Publications by authors named "Wan Mohd Aizat"

30 Publications

  • Page 1 of 1

Transcriptomic and Proteomic Analyses of and Reveal Parental Molecular Expression in the Pitchers of Their Hybrid, × .

Front Plant Sci 2020 20;11:625507. Epub 2021 Jan 20.

Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia.

is a genus comprising carnivorous tropical pitcher plants that have evolved trapping organs at the tip of their leaves for nutrient acquisition from insect trapping. Recent studies have applied proteomics approaches to identify proteins in the pitcher fluids for better understanding the carnivory mechanism, but protein identification is hindered by limited species-specific transcriptomes for . In this study, the proteomics informed by transcriptomics (PIT) approach was utilized to identify and compare proteins in the pitcher fluids of , , and their hybrid × through PacBio isoform sequencing (Iso-Seq) and liquid chromatography-mass spectrometry (LC-MS) proteomic profiling. We generated full-length transcriptomes from all three species of 80,791 consensus isoforms with an average length of 1,692 bp as a reference for protein identification. The comparative analysis found that transcripts and proteins identified in the hybrid × were more resembling , both of which are insectivorous compared with omnivorous that can derive nutrients from leaf litters. Previously reported hydrolytic proteins were detected, including proteases, glucanases, chitinases, phosphatases, nucleases, peroxidases, lipid transfer protein, thaumatin-like protein, pathogenesis-related protein, and disease resistance proteins. Many new proteins with diverse predicted functions were also identified, such as amylase, invertase, catalase, kinases, ligases, synthases, esterases, transferases, transporters, and transcription factors. Despite the discovery of a few unique enzymes in , we found no strong evidence of adaptive evolution to produce endogenous enzymes for the breakdown of leaf litter. A more complete picture of digestive fluid protein composition in this study provides important insights on the molecular physiology of pitchers and carnivory mechanism of species with distinct dietary habits.
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http://dx.doi.org/10.3389/fpls.2020.625507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7855304PMC
January 2021

A Review on Plant Bioactive Compounds and Their Modes of Action Against Coronavirus Infection.

Front Pharmacol 2020 11;11:589044. Epub 2021 Jan 11.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia.

The rapid outbreak of coronavirus disease 2019 (COVID-19) has demonstrated the need for development of new vaccine candidates and therapeutic drugs to fight against the underlying virus, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Currently, no antiviral treatment is available to treat COVID-19 as treatment is mostly directed to only relieving the symptoms. Retrospectively, herbal medicinal plants have been used for thousands of years as a medicinal alternative including for the treatment of various viral illnesses. However, a comprehensive description using various medicinal plants in treating coronavirus infection has not to date been described adequately, especially their modes of action. Most other reports and reviews have also only focused on selected ethnobotanical herbs such as Traditional Chinese Medicine, yet more plants can be considered to enrich the source of the anti-viral compounds. In this review, we have screened and identified potential herbal medicinal plants as anti-coronavirus medication across major literature databases without being limited to any regions or ethnobotanic criteria. As such we have successfully gathered experimentally validated , or findings of more than 30 plants in which these plant extracts or their related compounds, such as those of L., Thunb. and Nakai, are described through their respective modes of action against specific mechanisms or pathways during the viral infection. This includes inhibition of viral attachment and penetration, inhibition of viral RNA and protein synthesis, inhibition of viral key proteins such as 3-chymotrypsin-like cysteine protease (3CL) and papain-like protease 2 (PL), as well as other mechanisms including inhibition of the viral release and enhanced host immunity. We hope this compilation will help researchers and clinicians to identify the source of appropriate anti-viral drugs from plants in combating COVID-19 and, ultimately, save millions of affected human lives.
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http://dx.doi.org/10.3389/fphar.2020.589044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7845143PMC
January 2021

Toxicity and Sublethal Effect of Farnesyl Acetate on Diamondback Moth, (L.) (Lepidoptera: Plutellidae).

Insects 2021 Jan 27;12(2). Epub 2021 Jan 27.

Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.

