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Jiang D, Yang M, Xu J, Deng L, Hu C, Zhang L, Sun Y, Jiang J, Lu L. Three-stage fermentation of the feed and the application on weaned piglets. Front Vet Sci 2023; 10:1123563. [PMID: 36876012 PMCID: PMC9978217 DOI: 10.3389/fvets.2023.1123563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Numerous studies have demonstrated that soybean meal (SBM) contains high levels of anti-nutritional factors, which interrupt gastrointestinal homeostasis or metabolism normally of the weaned piglets. Here, the mixed probiotics, including Bacillus licheniformis (B. licheniformis, CGMCC 8147), Saccharomyces cerevisiae H11 (S. cerevisiae H11) and Lactobacillus casei (L. casei, CGMCC 8149) were applied to the three-stage fermentation of functional feed. Our research investigated the optimum ratio of inoculation, optimal time of inoculation, combination of substrates, and nutritional value of the fermented feed. The optimal microbial combination was B. licheniformis: S. cerevisiae: L. casei = 2:2:1, inoculating at 0, 12 and 24 h, respectively. The results revealed that crude protein and acid-soluble protein were remarkably improved and had lower pH. Trypsin inhibitor, glycine and β-glycine were reduced by 79.86, 77.18, and 69.29%, respectively. Moreover, animal trials further evaluated the growth-promoting effects of the fermented feed. It was noted that the average daily gain of weaned piglets was significantly higher, and the ratio of feed with weight, diarrhea incidence and mortality were lower significantly. The concentrations of serum immunoglobulin G(IgG), IgA, IgM, Complement C3 and interferon-γ (IFN-γ), and lysozyme activity were all increased. The relative abundance of fecal microbiota improved, especially lactobacillus, which increased the abundance of fecal dominant probiotics. Overall, the fermented feed may be conducive to the growth and health of weaned piglets by improving nutritional value, immunity properties, relative abundance of fecal microflora, and decreasing anti-nutritional factors of feed, thereby making them viable and usable feedstuffs for potential use in livestock industries.
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Affiliation(s)
- Dahai Jiang
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen, China.,College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Manqi Yang
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen, China.,College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Jun Xu
- Zhangzhou DaBeiNong Agriculture and Husbandry Science & Technology Co., Ltd., Zhangzhou, China
| | - Liping Deng
- Jiangxi DaBeiNong Technology Co., Ltd., Nanchang, China
| | - Cong Hu
- Beijing DaBeiNong Technology Group Co., Ltd., Beijing, China
| | - Liangliang Zhang
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen, China.,College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Yunzhang Sun
- The Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Jianchun Jiang
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen, China.,College of Chemical Engineering, Huaqiao University, Xiamen, China.,Institute of Chemical Industry of Forest Products, CAF, Nanjing, China
| | - Liming Lu
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen, China.,College of Chemical Engineering, Huaqiao University, Xiamen, China
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2
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Lentil allergens identification and quantification: An update from omics perspective. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 4:100109. [PMID: 35495776 PMCID: PMC9043643 DOI: 10.1016/j.fochms.2022.100109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 02/08/2023]
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3
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Malicka I, Lewińska I, Tymecki Ł. On-line 'protein shaker': A multicommutated flow analysis system for fluorometric creatinine determination in deproteinized serum. Anal Chim Acta 2022; 1191:339246. [PMID: 35033258 DOI: 10.1016/j.aca.2021.339246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 11/26/2022]
Abstract
A fully mechanized multicommutated flow analysis (MCFA) system for fluorometric determination of creatinine in serum samples is introduced in this paper. The flow system was constructed with microsolenoid pumps and valves and with a 3D-printed flow cell. Fluorometric assay relied on creatinine reaction with 3,5-dinitrobenzoic acid and hydrogen peroxide in an alkaline environment. To overcome significant interference from protein, a flow reactor for serum deproteinization was designed and implemented in the flow system. The deproteinization was carried out by precipitation with trichloroacetic acid and the addition of sodium chloride facilitated the precipitate sedimentation. The supernatant representative sample was pumped out and subjected to fluorometric creatinine assay. The obtained linear range was from 1.6 to 500 μmol L-1 and the precision, expressed as RSD, was below 3%. The proposed MCFA system was used to determine creatinine concentration in control serum samples. The results obtained with flow deproteinization correlated well with results obtained with conventional deproteinization (y = (0.91 ± 0.09) x + (37 ± 28)) with Pearson's r 0.979.
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Affiliation(s)
- Iga Malicka
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093, Warsaw, Poland
| | - Izabela Lewińska
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093, Warsaw, Poland.
| | - Łukasz Tymecki
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093, Warsaw, Poland
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4
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Röder M, Wiacek C, Lankamp F, Kreyer J, Weber W, Ueberham E. Improved Sensitivity of Allergen Detection by Immunoaffinity LC-MS/MS Using Ovalbumin as a Case Study. Foods 2021; 10:foods10122932. [PMID: 34945483 PMCID: PMC8700968 DOI: 10.3390/foods10122932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Food allergies are caused by severe hypersensitivity to specific food allergens such as the egg protein ovalbumin. It is therefore important to test food products for the presence of allergens to protect allergic people from accidental ingestion. For egg detection, ELISA is the only reasonable commercially available test format, although the recognition of target allergens can be affected by food processing, which may lead to false negative results. Current mass spectrometry-based detection methods may overcome this issue, but these approaches are often less sensitive. Here we combined the advantages of antibody-based and MS-based methods by developing an immunoaffinity LC-MS/MS technique to detect the common egg allergen Gal d 2. We investigated the principal functionality of this method with incurred cookie material containing whole egg powder. We found that the new method matched easily the sensitivity of egg specific ELISA tests. Further western blot experiments indicated that this strategy may be unaffected by food processing, providing an important alternative strategy for the detection and quantification of allergens in food.
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Affiliation(s)
- Martin Röder
- ifp Institut für Produktqualität GmbH, Wagner-Régeny-Str. 8, 12489 Berlin, Germany; (M.R.); (F.L.); (W.W.)
| | - Claudia Wiacek
- Institute of Food Hygiene, Leipzig University, An den Tierkliniken 1, 04103 Leipzig, Germany; (C.W.); (J.K.)
| | - Frauke Lankamp
- ifp Institut für Produktqualität GmbH, Wagner-Régeny-Str. 8, 12489 Berlin, Germany; (M.R.); (F.L.); (W.W.)
| | - Jonathan Kreyer
- Institute of Food Hygiene, Leipzig University, An den Tierkliniken 1, 04103 Leipzig, Germany; (C.W.); (J.K.)
| | - Wolfgang Weber
- ifp Institut für Produktqualität GmbH, Wagner-Régeny-Str. 8, 12489 Berlin, Germany; (M.R.); (F.L.); (W.W.)
| | - Elke Ueberham
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany
- Correspondence:
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5
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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Ippoushi K, Tanaka Y, Wakagi M, Hashimoto N. Evaluation of protein extraction methods for β-conglycinin quantification in soybeans and soybean products. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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7
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Al-Saedi N, Agarwal M, Ma W, Islam S, Ren Y. Study on Effect of Extraction Techniques and Seed Coat on Proteomic Distribution and Cheese Production from Soybean Milk. Molecules 2020; 25:E3237. [PMID: 32708569 PMCID: PMC7397084 DOI: 10.3390/molecules25143237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 11/25/2022] Open
Abstract
Soybean-based food products are a major source of protein. In the present study, proteins in soybean milk from seeds of the cultivar Bunya (Glycine max) were extracted using the cheesecloth and the centrifuge methods. The milk was produced through mechanical crushing of both whole and split seeds in water. Following separation by either the cheesecloth or centrifuge, proteins were isolated from the soybean milk by using thiourea/urea solubilisation and then separated them using two-dimensional polyacrylamide gel electrophoresis. The isolated proteins were identified by mass spectrometry. A total of 97 spots were identified including 49 that displayed different abundances. Of the two separation techniques, centrifuge separation gave higher protein extraction and more intense protein spots than cheesecloth separation. Eleven of the β-subunits of β-conglycinin, three of the α-subunits of β-conglycinin, and four of the mutant glycinin showed different levels of abundances between separation techniques, which might be related to subsequent cheese quality. Notably, split-seed soybean milk has less allergenic proteins with four α-subunits of β-conglycinin compared to whole-seed milk with eight of those proteins. The sensory evaluation showed that the cheese produced from split-soybean milk received higher consumer preferences compared to that of whole seed, which could be explained by their proteomic differences. The demonstrated reference map for whole and split-seed soybean milk could be further utilized in the research related to soybean cheesemaking.
