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Trájer AJ, Hoxha I, Xhekaj B, Platzgummer K, Dvořák V, Obwaller AG, Stefanovska J, Cvetkovikj A, Walochnik J, Sherifi K, Kniha E. Ecological setting of phlebotomine sand flies in the Republic of Kosovo. Heliyon 2024; 10:e33029. [PMID: 39021964 PMCID: PMC11253276 DOI: 10.1016/j.heliyon.2024.e33029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024] Open
Abstract
Sand flies (Diptera, Psychodidae) are the principal vectors of Leishmania spp., the causative agents of leishmaniasis, as well as phleboviruses. In the Balkans, the endemicity and spreading of sand fly-borne diseases are evident, particularly in the Republic of Kosovo, a country with a predominantly humid continental climate. To date, understanding the drivers behind the spatial structure and diversity patterns of sand fly communities in humid continental regions remains limited. Therefore, elucidating the geographical and ecological factors contributing to the presence of potential vector species in the country is crucial. We aimed to enhance our understanding of factors influencing sand fly occurrence in cool and wet wintering humid continental areas, which could serve as a model for other countries with similar climatic conditions. Therefore, we assessed the currently known sand fly fauna through detailed environmental analyses, including Voronoi tessellation patterns, entropy calculations, Principal Coordinate and Component Analyses, Hierarchical Clustering, Random Trees, and climatic suitability patterns. Notable differences in the ecological tolerance of the species were detected, and the most important climatic features limiting sand fly presence were wind speed and temperature seasonality. Sand flies were observed to prefer topographical environments with little roughness, and the modelled climatic suitability values indicated that, dominantly, the western plain regions of Kosovo harbour the most diverse sand fly fauna; and are the most threatened by sand fly-borne diseases. Phlebotomus neglectus and P. perfiliewi, both confirmed vectors for L. infantum and phleboviruses, were identified as two main species with vast distribution in Kosovo. Contrary to this, most other present species are relatively sparse and restricted to temperate rather than humid continental regions. Our findings reveal a diverse potential sand fly fauna in Kosovo, indicating the need for tailored strategies to address varying risks across the country's western and eastern regions in relation to leishmaniasis control amidst changing environmental conditions.
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Affiliation(s)
- Attila J. Trájer
- University of Pannonia, Sustainability Solutions Research Lab, Egyetem u. 10. H-8200, Hungary
| | - Ina Hoxha
- Center for Pathophysiology, Infectiology and Immunology, Institute of Specific Prophylaxis and Tropical Medicine, Medical University Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Betim Xhekaj
- Faculty of Agriculture and Veterinary, University of Prishtina ‘Hasan Prishtina’, Bulevardi ‘Bill Clinton’, P.N. 10000 Prishtinë, Kosovo
| | - Katharina Platzgummer
- Center for Pathophysiology, Infectiology and Immunology, Institute of Specific Prophylaxis and Tropical Medicine, Medical University Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Vit Dvořák
- Department of Parasitology, Faculty of Science, Charles University Prague, Viničná 7, 128 43, Prague, Czech Republic
| | - Adelheid G. Obwaller
- Division of Science, Research and Development, Federal Ministry of Defence, Roßauer Lände 1, 1090, Vienna, Austria
| | - Jovana Stefanovska
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine-Skopje, Ss. Cyril and Methodius University in Skopje, Lazar Pop-Trajkov 5–7, 1000, Skopje, North Macedonia
| | - Aleksandar Cvetkovikj
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine-Skopje, Ss. Cyril and Methodius University in Skopje, Lazar Pop-Trajkov 5–7, 1000, Skopje, North Macedonia
| | - Julia Walochnik
- Center for Pathophysiology, Infectiology and Immunology, Institute of Specific Prophylaxis and Tropical Medicine, Medical University Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Kurtesh Sherifi
- Faculty of Agriculture and Veterinary, University of Prishtina ‘Hasan Prishtina’, Bulevardi ‘Bill Clinton’, P.N. 10000 Prishtinë, Kosovo
| | - Edwin Kniha
- Center for Pathophysiology, Infectiology and Immunology, Institute of Specific Prophylaxis and Tropical Medicine, Medical University Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
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Dubery IA, Nephali LP, Tugizimana F, Steenkamp PA. Data-Driven Characterization of Metabolome Reprogramming during Early Development of Sorghum Seedlings. Metabolites 2024; 14:112. [PMID: 38393004 PMCID: PMC10891503 DOI: 10.3390/metabo14020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Specialized metabolites are produced via discrete metabolic pathways. These small molecules play significant roles in plant growth and development, as well as defense against environmental stresses. These include damping off or seedling blight at a post-emergence stage. Targeted metabolomics was followed to gain insights into metabolome changes characteristic of different developmental stages of sorghum seedlings. Metabolites were extracted from leaves at seven time points post-germination and analyzed using ultra-high performance liquid chromatography coupled to mass spectrometry. Multivariate statistical analysis combined with chemometric tools, such as principal component analysis, hierarchical clustering analysis, and orthogonal partial least squares-discriminant analysis, were applied for data exploration and to reduce data dimensionality as well as for the selection of potential discriminant biomarkers. Changes in metabolome patterns of the seedlings were analyzed in the early, middle, and late stages of growth (7, 14, and 29 days post-germination). The metabolite classes were amino acids, organic acids, lipids, cyanogenic glycosides, hormones, hydroxycinnamic acid derivatives, and flavonoids, with the latter representing the largest class of metabolites. In general, the metabolite content showed an increase with the progression of the plant growth stages. Most of the differential metabolites were derived from tryptophan and phenylalanine, which contribute to innate immune defenses as well as growth. Quantitative analysis identified a correlation of apigenin flavone derivatives with growth stage. Data-driven investigations of these metabolomes provided new insights into the developmental dynamics that occur in seedlings to limit post-germination mortality.
