Displaying publications 1 - 20 of 173 in total

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  1. Wang J, Tao C, Xu G, Ling J, Tong J, Goh BH, et al.
    Mol Omics, 2023 Dec 04;19(10):769-786.
    PMID: 37498608 DOI: 10.1039/d3mo00029j
    Chinese herbal medicine (CHM) exhibits a broad spectrum of clinical applications and demonstrates favorable therapeutic efficacy. Nonetheless, elucidating the underlying mechanism of action (MOA) of CHM in disease treatment remains a formidable task due to its inherent characteristics of multi-level, multi-linked, and multi-dimensional non-linear synergistic actions. In recent years, the concept of a Quality marker (Q-marker) proposed by Liu et al. has significantly contributed to the monitoring and evaluation of CHM products, thereby fostering the advancement of CHM research. Within this study, a Q-marker screening strategy for CHM formulas has been introduced, particularly emphasising efficacy and biological activities, integrating absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification. As an illustrative case, the Q-marker screening of Qianghuo Shengshi decoction (QHSSD) for treating rheumatoid arthritis (RA) has been conducted. Consequently, from a pool of 159 compounds within QHSSD, five Q-markers exhibiting significant in vitro anti-inflammatory effects have been identified. These Q-markers encompass notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Furthermore, by employing an integrated analysis of network pharmacology and metabolomics, several instructive insights into pharmacological mechanisms have been gleaned. This includes the identification of key targets and pathways through which QHSSD exerts its crucial roles in the treatment of RA. Notably, the inhibitory effect of QHSSD on AKT1 and MAPK3 activation has been validated through western blot analysis, underscoring its potential to mitigate RA-related inflammatory responses. In summary, this research demonstrates the proposed strategy's feasibility and provides a practical reference model for the systematic investigation of CHM formulas.
    Matched MeSH terms: Metabolomics
  2. Wang Y, Liu X, Dong L, Cheng KK, Lin C, Wang X, et al.
    Anal Chem, 2023 Apr 18;95(15):6203-6211.
    PMID: 37023366 DOI: 10.1021/acs.analchem.2c04603
    Drug combinations are commonly used to treat various diseases to achieve synergistic therapeutic effects or to alleviate drug resistance. Nevertheless, some drug combinations might lead to adverse effects, and thus, it is crucial to explore the mechanisms of drug interactions before clinical treatment. Generally, drug interactions have been studied using nonclinical pharmacokinetics, toxicology, and pharmacology. Here, we propose a complementary strategy based on metabolomics, which we call interaction metabolite set enrichment analysis, or iMSEA, to decipher drug interactions. First, a digraph-based heterogeneous network model was constructed to model the biological metabolic network based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Second, treatment-specific influences on all detected metabolites were calculated and propagated across the whole network model. Third, pathway activity was defined and enriched to quantify the influence of each treatment on the predefined functional metabolite sets, i.e., metabolic pathways. Finally, drug interactions were identified by comparing the pathway activity enriched by the drug combination treatments and the single drug treatments. A data set consisting of hepatocellular carcinoma (HCC) cells that were treated with oxaliplatin (OXA) and/or vitamin C (VC) was used to illustrate the effectiveness of the iMSEA strategy for evaluation of drug interactions. Performance evaluation using synthetic noise data was also performed to evaluate sensitivities and parameter settings for the iMSEA strategy. The iMSEA strategy highlighted synergistic effects of combined OXA and VC treatments including the alterations in the glycerophospholipid metabolism pathway and glycine, serine, and threonine metabolism pathway. This work provides an alternative method to reveal the mechanisms of drug combinations from the viewpoint of metabolomics.
    Matched MeSH terms: Metabolomics/methods
  3. Shi J, Zhao J, Zhang Y, Wang Y, Tan CP, Xu YJ, et al.
    Anal Chem, 2023 Dec 26;95(51):18793-18802.
    PMID: 38095040 DOI: 10.1021/acs.analchem.3c03785
    Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.