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Affiliation(s)
- Nadia Al-Saedi
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Perth 6150, Australia;
- Department of Food Science and Biotechnology, Faculty of Agriculture, University of Baghdad, Baghdad 10071, Iraq
| | - Manjree Agarwal
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Perth 6150, Australia;
| | - Wujun Ma
- Australia China Centre for Wheat Improvement (ACCWI), College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (W.M.); (S.I.)
| | - Shahidul Islam
- Australia China Centre for Wheat Improvement (ACCWI), College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (W.M.); (S.I.)
| | - Yonglin Ren
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Perth 6150, Australia;
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8
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Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation. mSystems 2020; 5:5/1/e00501-19. [PMID: 32047057 PMCID: PMC7018524 DOI: 10.1128/msystems.00501-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Solid-state fermentation (SSF) plays pivotal roles not only in human food but also farm animal diets. Soybean meal (SBM) and corn account for approximately 70% of the global feed consumption. However, the nutritional value of conventional SBM and corn mixed substrates (MS) is limited by antinutritional factors, causing substantial economic loss in livestock production. Although emerging studies have reported that SSF can improve the nutritional value of SBM-based substrates, the dynamic changes in the physicochemical features, microbiota, and metabolic functions of MS during SSF remain poorly understood, limiting further investigation. To provide insights into the dynamics of the physicochemical characteristics and the complex microbiome during the two-stage SSF of MS, multiple physicochemical analyses combined with high-throughput sequencing were applied here. These novel insights shed light on the complex changes that occur in the nutrition and microbiome during two-stage SSF of MS and are of great value for industrial feed-based practices and metabolomic research on SSF ecosystems. Substantial annual economic loss in livestock production is caused by antinutritional factors in soybean meal and corn mixed substrates, which can be degraded by microbial fermentation. Although considerable efforts have been made to explain the effects of fermentation on soybean meal and corn-based feed, the dynamics of the physicochemical characteristics, microbiota, and metabolic functions of soybean meal and corn mixed substrates during solid-state fermentation remain unclear. Here, multiple physicochemical analyses combined with high-throughput sequencing were performed to reveal the dynamic changes that occur during a novel two-stage solid-state fermentation process. Generally, inoculated bacteria rapidly proliferated in the initial 12-h aerobic fermentation (P = 0.002). Notably, most nutritional changes occurred during 12 to 24 h compared to 0 to 12 h. Second-stage anaerobic fermentation increased the bacterial abundance and lactic acid content (P < 0.00). Bacillus spp., Enterococcus spp., and Pseudomonas spp. were predominantly involved in the maturation of the fermented mixed substrates (P < 0.05). Additionally, the available phosphorus exhibited the greatest interaction with the microbial community structure. Cellular processes and environmental information processing might be the main metabolic processes of the microbiota during this fermentation. An in vivo model further evaluated the growth-promoting effects of the fermented products. These results characterized the dynamic changes that occur during two-stage solid-state fermentation and provided potential references for additional interventions to further improve the effectiveness and efficiency of solid-state fermentation of feed. IMPORTANCE Solid-state fermentation (SSF) plays pivotal roles not only in human food but also farm animal diets. Soybean meal (SBM) and corn account for approximately 70% of the global feed consumption. However, the nutritional value of conventional SBM and corn mixed substrates (MS) is limited by antinutritional factors, causing substantial economic loss in livestock production. Although emerging studies have reported that SSF can improve the nutritional value of SBM-based substrates, the dynamic changes in the physicochemical features, microbiota, and metabolic functions of MS during SSF remain poorly understood, limiting further investigation. To provide insights into the dynamics of the physicochemical characteristics and the complex microbiome during the two-stage SSF of MS, multiple physicochemical analyses combined with high-throughput sequencing were applied here. These novel insights shed light on the complex changes that occur in the nutrition and microbiome during two-stage SSF of MS and are of great value for industrial feed-based practices and metabolomic research on SSF ecosystems.
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Lin P, Xiaoli L, Li D, Jiang S, Zou Z, Lu Q, Chen Y. Rapidly and exactly determining postharvest dry soybean seed quality based on machine vision technology. Sci Rep 2019; 9:17143. [PMID: 31748535 PMCID: PMC6868226 DOI: 10.1038/s41598-019-53796-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 11/06/2019] [Indexed: 11/21/2022] Open
Abstract
The development of machine vision-based technologies to replace human labor for rapid and exact detection of agricultural product quality has received extensive attention. In this study, we describe a low-rank representation of jointly multi-modal bag-of-feature (JMBoF) classification framework for inspecting the appearance quality of postharvest dry soybean seeds. Two categories of speeded-up robust features and spatial layout of L*a*b* color features are extracted to characterize the dry soybean seed kernel. The bag-of-feature model is used to generate a visual dictionary descriptor from the above two features, respectively. In order to exactly represent the image characteristics, we introduce the low-rank representation (LRR) method to eliminate the redundant information from the long joint two kinds of modal dictionary descriptors. The multiclass support vector machine algorithm is used to classify the encoding LRR of the jointly multi-modal bag of features. We validate our JMBoF classification algorithm on the soybean seed image dataset. The proposed method significantly outperforms the state-of-the-art single-modal bag of features methods in the literature, which could contribute in the future as a significant and valuable technology in postharvest dry soybean seed classification procedure.
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Affiliation(s)
- Ping Lin
- College of Electrical Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China
| | - Li Xiaoli
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Du Li
- College of Electrical Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China
| | - Shanchao Jiang
- College of Electrical Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China
| | - Zhiyong Zou
- College of Mechanical and Electrical Engineering, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Qun Lu
- College of Electrical Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China
| | - Yongming Chen
- College of Electrical Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China.
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Xavier ADS, Furtado DZS, Assunção NA, Nascimento AN. Bioacessibility of Fe and Zn (associated to proteins) in cashew nut. J Food Compost Anal 2019. [DOI: 10.1016/j.jfca.2019.103259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Miranda C, Xu Q, Oehrle NW, Islam N, Garrett WM, Natarajan SS, Gillman JD, Krishnan HB. Proteomic Comparison of Three Extraction Methods Reveals the Abundance of Protease Inhibitors in the Seeds of Grass Pea, a Unique Orphan Legume. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10296-10305. [PMID: 31464437 DOI: 10.1021/acs.jafc.9b04307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Grass pea is an orphan legume that is grown in many places in the world. It is a high-protein, drought-tolerant legume that is capable of surviving extreme environmental challenges and can be a sole food source during famine. However, grass pea produces the neurotoxin β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which can cause a neurological disease. This crop is promising as a food source for both animals and humans if β-ODAP levels and other antinutritional factors such as protease inhibitors are lowered or removed. To understand more about these proteins, a proteomic analysis of grass pea was conducted using three different extraction methods to determine which was more efficient at isolating antinutritional factors. Seed proteins extracted with Tris-buffered saline (TBS), 30% ethanol, and 50% isopropanol were identified by mass spectrometry, resulting in the documentation of the most abundant proteins for each extraction method. Mass spectrometry spectral data and BLAST2GO analysis led to the identification of 1376 proteins from all extraction methods. The molecular function of the extracted proteins revealed distinctly different protein functional profiles. The majority of the TBS-extracted proteins were annotated with nutrient reservoir activity, while the isopropanol extraction yielded the highest percentage of endopeptidase proteinase inhibitors. Our results demonstrate that the 50% isopropanol extraction method was the most efficient at isolating antinutritional factors including protease inhibitors.
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Affiliation(s)
- Carrie Miranda
- Plant Genetics Research, USDA-Agricultural Research Service , University of Missouri , Columbia , Missouri 65211 , United States
| | - Quanle Xu
- College of Life Sciences , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Nathan W Oehrle
- Plant Genetics Research, USDA-Agricultural Research Service , University of Missouri , Columbia , Missouri 65211 , United States
| | - Nazrul Islam
- Soybean Genomics and Improvement Laboratory , USDA-ARS , Beltsville , Maryland 20705 , United States
| | - Wesley M Garrett
- Animal Bioscience and Biotechnology Laboratory , USDA-Agricultural Research Service , Beltsville 20705 , United States
| | - Savithiry S Natarajan
- Soybean Genomics and Improvement Laboratory , USDA-ARS , Beltsville , Maryland 20705 , United States
| | - Jason D Gillman
- Plant Genetics Research, USDA-Agricultural Research Service , University of Missouri , Columbia , Missouri 65211 , United States
| | - Hari B Krishnan
- Plant Genetics Research, USDA-Agricultural Research Service , University of Missouri , Columbia , Missouri 65211 , United States
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12
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Fan Y, Chen J, Wang Z, Tan T, Li S, Li J, Wang B, Zhang J, Cheng Y, Wu X, Yang W, Yang F. Soybean (Glycine max L. Merr.) seedlings response to shading: leaf structure, photosynthesis and proteomic analysis. BMC PLANT BIOLOGY 2019; 19:34. [PMID: 30665369 PMCID: PMC6341755 DOI: 10.1186/s12870-019-1633-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/07/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Intercropping and close planting are important cultivation methods that increase soybean yield in agricultural production. However, plant shading is a major abiotic stress factor that influences soybean growth and development. Although shade affects leaf morphological parameters and decreases leaf photosynthesis capacity, information on the responses of soybean leaf photosynthesis to shading at proteomic level is still lacking. RESULTS Compared with leaves under normal light (CK) treatment, leaves under shading treatment exhibited decreased palisade and spongy tissue thicknesses but significantly increased cell gap. Although shade increased the number of the chloroplast, the thickness of the grana lamella and the photosynthetic pigments per unit mass, but the size of the chloroplast and starch grains and the rate of net photosynthesis decreased compared with those of under CK treatment. A total of 248 differentially expressed proteins, among which 138 were upregulated, and 110 were downregulated, in soybean leaves under shading and CK treatments were detected via isobaric tags for relative and absolute quantification labeling in the three biological repeats. Differentially expressed proteins were classified into 3 large and 20 small groups. Most proteins involved in porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms were upregulated. By contrast, proteins involved in photosynthesis were downregulated. The gene family members corresponding to differentially expressed proteins, including protochlorophyllide reductase (Glyma06g247100), geranylgeranyl hydrogenase (Ggh), LHCB1 (Lhcb1) and ferredoxin (N/A) involved in the porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins and photosynthesis pathway were verified with real-time qPCR. The results showed that the expression patterns of the genes were consistent with the expression patterns of the corresponding proteins. CONCLUSIONS This study combined the variation of the soybean leaf structure and differentially expressed proteins of soybean leaves under shading. These results demonstrated that shade condition increased the light capture efficiency of photosystem II (PSII) in soybean leaves but decreased the capacity from PSII transmitted to photosystem II (PSI). This maybe the major reason that the photosynthetic capacity was decreased in shading.