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Affiliation(s)
- Ian A. Dubery
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa; (L.P.N.); (F.T.); (P.A.S.)
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Yang CR, Lin WJ, Shen PC, Liao PY, Dai YC, Hung YC, Lai HC, Mehmood S, Cheng WC, Ma WL. Phenotypic and metabolomic characteristics of mouse models of metabolic associated steatohepatitis. Biomark Res 2024; 12:6. [PMID: 38195587 PMCID: PMC10777576 DOI: 10.1186/s40364-023-00555-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/29/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Metabolic associated steatohepatitis (MASH) is metabolic disease that may progress to cirrhosis and hepatocellular carcinoma. Mouse models of diet-induced MASH, which is characterized by the high levels of fats, sugars, and cholesterol in diets, are commonly used in research. However, mouse models accurately reflecting the progression of MASH in humans remain to be established. Studies have explored the potential use of serological metabolites as biomarkers of MASH severity in relation to human MASH. METHODS We performed a comparative analysis of three mouse models of diet-induced MASH in terms of phenotypic and metabolomic characteristics; MASH was induced using different diets: a high-fat diet; a Western diet; and a high-fat, high-cholesterol diet. Liver cirrhosis was diagnosed using standard clinical approaches (e.g., METAVIR score, hyaluronan level, and collagen deposition level). Mouse serum samples were subjected to nuclear magnetic resonance spectroscopy-based metabolomic profiling followed by bioinformatic analyses. Metabolomic analysis of a retrospective cohort of patients with hepatocellular carcinoma was performed; the corresponding cirrhosis scores were also evaluated. RESULTS Using clinically relevant quantitative diagnostic methods, the severity of MASH was evaluated. Regarding metabolomics, the number of lipoprotein metabolites increased with both diet and MASH progression. Notably, the levels of very low-density lipoprotein (VLDL) and low-density lipoprotein (LDL) significantly increased with fibrosis progression. During the development of diet-induced MASH in mice, the strongest upregulation of expression was noted for VLDL receptor. Metabolomic analysis of a retrospective cohort of patients with cirrhosis indicated lipoproteins (e.g., VLDL and LDL) as predominant biomarkers of cirrhosis. CONCLUSIONS Our findings provide insight into the pathophysiology and metabolomics of experimental MASH and its relevance to human MASH. The observed upregulation of lipoprotein expression reveals a feedforward mechanism for MASH development that may be targeted for the development of noninvasive diagnosis.
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Affiliation(s)
- Cian-Ru Yang
- Program for Health Science and Industry, Graduate Institute of Biomedical Sciences, and Department of Medicine, and Tumor Biology Center, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Medical Research, Department of Gynecology and Obstetrics, and Department of Gastroenterology, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Jen Lin
- Program for Health Science and Industry, Graduate Institute of Biomedical Sciences, and Department of Medicine, and Tumor Biology Center, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Medical Research, Department of Gynecology and Obstetrics, and Department of Gastroenterology, China Medical University Hospital, Taichung, Taiwan
| | - Pei-Chun Shen
- Program for Health Science and Industry, Graduate Institute of Biomedical Sciences, and Department of Medicine, and Tumor Biology Center, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Medical Research, Department of Gynecology and Obstetrics, and Department of Gastroenterology, China Medical University Hospital, Taichung, Taiwan
| | - Pei-Yin Liao
- Program for Health Science and Industry, Graduate Institute of Biomedical Sciences, and Department of Medicine, and Tumor Biology Center, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Medical Research, Department of Gynecology and Obstetrics, and Department of Gastroenterology, China Medical University Hospital, Taichung, Taiwan
| | - Yuan-Chang Dai
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi City, Taiwan
| | - Yao-Ching Hung
- Department of Gynecology and Obstetrics, Asia University Hospital, Taichung, Taiwan
| | - Hsueh-Chou Lai
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Center for Digestive Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Shiraz Mehmood
- Program for Health Science and Industry, Graduate Institute of Biomedical Sciences, and Department of Medicine, and Tumor Biology Center, School of Medicine, China Medical University, Taichung, Taiwan
| | - Wei-Chung Cheng
- Program for Health Science and Industry, Graduate Institute of Biomedical Sciences, and Department of Medicine, and Tumor Biology Center, School of Medicine, China Medical University, Taichung, Taiwan.
| | - Wen-Lung Ma
- Program for Health Science and Industry, Graduate Institute of Biomedical Sciences, and Department of Medicine, and Tumor Biology Center, School of Medicine, China Medical University, Taichung, Taiwan.
- Department of Medical Research, Department of Gynecology and Obstetrics, and Department of Gastroenterology, China Medical University Hospital, Taichung, Taiwan.
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Hegde A, Gupta S, Kumari P, Joshi R, Srivatsan V. Wild Edible Flowers of Western Himalayas: Nutritional Characterization, UHPLC-QTOF-IMS-Based Phytochemical Profiling, Antioxidant Properties, and In Vitro Bioaccessibility of Polyphenols. ACS OMEGA 2023; 8:40212-40228. [PMID: 37929082 PMCID: PMC10620890 DOI: 10.1021/acsomega.3c03861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 11/07/2023]
Abstract
Four edible flowers commonly consumed in the Western Himalayan region, namely, Bauhinia variegata (Kachnar), Tropaeolum majus (Nasturtium), Matricaria chamomilla (Chamomile), and Tagetes erecta (Marigold), were characterized for their nutritional and phytochemical composition. Through the UHPLC-QTOF-IMS-based metabolomics approach, 131 compounds were tentatively identified consisting of phenolic acids, flavonoid glycosides, terpenoids, amino acids, and fatty acid derivatives. Kaempferol and quercetin glycosides for Kachnar, apigenin glycosides and caffeoylquinic acid derivatives for Chamomile, patulin and quercetin derivatives for Marigold, cyanidin and delphinidin glycosides for Nasturtium were the predicted marker metabolites identified through non-targeted metabolomics. Kachnar and Chamomile scored best in terms of macronutrients and essential micronutrients, respectively. Nasturtium contained high concentrations of α-linolenic acid, anthocyanins, and lutein. Kachnar contained the highest total phenolic acids (63.36 ± 0.38 mg GAE g-1), while Marigold contained the highest total flavonoids (118.90 ± 1.30 mg QUE g-1). Marigolds possessed excellent free radical scavenging and metal chelation activities. Chamomile exhibited strong α-glucosidase inhibition activity, followed by Nasturtium. The in vitro gastrointestinal digestibility of flower extracts indicated that the bioaccessibility of phenolic acids was higher than that of flavonoids. Polyphenols from Nasturtium and Chamomile showed the highest bioaccessibility. The study is an attempt to characterize traditionally consumed edible flowers and promote their wider utilization in gastronomy and nutraceuticals.