The diamondback moth, (L.) (Lepidoptera: Plutellidae), is the most important pest of cruciferous vegetables worldwide. In this study, we evaluated the properties of selected farnesyl derivative compounds against . The toxicity and sublethal concentration (LC) of farnesyl acetate, farnesyl acetone, farnesyl bromide, farnesyl chloride, and hexahydrofarnesyl acetone were investigated for 96 h. The leaf-dip bioassays showed that farnesyl acetate had a high level of toxicity against compared to other tested farnesyl derivatives. The LC value was 56.41 mg/L on the second-instar larvae of . Then, the sublethal effects of farnesyl acetate on biological parameters of were assessed. Compared to the control group, the sublethal concentration of farnesyl acetate decreased pupation and emergence rates, pupal weight, fecundity, egg hatching rate, female ratio, and oviposition period. Furthermore, the developmental time of was extended after being exposed to farnesyl acetate. Moreover, the application of farnesyl acetate on induced morphogenetic abnormalities in larval-pupal intermediates, adults that emerged with twisted wings, or complete adults that could not emerge from the cocoon. These results suggested that farnesyl acetate was highly effective against . The sublethal concentration of farnesyl acetate could reduce the population of by increasing abnormal pupal and adults, and by delaying its development period.
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http://dx.doi.org/10.3390/insects12020109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7910910PMC
January 2021

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology.

Front Plant Sci 2020 26;11:944. Epub 2020 Jun 26.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia.

Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.
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http://dx.doi.org/10.3389/fpls.2020.00944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371031PMC
June 2020

Comprehensive proteomics data on whole rice grain of selected pigmented and non-pigmented rice varieties using SWATH-MS approach.

Data Brief 2020 Aug 26;31:105927. Epub 2020 Jun 26.

Malaysian Agricultural Research & Development Institute (MARDI), 43300 Serdang, Selangor, Malaysia.

The proteome data of whole rice grain is considerably limited particularly for rice with pigmentations such as black and red rice. Hence, we performed proteome analysis of two black rice varieties (BALI and Pulut Hitam 9), two red rice varieties (MRM16 and MRQ100) and two white rice varieties (MR297 and MRQ76) using label-free liquid chromatography Triple TOF 6600 tandem mass spectrometry (LC-MS/MS). Our aim was to profile and identify proteins related to nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits based on peptide-centric scoring from the Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) approach. Both information dependent acquisition (IDA) and SWATH-MS run were performed in this analysis. Raw data was then processed using ProteinPilot software to identify and compare proteins from the six different varieties. In future, this proteomics data will be integrated with previously obtained genomics [1] and transcriptomics [2] data focusing on the above nutritional and quality traits, with an ultimate aim to develop a panel of functional biomarkers related to those traits for future rice breeding programme. The raw MS data of the pigmented and non-pigmented rice varieties have been deposited to ProteomeXchange database with accession number PXD018338.
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http://dx.doi.org/10.1016/j.dib.2020.105927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334386PMC
August 2020

In silico analysis on the functional and structural impact of Rad50 mutations involved in DNA strand break repair.

PeerJ 2020 22;8:e9197. Epub 2020 May 22.

Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.

Background: DNA double strand break repair is important to preserve the fidelity of our genetic makeup after DNA damage. Rad50 is one of the components in MRN complex important for DNA repair mechanism. Rad50 mutations can lead to microcephaly, mental retardation and growth retardation in human. However, Rad50 mutations in human and other organisms have never been gathered and heuristically compared for their deleterious effects. It is important to assess the conserved region in Rad50 and its homolog to identify vital mutations that can affect functions of the protein.

Method: In this study, Rad50 mutations were retrieved from SNPeffect 4.0 database and literature. Each of the mutations was analyzed using various bioinformatic analyses such as PredictSNP, MutPred, SNPeffect 4.0, I-Mutant and MuPro to identify its impact on molecular mechanism, biological function and protein stability, respectively.

Results: We identified 103 mostly occurred mutations in the Rad50 protein domains and motifs, which only 42 mutations were classified as most deleterious. These mutations are mainly situated at the specific motifs such as Walker A, Q-loop, Walker B, D-loop and signature motif of the Rad50 protein. Some of these mutations were predicted to negatively affect several important functional sites that play important roles in DNA repair mechanism and cell cycle signaling pathway, highlighting Rad50 crucial role in this process. Interestingly, mutations located at non-conserved regions were predicted to have neutral/non-damaging effects, in contrast with previous experimental studies that showed deleterious effects. This suggests that software used in this study may have limitations in predicting mutations in non-conserved regions, implying further improvement in their algorithm is needed. In conclusion, this study reveals the priority of acid substitution associated with the genetic disorders. This finding highlights the vital roles of certain residues such as K42E, C681A/S, CC684R/S, S1202R, E1232Q and D1238N/A located in Rad50 conserved regions, which can be considered for a more targeted future studies.
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http://dx.doi.org/10.7717/peerj.9197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7247530PMC
May 2020

The Impact of Plant Bioactive Compounds on Aging and Fertility of Diverse Organisms: A Review.

