Publications by authors named "Syarul Nataqain Baharum"

44 Publications

Metabolite profiling of endophytic spp. and its antiplasmodial potential.

PeerJ 2021 15;9:e10816. Epub 2021 Mar 15.

Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.

Background: Antiplasmodial drug discovery is significant especially from natural sources such as plant bacteria. This research aimed to determine antiplasmodial metabolites of spp. against 3D7 by using a metabolomics approach.

Methods: strains' growth curves, namely SUK 12 and SUK 48, were measured and . 3D7 IC values were calculated. Metabolomics analysis was conducted on both strains' mid-exponential and stationary phase extracts.

Results: The most successful antiplasmodial activity of SUK 12 and SUK 48 extracts shown to be at the stationary phase with IC values of 0.8168 ng/mL and 0.1963 ng/mL, respectively. In contrast, the IC value of chloroquine diphosphate (CQ) for antiplasmodial activity was 0.2812 ng/mL. The univariate analysis revealed that 854 metabolites and 14, 44 and three metabolites showed significant differences in terms of strain, fermentation phase, and their interactions. Orthogonal partial least square-discriminant analysis and S-loading plot putatively identified pavettine, aurantioclavine, and 4-butyldiphenylmethane as significant outliers from the stationary phase of SUK 48. For potential isolation, metabolomics approach may be used as a preliminary approach to rapidly track and identify the presence of antimalarial metabolites before any isolation and purification can be done.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.10816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971094PMC
March 2021

Streamlining Natural Products Biomanufacturing With Omics and Machine Learning Driven Microbial Engineering.

Front Bioeng Biotechnol 2020 21;8:608918. Epub 2020 Dec 21.

EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre, Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.

Increasing demands for the supply of biopharmaceuticals have propelled the advancement of metabolic engineering and synthetic biology strategies for biomanufacturing of bioactive natural products. Using metabolically engineered microbes as the bioproduction hosts, a variety of natural products including terpenes, flavonoids, alkaloids, and cannabinoids have been synthesized through the construction and expression of known and newly found biosynthetic genes primarily from model and non-model plants. The employment of omics technology and machine learning (ML) platforms as high throughput analytical tools has been increasingly leveraged in promoting data-guided optimization of targeted biosynthetic pathways and enhancement of the microbial production capacity, thereby representing a critical debottlenecking approach in improving and streamlining natural products biomanufacturing. To this end, this mini review summarizes recent efforts that utilize omics platforms and ML tools in strain optimization and prototyping and discusses the beneficial uses of omics-enabled discovery of plant biosynthetic genes in the production of complex plant-based natural products by bioengineered microbes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fbioe.2020.608918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779585PMC
December 2020

Metabolic Profile of - Co-Cultures Revealed the Alkaloids, Flavonoids and Fatty Acids that Contribute to Anti-Ganoderma Activity.

Molecules 2020 Dec 16;25(24). Epub 2020 Dec 16.

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

In solving the issue of basal stem rot diseases caused by Ganoderma, an investigation of as a biological control agent that suppresses Ganoderma infection has gained our interest, as it is more environmentally friendly. Recently, the fungal co-cultivation has emerged as a promising method to discover novel antimicrobial metabolites. In this study, an established technique of co-culturing and was applied to produce and induce metabolites that have antifungal activity against . The crude extract from the co-culture media was applied to a High Performance Liquid Chromatography (HPLC) preparative column to isolate the bioactive compounds, which were tested against . The fractions that showed inhibition against were sent for a Liquid Chromatography-Time of Flight-Mass Spectrometry (LC-TOF-MS) analysis to further identify the compounds that were responsible for the microbicidal activity. Interestingly, we found that eudistomin I, naringenin 7-O-beta-D-glucoside and penipanoid A, which were present in different abundances in all the active fractions, except in the control, could be the antimicrobial metabolites. In addition, the abundance of fatty acids, such as oleic acid and stearamide in the active fraction, also enhanced the antimicrobial activity. This comprehensive metabolomics study could be used as the basis for isolating biocontrol compounds to be applied in oil palm fields to combat a infection.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/molecules25245965DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7767070PMC
December 2020

The effects of amino acids and fatty acids on the disease resistance of in response to infection.

3 Biotech 2020 Dec 22;10(12):544. Epub 2020 Nov 22.

Metabolomics Research Laboratory, Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, Bangi, Malaysia.