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Affiliation(s)
- Athrinandan
S. Hegde
- Applied
Phycology and Food Technology Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC)
Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Smriti Gupta
- Applied
Phycology and Food Technology Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC)
Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Poonam Kumari
- Division
of Agrotechnology, CSIR-Institute of Himalayan
Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC)
Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Robin Joshi
- Applied
Phycology and Food Technology Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC)
Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Vidyashankar Srivatsan
- Applied
Phycology and Food Technology Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy
of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC)
Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
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Ghatak A, Chaturvedi P, Waldherr S, Subbarao GV, Weckwerth W. PANOMICS at the interface of root-soil microbiome and BNI. TRENDS IN PLANT SCIENCE 2023; 28:106-122. [PMID: 36229336 DOI: 10.1016/j.tplants.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.
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Affiliation(s)
- Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Steffen Waldherr
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guntur Venkata Subbarao
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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Chen J, Nie Y, Xu J, Huang S, Sheng J, Wang X, Zhong J. Sensory and metabolite migration from tilapia skin to soup during the boiling process: fast and then slow. NPJ Sci Food 2022; 6:52. [DOI: 10.1038/s41538-022-00168-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractThis study mainly studied sensory and metabolite migration from the skin to the soup in the boiling process of tilapia skin using content analysis, electronic nose technique, electronic tongue technique, and metabolomics technique based on ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry and gas chromatography-time-of-flight-mass spectrometry. The content changes, flavor changes, taste changes, metabolite numbers and differential metabolite numbers for both tilapia skin and soup mainly occurred in the initial 30 min. Moreover, the initial 10 min was the key period for the metabolite changes in the boiling process. Further, the differential metabolites in these three periods (0–10, 10–30, and 30–60 min) were identified to show the metabolites migration process. Six (adenine, gingerol, terephthalic acid, vanillin, pentanenitrile, and 2-pyrrolidinonede) and seven (butyramide, lysope(0:0/20:4(5z,8z,11z,14z)), lysope(22:6(4z,7z,10z,13z,16z,19z)/0:0), linoleic acid, N-acetylneuraminic acid, L-threose, and benzoin) chemicals were screened out in the differential metabolites of tilapia skin and soup, respectively, with Variable Importance in the Projection of >1 and p value of <0.05. This work would be beneficial to understand the sensory and metabolite migration in the preparation process of fish soup and provided a metabolomic analysis route to analyze metabolites migration in food.
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The use of ecological analytical tools as an unconventional approach for untargeted metabolomics data analysis: the case of Cecropia obtusifolia and its adaptive responses to nitrate starvation. Funct Integr Genomics 2022; 22:1467-1493. [PMID: 36199002 DOI: 10.1007/s10142-022-00904-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/04/2022]
Abstract
Plant metabolomics studies haves revealed new bioactive compounds. However, like other omics disciplines, the generated data are not fully exploited, mainly because the commonly performed analyses focus on elucidating the presence/absence of distinctive metabolites (and/or their precursors) and not on providing a holistic view of metabolomic changes and their participation in organismal adaptation to biotic and abiotic stress conditions. Therefore, spectral libraries generated from Cecropia obtusifolia cell suspension cultures in a previous study were considered as a case study and were reanalyzed herein. These libraries were obtained from a time-course experiment under nitrate starvation conditions using both electrospray ionization modes. The applied methodology included the use of ecological analytical tools in a systematic four-step process, including a population analysis of metabolite α diversity, richness, and evenness (i); a chemometrics analysis to identify discriminant groups (ii); differential metabolic marker identification (iii); and enrichment analyses and annotation of active metabolic pathways enriched by differential metabolites (iv). Our species α diversity results referring to the diversity of metabolites represented by mass-to-charge ratio (m/z) values detected at a specific retention time (rt) (an uncommon way to analyze untargeted metabolomic data) suggest that the metabolome is dynamic and is modulated by abiotic stress. A total of 147 and 371 m/z_rt pairs was identified as differential markers responsive to nitrate starvation in ESI- and ESI+ modes, respectively. Subsequent enrichment analysis showed a high degree of completeness of biosynthetic pathways such as those of brassinosteroids, flavonoids, and phenylpropanoids.