Mini Rev Med Chem 2020 ;20(13):1287-1299

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia.

It is expected that in 2050, there will be more than 20% of senior citizens aged over 60 years worldwide. Such alarming statistics require immediate attention to improve the health of the aging population. Since aging is closely related to the loss of antioxidant defense mechanisms, this situation eventually leads to numerous health problems, including fertility reduction. Furthermore, plant extracts have been used in traditional medicine as potent antioxidant sources. Although many experiments had reported the impact of various bioactive compounds on aging or fertility, there is a lack of review papers that combine both subjects. In this review, we have collected and discussed various bioactive compounds from 26 different plant species known to affect both longevity and fertility. These compounds, including phenolics and terpenes, are mostly involved in the antioxidant defense mechanisms of diverse organisms such as rats, mites, fruit flies, roundworms, and even roosters. A human clinical trial should be considered in the future to measure the effects of these bioactive compounds on human health and longevity. Ultimately, these plant-derived compounds could be developed into health supplements or potential medical drugs to ensure a healthy aging population.
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http://dx.doi.org/10.2174/1389557520666200429101942DOI Listing
April 2021

Modulation of Proteome Profile in AβPP/PS1 Mice Hippocampus, Medial Prefrontal Cortex, and Striatum by Palm Oil Derived Tocotrienol-Rich Fraction.

J Alzheimers Dis 2019 ;72(1):229-246

Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Japan.

Tocotrienol-rich fraction (TRF) is a mixture of vitamin E analogs derived from palm oil. We previously demonstrated that supplementation with TRF improved cognitive function and modulated amyloid pathology in AβPP/PS1 mice brains. The current study was designed to examine proteomic profiles underlying the therapeutic effect of TRF in the brain. Proteomic analyses were performed on samples of hippocampus, medial prefrontal cortex (mPFC), and striatum using liquid chromatography coupled to Q Exactive HF Orbitrap mass spectrometry. From these analyses, we profiled a total of 5,847 proteins of which 155 proteins were differentially expressed between AβPP/PS1 and wild-type mice. TRF supplementation of these mice altered the expression of 255 proteins in the hippocampus, mPFC, and striatum. TRF also negatively modulated the expression of amyloid beta A4 protein and receptor-type tyrosine-protein phosphatase alpha protein in the hippocampus. The expression of proteins in metabolic pathways, oxidative phosphorylation, and those involved in Alzheimer's disease were altered in the brains of AβPP/PS1 mice that received TRF supplementation.
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http://dx.doi.org/10.3233/JAD-181171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839455PMC
November 2020

Protein replenishment in pitcher fluids of Nepenthes × ventrata revealed by quantitative proteomics (SWATH-MS) informed by transcriptomics.

J Plant Res 2019 Sep 17;132(5):681-694. Epub 2019 Aug 17.

Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor Darul Ehsan, Malaysia.

Carnivorous plants capture and digest insects for nutrients, allowing them to survive in soil deprived of nitrogenous nutrients. Plants from the genus Nepenthes produce unique pitchers containing secretory glands, which secrete enzymes into the digestive fluid. We performed RNA-seq analysis on the pitcher tissues and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis on the pitcher fluids of Nepenthes × ventrata to study protein expression in this carnivory organ during early days of pitcher opening. This transcriptome provides a sequence database for pitcher fluid protein identification. A total of 32 proteins of diverse functions were successfully identified in which 19 proteins can be quantified based on label-free quantitative proteomics (SWATH-MS) analysis while 16 proteins were not reported previously. Our findings show that certain proteins in the pitcher fluid were continuously secreted or replenished after pitcher opening, even without any prey or chitin induction. We also discovered a new aspartic proteinase, Nep6, secreted into pitcher fluid. This is the first SWATH-MS analysis of protein expression in Nepenthes pitcher fluid using a species-specific reference transcriptome. Taken together, our study using a gel-free shotgun proteomics informed by transcriptomics (PIT) approach showed the dynamics of endogenous protein secretion in the digestive organ of N. × ventrata and provides insights on protein regulation during early pitcher opening prior to prey capture.
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http://dx.doi.org/10.1007/s10265-019-01130-wDOI Listing
September 2019

Valorization of mangosteen, "The Queen of Fruits," and new advances in postharvest and in food and engineering applications: A review.

J Adv Res 2019 Nov 29;20:61-70. Epub 2019 May 29.