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Affiliation(s)
- Yuanfang Fan
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Junxu Chen
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Zhonglin Wang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Tingting Tan
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
| | - Shenglan Li
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
| | - Jiafeng Li
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
| | - Beibei Wang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Jiawei Zhang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Yajiao Cheng
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Xiaoling Wu
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130 People’s Republic of China
| | - Feng Yang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130 People’s Republic of China
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13
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Leclerc S, Arntz Y, Taniguchi Y. Extending Single Molecule Imaging to Proteome Analysis by Quantitation of Fluorescent Labeling Homogeneity in Complex Protein Samples. Bioconjug Chem 2018; 29:2541-2549. [PMID: 29975043 DOI: 10.1021/acs.bioconjchem.8b00226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence-based electrophoresis has been widely used for proteome analysis in which every protein species in cells is labeled with a fluorescent dye, separated by electric migration, and quantified using fluorescence detection. The ultimate limit of sensitivity for this approach could be reached by single-molecule fluorescence imaging and counting individual proteins, requiring exhaustive fluorescent labeling of proteins across molecular populations and species. However, it remains unclear how homogeneous the fluorescence labeling of individual protein molecules of each species is across the proteome. To address this question, we developed a method to measure the labeling homogeneity based on a single-molecule fluorescence counting assay. Our results reveal that the proportion of proteins labeled with at least one dye, called labeling occupancy (LO), was 35% for fluorescently labeled BSA using existing protocols. We then found that the LO could be improved to 82% under high pH and surfactant-rich conditions. Furthermore, when a proteome sample from a human cell lysate was analyzed, the total LO was 71%, whereby the values varied between 50 and 90% for low and high molecular weight proteome fractions, respectively. The results support the possibility of sensitive detection of proteins using single-molecule counting with fluorescent labeling at the proteome scale.
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Affiliation(s)
- Simon Leclerc
- Laboratory for Cell Systems Control , RIKEN Center for Biosystems Dynamics Research , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan.,Laboratoire de Biomatériaux et Bioimagerie , INSERM 1121 Université de Strasbourg, Faculté de Médecine , 4 rue Human , F-67000 Strasbourg , France
| | - Youri Arntz
- Laboratoire de Biomatériaux et Bioimagerie , INSERM 1121 Université de Strasbourg, Faculté de Médecine , 4 rue Human , F-67000 Strasbourg , France
| | - Yuichi Taniguchi
- Laboratory for Cell Systems Control , RIKEN Center for Biosystems Dynamics Research , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan.,PRESTO, Japan Science and Technology Agency , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
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14
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Lu M, Jin Y, Cerny R, Ballmer-Weber B, Goodman RE. Combining 2-DE immunoblots and mass spectrometry to identify putative soybean (Glycine max) allergens. Food Chem Toxicol 2018; 116:207-215. [PMID: 29673863 DOI: 10.1016/j.fct.2018.04.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 04/14/2018] [Indexed: 12/25/2022]
Abstract
Soybean is recognized as a commonly allergenic food, but the identity of important allergens is not well studied. Recently, some global regulatory agencies started requiring quantitative analysis of individual allergens, including unproven allergens, as part of the risk assessment for genetically engineered (GE) soybeans. We sought to identify soybean proteins that bind IgE from any of 10 individual soybean-sensitized subjects. Soybean IgE binding proteins were identified by 2-DE immunoblots using sera from four soy-allergic and plasma from six soy-sensitized human subjects. Corresponding spots were excised from stained gels, digested, and analyzed using a quadrupole TOF Synapt G2-S tandem mass spectrometer. Results showed the major IgE binding proteins were subunits of either β-conglycinin (Gly m 5) or glycinin (Gly m 6). Soybean Kunitz trypsin inhibitor (SKTI) was a significant IgE binding protein for four subjects. Soybean agglutinin, seed biotinylated protein (SBP) of 65 kDa, late embryogenesis protein (LEP), and sucrose-binding protein were identified as IgE binding only for soy-sensitized subjects. We conclude that the major soybean allergens are isoforms of Gly m 5, Gly m 6, and possibly SKTI and that requirements for quantitative measurement of proteins that are not clear allergens is not relevant to safety.
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Affiliation(s)
- Mei Lu
- Department of Food Science and Technology, University of Nebraska-Lincoln, 1901 North 21st Street, Lincoln, NE, 68588, USA
| | - Yuan Jin
- Department of Food Science and Technology, University of Nebraska-Lincoln, 1901 North 21st Street, Lincoln, NE, 68588, USA
| | - Ron Cerny
- Department of Chemistry, University of Nebraska-Lincoln, 639 N. 12th Street, Lincoln, NE 68588, USA
| | - Barbara Ballmer-Weber
- Allergy Unit, Department of Dermatology, University Hospital Zürich, Zürich, Switzerland
| | - Richard E Goodman
- Department of Food Science and Technology, University of Nebraska-Lincoln, 1901 North 21st Street, Lincoln, NE, 68588, USA.
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15
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Kershaw JL, Botting CH, Brownlow A, Hall AJ. Not just fat: investigating the proteome of cetacean blubber tissue. CONSERVATION PHYSIOLOGY 2018; 6:coy003. [PMID: 29479430 PMCID: PMC5814904 DOI: 10.1093/conphys/coy003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/14/2017] [Accepted: 01/24/2018] [Indexed: 06/01/2023]
Abstract
Mammalian adipose tissue is increasingly being recognized as an endocrine organ involved in the regulation of a number of metabolic processes and pathways. It responds to signals from different hormone systems and the central nervous system, and expresses a variety of protein factors with important paracrine and endocrine functions. This study presents a first step towards the systematic analysis of the protein content of cetacean adipose tissue, the blubber, in order to investigate the kinds of proteins present and their relative abundance. Full depth blubber subsamples were collected from dead-stranded harbour porpoises (Phocoena phocoena) (n = 21). Three total protein extraction methods were trialled, and the highest total protein yields with the lowest extraction variability were achieved using a RIPA cell lysis and extraction buffer based protocol. Extracted proteins were separated using 1D Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE), and identified using nanoflow Liquid Chromatography Electrospray Ionization in tandem with Mass Spectrometry (nLC-ESI-MS/MS). A range of proteins were identified (n = 295) and classed into eight functional groups, the most abundant of which were involved in cell function and metabolism (45%), immune response and inflammation (15%) and lipid metabolism (11%). These proteins likely originate both from the various cell types within the blubber tissue itself, and from the circulation. They therefore have the potential to capture information on the cellular and physiological stresses experienced by individuals at the time of sampling. The importance of this proteomic approach is two-fold: Firstly, it could help to assign novel functions to marine mammal blubber in keeping with current understanding of the multi-functional role of adipose tissue in other mammals. Secondly, it could lead to the development of a suite of biomarkers to better monitor the physiological state and health of live individuals though remote blubber biopsy sampling.
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Affiliation(s)
- Joanna L Kershaw
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews KY16 8LB, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, School of Chemistry, Biomolecular Sciences Building Annexe, North Haugh, University of St Andrews, St Andrews KY16 9ST, UK
| | - Andrew Brownlow
- Scottish Marine Animals Strandings Scheme, SAC Consulting Veterinary Services, Inverness IV2 5NA, UK
| | - Ailsa J Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews KY16 8LB, UK
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16
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Lu M, Jin Y, Ballmer-Weber B, Goodman RE. A comparative study of human IgE binding to proteins of a genetically modified (GM) soybean and six non-GM soybeans grown in multiple locations. Food Chem Toxicol 2018; 112:216-223. [PMID: 29307601 DOI: 10.1016/j.fct.2018.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 12/28/2017] [Accepted: 01/01/2018] [Indexed: 10/18/2022]
Abstract
Prior to commercialization, genetically modified (GM) crops are evaluated to determine the allergenicity of the newly expressed protein. Some regulators require an evaluation of endogenous allergens in commonly allergenic crops including soybean to determine if genetic transformation increased endogenous allergen concentrations, even asking for IgE testing using sera from individual sensitized subjects. Little is known about the variability of the expression of endogenous allergens among non-GM varieties or under different environmental conditions. We tested IgE binding to endogenous allergenic proteins in an experimental non-commercial GM line, a non-GM near-isoline control, and five non-GM commercial soybean lines replicated at three geographically separated locations. One-dimensional (1D) and two-dimensional (2D) immunoblotting and ELISA were performed using serum or plasma from eleven soybean allergic patients. The results of immunoblots and ELISA showed no significant differences in IgE binding between the GM line and its non-GM near-isoline control. However, some distinct differences in IgE binding patterns were observed among the non-GM commercial soybean lines and between different locations, highlighting the inherent variability in endogenous allergenic proteins. Understanding the potential variability in the levels of endogenous allergens is necessary to establish a standard of acceptance for GM soybeans compared to non-GM soybean events and lines.