    Matched MeSH terms: Metabolomics/methods
  4. Zailani NNB, Ho PC
    Eur J Drug Metab Pharmacokinet, 2023 Sep;48(5):467-494.
    PMID: 37495930 DOI: 10.1007/s13318-023-00846-4
    This review provides an overview on the current applications of dried blood spots (DBS) as matrices for therapeutic drug (TDM) and drug or disease response monitoring (DRM). Compared with conventional methods using plasma/serum, DBS offers several advantages, including minimally invasiveness, a small blood volume requirement, reduced biohazardous risk, and improved sample stability. Numerous assays utilising DBS for TDM have been reported in the literature over the past decade, covering a wide range of therapeutic drugs. Several factors can affect the accuracy and reliability of the DBS sampling method, including haematocrit (HCT), blood volume, sampling paper and chromatographic effects. It is crucial to evaluate the correlation between DBS concentrations and conventional plasma/serum concentrations, as the latter has traditionally been used for clinical decision. The feasibility of using DBS sampling method as an option for home-based TDM is also discussed. Furthermore, DBS has also been used as a matrix for monitoring the drug or disease responses (DRM) through various approaches such as genotyping, viral load measurement, assessment of inflammatory factors, and more recently, metabolic profiling. Although this research is still in the development stage, advancements in technology are expected to lead to the identification of surrogate biomarkers for drug treatment in DBS and a better understanding of the correlation between DBS drug levels and drug responses. This will make DBS a valuable matrix for TDM and DRM, facilitating the achievement of pharmacokinetic and pharmacodynamic correlations and enabling personalised therapy.
    Matched MeSH terms: Metabolomics
  5. Wong C, Ling YS, Wee JLS, Mujahid A, Müller M
    Sci Rep, 2020 12 14;10(1):21861.
    PMID: 33318532 DOI: 10.1038/s41598-020-78873-3
    Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.
    Matched MeSH terms: Metabolomics*
  6. Xu J, Wang Y, Xu X, Cheng KK, Raftery D, Dong J
    Molecules, 2021 Sep 24;26(19).
    PMID: 34641330 DOI: 10.3390/molecules26195787
    In mass spectrometry (MS)-based metabolomics, missing values (NAs) may be due to different causes, including sample heterogeneity, ion suppression, spectral overlap, inappropriate data processing, and instrumental errors. Although a number of methodologies have been applied to handle NAs, NA imputation remains a challenging problem. Here, we propose a non-negative matrix factorization (NMF)-based method for NA imputation in MS-based metabolomics data, which makes use of both global and local information of the data. The proposed method was compared with three commonly used methods: k-nearest neighbors (kNN), random forest (RF), and outlier-robust (ORI) missing values imputation. These methods were evaluated from the perspectives of accuracy of imputation, retrieval of data structures, and rank of imputation superiority. The experimental results showed that the NMF-based method is well-adapted to various cases of data missingness and the presence of outliers in MS-based metabolic profiles. It outperformed kNN and ORI and showed results comparable with the RF method. Furthermore, the NMF method is more robust and less susceptible to outliers as compared with the RF method. The proposed NMF-based scheme may serve as an alternative NA imputation method which may facilitate biological interpretations of metabolomics data.
    Matched MeSH terms: Metabolomics/methods*
  7. Abdul-Hamid NA, Abas F, Maulidiani M, Ismail IS, Tham CL, Swarup S, et al.
    Anal Biochem, 2019 07 01;576:20-32.
    PMID: 30970239 DOI: 10.1016/j.ab.2019.04.001
    The variation in the extracellular metabolites of RAW 264.7 cells obtained from different passage numbers (passage 9, 12 and 14) was examined. The impact of different harvesting protocols (trypsinization and scraping) on recovery of intracellular metabolites was then assessed. The similarity and variation in the cell metabolome was investigated using 1H NMR metabolic profiling modeled using multivariate data analysis. The characterization and quantification of metabolites was performed to determine the passage-related and harvesting-dependent effects on impacted metabolic networks. The trypsinized RAW cells from lower passages gave higher intensities of most identified metabolites, including asparagine, serine and tryptophan. Principal component analysis revealed variation between cells from different passages and harvesting methods, as indicated by the formation of clusters in score plot. Analysis of S-plots revealed metabolites that acted as biomarkers in discriminating cells from different passages including acetate, serine, lactate and choline. Meanwhile lactate, glutamine and pyruvate served as biomarkers for differentiating trypsinized and scraped cells. In passage-dependent effects, glycolysis and TCA cycle were influential, whereas glycerophospholipid metabolism was affected by the harvesting method. Overall, it is proposed that typsinized RAW cells from lower passage numbers are more appropriate when conducting experiments related to NMR metabolomics.