Bioresource and Biorefinery Laboratory, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia.

One of the most prolific plants utilized in various applications is mangosteen ( L.). Rich in potent bioactive compounds, such as xanthones, mangosteen is known to possess pharmacologically important anti-inflammatory and anti-tumor properties. However, most previous reviews have only discussed the application of mangosteen in medicinal areas, yet more recent studies have diverged and valorized its usage in other scientific fields. In this review, the utilization of this exotic fruit in postharvest biology (phytohormone roles, metabolite profiling, bioactive compounds, isolation method optimization, chemical contaminant identification, and management of pests and fruit disorders), food science (food products, animal feed supplementation, and food shelf-life determination), and engineering fields (fabric and solar cell dyes, carbon dots, activated carbon, and biomedical advanced materials) is presented in detail. Research papers published from 2016 onward were selected and reviewed to show the recent research trends in these areas. In conclusion, mangosteen has been utilized for various purposes, ranging from usage in industrially important products to applications in advanced technologies and biomedical innovation.
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http://dx.doi.org/10.1016/j.jare.2019.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562293PMC
November 2019

Phenotypic subgrouping and multi-omics analyses reveal reduced diazepam-binding inhibitor (DBI) protein levels in autism spectrum disorder with severe language impairment.

PLoS One 2019 28;14(3):e0214198. Epub 2019 Mar 28.

Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.

Background: The mechanisms underlying autism spectrum disorder (ASD) remain unclear, and clinical biomarkers are not yet available for ASD. Differences in dysregulated proteins in ASD have shown little reproducibility, which is partly due to ASD heterogeneity. Recent studies have demonstrated that subgrouping ASD cases based on clinical phenotypes is useful for identifying candidate genes that are dysregulated in ASD subgroups. However, this strategy has not been employed in proteome profiling analyses to identify ASD biomarker proteins for specific subgroups.

Methods: We therefore conducted a cluster analysis of the Autism Diagnostic Interview-Revised (ADI-R) scores from 85 individuals with ASD to predict subgroups and subsequently identified dysregulated genes by reanalyzing the transcriptome profiles of individuals with ASD and unaffected individuals. Proteome profiling of lymphoblastoid cell lines from these individuals was performed via 2D-gel electrophoresis, and then mass spectrometry. Disrupted proteins were identified and compared to the dysregulated transcripts and reported dysregulated proteins from previous proteome studies. Biological functions were predicted using the Ingenuity Pathway Analysis (IPA) program. Selected proteins were also analyzed by Western blotting.

Results: The cluster analysis of ADI-R data revealed four ASD subgroups, including ASD with severe language impairment, and transcriptome profiling identified dysregulated genes in each subgroup. Screening via proteome analysis revealed 82 altered proteins in the ASD subgroup with severe language impairment. Eighteen of these proteins were further identified by nano-LC-MS/MS. Among these proteins, fourteen were predicted by IPA to be associated with neurological functions and inflammation. Among these proteins, diazepam-binding inhibitor (DBI) protein was confirmed by Western blot analysis to be expressed at significantly decreased levels in the ASD subgroup with severe language impairment, and the DBI expression levels were correlated with the scores of several ADI-R items.

Conclusions: By subgrouping individuals with ASD based on clinical phenotypes, and then performing an integrated transcriptome-proteome analysis, we identified DBI as a novel candidate protein for ASD with severe language impairment. The mechanisms of this protein and its potential use as an ASD biomarker warrant further study.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214198PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438570PMC
December 2019

Recent updates on metabolite composition and medicinal benefits of mangosteen plant.

PeerJ 2019 31;7:e6324. Epub 2019 Jan 31.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia.

Background: Mangosteen ( L.) fruit has a unique sweet-sour taste and is rich in beneficial compounds such as xanthones. Mangosteen originally been used in various folk medicines to treat diarrhea, wounds, and fever. More recently, it had been used as a major component in health supplement products for weight loss and for promoting general health. This is perhaps due to its known medicinal benefits, including as anti-oxidant and anti-inflammation. Interestingly, publications related to mangosteen have surged in recent years, suggesting its popularity and usefulness in research laboratories. However, there are still no updated reviews (up to 2018) in this booming research area, particularly on its metabolite composition and medicinal benefits.

Method: In this review, we have covered recent articles within the years of 2016 to 2018 which focus on several aspects including the latest findings on the compound composition of mangosteen fruit as well as its medicinal usages.