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Qian Z, Tan R, Zhang X, Leng Y, Chen Z. MnO2 Nanosheet-Based colorimetric sensor Array: Toward identification of organophosphorus pesticides. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mafata M, Brand J, Medvedovici A, Buica A. Chemometric and sensometric techniques in enological data analysis. Crit Rev Food Sci Nutr 2022; 63:10995-11009. [PMID: 35730201 DOI: 10.1080/10408398.2022.2089624] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Enological evaluations capture the chemical and sensory space of wine using different techniques; many sensory methods as well as a variety of analytical chemistry techniques contribute to the amount of information generated. Data fusion, especially integrating data sets, is important when working with complex systems. The success reported when trying to integrate different modalities is generally low and has been attributed to the lack of statistically considerate strategies focusing on the data handling process. Multiple stages of data handling must be carefully considered when dealing with multi-modal data. In this review, the different stages in the data analysis process were examined. The study revealed misconceptions surrounding the process and elucidated rules for purpose-driven approaches by examining the complexities of each stage and the impact the decisions made at each stage have on the resulting models. The two major modeling approaches are either supervised (discrimination, classification, prediction) or unsupervised (exploration). Supervised approaches were emphatic on the pre-processing steps and prioritized increasing performance. Unsupervised approaches were mostly used for preliminary steps. The review found aspects often neglected when it came to the data collection and capturing which in the end contributed to the low success in combining sensory and chemistry data.
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Affiliation(s)
- Mpho Mafata
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, South Africa
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Jeanne Brand
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, South Africa
| | - Andrei Medvedovici
- Department of Analytical Chemistry, Faculty of Chemistry, University of Bucharest, Bucharest, Romania
| | - Astrid Buica
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, South Africa
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
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Targeted and Untargeted Mass Spectrometry-Based Metabolomics for Chemical Profiling of Three Coffee Species. Molecules 2022; 27:molecules27103152. [PMID: 35630628 PMCID: PMC9143251 DOI: 10.3390/molecules27103152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022] Open
Abstract
While coffee beans have been studied for many years, researchers are showing a growing interest in coffee leaves and by-products, but little information is currently available on coffee species other than Coffea arabica and Coffea canephora. The aim of this work was to perform a targeted and untargeted metabolomics study on Coffea arabica, Coffea canephora and Coffea anthonyi. The application of the recent high-resolution mass spectrometry-based metabolomics tools allowed us to gain a clear overview of the main differences among the coffee species. The results showed that the leaves and fruits of Coffea anthonyi had a different metabolite profile when compared to the two other species. In Coffea anthonyi, caffeine levels were found in lower concentrations while caffeoylquinic acid and mangiferin-related compounds were found in higher concentrations. A large number of specialized metabolites can be found in Coffea anthonyi tissues, making this species a valid candidate for innovative healthcare products made with coffee extracts.
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Zeng L, Bi Y, Guo P, Bi Y, Wang T, Dong L, Wang F, Chen L, Zhang W. Metabolic Analysis of Schizochytrium Mutants With High DHA Content Achieved With ARTP Mutagenesis Combined With Iodoacetic Acid and Dehydroepiandrosterone Screening. Front Bioeng Biotechnol 2021; 9:738052. [PMID: 34869256 PMCID: PMC8637758 DOI: 10.3389/fbioe.2021.738052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
High DHA production cost caused by low DHA titer and productivity of the current Schizochytrium strains is a bottleneck for its application in competition with traditional fish-oil based approach. In this study, atmospheric and room-temperature plasma with iodoacetic acid and dehydroepiandrosterone screening led to three mutants, 6–8, 6–16 and 6–23 all with increased growth and DHA accumulations. A LC/MS metabolomic analysis revealed the increased metabolism in PPP and EMP as well as the decreased TCA cycle might be relevant to the increased growth and DHA biosynthesis in the mutants. Finally, the mutant 6–23, which achieved the highest growth and DHA accumulation among all mutants, was evaluated in a 5 L fermentor. The results showed that the DHA concentration and productivity in mutant 6–23 were 41.4 g/L and 430.7 mg/L/h in fermentation for 96 h, respectively, which is the highest reported so far in literature. The study provides a novel strain improvement strategy for DHA-producing Schizochytrium.
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Affiliation(s)
- Lei Zeng
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Yanqi Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Pengfei Guo
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Yali Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Tiantian Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Liang Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Fangzhong Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
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12
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Hernández-Guerrero CJ, Villa-Ruano N, Zepeda-Vallejo LG, Hernández-Fuentes AD, Ramirez-Estrada K, Zamudio-Lucero S, Hidalgo-Martínez D, Becerra-Martínez E. Bean cultivars (Phaseolus vulgaris L.) under the spotlight of NMR metabolomics. Food Res Int 2021; 150:110805. [PMID: 34865815 DOI: 10.1016/j.foodres.2021.110805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/08/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
The seeds of Phaseolus vulgaris are a rich source of protein consumed around the world and are considered as the most important source of proteins and antioxidants in the Mexican diet. This work reports on the 1H NMR metabolomics profiling of the cultivars Peruano (FPe), Pinto (FPi), Flor de mayo (FM), Negro (FN) and Flor de junio (FJ). Total phenolics, total flavonoids and total protein contents were determined to complement the nutritional facts in seeds and leaves. According to our results, the metabolomics fingerprint of beans seeds and leaves were very similar, showing the presence of 52 metabolites, 46 in seeds and 48 in leaves, including 8 sugars, 17 amino acids, 15 organic acids, 5 nucleosides and 7 miscellaneous compounds. In seeds, free amino acids were detected in higher concentrations than in the leaves, whereas organic acids were more abundant in leaves than in seeds. With multivariate and cluster analysis it was possible to rank the cultivars according to their nutritional properties according to NMR profiling, then a machine learning algorithm was used to reveal the most important differential metabolites which are the key for correct classification. The results coincide in highlighting the FN seeds and FPe leaves for the best nutritional facts. Finally, in terms of cultivars, FN and FM present the best nutritional properties, with high protein and flavonoids content, as well as, a high concentration of amino acids and nucleosides.