    Matched MeSH terms: Metabolomics/methods*
  8. Aizat WM, Ismail I, Noor NM
    Adv Exp Med Biol, 2018 11 2;1102:1-9.
    PMID: 30382565 DOI: 10.1007/978-3-319-98758-3_1
    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.
    Matched MeSH terms: Metabolomics/trends*
  9. Lee LK, Foo KY
    Clin Biochem, 2014 Jul;47(10-11):973-82.
    PMID: 24875852 DOI: 10.1016/j.clinbiochem.2014.05.053
    Infertility is a worldwide reproductive health problem which affects approximately 15% of couples, with male factor infertility dominating nearly 50% of the affected population. The nature of the phenomenon is underscored by a complex array of transcriptomic, proteomic and metabolic differences which interact in unknown ways. Many causes of male factor infertility are still defined as idiopathic, and most diagnosis tends to be more descriptive rather than specific. As such, the emergence of novel transcriptomic and metabolomic studies may hold the key to more accurately diagnose and treat male factor infertility. This paper provides the most recent evidence underlying the role of transcriptomic and metabolomic analysis in the management of male infertility. A summary of the current knowledge and new discovery of noninvasive, highly sensitive and specific biomarkers which allow the expansion of this area is outlined.
    Matched MeSH terms: Metabolomics/methods
  10. Selamat J, Rozani NAA, Murugesu S
    Molecules, 2021 Dec 14;26(24).
    PMID: 34946647 DOI: 10.3390/molecules26247565
    The authentication of food products is essential for food quality and safety. Authenticity assessments are important to ensure that the ingredients or contents of food products are legitimate and safe to consume. The metabolomics approach is an essential technique that can be utilized for authentication purposes. This study aimed to summarize food authentication through the metabolomics approach, to study the existing analytical methods, instruments, and statistical methods applied in food authentication, and to review some selected food commodities authenticated using metabolomics-based methods. Various databases, including Google Scholar, PubMed, Scopus, etc., were used to obtain previous research works relevant to the objectives. The review highlights the role of the metabolomics approach in food authenticity. The approach is technically implemented to ensure consumer protection through the strict inspection and enforcement of food labeling. Studies have shown that the study of metabolomics can ultimately detect adulterant(s) or ingredients that are added deliberately, thus compromising the authenticity or quality of food products. Overall, this review will provide information on the usefulness of metabolomics and the techniques associated with it in successful food authentication processes, which is currently a gap in research that can be further explored and improved.
    Matched MeSH terms: Metabolomics*
  11. Ismail SN, Maulidiani M, Akhtar MT, Abas F, Ismail IS, Khatib A, et al.
    Molecules, 2017 Sep 25;22(10).
    PMID: 28946701 DOI: 10.3390/molecules22101612
    Gaharu (agarwood, Aquilaria malaccensis Lamk.) is a valuable tropical rainforest product traded internationally for its distinctive fragrance. It is not only popular as incense and in perfumery, but also favored in traditional medicine due to its sedative, carminative, cardioprotective and analgesic effects. The current study addresses the chemical differences and similarities between gaharu samples of different grades, obtained commercially, using ¹H-NMR-based metabolomics. Two classification models: partial least squares-discriminant analysis (PLS-DA) and Random Forests were developed to classify the gaharu samples on the basis of their chemical constituents. The gaharu samples could be reclassified into a 'high grade' group (samples A, B and D), characterized by high contents of kusunol, jinkohol, and 10-epi-γ-eudesmol; an 'intermediate grade' group (samples C, F and G), dominated by fatty acid and vanillic acid; and a 'low grade' group (sample E and H), which had higher contents of aquilarone derivatives and phenylethyl chromones. The results showed that ¹H- NMR-based metabolomics can be a potential method to grade the quality of gaharu samples on the basis of their chemical constituents.