Mass mortality resulting from bacterial infection poses a major problem in the grouper aquaculture industry. The purpose of this study was to profile the metabolites released in challenged fish and to reconstruct the metabolic pathways of brown marble grouper ( in response to infection. Metabolite profiles from control and challenged treatment groups after feeding were determined using gas chromatography-mass spectrometry (GC-MS). Forty metabolites were identified from the GC-MS analysis. These metabolites comprised of amino acids, fatty acids, organic acids and carbohydrates. The profiles showed the highest percent area (33.1%) for leucine from the amino acid class in infected fish compared to the control treatment group (12.3%). Regarding the fatty acid class, a higher percent area of the metabolite 8,11-eicosadienoic acid (27.04%) was observed in fish infected with than in the control treatment group (22.5%). Meanwhile, in the carbohydrate class, glucose (47.0%) was the metabolite in the carbohydrate class present at highest percentage in the control treatment group compared to infected fish (30.0%). Our findings highlight the importance of a metabolic analysis for understanding the changes of metabolites in in response to bacterial infections.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13205-020-02543-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7680817PMC
December 2020

Comparative metabolomics of Phialemonium curvatum as an omnipotent fungus cultivated on crude palm oil versus glucose.

Microb Cell Fact 2020 Sep 9;19(1):179. Epub 2020 Sep 9.

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

Background: Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lacking. Selected fungi that can grow in acidic mineral salt media (MSM) with vegetable oil had been identified recently. Hence, this study aimed to investigate the overall metabolite changes of an omnipotent fungus and to reveal changes at central carbon metabolism corresponding to both carbon sources.

Results: Targeted and non-targeted metabolomics for both polar and semi-polar metabolites of Phialemonium curvatum AWO2 (DSM 23903) cultivated in MSM with palm oil (MSM-P) or glucose (MSM-G) as carbon sources were obtained. Targeted metabolomics on central carbon metabolism of tricarboxylic acid (TCA) cycle and glyoxylate cycle were analysed using LC-MS/MS-TripleQ and GC-MS, while untargeted metabolite profiling was performed using LC-MS/MS-QTOF followed by multivariate analysis. Targeted metabolomics analysis showed that glyoxylate pathway and TCA cycle were recruited at central carbon metabolism for triglyceride and glucose catabolism, respectively. Significant differences in organic acids concentration of about 4- to 8-fold were observed for citric acid, succinic acid, malic acid, and oxaloacetic acid. Correlation of organic acids concentration and key enzymes involved in the central carbon metabolism was further determined by enzymatic assays. On the other hand, the untargeted profiling revealed seven metabolites undergoing significant changes between MSM-P and MSM-G cultures.

Conclusions: Overall, this study has provided insights on the understanding on the effect of triglycerides and sugar as carbon source in fungi global metabolic pathway, which might become important for future optimization of carbon flux engineering in fungi to improve organic acids production when vegetable oil is applied as the sole carbon source.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12934-020-01434-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487481PMC
September 2020

Application of Reverse Genetics in Functional Genomics of Potyvirus.

Viruses 2020 07 26;12(8). Epub 2020 Jul 26.

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

Numerous potyvirus studies, including virus biology, transmission, viral protein function, as well as virus-host interaction, have greatly benefited from the utilization of reverse genetic techniques. Reverse genetics of RNA viruses refers to the manipulation of viral genomes, transfection of the modified cDNAs into cells, and the production of live infectious progenies, either wild-type or mutated. Reverse genetic technology provides an opportunity of developing potyviruses into vectors for improving agronomic traits in plants, as a reporter system for tracking virus infection in hosts or a production system for target proteins. Therefore, this review provides an overview on the breakthroughs achieved in potyvirus research through the implementation of reverse genetic systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v12080803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472138PMC
July 2020

Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15.

Microbiol Res 2020 Mar 9;233:126410. Epub 2020 Jan 9.

Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. Electronic address:

Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.micres.2020.126410DOI Listing
March 2020

Insight into plant cell wall degradation and pathogenesis of via comparative genome analysis.

PeerJ 2019 18;7:e8065. Epub 2019 Dec 18.

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

Background: is a hemibiotrophic fungus that infects oil palms ( Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels.

Methods: In this study, comparative genome analysis was carried out using the NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from NJ3 was made against , a well-studied model sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of NJ3.