Result: Mangosteen has been vastly used in medicinal areas including in anti-cancer, anti-microbial, and anti-diabetes treatments. Furthermore, we have also described the benefits of mangosteen extract in protecting various human organs such as liver, skin, joint, eye, neuron, bowel, and cardiovascular tissues against disorders and diseases.

Conclusion: All in all, this review describes the numerous manipulations of mangosteen extracted compounds in medicinal areas and highlights the current trend of its research. This will be important for future directed research and may allow researchers to tackle the next big challenge in mangosteen study: drug development and human applications.
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http://dx.doi.org/10.7717/peerj.6324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368837PMC
January 2019

LC-MS data for metabolomics analysis of L. seed germination.

Data Brief 2018 Dec 17;21:2221-2223. Epub 2018 Nov 17.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia.

Metabolic regulation is important during seed germination for the establishment of seedling. The germination strategy of mangosteen ( L.) seed is thought to be unique due to its recalcitrant characteristic (sensitive to coldness and drying). To investigate the metabolic changes during seed germination, we performed metabolomics analysis on germinating mangosteen seed sown after zero, one, three, five, seven and nine days. Sampled mangosteen seeds were subjected to methanol extraction prior analysis using Liquid Chromatography-Time of Flight-Mass Spectrometry (LC-TOF-MS). MS data were further analyzed using ProfileAnalysis (version 2.1). This is one of the earliest reports in metabolite identification and profiling of mangosteen seed at different germination stages. This data article refers to the article entitled "Metabolite profiling of mangosteen seed germination highlights metabolic changes related to carbon utilization and seed protection" (Mazlan et al., 2019) [1].
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http://dx.doi.org/10.1016/j.dib.2018.11.072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276546PMC
December 2018

Proteomics in Systems Biology.

Adv Exp Med Biol 2018;1102:31-49

Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia.

Proteomics is the study of proteins, the workhorses of cells. Proteins can be subjected to various post-translational modifications, making them dynamic to external perturbation. Proteomics can be divided into four areas: sequence, structural, functional and interaction and expression proteomics. These different areas used different instrumentations and have different focuses. For example, sequence and structural proteomics mainly focus on elucidating a particular protein sequence and structure, respectively. Meanwhile, functional and interaction proteomics concentrate on protein function and interaction partners, whereas expression proteomics allows the cataloguing of total proteins in any given samples, hence providing a holistic overview of various proteins in a cell. The application of expression proteomics in cancer and crop research is detailed in this chapter. The general workflow of expression proteomics consisting the use of mass spectrometry instrumentation has also been described, and some examples of proteomics studies are also presented.
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http://dx.doi.org/10.1007/978-3-319-98758-3_3DOI Listing
July 2019

Recent Development in Omics Studies.

Adv Exp Med Biol 2018;1102:1-9

Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia.

The central dogma of molecular biology (DNA, RNA, protein and metabolite) has engraved our understanding of genetics in all living organisms. While the concept has been embraced for many decades, the development of high-throughput technologies particularly omics (genomics, transcriptomics, proteomics and metabolomics) has revolutionised the field to incorporate big data analysis including bioinformatics and systems biology as well as synthetic biology area. These omics approaches as well as systems and synthetic biology areas are now increasingly popular as seen by the growing numbers of publication throughout the years. Several journals which have published most of these related fields are also listed in this chapter to overview their impact and target journals.
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http://dx.doi.org/10.1007/978-3-319-98758-3_1DOI Listing
July 2019

Mass spectrometry dataset for LC-MS metabolomics analysis of L. seed development.

Data Brief 2018 Dec 12;21:548-551. Epub 2018 Oct 12.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia.

L. (mangosteen) seed is recalcitrant, prone to low temperature and drying which limit its long-term storage. Therefore, it is imperative to understand the metabolic changes throughout its development, to shed some light into the recalcitrant nature of this seed. We performed metabolomics analysis on mangosteen seed at different stages of development; six, eight, ten, twelve and fourteen weeks after anthesis. Seed samples were subjected to methanol extraction prior analysis using liquid chromatography - mass spectrometry (LC-MS). The MS data acquired were analyzed using ProfileAnalysis (version 2.1). This data article refers to the article entitled "Metabolomics analysis of developing seed reveals modulated levels of sugars, organic acids and phenylpropanoid compounds" (Mazlan et al., 2018) [1].
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http://dx.doi.org/10.1016/j.dib.2018.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199813PMC
December 2018

Improved Fertility of Diabetic Rats: Preliminary Study of Sperm Proteomic.