    Matched MeSH terms: Metabolomics/methods*
  12. Abdulazeez I, Ismail IS, Mohd Faudzi SM, Christianus A, Chong SG
    Drug Chem Toxicol, 2024 Jan;47(1):115-130.
    PMID: 37548163 DOI: 10.1080/01480545.2023.2242005
    Sodium taurocholate (NaT) is a hydrophobic bile salt that exhibits varying toxicity and antimicrobial activity. The accumulation of BSs during their entero-hepatic cycle causes cytotoxicity in the liver and intestine and could also alter the intestinal microbiome leading to various diseases. In this research, the acute toxicity of sodium taurocholate in different concentrations (3000 mg/L, 1500 mg/L, 750 mg/L, 375 mg/L, and 0 mg/L) was investigated on four months old zebrafish by immersion in water for 96 h. The results were determined based on the fish mortality, behavioral response, and NMR metabolomics analysis which revealed LC50 of 1760.32 mg/L and 1050.42 mg/L after 72 and 96 h treatment, respectively. However, the non-lethal NaT concentrations of 750 mg/L and 375 mg/L at 96 h exposure significantly (p ≤ 0.05) decreased the total distance traveled and the activity duration, also caused surface respiration on the zebrafish. Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) revealed that the metabolome of the fish treated with 750 mg/L was discriminated from that of the control by PC1. Major significantly downregulated metabolites by NaT-induction include valine, isoleucine, 2-hydroxyvalerate, glycine, glycerol, choline, glucose, pyruvate, anserine, threonine, carnitine and homoserine. On the contrary, taurine, creatine, lactate, acetate and 3-hydroxybutyrate were upregulated suggesting cellular consumption of lipids, glucose and amino acids for adenosine triphosphate (ATP) generation during immune and inflammatory response. whereby these metabolites were released in the process. In conclusion, the research revealed the toxic effect of NaT and its potential to trigger changes in zebrafish metabolism.
    Matched MeSH terms: Metabolomics/methods
  13. Wong PL, Ramli NS, Tan CP, Azlan A, Abas F
    Phytochem Anal, 2021 Sep;32(5):685-697.
    PMID: 33295100 DOI: 10.1002/pca.3015
    INTRODUCTION: Ardisia elliptica Thunb. (Primulaceae) is a medicinal herb that is traditionally used for the treatment of fever, diarrhoea, measles and herpes. However, there is limited information regarding the correlation of its phytoconstituents with the bioactivity. Optimisation of solvent extraction is vital for maximising retention of bioactive molecules.

    OBJECTIVE: This study investigated the metabolite variations in A. elliptica leaves and the correlation with antioxidant activities.

    METHODOLOGY: Total phenolic content (TPC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) and nitric oxide (NO) radicals scavenging assays were performed on A. elliptica leaves extracted with four different ethanol ratios (0%, 50%, 70% and absolute ethanol). The correlation of metabolites with antioxidant activities was evaluated using a nuclear magnetic resonance (NMR)-based metabolomics approach.

    RESULTS: The results showed that the 50% and 70% ethanolic extracts retained the highest TPC, and the 70% ethanolic extract was the most active, exhibiting half maximal inhibitory concentration (IC50 ) values of 10.18 ± 0.83 and 43.05 ± 1.69 μg/mL, respectively, in both radical scavenging assays. A total of 46 metabolites were tentatively identified, including flavonoids, benzoquinones, triterpenes and phenolic derivatives. The 50% and 70% ethanolic extracts showed similarities in metabolites content and were well discriminated from water and absolute ethanol extracts in a principal component analysis (PCA) model. Moreover, 31 metabolites were found to contribute significantly to the differentiation and antioxidant activity.