Results: was enriched with CAZymes and CWDEs in a similar fashion to that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of was investigated by analyzing the fungal CAZymes with necrotrophic , , biotrophic , and hemibiotrophic . Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis.

Discussion: This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by . Identification of CAZymes and CWDE-related PHI genes in would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.8065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927665PMC
December 2019

Comparative genome analysis reveals a distinct influence of nucleotide composition on virus-host species-specific interaction of prawn-infecting nodavirus.

J Fish Dis 2019 Dec 21;42(12):1761-1772. Epub 2019 Oct 21.

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

Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus-host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jfd.13093DOI Listing
December 2019

Recent advancement of engineering microbial hosts for the biotechnological production of flavonoids.

Mol Biol Rep 2019 Dec 18;46(6):6647-6659. Epub 2019 Sep 18.

Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Malaysia.

Flavonoids are polyphenols that are important organic chemicals in plants. The health benefits of flavonoids that result in high commercial values make them attractive targets for large-scale production through bioengineering. Strategies such as engineering a flavonoid biosynthetic pathway in microbial hosts provide an alternative way to produce these beneficial compounds. Escherichia coli, Saccharomyces cerevisiae and Streptomyces sp. are among the expression systems used to produce recombinant products, as well as for the production of flavonoid compounds through various bioengineering approaches including clustered regularly interspaced short palindromic repeats (CRISPR)-based genome engineering and genetically encoded biosensors to detect flavonoid biosynthesis. In this study, we review the recent advances in engineering model microbial hosts as being the factory to produce targeted flavonoid compounds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11033-019-05066-1DOI Listing
December 2019

Complete Genome Sequence of Infecting Asian Rice (Oryza sativa) in Malaysia.

Microbiol Resour Announc 2019 May 16;8(20). Epub 2019 May 16.

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

Rice tungro disease was discovered in Malaysia in the 1930s. The first and only genome of (RTBV) isolated from rice in Malaysia was sequenced in 1999. After nearly two decades, here, we present the complete genome sequence of an RTBV isolate in rice from Seberang Perai, Malaysia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00262-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522785PMC
May 2019

A Review on Viruses Infecting Taro ( (L.) Schott).

Pathogens 2019 Apr 25;8(2). Epub 2019 Apr 25.

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

Taro is an important crop in parts of the world, especially in the Pacific Islands. Like all plants, it is also susceptible to virus infections that could result in diseases, which negatively affects the source of food and trade revenue. Understanding the biology of taro viruses could improve current knowledge regarding the relationship between viruses and taro, thus allowing for a better approach towards the management of the diseases that are associated with them. By compiling and discussing the research on taro and its four major viruses (, , and ) and a relatively new one (, this paper explores the details of each virus by examining their characteristics and highlighting information that could be used to mitigate taro infections and disease management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/pathogens8020056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630990PMC
April 2019

Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation.

PeerJ 2019 5;7:e6568. Epub 2019 Apr 5.

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

Pathologically relevant behaviors of , such as the expression of virulence factors, biofilm production, and swarming motility, have been shown to be controlled by quorum sensing. The autoinducer-2 quorum sensing receptor protein LuxP is one of the target proteins for drug development to suppress the virulence of . Here, we reported the potential molecular interaction of fatty acids identified in vibriosis-resistant grouper with LuxP. Fatty acid, 4-oxodocosahexaenoic acid (4R8) showed significant binding affinity toward LuxP (-6.0 kcal/mol) based on molecular docking analysis. The dynamic behavior of the protein-ligand complex was illustrated by molecular dynamic simulations. The fluctuation of the protein backbone, the stability of ligand binding, and hydrogen bond interactions were assessed, suggesting 4R8 possesses potential interaction with LuxP, which was supported by the low binding free energy (-29.144 kJ/mol) calculated using the molecular mechanics Poisson-Boltzmann surface area.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.6568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452917PMC
April 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214198PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438570PMC
December 2019

Metabolite profiling of Epinephelus fuscoguttatus infected with vibriosis reveals Omega 9 as potential metabolite biomarker.

Fish Physiol Biochem 2019 Jun 26;45(3):1203-1215. Epub 2019 Mar 26.