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Affiliation(s)
- Claudia J Hernández-Guerrero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. IPN s/n, CP 23096. La Paz, Baja California Sur, Mexico
| | - Nemesio Villa-Ruano
- CONACyT-Centro Universitario de Vinculación y Transferencia de Tecnología, Benemérita Universidad Autónoma de Puebla, CP 72570 Puebla, Mexico
| | - L Gerardo Zepeda-Vallejo
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Alma D Hernández-Fuentes
- Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico
| | - Karla Ramirez-Estrada
- Laboratorio de Metabolismo Celular, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Av. Universidad S/N, Ciudad Universitaria, San Nicolás de los Garza, NL 66451, Mexico
| | - Sergio Zamudio-Lucero
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Av. Luis Enrique Erro S/N, Unidad Profesional Adolfo López Mateos, Zacatenco, Delegación Gustavo A. Madero, Ciudad de México 07738, Mexico
| | - Diego Hidalgo-Martínez
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, United States.
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Av. Luis Enrique Erro S/N, Unidad Profesional Adolfo López Mateos, Zacatenco, Delegación Gustavo A. Madero, Ciudad de México 07738, Mexico.
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13
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Correia MSP, Thapa B, Vujasinovic M, Löhr JM, Globisch D. Investigation of the individual human sulfatome in plasma and urine samples reveals an age-dependency. RSC Adv 2021; 11:34788-34794. [PMID: 35494758 PMCID: PMC9042682 DOI: 10.1039/d1ra05994g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/12/2021] [Indexed: 12/30/2022] Open
Abstract
Metabolic microbiome interaction with the human host has been linked to human physiology and disease development. The elucidation of this interspecies metabolite exchange will lead to identification of beneficial metabolites and disease modulators. Their discovery and quantitative analysis requires the development of specific tools and analysis of specific compound classes. Sulfated metabolites are considered a readout for the co-metabolism of the microbiome and their host. This compound class is part of the human phase II clearance process of xenobiotics and is the main focus in drug or doping metabolism and also includes dietary components and microbiome-derived compounds. Here, we report the targeted analysis of sulfated metabolites in plasma and urine samples in the same individuals to identify the core sulfatome and similarities between these two sample types. This analysis of 27 individuals led to the identification of the core sulfatome of 41 metabolites in plasma and urine samples as well as an age effect for 15 metabolites in both sample types.
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Affiliation(s)
- Mário S P Correia
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University Box 599 SE-75124 Uppsala Sweden
| | - Bhawana Thapa
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University Box 599 SE-75124 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute Stockholm Sweden
| | - Daniel Globisch
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University Box 599 SE-75124 Uppsala Sweden
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14
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Chemometric applications in metabolomic studies using chromatography-mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116165] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Yu CS, Lin YJ, Lin CH, Lin SY, Wu JL, Chang SS. Development of an Online Health Care Assessment for Preventive Medicine: A Machine Learning Approach. J Med Internet Res 2020; 22:e18585. [PMID: 32501272 PMCID: PMC7305560 DOI: 10.2196/18585] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/13/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In the era of information explosion, the use of the internet to assist with clinical practice and diagnosis has become a cutting-edge area of research. The application of medical informatics allows patients to be aware of their clinical conditions, which may contribute toward the prevention of several chronic diseases and disorders. OBJECTIVE In this study, we applied machine learning techniques to construct a medical database system from electronic medical records (EMRs) of subjects who have undergone health examination. This system aims to provide online self-health evaluation to clinicians and patients worldwide, enabling personalized health and preventive health. METHODS We built a medical database system based on the literature, and data preprocessing and cleaning were performed for the database. We utilized both supervised and unsupervised machine learning technology to analyze the EMR data to establish prediction models. The models with EMR databases were then applied to the internet platform. RESULTS The validation data were used to validate the online diagnosis prediction system. The accuracy of the prediction model for metabolic syndrome reached 91%, and the area under the receiver operating characteristic (ROC) curve was 0.904 in this system. For chronic kidney disease, the prediction accuracy of the model reached 94.7%, and the area under the ROC curve (AUC) was 0.982. In addition, the system also provided disease diagnosis visualization via clustering, allowing users to check their outcome compared with those in the medical database, enabling increased awareness for a healthier lifestyle. CONCLUSIONS Our web-based health care machine learning system allowed users to access online diagnosis predictions and provided a health examination report. Users could understand and review their health status accordingly. In the future, we aim to connect hospitals worldwide with our platform, so that health care practitioners can make diagnoses or provide patient education to remote patients. This platform can increase the value of preventive medicine and telemedicine.