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Affiliation(s)
- Mei Lu
- Department of Food Science and Technology, University of Nebraska Lincoln, Lincoln, NE, USA.
| | - Yuan Jin
- Department of Food Science and Technology, University of Nebraska Lincoln, Lincoln, NE, USA.
| | - Barbara Ballmer-Weber
- Allergy Unit, Department of Dermatology, University Hospital Zürich, Zürich, Switzerland.
| | - Richard E Goodman
- Department of Food Science and Technology, University of Nebraska Lincoln, Lincoln, NE, USA.
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17
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John KMM, Khan F, Luthria DL, Matthews B, Garrett WM, Natarajan S. Proteomic and metabolomic analysis of minimax and Williams 82 soybeans grown under two different conditions. J Food Biochem 2017. [DOI: 10.1111/jfbc.12404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- K. M. Maria John
- Beltsville Human Nutrition Research Center; USDA-ARS; Beltsville Maryland 20705 USA
| | - Farooq Khan
- Department of Plant Science & Landscape Architecture; University of Maryland, College Park; Maryland 20742 USA
| | - Davanand L. Luthria
- Beltsville Human Nutrition Research Center; USDA-ARS; Beltsville Maryland 20705 USA
| | - Benjamin Matthews
- Soybean Genomics and Improvement Laboratory; USDA-ARS; Beltsville Maryland 20705 USA
| | - Wesley M. Garrett
- Animal Biosciences and Biotechnology Laboratory; USDA-ARS; Beltsville Maryland 20705 USA
| | - Savithiry Natarajan
- Soybean Genomics and Improvement Laboratory; USDA-ARS; Beltsville Maryland 20705 USA
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18
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Hill RC, Oman TJ, Wang X, Shan G, Schafer B, Herman RA, Tobias R, Shippar J, Malayappan B, Sheng L, Xu A, Bradshaw J. Development, Validation, and Interlaboratory Evaluation of a Quantitative Multiplexing Method To Assess Levels of Ten Endogenous Allergens in Soybean Seed and Its Application to Field Trials Spanning Three Growing Seasons. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5531-5544. [PMID: 28635260 DOI: 10.1021/acs.jafc.7b01018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
As part of the regulatory approval process in Europe, comparison of endogenous soybean allergen levels between genetically engineered (GE) and non-GE plants has been requested. A quantitative multiplex analytical method using tandem mass spectrometry was developed and validated to measure 10 potential soybean allergens from soybean seed. The analytical method was implemented at six laboratories to demonstrate the robustness of the method and further applied to three soybean field studies across multiple growing seasons (including 21 non-GE soybean varieties) to assess the natural variation of allergen levels. The results show environmental factors contribute more than genetic factors to the large variation in allergen abundance (2- to 50-fold between environmental replicates) as well as a large contribution of Gly m 5 and Gly m 6 to the total allergen profile, calling into question the scientific rational for measurement of endogenous allergen levels between GE and non-GE varieties in the safety assessment.
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Affiliation(s)
- Ryan C Hill
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Trent J Oman
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Xiujuan Wang
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Guomin Shan
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Barry Schafer
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Rod A Herman
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Rowel Tobias
- EAG Laboratories , 4780 Discovery Drive, Columbia, Missouri 65201, United States
| | - Jeff Shippar
- Covance Laboratories , 3301 Kinsman Blvd., Madison, Wisconsin 53704, United States
| | - Bhaskar Malayappan
- Critical Path Services LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
| | - Li Sheng
- EPL Bioanalytical Services , 9095 W. Harristown Blvd, Niantic, Illinois 62551, United States
| | - Austin Xu
- Primera Analytical Solutions , 259 Wall Street, Princeton, New Jersey 08540, United States
| | - Jason Bradshaw
- Pyxant Laboratories , 4720 Forge Road #106, Colorado Springs, Colorado 80907, United States
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19
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Maria John KM, Khan F, Luthria DL, Garrett W, Natarajan S. Proteomic analysis of anti-nutritional factors (ANF's) in soybean seeds as affected by environmental and genetic factors. Food Chem 2017; 218:321-329. [PMID: 27719916 DOI: 10.1016/j.foodchem.2016.09.072] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/02/2016] [Accepted: 09/12/2016] [Indexed: 11/30/2022]
Abstract
The genotype (G), environment (E), and the relationship between G and E on soybean seed anti-nutritional factors (ANF's) were examined under three different agro-climatic conditions. The field trials were conducted at Maryland, South Carolina and South Dakota using nine region specific genotypes. At each location, the nine genotypes were grown with two planting/sowing dates. Differentially expressed protein spots from the two-dimensional gel electrophoresis were analyzed using mass spectrometry. Seven ANF's corresponding to soybean agglutinin and Kunitz trypsin inhibitor were identified based on the statistical significance levels at p<0.005. The G and E conditions (planting/sowing season) influences the ANF's content. This initial study suggests that early sowing reduces the total ANF's content irrespective of genotypes and their growing locations.
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Affiliation(s)
- K M Maria John
- USDA-ARS, Beltsville Human Nutrition Research Center, Beltsville, MD 20705, USA
| | - Farooq Khan
- University of Maryland, Department of Plant Science & Landscape Architecture, College Park, MD 20742, USA
| | - Davanand L Luthria
- USDA-ARS, Beltsville Human Nutrition Research Center, Beltsville, MD 20705, USA
| | - Wesley Garrett
- USDA-ARS, Animal Biosciences and Biotechnology Laboratory, Beltsville, MD 20705, USA
| | - Savithiry Natarajan
- USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA.
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20
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Nano-LC-ESI MS/MS analysis of proteins in dried sea dragon Solenognathus hardwickii and bioinformatic analysis of its protein expression profiling. Chin J Nat Med 2017; 14:709-713. [PMID: 27667517 DOI: 10.1016/s1875-5364(16)30084-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 11/23/2022]
Abstract
The sea dragon Solenognathus hardwickii has long been used as a traditional Chinese medicine for the treatment of various diseases, such as male impotency. To gain a comprehensive insight into the protein components of the sea dragon, shotgun proteomic analysis of its protein expression profiling was conducted in the present study. Proteins were extracted from dried sea dragon using a trichloroacetic acid/acetone precipitation method and then separated by SDS-PAGE. The protein bands were cut from the gel and digested by trypsin to generate peptide mixture. The peptide fragments were then analyzed using nano liquid chromatography tandem mass spectrometry (nano-LC-ESI MS/MS). 810 proteins and 1 577 peptides were identified in the dried sea dragon. The identified proteins exhibited molecular weight values ranging from 1 900 to 3 516 900 Da and pI values from 3.8 to 12.18. Bioinformatic analysis was conducted using the DAVID Bioinformatics Resources 6.7 Gene Ontology (GO) analysis tool to explore possible functions of the identified proteins. Ascribed functions of the proteins mainly included intracellular non-membrane-bound organelle, non-membrane-bounded organelle, cytoskeleton, structural molecule activity, calcium ion binding and etc. Furthermore, possible signal networks of the identified proteins were predicted using STRING (Search Tool for the Retrieval of Interacting Genes) database. Ribosomal protein synthesis was found to play an important role in the signal network. The results of this study, to best of our knowledge, were the first to provide a reference proteome profile for the sea dragon, and would aid in the understanding of the expression and functions of the identified proteins.
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21
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Mohammad SA, Ghanemi K, Larki A. Simultaneous extraction of polycyclic aromatic hydrocarbons through the complete dissolution of solid biological samples in sodium hydroxide/urea/thiourea aqueous solution. J Chromatogr A 2016; 1476:9-18. [DOI: 10.1016/j.chroma.2016.11.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/12/2016] [Accepted: 11/15/2016] [Indexed: 01/03/2023]
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22
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Yang A, Yu X, Zheng A, James AT. Rebalance between 7S and 11S globulins in soybean seeds of differing protein content and 11SA4. Food Chem 2016; 210:148-55. [PMID: 27211633 DOI: 10.1016/j.foodchem.2016.04.095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/31/2016] [Accepted: 04/20/2016] [Indexed: 11/22/2022]
Abstract
Protein content and globulin subunit composition of soybean seeds affect the quality of soy foods. In this proteomic study, the protein profile of soybean seeds with high (∼45.5%) or low (∼38.6%) protein content and with or without the glycinin (11S) subunit 11SA4 was examined. 44 unique proteins and their homologues were identified and showed that both protein content and 11SA4 influenced the abundance of a number of proteins. The absence of 11SA4 exerted a greater impact than the protein content, and led to a decreased abundance of glycinin G2/A2B1 and G5/A5A4B3 subunits, which resulted in lower total 11S with a concomitant higher total β-conglycinin (7S). Low protein content was associated with higher glycinin G3/A1aB1b and lower glycinin G4/A5A4B3. Using the proteomic approach, it was demonstrated that 11SA4 deficiency induced compensatory accumulation of 7S globulins and led to a similar total abundance for 7S+11S irrespective of protein content or 11SA4.