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

In this study, we report the starvation effect and vibriosis infection on a tropical fish, the tiger grouper (Epinephelus fuscoguttatus). The tiger groupers were infected with Vibrio vulnificus for 21 days. Gas chromatography-mass spectrometry combined with multivariate analysis was used to assess the variation in metabolite profiles of E. fuscoguttatus. Metabolite productions in infected fishes were significantly influenced by fatty acid production. The Omega 9 (ω-9) was abundant under the challenged conditions compared to Omega 3 (ω-3) and Omega 6 (ω-6). A total of six fatty acids from the ω-9 group were detected in high concentration in the infected fishes compared to the control groupers. These metabolites are Oleic acid, Palmitoleic acid, 6,9-Octadecenoic acid, 8,11-Eicosadienoic acid, cis-Erucic acid and 5,8,11-Eicosatrienoic acid. The production of ω-9 differed significantly (p ≤ 0.001) in the challenged samples. The detected ω-9 compounds were quantified based on three different extraction techniques with Supelco 37-component FAME mix (Supelco, USA). The highest concentration of ω-9 groups compared to the other fatty acids detected is 1320.79 mg/4 g and the lowest is 939 mg/4 g in challenged-starved; meanwhile, in challenged-fed, the highest concentration detected is 1220.87 mg/4 g and the lowest is 917.25 mg/4 g. These changes demonstrate that ω-9 can be used as a biomarker of infection in fish.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10695-019-00633-6DOI Listing
June 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].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2018.11.072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276546PMC
December 2018

Metabolomics in Systems Biology.

Adv Exp Med Biol 2018;1102:51-68

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

Over the last decade, metabolomics has continued to grow rapidly and is considered a dynamic technology in envisaging and elucidating complex phenotypes in systems biology area. The advantage of metabolomics compared to other omics technologies such as transcriptomics and proteomics is that these later omics only consider the intermediate steps in the central dogma pathway (mRNA and protein expression). Meanwhile, metabolomics reveals the downstream products of gene and expression of proteins. The most frequently used tools are nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). Some of the common MS-based analyses are gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These high-throughput instruments play an extremely crucial role in discovery metabolomics to generate data needed for further analysis. In this chapter, the concept of metabolomics in the context of systems biology is discussed and provides examples of its application in human disease studies, plant responses towards stress and abiotic resistance and also microbial metabolomics for biotechnology applications. Lastly, a few case studies of metabolomics analysis are also presented, for example, investigation of an aromatic herbal plant, Persicaria minor metabolome and microbial metabolomics for metabolic engineering applications.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-3-319-98758-3_4DOI 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].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2018.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199813PMC
December 2018

Transcriptome-wide effects of expansin gene manipulation in etiolated Arabidopsis seedling.

J Plant Res 2019 Mar 19;132(2):159-172. Epub 2018 Oct 19.

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

Expansin is a non-enzymatic protein which plays a pivotal role in cell wall loosening by inducing stress relaxation and extension in the plant cell wall. Previous studies on Arabidopsis, Petunia × hybrida, and tomato demonstrated that the suppression of expansin gene expression reduced plant growth but expansin overexpression does not necessarily promotes growth. In this study, both expansin gene suppression and overexpression in dark-grown transgenic Arabidopsis seedlings resulted in reduced hypocotyl length at late growth stages with a more pronounced effect for the overexpression. This defect in hypocotyl elongation raises questions about the molecular effect of expansin gene manipulation. RNA-seq analysis of the transcriptomic changes between day 3 and day 5 seedlings for both transgenic lines found numerous differentially expressed genes (DEGs) including transcription factors and hormone-related genes involved in different aspects of cell wall development. These DEGs imply that the observed hypocotyl growth retardation is a consequence of the concerted effect of regulatory factors and multiple cell-wall related genes, which are important for cell wall remodelling during rapid hypocotyl elongation. This is further supported by co-expression analysis through network-centric approach of differential network cluster analysis. This first transcriptome-wide study of expansin manipulation explains why the effect of expansin overexpression is greater than suppression and provides insights into the dynamic nature of molecular regulation during etiolation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10265-018-1067-0DOI Listing
March 2019

Metabolite profiles of callus and cell suspension cultures of mangosteen.