    CONCLUSION: This study provides information on bioactive compounds in A. elliptica leaves, which is promising as a functional ingredient for food production or for the development of phytomedicinal products.

    Matched MeSH terms: Metabolomics
  14. Ma NL, Lam SD, Che Lah WA, Ahmad A, Rinklebe J, Sonne C, et al.
    Environ Pollut, 2021 Oct 01;286:117214.
    PMID: 33971466 DOI: 10.1016/j.envpol.2021.117214
    Salinisation of soil is associated with urban pollution, industrial development and rising sea level. Understanding how high salinity is managed at the plant cellular level is vital to increase sustainable farming output. Previous studies focus on plant stress responses under salinity tolerance. Yet, there is limited knowledge about the mechanisms involved from stress state until the recovery state; our research aims to close this gap. By using the most tolerance genotype (SS1-14) and the most susceptible genotype (SS2-18), comparative physiological, metabolome and post-harvest assessments were performed to identify the underlying mechanisms for salinity stress recovery in plant cells. The up-regulation of glutamine, asparagine and malonic acid were found in recovered-tolerant genotype, suggesting a role in the regulation of panicle branching and spikelet formation for survival. Rice could survive up to 150 mM NaCl (∼15 ds/m) with declined of production rate 5-20% ranged from tolerance to susceptible genotype. This show that rice farming may still be viable on the high saline affected area with the right selection of salt-tolerant species, including glycophytes. The salt recovery biomarkers identified in this study and the adaption underlined could be empowered to address salinity problem in rice field.
    Matched MeSH terms: Metabolomics
  15. Mazlan NW, Tate R, Yusoff YM, Clements C, Edrada-Ebel R
    Curr Med Chem, 2020;27(11):1815-1835.
    PMID: 31272343 DOI: 10.2174/0929867326666190704130105
    Endophytic fungi have been explored not just for their ecological functions but also for their secondary metabolites as a new source of these pharmacologically active natural products. Accordingly, many structurally unique and biologically active compounds have been obtained from the cultures of endophytic fungi. Fusarium sp. and Lasiodiplodia theobromae were isolated from the root and stem of the mangrove plant Avicennia lanata, respectively, collected from Terengganu, Malaysia. High-resolution mass spectrometry and NMR spectroscopy were used as metabolomics profiling tools to identify and optimize the production of bioactive secondary metabolites in both strains at different growth stages and culture media. The spectral data was processed by utilizing Mzmine 2, a quantitative expression analysis software and an in house MS-Excel macro coupled with the Dictionary of Natural Products databases for dereplication studies. The investigation for the potential bioactive metabolites from a 15-day rice culture of Fusarium sp. yielded four 1,4- naphthoquinone with naphthazarin structures (1-4). On the other hand, the endophytic fungus L. theobromae grown on the 15-day solid rice culture produced dihydroisocoumarins (5-8). All the isolated compounds (1-8) showed significant activity against Trypanosoma brucei brucei with MIC values of 0.32-12.5 µM. Preliminary cytotoxicity screening against normal prostate cells (PNT2A) was also performed. All compounds exhibited low cytotoxicity, with compounds 3 and 4 showing the lowest cytotoxicity of only 22.3% and 38.6% of the control values at 100 µg/mL, respectively. Structure elucidation of the isolated secondary metabolites was achieved using 2D-NMR and HRESI-MS as well as comparison with literature data.
    Matched MeSH terms: Metabolomics
  16. Ma NL, Hansen M, Roland Therkildsen O, Kjær Christensen T, Skjold Tjørnløv R, Garbus SE, et al.
    Environ Int, 2020 09;142:105866.