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Affiliation(s)
- A Yang
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD 4067, Australia.
| | - X Yu
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD 4067, Australia; College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - A Zheng
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD 4067, Australia; Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - A T James
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD 4067, Australia
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23
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Botsios S, Tittman S, Manuelidis L. Rapid chemical decontamination of infectious CJD and scrapie particles parallels treatments known to disrupt microbes and biofilms. Virulence 2016; 6:787-801. [PMID: 26556670 DOI: 10.1080/21505594.2015.1098804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Neurodegenerative human CJD and sheep scrapie are diseases caused by several different transmissible encephalopathy (TSE) agents. These infectious agents provoke innate immune responses in the brain, including late-onset abnormal prion protein (PrP-res) amyloid. Agent particles that lack detectable PrP sequences by deep proteomic analysis are highly infectious. Yet these agents, and their unusual resistance to denaturation, are often evaluated by PrP amyloid disruption. To reexamine the intrinsic resistance of TSE agents to denaturation, a paradigm for less resistant viruses and microbes, we developed a rapid and reproducible high yield agent isolation procedure from cultured cells that minimized PrP amyloid and other cellular proteins. Monotypic neuronal GT1 cells infected with the FU-CJD or 22L scrapie agents do not have complex brain changes that can camouflage infectious particles and prevent their disruption, and there are only 2 reports on infectious titers of any human CJD strain treated with chemical denaturants. Infectious titers of both CJD and scrapie were reduced by >4 logs with Thiourea-urea, a treatment not previously tested. A mere 5 min exposure to 4M GdnHCl at 22°C reduced infectivity by >5 logs. Infectious 22L particles were significantly more sensitive to denaturation than FU-CJD particles. A protocol using sonication with these chemical treatments may effectively decontaminate complicated instruments, such as duodenoscopes that harbor additional virulent microbes and biofilms associated with recent iatrogenic infections.
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Affiliation(s)
- Sotirios Botsios
- a Yale Medical School; Section of Neuropathology (Surgery) ; New Haven , CT USA
| | - Sarah Tittman
- a Yale Medical School; Section of Neuropathology (Surgery) ; New Haven , CT USA
| | - Laura Manuelidis
- a Yale Medical School; Section of Neuropathology (Surgery) ; New Haven , CT USA
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24
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Subramanian S, Ricci E, Souleimanov A, Smith DL. A Proteomic Approach to Lipo-Chitooligosaccharide and Thuricin 17 Effects on Soybean GerminationUnstressed and Salt Stress. PLoS One 2016; 11:e0160660. [PMID: 27560934 PMCID: PMC4999219 DOI: 10.1371/journal.pone.0160660] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/23/2016] [Indexed: 12/13/2022] Open
Abstract
Salt stress is an important abiotic stressor affecting crop growth and productivity. Of the 20 percent of the terrestrial earth's surface available as agricultural land, 50 percent is estimated by the United Nations Environment Program to be salinized to the level that crops growing on it will be salt-stressed. Increased soil salinity has profound effects on seed germination and germinating seedlings as they are frequently confronted with much higher salinities than vigorously growing plants, because germination usually occurs in surface soils, the site of greatest soluble salt accumulation. The growth of soybean exposed to 40 mM NaCl is negatively affected, while an exposure to 80 mM NaCl is often lethal. When treated with the bacterial signal compounds lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17), soybean seeds (variety Absolute RR) responded positively at salt stress of up to 150 mM NaCl. Shotgun proteomics of unstressed and 100 mM NaCl stressed seeds (48 h) in combination with the LCO and Th17 revealed many known, predicted, hypothetical and unknown proteins. In all, carbon, nitrogen and energy metabolic pathways were affected under both unstressed and salt stressed conditions when treated with signals. PEP carboxylase, Rubisco oxygenase large subunit, pyruvate kinase, and isocitrate lyase were some of the noteworthy proteins enhanced by the signals, along with antioxidant glutathione-S-transferase and other stress related proteins. These findings suggest that the germinating seeds alter their proteome based on bacterial signals and on stress, the specificity of this response plays a crucial role in organ maturation and transition from one stage to another in the plants' life cycle; understanding this response is of fundamental importance in agriculture and, as a result, global food security. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD004106.
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Affiliation(s)
- Sowmyalakshmi Subramanian
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
| | - Emily Ricci
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
| | - Alfred Souleimanov
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
| | - Donald L. Smith
- Department of Plant Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte Anne de Bellevue, Quebec, H9X3V9, Canada
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25
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Jiang MX, Zhai LJ, Yang H, Zhai SM, Zhai CK. Analysis of Active Components and Proteomics of Chinese Wild Rice (Zizania latifolia (Griseb) Turcz) and Indica Rice (Nagina22). J Med Food 2016; 19:798-804. [DOI: 10.1089/jmf.2015.3612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Ming-xia Jiang
- School of Public Health, Southeast University, Nanjing, China
| | - Li-jie Zhai
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hua Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Shu-menghui Zhai
- Department of Public Health, Center for Asian Health, Temple University, Philadelphia, Pennsylvania, USA
| | - Cheng-kai Zhai
- School of Public Health, Southeast University, Nanjing, China
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Seo SH, Cho SJ. Changes in allergenic and antinutritional protein profiles of soybean meal during solid-state fermentation with Bacillus subtilis. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.02.035] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Jia YL, Chen H, Zhang C, Gao LJ, Wang XC, Qiu LL, Wu JF. Proteomic analysis of halotolerant proteins under high and low salt stress in Dunaliella salina using two-dimensional differential in-gel electrophoresis. Genet Mol Biol 2016; 39:239-47. [PMID: 27192131 PMCID: PMC4910558 DOI: 10.1590/1678-4685-gmb-2015-0108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/06/2015] [Indexed: 11/22/2022] Open
Abstract
Dunaliella salina, a single-celled marine alga with extreme salt tolerance, is an important model organism for studying fundamental extremophile survival mechanisms and their potential practical applications. In this study, two-dimensional differential in-gel electrophoresis (2D-DIGE) was used to investigate the expression of halotolerant proteins under high (3 M NaCl) and low (0.75 M NaCl) salt concentrations. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and bioinformatics were used to identify and characterize the differences among proteins. 2D-DIGE analysis revealed 141 protein spots that were significantly differentially expressed between the two salinities. Twenty-four differentially expressed protein spots were successfully identified by MALDI-TOF/TOF MS, including proteins in the following important categories: molecular chaperones, proteins involved in photosynthesis, proteins involved in respiration and proteins involved in amino acid synthesis. Expression levels of these proteins changed in response to the stress conditions, which suggests that they may be involved in the maintenance of intracellular osmotic pressure, cellular stress responses, physiological changes in metabolism, continuation of photosynthetic activity and other aspects of salt stress. The findings of this study enhance our understanding of the function and mechanisms of various proteins in salt stress.
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Affiliation(s)
- Yan-Long Jia
- Pharmacy College, Xinxiang Medical University, Xinxiang 453003, Henan, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Hui Chen
- Pharmacy College, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Chong Zhang
- Pharmacy College, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Li-Jie Gao
- School of Basic Medicine, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Xi-Cheng Wang
- Pharmacy College, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Le-Le Qiu
- School of Basic Medicine, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Jun-Fang Wu
- School of Basic Medicine, Xinxiang Medical University, Xinxiang 453003, Henan, China
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Lakshman DK, Roberts DP, Garrett WM, Natarajan SS, Darwish O, Alkharouf N, Pain A, Khan F, Jambhulkar PP, Mitra A. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with Roles in Plant Cell Wall Degradation and Virulence. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3101-3110. [PMID: 27019116 DOI: 10.1021/acs.jafc.5b05735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rhizoctonia solani AG 4 is a soilborne necrotrophic fungal plant pathogen that causes economically important diseases on agronomic crops worldwide. This study used a proteomics approach to characterize both intracellular proteins and the secretome of R. solani AG 4 isolate Rs23A under several growth conditions, the secretome being highly important in pathogenesis. From over 500 total secretome and soluble intracellular protein spots from 2-D gels, 457 protein spots were analyzed and 318 proteins positively matched with fungal proteins of known function by comparison with available R. solani genome databases specific for anastomosis groups 1-IA, 1-IB, and 3. These proteins were categorized to possible cellular locations and functional groups and for some proteins their putative roles in plant cell wall degradation and virulence. The majority of the secreted proteins were grouped to extracellular regions and contain hydrolase activity.
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Affiliation(s)
- Dilip K Lakshman
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Daniel P Roberts
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Wesley M Garrett
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Savithiry S Natarajan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Omar Darwish
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Nadim Alkharouf
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Arnab Pain
- Pathogen Genomics, KAUST , Thuwal, Saudi Arabia 23955
| | - Farooq Khan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | | | - Amitava Mitra
- Department of Plant Pathology, University of Nebraska , Lincoln, Nebraska 68583, United States
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Jungsukcharoen J, Chokchaichamnankit D, Srisomsap C, Cherdshewasart W, Sangvanich P. Proteome analysis of Pueraria mirifica tubers collected in different seasons. Biosci Biotechnol Biochem 2016; 80:1070-80. [PMID: 26940377 DOI: 10.1080/09168451.2016.1141035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pueraria mirifica-derived tuberous powder has been long-term consumed in Thailand as female hormone-replacement traditional remedies. The protein profiles of tubers collected in different seasons were evaluated. Phenol extraction, 2D-PAGE, and mass spectrometry were employed for tuberous proteome analysis. Out of the 322 proteins detected, over 59% were functionally classified as being involved in metabolism. The rest proteins were involved in defense, protein synthesis, cell structure, transportation, stress, storage, and also unidentified function. The proteins were found to be differentially expressed with respect to harvest season. Importantly, chalcone isomerase, isoflavone synthase, cytochrome p450, UDP-glycosyltransferase, and isoflavone reductase, which are all involved in the biosynthesis pathway of bioactive isoflavonoids, were most abundantly expressed in the summer-collected tubers. This is the first report on the proteomic patterns in P. mirifica tubers in relevant with seasonal variation. The study enlights the understanding of variance isoflavonoid production in P. mirifica tubers.