3 Biotech 2018 Aug 17;8(8):322. Epub 2018 Jul 17.

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

Callus was induced from mangosteen ( L.) young purple-red leaves on Murashige and Skoog basal medium with various combinations of plant growth regulators. Murashige and Skoog medium with 4.44 µM 6-benzylaminopurine and 4.52 µM 2,4-dichlorophenoxyacetic acid was the best for friable callus induction. This friable callus was used for the initiation of cell suspension culture. The effects of different combinations of 6-benzylaminopurine and 2,4-dichlorophenoxyacetic acid, carbon sources and inoculum sizes were tested. It was found that combination of 2.22 µM 6-benzylaminopurine + 2.26 µM 2,4-dichlorophenoxyacetic acid, glucose (30 g/l) and 1.5 g/50 ml inoculum size was the best for cell growth. Callus and cell suspension cultures were then treated either with 100 µM methyl jasmonate as an elicitor for 5 days, or 0.5 g/l casein hydrolysate as an organic supplement for 7 days. Metabolites were then extracted and profiled using liquid chromatography-time of flight mass spectrometry. Multivariate discriminant analyses revealed significant metabolite differences ( ≤ 0.05) for callus and suspension cells treated either with methyl jasmonate or casein hydrolysate. Based on MS/MS data, methyl jasmonate stimulated the production of an alkaloid (thalsimine) and fatty acid (phosphatidyl ethanolamine) in suspension cells while in callus, an alkaloid (thiacremonone) and glucosinolate (7-methylthioheptanaldoxime) was produced. Meanwhile casein hydrolysate stimulated the production of alkaloids such as 3ß,6ß-dihydroxynortropane and cis-hinokiresinol and triterpenoids such as schidigerasaponin and talinumoside in suspension cells. This study provides evidence on the potential of secondary metabolite production from in vitro culture of mangosteen.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13205-018-1336-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6049810PMC
August 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 .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2018.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996727PMC
June 2018

Functional Characterisation of New Sesquiterpene Synthase from the Malaysian Herbal Plant, .

Molecules 2018 06 6;23(6). Epub 2018 Jun 6.

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

(syn. ) 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 STPS1 and STPS2, two sesquiterpene synthase genes that were identified from transcriptome data mining. The full-length sequences of the STPS1 and STPS2 genes were expressed in the pQE-2 expression vector. The sizes of STPS1 and STPS2 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 STPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the STPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of STPS1 and STPS2 in the biosynthesis pathway of , to produce aromatic sesquiterpenes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/molecules23061370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6100370PMC
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2018.02.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988417PMC
April 2018

Polygonumins A, a newly isolated compound from the stem of Polygonum minus Huds with potential medicinal activities.

Sci Rep 2018 03 9;8(1):4202. Epub 2018 Mar 9.

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

Polygonumins A, a new compound, was isolated from the stem of Polygonum minus. Based on NMR results, the compound's structure is identical to that of vanicoside A, comprising four phenylpropanoid ester units and a sucrose unit. The structure differences were located at C-3″″'. The cytotoxic activity of polygonumins A was evaluated on several cancer cell lines by a cell viability assay using tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The compound showed the highest antiproliferative (p < 0.05) activities against K562 (Human Leukaemia Cell Line), MCF7 (Human breast adenocarcinoma cell line), and HCT116 (Colorectal cancer cells) cells. Cytotoxic studies against V79-4 cells were carried out and showed that polygonumins A was toxic at 50 µg/ml, suggesting that this compound may be used as an anticancer drug without affecting normal cells. Polygonumins A also showed promising activity as an HIV-1 protease inhibitor with 56% relative inhibition. Molecular docking results indicated that the compound possesses high binding affinity towards the HIV protease over the low binding free energy range of -10.5 to -11.3 kcal/mol. P. minus is used in Malaysian traditional medicine for the treatment of tumour cells. This is the first report on the use of P. minus as an HIV-1 protease inhibitor.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-22485-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5845017PMC
March 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2017.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724979PMC
February 2018

Transcriptomic data of hypocotyl overexpressing a heterologous gene.

Data Brief 2017 Dec 22;15:320-323. Epub 2017 Sep 22.