Evid Based Complement Alternat Med 2018 30;2018:9201539. Epub 2018 Sep 30.

Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia.

(GP) is a medicinal herb that has long been known as anti-inflammatory and antihyperglycaemic. Recently, this herbal extract has been associated with a profertility effect, suggesting its applicability in treating both diabetes and male infertility. In this study, the effects of GP aqueous extract (GPAE) on diabetic rats were investigated through evaluating testes histology and androgen hormone levels as well as the implantation sites of female rats on copulation with the treated male rats. Three dosages of GPAE were used (150, 300, and 450 mg/kg), and there were three control groups [normal, diabetic, and metformin-treated diabetic]. Testes histology, androgen hormone levels, and number of implantation sites of the GPAE-treated groups matched those of the normal group in contrast to the diabetic and metformin-treated diabetic controls. Sperm proteomics analysis identified 666 proteins, but only 88 were consistently found in all the control and 450-mg/kg GPAE-treated groups. Four proteins, including cysteine-rich secretory protein 1, carboxylesterase 5A, zona pellucida binding protein, and phosphatidylethanolamine-binding protein 1, were significantly upregulated with GPAE treatment compared with the diabetic control, matching the protein levels of the normal group. These proteins were mainly involved in sperm maturation, sperm capacitation, and sperm-egg interaction, suggesting that GP treatment was able to restore the fertility of male diabetic rats at molecular protein level. In conclusion, GP treatment effectively treats infertility of male diabetic rats, possibly through the upregulation of proteins related to sperm maturation and sperm-egg interaction.
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http://dx.doi.org/10.1155/2018/9201539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186343PMC
September 2018

Cytotoxicity and Toxicity Evaluation of Xanthone Crude Extract on Hypoxic Human Hepatocellular Carcinoma and Zebrafish () Embryos.

Toxics 2018 Oct 9;6(4). Epub 2018 Oct 9.

Danish Cancer Society Research Centre, Strandboulevarden 49, 2100 Copenhagen, Denmark.

Xanthone is an organic compound mostly found in mangosteen pericarp and widely known for its anti-proliferating effect on cancer cells. In this study, we evaluated the effects of xanthone crude extract (XCE) and α-mangostin (α-MG) on normoxic and hypoxic human hepatocellular carcinoma (HepG2) cells and their toxicity towards zebrafish embryos. XCE was isolated using a mixture of acetone and water (80:20) and verified via high performance liquid chromatography (HPLC). Both XCE and α-MG showed higher anti-proliferation effects on normoxic HepG2 cells compared to the control drug, 5-fluorouracil (IC = 50.23 ± 1.38, 8.39 ± 0.14, and 143.75 ± 15.31 μg/mL, respectively). In hypoxic conditions, HepG2 cells were two times less sensitive towards XCE compared to normoxic HepG2 cells (IC = 109.38 ± 1.80 μg/mL) and three times less sensitive when treated with >500 μg/mL 5-fluorouracil (5-FU). A similar trend was seen with the α-MG treatment on hypoxic HepG2 cells (IC = 10.11 ± 0.05 μg/mL) compared to normoxic HepG2 cells. However, at a concentration of 12.5 μg/mL, the α-MG treatment caused tail-bend deformities in surviving zebrafish embryos, while no malformation was observed when embryos were exposed to XCE and 5-FU treatments. Our study suggests that both XCE and α-MG are capable of inhibiting HepG2 cell proliferation during normoxic and hypoxic conditions, more effectively than 5-FU. However, XCE is the preferred option as no malformation was observed in surviving zebrafish embryos and it is more cost efficient than α-MG.
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http://dx.doi.org/10.3390/toxics6040060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316214PMC
October 2018

Crystal structure and functional analysis of human C1ORF123.

PeerJ 2018 28;6:e5377. Epub 2018 Sep 28.

Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.

Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.
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http://dx.doi.org/10.7717/peerj.5377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6166629PMC
September 2018

Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb leaves upon methyl jasmonate elicitation.

PeerJ 2018 28;6:e5525. Epub 2018 Aug 28.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.

Background: Jasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, , which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like is unknown.

Method: In this study, plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression.

Results: From this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson's  = 0.677) while a weak correlation was observed for downregulated proteins ( = 0.147).

Discussion: MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak ( = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.
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http://dx.doi.org/10.7717/peerj.5525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118203PMC
August 2018

Proteome profiling in the hippocampus, medial prefrontal cortex, and striatum of aging rat.

Exp Gerontol 2018 10 5;111:53-64. Epub 2018 Jul 5.

Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan. Electronic address:

Decrease in multiple functions occurs in the brain with aging, all of which can contribute to age-related cognitive and locomotor impairments. Brain atrophy specifically in hippocampus, medial prefrontal cortex (mPFC), and striatum, can contribute to this age-associated decline in function. Our recent metabolomics analysis showed age-related changes in these brain regions. To further understand the aging processes, analysis using a proteomics approach was carried out. This study was conducted to identify proteome profiles in the hippocampus, mPFC, and striatum of 14-, 18-, 23-, and 27-month-old rats. Proteomics analysis using ultrahigh performance liquid chromatography coupled with Q Exactive HF Orbitrap mass spectrometry identified 1074 proteins in the hippocampus, 871 proteins in the mPFC, and 241 proteins in the striatum. Of these proteins, 97 in the hippocampus, 25 in mPFC, and 5 in striatum were differentially expressed with age. The altered proteins were classified into three ontologies (cellular component, molecular function, and biological process) containing 44, 38, and 35 functional groups in the hippocampus, mPFC, and striatum, respectively. Most of these altered proteins participate in oxidative phosphorylation (e.g. cytochrome c oxidase and ATP synthase), glutathione metabolism (e.g. peroxiredoxins), or calcium signaling pathway (e.g. protein S100B and calmodulin). The most prominent changes were observed in the oldest animals. These results suggest that alterations in oxidative phosphorylation, glutathione metabolism, and calcium signaling pathway are involved in cognitive and locomotor impairments in aging.
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http://dx.doi.org/10.1016/j.exger.2018.07.002DOI Listing
October 2018

Metabolomics data of leaf using LC-ESI-TOF-MS.

Data Brief 2018 Jun 4;18:1212-1216. Epub 2018 Apr 4.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia.

is a psychoactive plant known as "ketum" in Malaysia and "kratom" in Thailand. This plant is distinctly known to produce two important alkaloids, namely mitragynine (MG) and 7-hydroxymitragynine (7-OH-MG) that can bind to opioid receptors [1]. MG was reported to exhibit antidepressant properties in animal studies [2]. These compounds were also proposed to have the potential to replace opioid analgesics with much lower risks of side effects [3]. To date, there are only over 40 metabolites identified in [4,5]. To obtain a more complete profile of secondary metabolites in ketum, we performed metabolomics study using mature leaves of the green variety. The leaf samples were extracted using methanol prior to liquid chromatography-electrospray ionization-time of flight-mass spectrometry (LC-ESI-TOF-MS) analysis. This data can be useful to for the identification of unknown metabolites that are associated with alkaloid biosynthesis pathway in .
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http://dx.doi.org/10.1016/j.dib.2018.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996727PMC
June 2018

ESI-LC-MS based-metabolomics data of mangosteen ( Linn.) fruit pericarp, aril and seed at different ripening stages.

Data Brief 2018 Apr 15;17:1074-1077. Epub 2018 Feb 15.

Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia.

Fruit ripening is a complex phenomenon involving a series of biochemical, physiological and organoleptic changes. Ripening process in mangosteen ( Linn.) is unique of which the fruit will only ripen properly if harvested during its middle stage (emergence of purple/pink colour) but not earlier (green stage). The knowledge on the molecular mechanism and regulation behind this phenomenon is still limited. Hence, electrospray ionization liquid chromatography mass spectrometry (ESI-LC-MS) based metabolomics analysis was applied to determine the metabolome of mangosteen ripening. Specifically, mangosteen pericarp, aril and seed were collected at four different ripening stages (stage 0: green, stage 2: yellowish with pink patches, stage 4: brownish red and stage 6: dark purple) and subjected to metabolite profiling analysis. The data provided in this article have been deposited to the EMBL-EBI MetaboLights database (DOI: 10.1093/nar/gks1004. PubMed PMID: 23109552) with the identifier MTBLS595. The complete dataset can be accessed here https://www.ebi.ac.uk/metabolights/MTBLS595.
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http://dx.doi.org/10.1016/j.dib.2018.02.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988417PMC
April 2018

Proteomic analysis of pitcher fluid from × .

Data Brief 2018 Apr 2;17:517-519. Epub 2018 Feb 2.

Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600 Selangor Darul Ehsan, Malaysia.