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Affiliation(s)
- Jutarmas Jungsukcharoen
- a Faculty of Science, Program in Biotechnology , Chulalongkorn University , Bangkok , Thailand
| | | | - Chantragan Srisomsap
- b Laboratory of Biochemistry , Chulabhorn Research Institute , Bangkok , Thailand
| | - Wichai Cherdshewasart
- c Faculty of Science, Department of Biology , Chulalongkorn University , Bangkok , Thailand
| | - Polkit Sangvanich
- d Faculty of Science, Department of Chemistry , Chulalongkorn University , Bangkok , Thailand
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30
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Natarajan S, Khan F, Song Q, Lakshman S, Cregan P, Scott R, Shipe E, Garrett W. Characterization of Soybean Storage and Allergen Proteins Affected by Environmental and Genetic Factors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:1433-45. [PMID: 26807503 DOI: 10.1021/acs.jafc.5b05172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
There is limited information on the influence of genetic and environmental variability on soybean protein composition. This study aimed to determine the role of genotype (G), environments (E), and the interrelationship of genotype and environment (G×E) on soybean seed protein. Three sets of nine soybean genotypes were grown in replicated trials at Maryland, South Carolina, and South Dakota. At each location, the nine genotypes were grown with two planting/sowing dates. We applied two-dimensional gel electrophoresis and mass spectrometry to study the variability of soybean storage and allergen proteins. Statistical analysis of 47 storage and 8 allergen proteins, in terms of differentially expressed protein spots significant at the p<0.005 level, was performed. We found more spots that showed statistically significant differences in expression among E compared to G and G×E interaction.
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Affiliation(s)
- Savithiry Natarajan
- Soybean Genomics and Improvement Laboratory, USDA-ARS , Beltsville, Maryland 20705, United States
| | - Farooq Khan
- Department of Plant Science & Landscape Architecture, University of Maryland , College Park, Maryland 20742, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS , Beltsville, Maryland 20705, United States
| | - Sukla Lakshman
- Diet, Genomics and Immunology Laboratory, USDA-ARS , Beltsville, Maryland 20705, United States
| | - Perry Cregan
- Soybean Genomics and Improvement Laboratory, USDA-ARS , Beltsville, Maryland 20705, United States
| | - Roy Scott
- Crop Production and Protection, Oilseeds & Bioscience, USDA-ARS , Beltsville, Maryland 20705, United States
| | - Emerson Shipe
- Clemson University , Department of Entomology, Soils, & Plant Sciences, Clemson, South Carolina 29634, United States
| | - Wesley Garrett
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS , Beltsville, Maryland 20705, United States
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31
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Latef AAHA, Jan S, Abd‐Allah EF, Rashid B, John R, Ahmad P. Soybean under abiotic stress. PLANT‐ENVIRONMENT INTERACTION 2016:28-42. [DOI: 10.1002/9781119081005.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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32
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Ling X, Guo J, Zheng C, Ye C, Lu Y, Pan X, Chen Z, Ng IS. Simple, effective protein extraction method and proteomics analysis from polyunsaturated fatty acids-producing micro-organisms. Bioprocess Biosyst Eng 2015; 38:2331-41. [DOI: 10.1007/s00449-015-1467-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/25/2015] [Indexed: 11/30/2022]
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VILHENA MILCAB, FRANCO MÔNICAR, SCHMIDT DAIANA, CARVALHO GISELLE, AZEVEDO RICARDOA. Evaluation of protein extraction methods for enhanced proteomic analysis of tomato leaves and roots. ACTA ACUST UNITED AC 2015; 87:1853-63. [DOI: 10.1590/0001-3765201520150116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteomics is an outstanding area in science whose increasing application has advanced to distinct purposes. A crucial aspect to achieve a good proteome resolution is the establishment of a methodology that results in the best quality and wide range representation of total proteins. Another important aspect is that in many studies, limited amounts of tissue and total protein in the tissue to be studied are found, making difficult the analysis. In order to test different parameters, combinations using minimum amount of tissue with 4 protocols for protein extraction from tomato (Solanum lycopersicum L.) leaves and roots were evaluated with special attention to their capacity for removing interferents and achieving suitable resolution in bidimensional gel electrophoresis, as well as satisfactory protein yield. Evaluation of the extraction protocols revealed large protein yield differences obtained for each one. TCA/acetone was shown to be the most efficient protocol, which allowed detection of 211 spots for leaves and 336 for roots using 500 µg of leaf protein and 800 µg of root protein per gel.
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34
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Malafaia CB, Guerra ML, Silva TD, Paiva PM, Souza EB, Correia MT, Silva MV. Selection of a protein solubilization method suitable for phytopathogenic bacteria: a proteomics approach. Proteome Sci 2015; 13:5. [PMID: 25670925 PMCID: PMC4322814 DOI: 10.1186/s12953-015-0062-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/12/2015] [Indexed: 12/12/2022] Open
Abstract
Background Finding the best extraction method of proteins from lysed cells is the key step for detection and identification in all proteomics applications. These are important to complement the knowledge about the mechanisms of interaction between plants and phytopathogens causing major economic losses. To develop an optimized extraction protocol, strains of Acidovorax citrulli, Pectobacterium carotovorum subsp. carotovorum and Ralstonia solanacearum were used as representative cells in the study of phytopathogenic bacteria. This study aims to compare four different protein extraction methods, including: Trizol, Phenol, Centrifugation and Lysis in order to determine which are more suitable for proteomic studies using as parameters the quantity and quality of extracted proteins observed in two-dimensional gels. Results The bacteria studied showed different results among the tested methods. The Lysis method was more efficient for P. carotovorum subsp. carotovorum and R. solanacearum phytobacteria, as well as simple and fast, while for A. citrulli, the Centrifugation method was the best. This evaluation is based on results obtained in polyacrylamide gels that presented a greater abundance of spots and clearer and more consistent strips as detected by two-dimensional gels. Conclusions These results attest to the adequacy of these proteins extraction methods for proteomic studies.
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Affiliation(s)
- Carolina B Malafaia
- Programa de Pós-Graduação em Ciências Biológicas - Centro de Ciências Biológicas - Universidade Federal de Pernambuco, Rua Prof. Nelson Chaves s/n, Cidade Universitária, CEP 50670-901 Recife, PE Brasil
| | - Myrzânia L Guerra
- Programa de Pós-Graduação em Fitopatologia - Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n - Dois Irmãos, CEP: 52171-900 Recife, PE Brasil
| | - Túlio D Silva
- Programa de Pós-Graduação em Ciências Biológicas - Centro de Ciências Biológicas - Universidade Federal de Pernambuco, Rua Prof. Nelson Chaves s/n, Cidade Universitária, CEP 50670-901 Recife, PE Brasil
| | - Patrícia Mg Paiva
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Rua Prof. Moraes Rego s/n, Cidade Universitária, 50670-420 Recife, PE Brasil
| | - Elineide B Souza
- Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n - Dois Irmãos, CEP: 52171-900 Recife, PE Brasil
| | - Maria Ts Correia
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Rua Prof. Moraes Rego s/n, Cidade Universitária, 50670-420 Recife, PE Brasil
| | - Márcia V Silva
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Rua Prof. Moraes Rego s/n, Cidade Universitária, 50670-420 Recife, PE Brasil
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Yin Y, Yang R, Han Y, Gu Z. Comparative proteomic and physiological analyses reveal the protective effect of exogenous calcium on the germinating soybean response to salt stress. J Proteomics 2015; 113:110-26. [PMID: 25284050 DOI: 10.1016/j.jprot.2014.09.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/22/2014] [Accepted: 09/26/2014] [Indexed: 01/16/2023]
Abstract
Calcium enhances salt stress tolerance of soybeans. Nevertheless, the molecular mechanism of calcium's involvement in resistance to salt stress is unclear. A comparative proteomic approach was used to investigate protein profiles in germinating soybeans under NaCl-CaCl2 and NaCl-LaCl3 treatments. A total of 80 proteins affected by calcium in 4-day-old germinating soybean cotyledons and 71 in embryos were confidently identified. The clustering analysis showed proteins were subdivided into 5 and 6 clusters in cotyledon and embryo, respectively. Among them, proteins involved in signal transduction and energy pathways, in transportation, and in protein biosynthesis were largely enriched while those involved in proteolysis were decreased. Abundance of nucleoside diphosphate kinase and three antioxidant enzymes were visibly increased by calcium. Accumulation of gamma-aminobutyric acid and polyamines was also detected after application of exogenous calcium. This was consistent with proteomic results, which showed that proteins involved in the glutamate and methionine metabolism were mediated by calcium. Calcium could increase the salt stress tolerance of germinating soybeans via enriching signal transduction, energy pathway and transportation, promoting protein biosynthesis, inhibiting proteolysis, redistributing storage proteins, regulating protein processing in endoplasmic reticulum, enriching antioxidant enzymes and activating their activities, accumulating secondary metabolites and osmolytes, and other adaptive responses. Biological significance Soybean (Glycine max L.), as a traditional edible legume, is being targeted for designing functional foods. During soybean germination under stressful conditions especially salt stress, newly discovered functional components such as gamma-aminobutyric acid (GABA) are rapidly accumulated. However, soybean plants are relatively salt-sensitive and the growth, development and biomass of germinating soybeans are significantly suppressed under salt stress condition. According to previous studies, exogenous calcium counters the harmful effect of salt stress and increases the biomass and GABA content of germinating soybeans. Nevertheless, the precise molecular mechanism underlying the role of calcium in resistance to salt stress is still unknown. This paper is the first study employing comparative proteomic and physiological analyses to reveal the protective effect of exogenous calcium in the germinating soybean response to salt stress. Our study links the biological events with proteomic information and provides detailed peptide information on all identified proteins. The functions of those significantly changed proteins are also analyzed. The physiological and comparative proteomic analyses revealed the putative molecular mechanism of exogenous calcium treatment induced salt stress responses. The findings from this paper are beneficial to high GABA-rich germinating soybean biomass. Additionally, these findings also might be applicable to the genetic engineering of soybean plants to improve stress tolerance.