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Affiliation(s)
- Cheng-Sheng Yu
- Department of Family Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Jiun Lin
- Department of Family Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chang-Hsien Lin
- Department of Family Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shiyng-Yu Lin
- Department of Family Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jenny L Wu
- Department of Family Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shy-Shin Chang
- Department of Family Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
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16
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Sun Z, Fan YZ, Du SZ, Yang YZ, Ling Y, Li NB, Luo HQ. Conversion of Fluorescence Signals into Optical Fingerprints Realizing High-Throughput Discrimination of Anionic Sulfonate Surfactants with Similar Structure Based on a Statistical Strategy and Luminescent Metal–Organic Frameworks. Anal Chem 2020; 92:7273-7281. [DOI: 10.1021/acs.analchem.0c00907] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhe Sun
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yu Zhu Fan
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Shi Zhe Du
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yu Zhu Yang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yu Ling
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Nian Bing Li
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Hong Qun Luo
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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17
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Shameh S, Alirezalu A, Hosseini B, Maleki R. Fruit phytochemical composition and color parameters of 21 accessions of five Rosa species grown in North West Iran. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:5740-5751. [PMID: 31166009 DOI: 10.1002/jsfa.9842] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND The genus Rosa comprises economically important horticultural plants belonging to the family Rosaceae. Recently, the use of different Rosa species has increased owing to their multipurpose properties (ornamental, food and medicinal uses). In this study, 21 accessions of Rosa genotypes were compared for fruit phytochemical composition and color parameters. RESULTS The highest antioxidant activity (37.86 mg AAE g-1 FW) and total phenolic (8.17 mg GAE g-1 FW), total flavonoid (2.53 mg QUE g-1 FW), total carotenoid (20.21 mg g-1 FW) and ascorbic acid (84.27 mg g-1 FW) contents were observed in G20 (R. canina), G8 (R. canina), G9 (R. canina), G5 (R. damascena) and G10 (R. moschata) respectively. Chlorogenic acid and gallic acid were found as the main phenolic constituents of Rosa fruits. High amounts of apigenin, rutin, quercetin, p-coumaric acid, cinnamic acid, chlorogenic acid, caffeic acid and gallic acid were obtained in fruit extracts of G6, G14, G6, G8, G19, G9, G19 and G12 respectively. Moreover, the level of color parameters also varied among genotypes. The highest values of a*, b*, L* and chroma were obtained in G4 (R. canina). Based on hierarchical clustering analysis with heat-map, five groups of accessions were identified. CONCLUSION Different Rosa genotypes are rich in certain phytochemical compounds, with significant variations in their levels being observed. Hence evaluation of Rosa genetic resources can supply valuable data for screening accessions containing high levels of individual phenolics, antioxidants and other bioactive compounds for use in breeding programs and food and pharma industries. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Shahla Shameh
- Department of Horticultural Sciences, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Abolfazl Alirezalu
- Department of Horticultural Sciences, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Bahman Hosseini
- Department of Horticultural Sciences, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Ramin Maleki
- Research Department of Chromatography, Iranian Academic Center for Education, Culture and Research (ACECR), Urmia, Iran
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18
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Chen YY, Shen J, Tang YP, Yu JG, Wang J, Yue SJ, Yang J, Chen JQ, Feng LM, Zhu ZH, Tao WW, Zhang L, Duan JA. Elucidating the interaction of kansui and licorice by comparative plasma/tissue metabolomics and a heatmap with relative fold change. J Pharm Anal 2019; 9:312-323. [PMID: 31929940 PMCID: PMC6951493 DOI: 10.1016/j.jpha.2019.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/13/2019] [Accepted: 05/29/2019] [Indexed: 11/25/2022] Open
Abstract
Although compatibility is highly advocated in traditional Chinese medicine (TCM), inappropriate combination of some herbs may reduce the therapeutic action and even produce toxic effects. Kansui and licorice, one of TCM "Eighteen Incompatible Medicaments", are the most representative cases of improper herbal combination, which may still be applied simultaneously under given conditions. However, the potential mechanism of their compatibility and incompatibility is unclear. In the present study, two different ratios of kansui and licorice, representing their compatibility and incompatibility respectively, were designed to elucidate their interaction by comparative plasma/tissue metabolomics and a heatmap with relative fold change. As a result, glycocholic acid, prostaglandin F2a, dihydroceramide and sphinganine were screened out as the principal alternative biomarkers of compatibility group; sphinganine, dihydroceramide, arachidonic acid, leukotriene B4, acetoacetic acid and linoleic acid were those of incompatibility group. Based on the values of biomarkers in each tissue, the liver was identified as the compatible target organ, while the heart, liver, and kidney were the incompatible target organs. Furthermore, important pathways for compatibility and incompatibility were also constructed. These results help us to better understand and utilize the two herbs, and the study was the first to reveal some innate characters of herbs related to TCM "Eighteen Incompatible Medicaments".
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Affiliation(s)
- Yan-Yan Chen
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Juan Shen
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Yu-Ping Tang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Jin-Gao Yu
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Jing Wang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Shi-Jun Yue
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Jie Yang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Jia-Qian Chen
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Li-Mei Feng
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Zhen-Hua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Wei-Wei Tao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Li Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
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Qi J, Pang Y, An P, Jiang G, Kong Q, Ren X. Determination of metabolites of Geotrichum citri-aurantii treated with peppermint oil using liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. J Food Biochem 2018; 43:e12745. [PMID: 31353560 DOI: 10.1111/jfbc.12745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/12/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023]
Abstract
Sour rot is a leading disease of citrus fruit caused by the postharvest pathogen Geotrichum citri-aurantii. It has been reported that essential oils can be used as substitutes for synthetic fungicides to control the pathogen. In this study, changes in metabolites and antifungal effects of G. citri-aurantii treated with peppermint oil (PO) were investigated. The inhibition rate of the mycelial growth increased as the PO concentration increased, and 6 μl PO/disk resulted in a radial growth inhibition of 79.2%. The electrical conductivity of G. citri-aurantii treated with PO increased compared to the control. By comparing the metabolic profiles of treated and untreated G. citri-aurantii cells, a total of 53 distinct metabolites 9 were up-regulated and 44 were down-regulated were found, including 16 lipid metabolites, 6 carbohydrate metabolites, 2 amino acid metabolites, 5 alcohols, 2 glycoside metabolites, and 3 ketone metabolites, etc, and these metabolites are involved in 25 major metabolic pathways. PRACTICAL APPLICATIONS: Chemical fungicides can effectively control G. citri-aurantii during fruit postharvest period. However, synthetic chemical fungicides have gradually led to buildup of resistance of fungil, which seriously causes the frequent of food-borne diseases. PO extracted from natural plants can be used as natural additive in many foods due to their antioxidant, antibacterial, and antifungal properties. Therefore, PO can be considered as a promising bacteriostatic agent for the defense of G. citri-aurantii during fruit postharvest period.