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

Expansin increases cell wall extensibility to allow cell wall loosening and cell expansion even in the absence of hydrolytic activity. Previous studies showed that excessive overexpression of expansin gene resulted in defective growth (Goh et al., 2014; Rochange et al., 2001) [1,2] and altered cell wall chemical composition (Zenoni et al., 2011) [3]. However, the molecular mechanism on how the overexpression of non-enzymatic cell wall protein expansin can result in widespread effects on plant cell wall and organ growth remains unclear. We acquired transcriptomic data on previously reported transgenic Arabidopsis line (Goh et al., 2014) [1] to investigate the effects of overexpressing a heterologus cucumber expansin gene () on the global gene expression pattern during early and late phases of etiolated hypocotyl growth.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2017.09.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712050PMC
December 2017

Discovery of Antimalarial Drugs from Streptomycetes Metabolites Using a Metabolomic Approach.

J Trop Med 2017 16;2017:2189814. Epub 2017 Oct 16.

Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Science, Universiti Kebangsaan Malaysia (UKM), 50300 Kuala Lumpur, Malaysia.

Natural products continue to play an important role as a source of biologically active substances for the development of new drug. , Gram-positive bacteria which are widely distributed in nature, are one of the most popular sources of natural antibiotics. Recently, by using a bioassay-guided fractionation, an antimalarial compound, Gancidin-W, has been discovered from these bacteria. However, this classical method in identifying potentially novel bioactive compounds from the natural products requires considerable effort and is a time-consuming process. Metabolomics is an emerging "omics" technology in systems biology study which integrated in process of discovering drug from natural products. Metabolomics approach in finding novel therapeutics agent for malaria offers dereplication step in screening phase to shorten the process. The highly sensitive instruments, such as Liquid Chromatography-Mass Spectrophotometry (LC-MS), Gas Chromatography-Mass Spectrophotometry (GC-MS), and Nuclear Magnetic Resonance (H-NMR) spectroscopy, provide a wide range of information in the identification of potentially bioactive compounds. The current paper reviews concepts of metabolomics and its application in drug discovery of malaria treatment as well as assessing the antimalarial activity from natural products. Metabolomics approach in malaria drug discovery is still new and needs to be initiated, especially for drug research in Malaysia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1155/2017/2189814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662797PMC
October 2017

Mass spectrometry data of metabolomics analysis of Nepenthes pitchers.

Data Brief 2017 Oct 29;14:295-297. Epub 2017 Jul 29.

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

Hybridisation plays a significant role in the evolution and diversification of plants. Hybridisation among Nepenthes species is extensive, either naturally or man-made. To investigate the effects of hybridisation on the chemical compositions, we carried out metabolomics study on pitcher tissue of and their hybrid, . Pitcher samples were harvested and extracted in methanol:chloroform:water via sonication-assisted extraction before analysed using LC-TOF-MS. MS data were analysed using XCMS online version 2.2.5. This is the first MS data report towards the profiling, identification and comprehensive comparison of metabolites present in Nepenthes species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dib.2017.07.068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540702PMC
October 2017

C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses.

PeerJ 2017 5;5:e3451. Epub 2017 Jul 5.

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

subsp. MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of to several stresses has been described, the adaptation mechanisms at the level of fluxes have seldom been described. To gain insights into cellular metabolism, C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS) were used to measure the flux ratios of active pathways in the central metabolism of when subjected to three conditions varying in temperature (30°C, 37°C) and agitation (with and without agitation at 150 rpm). Collectively, the concentrations of proteinogenic amino acids (PAAs) and free fatty acids (FAAs) were compared, and Pearson correlation analysis () was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP) pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA). Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA) from pyruvate (PYR) reaction in all conditions suggested the activation of pyruvate carboxylate (pycA) in , in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP) pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in . Overall, the integration of systematic analysis of amino acids and flux ratio analysis provides a systems-level understanding of how regulates central metabolism under various conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.3451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501154PMC
July 2017

Transcriptomic data of hypocotyl upon suppression of expansin genes.

Genom Data 2017 Jun 3;12:132-133. Epub 2017 May 3.

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

Expansin is a cell wall loosening protein without hydrolytic activity, which allows cell expansion by influencing cell wall extensibility. Previous studies showed that the suppression of expansin genes (, , and ) resulted in defective organ growth and altered cell wall chemical composition [1,2]. However, the molecular mechanism on how the suppression of non-enzymatic expansin expression can result in widespread effects on plant cell wall and organ growth is still unclear. In this study, we performed transcriptomic analysis on the hypocotyls of previously reported transgenic line [1] to investigate the effects of expansin gene suppression on the global gene expression pattern, particularly on the cell wall related genes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gdata.2017.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429223PMC
June 2017