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Affiliation(s)
- Yongqi Yin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China; College of Food Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225127, PR China
| | - Runqiang Yang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yongbin Han
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Zhenxin Gu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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36
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Protein extraction method for the proteomic study of a Mexican traditional fermented starchy food. J Proteomics 2014; 111:139-47. [DOI: 10.1016/j.jprot.2014.06.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/19/2014] [Accepted: 06/28/2014] [Indexed: 01/31/2023]
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37
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Capriotti AL, Caruso G, Cavaliere C, Samperi R, Stampachiacchiere S, Zenezini Chiozzi R, Laganà A. Protein profile of mature soybean seeds and prepared soybean milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9893-9. [PMID: 25229310 DOI: 10.1021/jf5034152] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The soybean (Glycine max (L.) Merrill) is economically the most important bean in the world, providing a wide range of vegetable proteins. Soybean milk is a colloidal solution obtained as water extract from swelled and ground soybean seeds. Soybean proteins represent about 35-40% on a dry weight basis and they are receiving increasing attention with respect to their health effects. However, the soybean is a well-recognized allergenic food, and therefore, it is urgent to define its protein components responsible for the allergenicity in order to develop hypoallergenic soybean products for sensitive people. The main aim of this work was the characterization of seed and milk soybean proteome and their comparison in terms of protein content and specific proteins. Using a shotgun proteomics approach, 243 nonredundant proteins were identified in mature soybean seeds.
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Affiliation(s)
- Anna Laura Capriotti
- Dipartimento di Chimica, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, 00185 Rome, Italy
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Tavakolan M, Alkharouf NW, Matthews BF, Natarajan SS. SoyProLow: A protein database enriched in low abundant soybean proteins. Bioinformation 2014; 10:599-601. [PMID: 25352730 PMCID: PMC4209371 DOI: 10.6026/97320630010599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/31/2014] [Indexed: 11/23/2022] Open
Abstract
Soybeans are an important legume crop that contain 2 major storage proteins, β-conglycinin and glycinin, which account about 70-
80% of total seed proteins. These abundant proteins hinder the isolation and characterization of several low abundant proteins in
soybean seeds. Several protein extraction methodologies were developed in our laboratory to decrease these abundant storage
proteins in seed extracts and to also decrease the amount of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO), which is
normally very abundant in leaf extracts. One of the extraction methodologies used 40% isopropanol and was more effective in
depleting soybean storage proteins and enhancing low abundant seed proteins than similar methods using 10-80% isopropanol.
Extractions performed with 40% isopropanol decreased the amount of storage proteins and revealed 107 low abundant proteins
when using the combined approaches of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and Mass Spectrometry
(MS). The separation of proteins was achieved by iso-electric focusing (IEF) and 2D-PAGE. The proteins were analyzed with MS
techniques to provide amino acid sequence. The proteins were identified by comparing their amino acid sequences with those in
different databases including NCBI-non redundant, UniprotKB and MSDB databases. In this investigation, previously published
results on low abundant soybean seed proteins were used to create an online database (SoyProLow) to provide a data repository
that can be used as a reference to identify and characterize low abundance proteins. This database is freely accessible to individuals
using similar techniques and can be for the subsequent genetic manipulation to produce value added soybean traits. An intuitive
user interface based on dynamic HTML enables users to browse the network and the profiles of the low abundant proteins.
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Affiliation(s)
- Mona Tavakolan
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA
| | - Nadim W Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA
| | - Benjamin F Matthews
- USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
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Yin Y, Yang R, Gu Z. Organ-specific proteomic analysis of NaCl-stressed germinating soybeans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:7233-44. [PMID: 24960070 DOI: 10.1021/jf500851r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A comparative proteomic approach was employed to explore proteome expression patterns in germinating soybeans under NaCl stress and NaCl-aminoguanidine treatment. The proteins were extracted from 4-day-old germinating soybean cotyledons and noncotyledons (hypocotyl and radicle) and were separated using two-dimensional polyacrylamide gel electrophoresis. A total of 63 and 72 differentially expressed proteins were confidently identified by MALDI-TOF/TOF in the noncotyledons and cotyledons, respectively. These identified proteins were divided into ten functional groups and most of them were predicted to be cytoplasmic proteins in noncotyledons. Moreover, γ-aminobutyric acid was accumulated while the major allergen (Bd 30K protein) was reduced in the germinating soybeans. The proteins involved in energy metabolism and in protein processing in endoplasmic reticulum were enriched under NaCl stress. Meanwhile, the negative effect of stress was aggravated once polyamine degradation was inhibited. Redistribution of storage proteins under stress indicated that storage proteins might not only function as seed storage reserves but also have additional roles in plant defense.
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Affiliation(s)
- Yongqi Yin
- College of Food Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
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40
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Lee H, Garrett WM, Sullivan J, Forseth I, Natarajan SS. Proteomic analysis of the pulvinus, a heliotropic tissue, in Glycine max. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2014. [DOI: 10.4081/pb.2014.4887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Certain plant species respond to light, dark, and other environmental factors by leaf movement. Leguminous plants both track and avoid the sun through turgor changes of the pulvinus tissue at the base of leaves. Mechanisms leading to pulvinar turgor flux, particularly knowledge of the proteins involved, are not well-known. In this study we used two-dimensional gel electrophoresis and liquid chromatography-tandom mass spectrometry to separate and identify the proteins located in the soybean pulvinus. A total of 183 spots were separated and 195 proteins from 165 spots were identified and functionally analyzed using single enrichment analysis for gene ontology terms. The most significant terms were related to proton transport. Comparison with guard cell proteomes revealed similar significant processes but a greater number of pulvinus proteins are required for comparable analysis. To our knowledge, this is a novel report on the analysis of proteins found in soybean pulvinus. These findings provide a better understanding of the proteins required for turgor change in the pulvinus.
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Pereira JL, Queiroz RML, Charneau SO, Felix CR, Ricart CAO, da Silva FL, Steindorff AS, Ulhoa CJ, Noronha EF. Analysis of Phaseolus vulgaris response to its association with Trichoderma harzianum (ALL-42) in the presence or absence of the phytopathogenic fungi Rhizoctonia solani and Fusarium solani. PLoS One 2014; 9:e98234. [PMID: 24878929 PMCID: PMC4039509 DOI: 10.1371/journal.pone.0098234] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/30/2014] [Indexed: 12/22/2022] Open
Abstract
The present study was carried out to evaluate the ability of Trichoderma harzianum (ALL 42-isolated from Brazilian Cerrado soil) to promote common bean growth and to modulate its metabolism and defense response in the presence or absence of the phytopathogenic fungi Rhizoctonia solani and Fusarium solani using a proteomic approach. T. harzianum was able to promote common bean plants growth as shown by the increase in root/foliar areas and by size in comparison to plants grown in its absence. The interaction was shown to modulate the expression of defense-related genes (Glu1, pod3 and lox1) in roots of P. vulgaris. Proteomic maps constructed using roots and leaves of plants challenged or unchallenged by T. harzianum and phytopathogenic fungi showed differences. Reference gels presented differences in spot distribution (absence/presence) and relative volumes of common spots (up or down-regulation). Differential spots were identified by peptide fingerprinting MALDI-TOF mass spectrometry. A total of 48 identified spots (19 for leaves and 29 for roots) were grouped into protein functional classes. For leaves, 33%, 22% and 11% of the identified proteins were categorized as pertaining to the groups: metabolism, defense response and oxidative stress response, respectively. For roots, 17.2%, 24.1% and 10.3% of the identified proteins were categorized as pertaining to the groups: metabolism, defense response and oxidative stress response, respectively.
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Affiliation(s)
- Jackeline L. Pereira
- Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Rayner M. L. Queiroz
- Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Sébastien O. Charneau
- Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Carlos R. Felix
- Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Carlos A. O. Ricart
- Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | | | - Andrei Stecca Steindorff
- Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Cirano J. Ulhoa
- Biological Sciences Institute, Federal University of Goiás (UFG), Goiânia, Goiás, Brazil
- * E-mail:
| | - Eliane F. Noronha
- Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
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42
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Hossain Z, Komatsu S. Potentiality of Soybean Proteomics in Untying the Mechanism of Flood and Drought Stress Tolerance. Proteomes 2014; 2:107-127. [PMID: 28250373 PMCID: PMC5302732 DOI: 10.3390/proteomes2010107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 11/17/2022] Open
Abstract
Dissecting molecular pathways at protein level is essential for comprehensive understanding of plant stress response mechanism. Like other legume crops, soybean, the world's most widely grown seed legume and an inexpensive source of protein and vegetable oil, is also extremely sensitive to abiotic stressors including flood and drought. Irrespective of the kind and severity of the water stress, soybean exhibits a tight control over the carbon metabolism to meet the cells required energy demand for alleviating stress effects. The present review summarizes the major proteomic findings related to changes in soybean proteomes in response to flood and drought stresses to get a clear insight into the complex mechanisms of stress tolerance. Furthermore, advantages and disadvantages of different protein extraction protocols and challenges and future prospects of soybean proteome study are discussed in detail to comprehend the underlying mechanism of water stress acclimation.
