sequence database is used as the protein sequence database. In this current study, the proteome profile were profiled using SWATH-MS technology complemented with documented transcriptome profiling [2], the first such report in this tropical herb. The plant was also elicited using a phytohormone, methyl jasmonate (MeJA) and protein changes were elucidated using label-free quantification of SWATH-MS to understand the role of such signal molecule in this herbal species. The mass spectrometry proteomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD005749. This data article refers to the article entitled "Proteomics (SWATH-MS)-informed by transcriptomics approach of Persicaria minor leaves upon methyl jasmonate elicitation" [3].
  13. Fulltext Functional Characterisation of New Sesquiterpene Synthase from the Malaysian Herbal Plant, Polygonum Minus
    Rusdi NA, Goh HH, Sabri S, Ramzi AB, Mohd Noor N, Baharum SN
    Molecules, 2018 06 06;23(6).
    PMID: 29882808 DOI: 10.3390/molecules23061370
    Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that were identified from P. minus transcriptome data mining. The full-length sequences of the PmSTPS1 and PmSTPS2 genes were expressed in the E. coli pQE-2 expression vector. The sizes of PmSTPS1 and PmSTPS2 were 1098 bp and 1967 bp, respectively, with open reading frames (ORF) of 1047 and 1695 bp and encoding polypeptides of 348 and 564 amino acids, respectively. The proteins consist of three conserved motifs, namely, Asp-rich substrate binding (DDxxD), metal binding residues (NSE/DTE), and cytoplasmic ER retention (RxR), as well as the terpene synthase family N-terminal domain and C-terminal metal-binding domain. From the in vitro enzyme assays, using the farnesyl pyrophosphate (FPP) substrate, the PmSTPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the PmSTPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of PmSTPS1 and PmSTPS2 in the biosynthesis pathway of P. minus, to produce aromatic sesquiterpenes.
  14. Functional Genomics
    Goh HH, Ng CL, Loke KK
    Adv Exp Med Biol, 2018 11 2;1102:11-30.
    PMID: 30382566 DOI: 10.1007/978-3-319-98758-3_2
    Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
  15. Fulltext Genome-wide transcriptome profiling ofCarica papayaL. embryogenic callus
    Jamaluddin ND, Mohd Noor N, Goh HH
    Physiol Mol Biol Plants, 2017 Apr;23(2):357-368.
    PMID: 28461724 DOI: 10.1007/s12298-017-0429-8
    Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3' mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.
  16. 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.
  17. 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.
  18. 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.
  19. Integrative Multi-Omics Through Bioinformatics
    Goh HH
    Adv Exp Med Biol, 2018 11 2;1102:69-80.
    PMID: 30382569 DOI: 10.1007/978-3-319-98758-3_5
    This chapter introduces different aspects of bioinformatics with a brief discussion in the systems biology context. Example applications in network pharmacology of traditional Chinese medicine, systems metabolic engineering, and plant genome-scale modelling are described. Lastly, this chapter concludes on how bioinformatics helps to integrate omics data derived from various studies described in previous chapters for a holistic understanding of secondary metabolite production in P. minus.
  20. Fulltext Iso-Seq analysis of Nepenthes ampullaria, Nepenthes rafflesiana and Nepenthes × hookeriana for hybridisation study in pitcher plants
    Zulkapli MM, Rosli MAF, Salleh FIM, Mohd Noor N, Aizat WM, Goh HH
    Genom Data, 2017 Jun;12:130-131.
    PMID: 28529881 DOI: 10.1016/j.gdata.2017.05.003
    Tropical pitcher plants in the species-rich Nepenthaceae family of carnivorous plants possess unique pitcher organs. Hybridisation, natural or artificial, in this family is extensive resulting in pitchers with diverse features. The pitcher functions as a passive insect trap with digestive fluid for nutrient acquisition in nitrogen-poor habitats. This organ shows specialisation according to the dietary habit of different Nepenthes species. In this study, we performed the first single-molecule real-time isoform sequencing (Iso-Seq) analysis of full-length cDNA from Nepenthes ampullaria which can feed on leaf litter, compared to carnivorous Nepenthes rafflesiana, and their carnivorous hybrid Nepenthes × hookeriana. This allows the comparison of pitcher transcriptomes from the parents and the hybrid to understand how hybridisation could shape the evolution of dietary habit in Nepenthes. Raw reads have been deposited to SRA database with the accession numbers SRX2692198 (N. ampullaria), SRX2692197 (N. rafflesiana), and SRX2692196 (N. × hookeriana).
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