    PMID: 32590281 DOI: 10.1016/j.envint.2020.105866
    The Baltic/Wadden Sea Flyway of common eiders has declined over the past three decades. Multiple factors such as contaminant exposure, global warming, hunting, white-tailed eagle predation, decreased agricultural eutrophication and infectious diseases have been suggested to explain the decline. We collected information on body mass, mercury (Hg) concentration, biochemistry and untargeted metabolomics of incubating birds in two colonies in the Danish Straits (Hov Røn, n = 100; Agersø, n = 29) and in one colony in the Baltic proper (Christiansø, n = 23) to look into their metabolisms and energy balance. Body mass was available from early and late incubation for Hov Røn and Christiansø, showing a significant decline (25-30%) in both colonies with late body mass at Christiansø being the lowest. Whole blood concentrations of total mercury Hg were significantly higher in birds at Christiansø in the east compared to Hov Røn in the west. All birds in the three colonies had Hg concentrations in the range of ≤1.0 μg/g ww, which indicates that the risk of effects on reproduction is in the no to low risk category for wild birds. Among the biochemical measures, glucose, fructosamine, amylase, albumin and protein decreased significantly from early to late incubation at Hov Røn and Christiansø, reflecting long-term fastening as supported by the decline in body mass. Untargeted metabolomics performed on Christiansø eiders revealed presence of 8,433 plasma metabolites. Of these, 3,179 metabolites changed significantly (log2-fold change ≥1, p ≤ 0.05) from the early to late incubation. For example, smaller peptides and vitamin B2 (riboflavin) were significantly down-regulated while 11-deoxycorticosterone and palmitoylcarnitine were significantly upregulated. These results show that cumulative stress including fasting during incubation affect the eiders' biochemical profile and energy metabolism and that this may be most pronounced for the Christiansø colony in the Baltic proper. This amplify the events of temperature increases and food web changes caused by global warming that eventually accelerate the loss in body weight. Future studies should examine the relationship between body condition, temperature and reproductive outcomes and include mapping of food web contaminant, energy and nutrient content to better understand, manage and conserve the populations.
    Matched MeSH terms: Metabolomics
  17. Ma NL, Rahmat Z, Lam SS
    Int J Mol Sci, 2013;14(4):7515-41.
    PMID: 23567269 DOI: 10.3390/ijms14047515
    Physiological and ecological constraints that cause the slow growth and depleted production of crops have raised a major concern in the agriculture industry as they represent a possible threat of short food supply in the future. The key feature that regulates the stress signaling pathway is always related to the reactive oxygen species (ROS). The accumulation of ROS in plant cells would leave traces of biomarkers at the genome, proteome, and metabolome levels, which could be identified with the recent technological breakthrough coupled with improved performance of bioinformatics. This review highlights the recent breakthrough in molecular strategies (comprising transcriptomics, proteomics, and metabolomics) in identifying oxidative stress biomarkers and the arising opportunities and obstacles observed in research on biomarkers in rice. The major issue in incorporating bioinformatics to validate the biomarkers from different omic platforms for the use of rice-breeding programs is also discussed. The development of powerful techniques for identification of oxidative stress-related biomarkers and the integration of data from different disciplines shed light on the oxidative response pathways in plants.
    Matched MeSH terms: Metabolomics/methods*
  18. Watanabe M, Roth TL, Bauer SJ, Lane A, Romick-Rosendale LE
    PLoS One, 2016;11(5):e0156318.
    PMID: 27232336 DOI: 10.1371/journal.pone.0156318
    A variety of wildlife species maintained in captivity are susceptible to iron storage disease (ISD), or hemochromatosis, a disease resulting from the deposition of excess iron into insoluble iron clusters in soft tissue. Sumatran rhinoceros (Dicerorhinus sumatrensis) is one of the rhinoceros species that has evolutionarily adapted to a low-iron diet and is susceptible to iron overload. Hemosiderosis is reported at necropsy in many African black and Sumatran rhinoceroses but only a small number of animals reportedly die from hemochromatosis. The underlying cause and reasons for differences in susceptibility to hemochromatosis within the taxon remains unclear. Although serum ferritin concentrations have been useful in monitoring the progression of ISD in many species, there is some question regarding their value in diagnosing hemochromatosis in the Sumatran rhino. To investigate the metabolic changes during the development of hemochromatosis and possibly increase our understanding of its progression and individual susceptibility differences, the serum metabolome from a Sumatran rhinoceros was investigated by nuclear magnetic resonance (NMR)-based metabolomics. The study involved samples from female rhinoceros at the Cincinnati Zoo (n = 3), including two animals that died from liver failure caused by ISD, and the Sungai Dusun Rhinoceros Conservation Centre in Peninsular Malaysia (n = 4). Principal component analysis was performed to visually and statistically compare the metabolic profiles of the healthy animals. The results indicated that significant differences were present between the animals at the zoo and the animals in the conservation center. A comparison of the 43 serum metabolomes of three zoo rhinoceros showed two distinct groupings, healthy (n = 30) and unhealthy (n = 13). A total of eighteen altered metabolites were identified in healthy versus unhealthy samples. Results strongly suggest that NMR-based metabolomics is a valuable tool for animal health monitoring and may provide insight into the progression of this and other insidious diseases.