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Affiliation(s)
- Zahed Hossain
- Plant Stress Biology Lab, Department of Botany, West Bengal State University, Kolkata-700126, India.
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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43
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Alam M, Ghosh W. Optimization of a phenol extraction-based protein preparation method amenable to downstream 2DE and MALDI-MS based analysis of bacterial proteomes. Proteomics 2014; 14:216-21. [DOI: 10.1002/pmic.201300146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 10/25/2013] [Accepted: 11/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Masrure Alam
- Department of Microbiology; Bose Institute; Kolkata India
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44
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Marzban G, Herndl A, Maghuly F, Katinger H, Laimer M. Mapping of fruit allergens by 2D electrophoresis and immunodetection. Expert Rev Proteomics 2014; 5:61-75. [DOI: 10.1586/14789450.5.1.61] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Abstract
Soybean, the world's most widely grown seed legume, is an important global source of vegetable oil and protein. Though, complete draft genome sequence of soybean is now available, but functional genomics studies remain in their infancy, as this agricultural legume species exhibits genetic constrains like genome duplications and self-incompatibilities. The techniques of proteomics provide much powerful tool for functional analysis of soybean. In the present review, an attempt has been made to summarize all significant contributions in the field of soybean proteomics. Special emphasis is given to subcellular proteomics in response to abiotic stresses for better understanding molecular basis of acquisition of stress tolerance mechanism. Detailed protocols of protein extraction, solubilization, fractionation of subcellular organelle, and proteins identification are explained for soybean proteomics. All this information would not only enrich us in understanding the plants response to environmental stressors but would also enable us to design genetically engineered stress tolerant soybean.
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Affiliation(s)
- Zahed Hossain
- Department of Botany, West Bengal State University, Kolkata, West Bengal, India
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46
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Wang T, Qin GX, Sun ZW, Zhao Y. Advances of research on glycinin and β-conglycinin: a review of two major soybean allergenic proteins. Crit Rev Food Sci Nutr 2014; 54:850-62. [PMID: 24499064 DOI: 10.1080/10408398.2011.613534] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Being an important crop, soybean is widely used in the world and plays a vital role in human and animal nutrition. However, it contains several antinutritional factors (ANFs) including soybean agglutinin, soybean protease inhibitors, soybean allergenic proteins, etc., that may result in poor food utilization, decreased growth performance, and even disease. Among these ANFs, soybean allergenic proteins can lead to allergic reactions in human and animals, which has become a public problem all over the world, but our knowledge on it is still inadequate. This paper aims to provide an update on the characteristics, detection or exploration methods, and in vivo research models of soybean allergenic proteins; especially glycinin and β-conglycinin are deeply discussed. Through this review, we may have a better understanding on the advances of research on these two soybean allergenic proteins. Besides, the ingredient processing used to reduce the allergenicity of soybean is also reviewed.
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Affiliation(s)
- Tao Wang
- a College of Animal Science and Technology , Jilin Agricultural University , Changchun , 130118 , P. R. China
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47
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Hossain Z, Khatoon A, Komatsu S. Soybean proteomics for unraveling abiotic stress response mechanism. J Proteome Res 2013; 12:4670-84. [PMID: 24016329 DOI: 10.1021/pr400604b] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Plant response to abiotic stresses depends upon the fast activation of molecular cascades involving stress perception, signal transduction, changes in gene and protein expression and post-translational modification of stress-induced proteins. Legumes are extremely sensitive to flooding, drought, salinity and heavy metal stresses, and soybean is not an exception of that. Invention of immobilized pH gradient strips followed by advancement in mass spectrometry has made proteomics a fast, sensitive and reliable technique for separation, identification and characterization of stress-induced proteins. As the functional translated portion of the genome plays an essential role in plant stress response, proteomic studies provide us a finer picture of protein networks and metabolic pathways primarily involved in stress tolerance mechanism. Identifying master regulator proteins that play key roles in the abiotic stress response pathway is fundamental in providing opportunities for developing genetically engineered stress-tolerant crop plants. This review highlights recent contributions in the field of soybean biology to comprehend the complex mechanism of abiotic stress acclimation. Furthermore, strengths and weaknesses of different proteomic methodologies of extracting complete proteome and challenges and future prospects of soybean proteome study both at organ and whole plant levels are discussed in detail to get new insights into the plant abiotic stress response mechanism.
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Affiliation(s)
- Zahed Hossain
- Plant Stress Biology Lab, Department of Botany, West Bengal State University , Kolkata 700126, West Bengal, India
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48
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Goodman RE, Panda R, Ariyarathna H. Evaluation of endogenous allergens for the safety evaluation of genetically engineered food crops: review of potential risks, test methods, examples and relevance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:8317-32. [PMID: 23848840 DOI: 10.1021/jf400952y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The safety of food produced from genetically engineered (GE) crops is assessed for potential risks of food allergy on the basis of an international consensus guideline outlined by the Codex Alimentarius Commission (2003). The assessment focuses on evaluation of the potential allergenicity of the newly expressed protein(s) as the primary potential risk using a process that markedly limits risks to allergic consumers. However, Codex also recommended evaluating a second concern, potential increases in endogenous allergens of commonly allergenic food crops that might occur due to insertion of the gene. Unfortunately, potential risks and natural variation of endogenous allergens in non-GE varieties are not understood, and risks from increases have not been demonstrated. Because regulatory approvals in some countries are delayed due to increasing demands for measuring endogenous allergens, we present a review of the potential risks of food allergy, risk management for food allergy, and test methods that may be used in these evaluations. We also present new data from our laboratory studies on the variation of the allergenic lipid transfer protein in non-GE maize hybrids as well as data from two studies of endogenous allergen comparisons for three GE soybean lines, their nearest genetic soy lines, and other commercial lines. We conclude that scientifically based limits of acceptable variation cannot been established without an understanding of natural variation in non-GE crops. Furthermore, the risks from increased allergen expression are minimal as the risk management strategy for food allergy is for allergic individuals to avoid consuming any food containing their allergenic source, regardless of the crop variety.
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Affiliation(s)
- Richard E Goodman
- Food Allergy Research and Resource Program, University of Nebraska-Lincoln , 143 Food Industry Complex, Lincoln, Nebraska 68583-0955, United States
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Zhang M, Shen S. Effective protein extraction protocol for proteomics studies of Jerusalem artichoke leaves. J Sep Sci 2013; 36:2203-9. [PMID: 23630184 DOI: 10.1002/jssc.201300199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 11/11/2022]
Abstract
Protein extraction is a crucial step for proteomics studies. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis (2DE) analysis in Jerusalem artichoke (Helianthus tuberosus L.), three different protein extraction methods-trichloroacetic acid/acetone, Mg/NP-40, and phenol/ammonium acetate-were evaluated using Jerusalem artichoke leaves as source materials. Of the three methods, trichloroacetic acid/acetone yielded the best protein separation pattern and highest number of protein spots in 2DE analysis. Proteins highly abundant in leaves, such as Rubisco, are typically problematic during leaf 2DE analysis, however, and this disadvantage was evident using trichloroacetic acid/acetone. To reduce the influence of abundant proteins on the detection of low-abundance proteins, we optimized the trichloroacetic acid/acetone method by incorporating a PEG fractionation approach. After optimization, 363 additional (36.2%) protein spots were detected on the 2DE gel. Our results suggest that trichloroacetic acid/acetone method is a better protein extraction technique than Mg/NP-40 and phenol/ammonium acetate in Jerusalem artichoke leaf 2DE analysis, and that trichloroacetic acid/acetone method combined with PEG fractionation procedure is the most effective approach for leaf 2DE analysis of Jerusalem artichoke.
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Affiliation(s)
- Meide Zhang
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi, China.
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50
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Proteomics-based allergen analysis in plants. J Proteomics 2013; 93:40-9. [PMID: 23568023 DOI: 10.1016/j.jprot.2013.03.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 03/16/2013] [Accepted: 03/19/2013] [Indexed: 01/12/2023]
Abstract
UNLABELLED Plants may trigger hypersensitivity reactions when individuals with allergies consume foods derived from plant materials or inhale plant pollen. As each plant food or pollen contains multiple allergens, proteomics is a powerful tool to detect the allergens present. Allergen-targeted proteomics, termed allergenomics, has been used for comprehensive identification and/or quantification of plant allergens, because it is a simple and inexpensive tool for rapid detection of proteins that bind to IgE. There are increasing numbers of reports on the applications of allergenomics. In this review, we outline some of the applications of proteomics, including: (i) identification of novel allergens, (ii) allergic diagnoses, (iii) quantification of allergens, and (iv) natural diversity of allergens, and finally discuss (v) the use of allergenomics for safety assessment of genetically modified (GM) plants. BIOLOGICAL SIGNIFICANCE Recently, the number of allergic patients is increasing. Therefore, a comprehensive analysis of allergens (allergenomics) in plants is highly important for not only risk assessment of food plants but also diagnosis of allergic symptoms. In this manuscript, we reviewed the recent progress of allergenomics for identification, quantification and profiling of allergens. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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