The carnivorous plants of genus produce unique pitchers containing secretory glands, which secrete proteins into the digestive fluid. We investigated protein profile in the pitcher fluid during the first three days of opening to understand carnivory trait of × . The proteome analysis of pitcher fluid from × was performed by label-free quantitative liquid chromatography mass spectrometry (nLC-MS/MS). Raw MS data have been deposited to the ProteomeXchange with identifier PXD007251. This dataset allows the identification and quantification of proteins from pitcher fluids to elucidate proteins involved in carnivory physiology of species.
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http://dx.doi.org/10.1016/j.dib.2018.01.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988297PMC
April 2018

Extensive mass spectrometry proteomics data of herb upon methyl jasmonate treatment.

Data Brief 2018 Feb 8;16:1091-1094. Epub 2018 Feb 8.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.

Proteomics is often hindered by the lack of protein sequence database particularly for non-model species such as 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 leaves upon methyl jasmonate elicitation" [3].
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http://dx.doi.org/10.1016/j.dib.2017.09.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972844PMC
February 2018

Transcriptome data of infected by .

Data Brief 2018 Feb 13;16:466-469. Epub 2017 Nov 13.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Selangor, Malaysia.

Vibriosis disease by spp. greatly reduced productivity of aquaculture, such as brown-marbled grouper (), which is an economically important fish species in Malaysia. Preventive measures and immediate treatment are critical to reduce the mortality of from vibriosis. To investigate the molecular mechanisms associated with immune response and host-bacteria interaction, a transcriptomic analysis was performed to compare between healthy and -infected groupers. This permits the discovery of immune-related genes, specifically the resistance genes upon infection. Herein, we provide the raw transcriptome data from Illumina HiSeq. 4000 that have been deposited into NCBI SRA database with the BioProject accession number PRJNA396437. A total of 493,403,076 raw sequences of 74.5 Gb were obtained. Trimming of the raw data produced 437,186,232 clean reads of ~58 Gb. These datasets will be useful to elucidate the defence mechanisms of against infection for future development of effective prevention and treatment of vibriosis.
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http://dx.doi.org/10.1016/j.dib.2017.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724979PMC
February 2018

Data on RNA-seq analysis of L. seed development.

Data Brief 2018 Feb 7;16:90-93. Epub 2017 Nov 7.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia.

Mangosteen ( 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.
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http://dx.doi.org/10.1016/j.dib.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694954PMC
February 2018

Whole-genome shotgun sequence of phenazine-producing endophytic SUK12.

Genom Data 2017 Sep 24;13:7-10. Epub 2017 May 24.

School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300 Kuala Lumpur, Malaysia.

sp. produces bioactive compounds with a broad spectrum of activities. SUK12 has been identified as a novel endophytic bacteria isolated from ethnomedicinal plant , and was found to produce the phenazine class of biologically active antimicrobial metabolites. The potential use of the phenazines has led to our research interest in determining the genome sequence of SUK12. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PRJNA269542. The raw sequence data are available [https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP105770].
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http://dx.doi.org/10.1016/j.gdata.2017.05.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447654PMC
September 2017

RNA-seq analysis of mangosteen ( L.) fruit ripening.

Genom Data 2017 Jun 13;12:159-160. Epub 2017 May 13.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.

Mangosteen ( L.) is known for its delectable taste and contains high amount of xanthones which have been reported to possess anti-cancer, anti-inflammatory and other bioactive properties. However, stage-specific regulation of mangosteen fruit ripening has never been studied in detail. We have performed a comparative transcriptomic analysis of three ripening stages (Stage 0, 2 and 6) of mangosteen. We have obtained a raw data from six libraries through Illumina HiSeq 4000. A total of ~ 40 Gb of raw data were generated. Clean reads of 650,887,650 (bp) were obtained from 656,913,570 (bp) raw reads. The raw transcriptome data were deposited to SRA database, with the BioProject accession number of PRJNA339916. These data will be beneficial for transcriptome profiling in order to study the regulation of mangosteen fruit ripening. The lack of a complete sequence database from this species impedes protein identification. These data sets provide a reference data for the exploration of novel genes or proteins to understand mangosteen fruit ripening behaviour.
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http://dx.doi.org/10.1016/j.gdata.2017.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435573PMC
June 2017

Iso-Seq analysis of , and  ×  for hybridisation study in pitcher plants.

Genom Data 2017 Jun 3;12:130-131. Epub 2017 May 3.

Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.

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 which can feed on leaf litter, compared to carnivorous , and their carnivorous hybrid  × . 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 (), SRX2692197 (), and SRX2692196 ( × ).
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http://dx.doi.org/10.1016/j.gdata.2017.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429222PMC
June 2017