    Matched MeSH terms: Metabolomics*
  19. Saleh MSM, Siddiqui MJ, Mediani A, Ahmed QU, Mat So'ad SZ, Saidi-Besbes S, et al.
    Food Res Int, 2020 11;137:109547.
    PMID: 33233172 DOI: 10.1016/j.foodres.2020.109547
    Fruit of salak (Salacca zalacca) is traditionally used and commercialized as an antidiabetic agent. However, the scientific evidence to prove this traditional use is lacking. This research was aimed to evaluate the metabolic changes of obese-diabetic (OBDC) rats treated with S. zalacca fruit extract using proton-nuclear magnetic resonance (1H NMR)-based metabolomics approach. This research presents the first report on the in vitro antidiabetic effect of S. zalacca fruits extract using this approach. The obtained results indicated that the administration of 400 mg/kg bw of 60% ethanolic S. zalacca extract for 6 weeks significantly decreased the blood glucose level and normalized the blood lipid profile of the OBDC rats. The potential biomarkers in urine were 2-oxoglutarate, alanine, leucine, succinate 3-hydroxybutyrate, taurine, betaine, allantoin, acetate, dimethylamine, creatine, creatinine, glucose, phenyl-acetylglycine, and hippurate. Based on the data obtained, the 60% ethanolic extract could not fully improved the metabolic complications of diabetic rats. The extract of S. zalacca fruit was able to decrease the ketones bodies as 3-hydroxybutyrate and acetoacetate. It also improved energy metabolism, involving glucose, acetate, lactate, 2-hydroxybutyrate, 2-oxoglutarate, citrate, and succinate. Moreover, it decreased metabolites from gut microflora, including choline. This extract had significant effect on amino acid metabolism, metabolites from gut microflora, bile acid metabolism and creatine. The result can further support the traditional claims of S. zalacca fruits in management of diabetes. This finding might be valuable in understanding the molecular mechanism and pharmacological properties of this medicinal plant for managing diabetes mellitus.
    Matched MeSH terms: Metabolomics*
  20. Enche Ady CNA, Lim SM, Teh LK, Salleh MZ, Chin AV, Tan MP, et al.
    J Neurosci Res, 2017 Oct;95(10):2005-2024.
    PMID: 28301062 DOI: 10.1002/jnr.24048
    The rapid increase in the older population has made age-related diseases like Alzheimer's disease (AD) a global concern. Given that there is still no cure for this neurodegenerative disease, the drastic growth in the number of susceptible individuals represents a major emerging threat to public health. The poor understanding of the mechanisms underlying AD is deemed the greatest stumbling block against progress in definitive diagnosis and management of this disease. There is a dire need for biomarkers that can facilitate early diagnosis, classification, prognosis, and treatment response. Efforts have been directed toward discovery of reliable and distinctive AD biomarkers but with very little success. With the recent emergence of high-throughput technology that is able to collect and catalogue vast datasets of small metabolites, metabolomics offers hope for a better understanding of AD and subsequent identification of biomarkers. This review article highlights the potential of using multiple metabolomics platforms as useful means in uncovering AD biomarkers from body fluids. © 2017 Wiley Periodicals, Inc.
    Matched MeSH terms: Metabolomics/methods*
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