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Affiliation(s)
- Jianrui Qi
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Yaxing Pang
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Peipei An
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Guoshan Jiang
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Qingjun Kong
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Xueyan Ren
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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20
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Galeano Garcia P, Neves Dos Santos F, Zanotta S, Eberlin MN, Carazzone C. Metabolomics of Solanum lycopersicum Infected with Phytophthora infestans Leads to Early Detection of Late Blight in Asymptomatic Plants. Molecules 2018; 23:E3330. [PMID: 30558273 PMCID: PMC6320815 DOI: 10.3390/molecules23123330] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 02/07/2023] Open
Abstract
Tomato crops suffer attacks of various pathogens that cause large production losses. Late blight caused by Phytophthora infestans is a devastating disease in tomatoes because of its difficultly to control. Here, we applied metabolomics based on liquid chromatography⁻mass spectrometry (LC-MS) and metabolic profiling by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) in combination with multivariate data analysis in the early detection of late blight on asymptomatic tomato plants and to discriminate infection times of 4, 12, 24, 36, 48, 60, 72 and 96 h after inoculation (hpi). MALDI-MS and LC-MS profiles of metabolites combined with multivariate data analysis are able to detect early-late blight-infected tomato plants, and metabolomics based on LC-MS discriminates infection times in asymptomatic plants. We found the metabolite tomatidine as an important biomarker of infection, saponins as early infection metabolite markers and isocoumarin as early and late asymptomatic infection marker along the post infection time. MALDI-MS and LC-MS analysis can therefore be used as a rapid and effective method for the early detection of late blight-infected tomato plants, offering a suitable tool to guide the correct management and application of sanitary defense approaches. LC-MS analysis also appears to be a suitable tool for identifying major metabolites of asymptomatic late blight-infected tomato plants.
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Affiliation(s)
- Paula Galeano Garcia
- Laboratory of Advanced Analytical Techniques in Natural Products, Universidad de los Andes, Bogotá 111711, Colombia.
- Bioprospección de los Productos Naturales Amazónicos, Facultad de Ciencias Básicas, Universidad de la Amazonia, Florencia 180002, Colombia.
- ThoMSon Mass Spectrometry Laboratory, University of Campinas, Institute of Chemistry, Campinas 13083-970, Brazil.
| | - Fábio Neves Dos Santos
- ThoMSon Mass Spectrometry Laboratory, University of Campinas, Institute of Chemistry, Campinas 13083-970, Brazil.
| | - Samantha Zanotta
- Laboratório de Diagnostico Fitopatológico, Instituto Biológico, São Paulo 04014-900, Brazil.
| | - Marcos Nogueira Eberlin
- ThoMSon Mass Spectrometry Laboratory, University of Campinas, Institute of Chemistry, Campinas 13083-970, Brazil.
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products, Universidad de los Andes, Bogotá 111711, Colombia.
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21
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Qazi SS, Lombardo DA, Abou-Zaid MM. A Metabolomic and HPLC-MS/MS Analysis of the Foliar Phenolics, Flavonoids and Coumarins of the Fraxinus Species Resistant and Susceptible to Emerald Ash Borer. Molecules 2018; 23:E2734. [PMID: 30360500 PMCID: PMC6278661 DOI: 10.3390/molecules23112734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/15/2018] [Accepted: 10/20/2018] [Indexed: 11/25/2022] Open
Abstract
The Emerald Ash Borer (EAB), Agrilus planipennis, Fairmaire, an Asian invasive alien buprestid has devastated tens of millions of ash trees (Fraxinus spp.) in North America. Foliar phytochemicals of the genus Fraxinus (Oleaceae): Fraxinus pennsylvanica (Green ash), F. americana (White ash), F. profunda (Bush) Bush. (Pumpkin ash), F. quadrangulata Michx. (Blue ash), F. nigra Marsh. (Black ash) and F. mandshurica (Manchurian ash) were investigated using HPLC-MS/MS and untargeted metabolomics. HPLC-MS/MS help identified 26 compounds, including phenolics, flavonoids and coumarins in varying amounts. Hydroxycoumarins, esculetin, esculin, fraxetin, fraxin, fraxidin and scopoletin were isolated from blue, black and Manchurian ashes. High-throughput metabolomics revealed 35 metabolites, including terpenes, secoiridoids and lignans. Metabolomic profiling indicated several upregulated putative compounds from Manchurian ash, especially fraxinol, ligstroside, oleuropin, matairesinol, pinoresinol glucoside, 8-hydroxypinoresinol-4-glucoside, verbenalin, hydroxytyrosol-1-O-glucoside, totarol and ar-artemisene. Further, dicyclomine, aphidicolin, parthenolide, famciclovir, ar-turmerone and myriocin were identified upregulated in blue ash. Principal component analysis demonstrated a clear separation between Manchurian and blue ashes from black, green, white and pumpkin ashes. The presence of defensive compounds upregulated in Manchurian ash, suggests their potential role in providing constitutive resistance to EAB, and reflects its co-evolutionary history with A. planipennis, where they appear to coexist in their native habitats.
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Affiliation(s)
- Sohail S Qazi
- Natural Resources Canada, Canadian Forest Service, Great Lake Forestry Centre, Sault Ste. Marie, ON P6A 2E5, Canada.
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Domenic A Lombardo
- Natural Resources Canada, Canadian Forest Service, Great Lake Forestry Centre, Sault Ste. Marie, ON P6A 2E5, Canada.
| | - Mamdouh M Abou-Zaid
- Natural Resources Canada, Canadian Forest Service, Great Lake Forestry Centre, Sault Ste. Marie, ON P6A 2E5, Canada.
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON N6A 5B9, Canada.
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Tsuchiya S, Cho Y, Yoshioka R, Konoki K, Nagasawa K, Oshima Y, Yotsu-Yamashita M. Synthesis and Identification of Key Biosynthetic Intermediates for the Formation of the Tricyclic Skeleton of Saxitoxin. Angew Chem Int Ed Engl 2017; 56:5327-5331. [DOI: 10.1002/anie.201612461] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Shigeki Tsuchiya
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Yuko Cho
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Renpei Yoshioka
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Keiichi Konoki
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Kazuo Nagasawa
- Faculty of Technology; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei-shi Tokyo 184-8588 Japan
| | - Yasukatsu Oshima
- Graduate School of Life Sciences; Tohoku University; 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
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Tsuchiya S, Cho Y, Yoshioka R, Konoki K, Nagasawa K, Oshima Y, Yotsu-Yamashita M. Synthesis and Identification of Key Biosynthetic Intermediates for the Formation of the Tricyclic Skeleton of Saxitoxin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Shigeki Tsuchiya
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Yuko Cho
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Renpei Yoshioka
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Keiichi Konoki
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
| | - Kazuo Nagasawa
- Faculty of Technology; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei-shi Tokyo 184-8588 Japan
| | - Yasukatsu Oshima
- Graduate School of Life Sciences; Tohoku University; 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science; Tohoku University; 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-0845 Japan
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Antioxidant Activity of the Lignins Derived from Fluidized-Bed Fast Pyrolysis. Molecules 2017; 22:molecules22030372. [PMID: 28257062 PMCID: PMC6155384 DOI: 10.3390/molecules22030372] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/13/2017] [Accepted: 02/16/2017] [Indexed: 01/28/2023] Open
Abstract
A challenge in recent years has been the rational use of forest and agriculture residues for the production of bio-fuel, biochemical, and other bioproducts. In this study, potentially useful compounds from pyrolytic lignins were identified by HPLC-MS/MS and untargeted metabolomics. The metabolites identified were 2-(4-allyl-2-methoxyphenoxy)-1-(4-hydroxy-3-methoxyphenyl)-1-propanol, benzyl benzoate, fisetinidol, phenyllactic acid, 2-phenylpropionic acid, 6,3′-dimethoxyflavone, and vanillin. The 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH), trolox equivalent antioxidant capacity (TEAC), and total phenolics content (TPC) per gram of pyrolytic lignin ranged from 14 to 503 mg ascorbic acid equivalents, 35 to 277 mg trolox equivalents, and 0.42 to 50 mg gallic acid equivalents, respectively. A very significant correlation was observed between the DPPH and TPC (r = 0.8663, p ≤ 0.0001), TEAC and TPC (r = 0.8044, p ≤ 0.0001), and DPPH and TEAC (r = 0.8851, p ≤ 0.0001). The polyphenolic compounds in the pyrolytic lignins which are responsible for radical scavenging activity and antioxidant properties can be readily profiled with HPLC-MS/MS combined with untargeted metabolomics. The results also suggest that DPPH, TEAC, and TPC assays are suitable methods for the measurement of antioxidant activity in a variety of pyrolytic lignins. These data show that the pyrolytic lignins can be considered as promising sources of natural antioxidants and value-added chemicals.
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Ma C, Luciani T, Terebus A, Liang J, Marai GE. PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space. BMC Bioinformatics 2017; 18:24. [PMID: 28251874 PMCID: PMC5333168 DOI: 10.1186/s12859-016-1447-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Visualizing the complex probability landscape of stochastic gene regulatory networks can further biologists’ understanding of phenotypic behavior associated with specific genes. Results We present PRODIGEN (PRObability DIstribution of GEne Networks), a web-based visual analysis tool for the systematic exploration of probability distributions over simulation time and state space in such networks. PRODIGEN was designed in collaboration with bioinformaticians who research stochastic gene networks. The analysis tool combines in a novel way existing, expanded, and new visual encodings to capture the time-varying characteristics of probability distributions: spaghetti plots over one dimensional projection, heatmaps of distributions over 2D projections, enhanced with overlaid time curves to display temporal changes, and novel individual glyphs of state information corresponding to particular peaks. Conclusions We demonstrate the effectiveness of the tool through two case studies on the computed probabilistic landscape of a gene regulatory network and of a toggle-switch network. Domain expert feedback indicates that our visual approach can help biologists: 1) visualize probabilities of stable states, 2) explore the temporal probability distributions, and 3) discover small peaks in the probability landscape that have potential relation to specific diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1447-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chihua Ma
- Electronic Visualization Laboratory, Department of Computer Science, University of Illinois at Chicago, 851 S. Morgan St (M/C 152), Room 1120 SEO, Chicago, 60607, IL, US.
| | - Timothy Luciani
- Electronic Visualization Laboratory, Department of Computer Science, University of Illinois at Chicago, 851 S. Morgan St (M/C 152), Room 1120 SEO, Chicago, 60607, IL, US
| | - Anna Terebus
- Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan St (M/C 063), Room 218 SEO, Chicago, 60607, IL, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan St (M/C 063), Room 218 SEO, Chicago, 60607, IL, USA
| | - G Elisabeta Marai
- Electronic Visualization Laboratory, Department of Computer Science, University of Illinois at Chicago, 851 S. Morgan St (M/C 152), Room 1120 SEO, Chicago, 60607, IL, US
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van Dam NM, Bouwmeester HJ. Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication. TRENDS IN PLANT SCIENCE 2016; 21:256-265. [PMID: 26832948 DOI: 10.1016/j.tplants.2016.01.008] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 05/19/2023]
Abstract
The rhizosphere is densely populated with a variety of organisms. Interactions between roots and rhizosphere community members are mostly achieved via chemical communication. Root exudates contain an array of primary and secondary plant metabolites that can attract, deter, or kill belowground insect herbivores, nematodes, and microbes, and inhibit competing plants. Metabolomics of root exudates can potentially help us to better understand this chemical dialogue. The main limitations are the proper sampling of the exudate, the sensitivity of the metabolomics platforms, and the multivariate data analysis to identify causal relations. Novel technologies may help to generate a spatially explicit metabolome of the root and its exudates at a scale that is relevant for the rhizosphere community.
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Affiliation(s)
- Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany; Institute of Ecology, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany; Molecular Interaction Ecology, Institute of Water and Wetland Research (IWWR), Radboud University, PO Box 9010, Nijmegen, GL 6500, The Netherlands.
| | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, PB 6708, The Netherlands.
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