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Liu J, Feng X, Liang L, Sun L, Meng D. Enzymatic biosynthesis of D-galactose derivatives: Advances and perspectives. Int J Biol Macromol 2024; 267:131518. [PMID: 38615865 DOI: 10.1016/j.ijbiomac.2024.131518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
D-Galactose derivatives, including galactosyl-conjugates and galactose-upgrading compounds, provide various physiological benefits and find applications in industries such as food, cosmetics, feed, pharmaceuticals. Many research on galactose derivatives focuses on identification, characterization, development, and mechanistic aspects of their physiological function, providing opportunities and challenges for the development of practical approaches for synthesizing galactose derivatives. This study focuses on recent advancements in enzymatic biosynthesis of galactose derivatives. Various strategies including isomerization, epimerization, transgalactosylation, and phosphorylation-dephosphorylation were extensively discussed under the perspectives of thermodynamic feasibility, theoretical yield, cost-effectiveness, and by-product elimination. Specifically, the enzymatic phosphorylation-dephosphorylation cascade is a promising enzymatic synthesis route for galactose derivatives because it can overcome the thermodynamic equilibrium of isomerization and utilize cost-effective raw materials. The study also elucidates the existing challenges and future trends in enzymatic biosynthesis of galactose derivatives. Collectively, this review provides a real-time summary aimed at promoting the practical biosynthesis of galactose derivatives through enzymatic catalysis.
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Affiliation(s)
- Juanjuan Liu
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Xinming Feng
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China
| | - Likun Liang
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Liqin Sun
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China.
| | - Dongdong Meng
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China.
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Wang K, Xu Y, Xuan Z, Xiao X, Gu G, Lu L. Enzymatic synthesis of prebiotic galactooligosaccharides from galactose derived from gum arabic. Food Chem 2023; 429:136987. [PMID: 37523914 DOI: 10.1016/j.foodchem.2023.136987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
A novel enzymatic process was established for galactooligosaccharides (GOS) synthesis by using plant-derived galactose as substrate, without producing any byproducts. The galactose was prepared from the acid hydrolysate of gum arabic. The yeast Kluyveromyces lactis producing β-galactosidase capable of catalyzing GOS synthesis from galactose was screened out. The synthesis conditions using the yeast cells as enzyme source were optimized by both single-factor experiment and response surface methodology, with the highest GOS yield reached 45%. The composition of reaction mixture contained only GOS and unreacted galactose, which could be easily separated by the cation exchange resin column. The structures of major GOS products were identified as Gal-β-D-(1 → 6)-Gal, Gal-β-D-(1 → 3)-Gal, and Gal-β-D-(1 → 6)-Gal-β-D-(1 → 6)-Gal by MS and NMR spectra. Moreover, the β-galactosidase-containing cells can be recycled for at least 30 batches of GOS synthesis at 35 °C, with the enzyme activity remaining above 60%.
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Affiliation(s)
- Ke Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yihong Xu
- Hegeng Biotech Engineering Co., Ltd., Chuzhou 239000, China
| | - Zehui Xuan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xina Xiao
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Lili Lu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Dilshad R, Khan KUR, Ahmad S, Shaik Mohammad AA, Sherif AE, Rao H, Ahmad M, Ghalloo BA, Begum MY. Phytochemical characterization of Typha domingensis and the assessment of therapeutic potential using in vitro and in vivo biological activities and in silico studies. Front Chem 2023; 11:1273191. [PMID: 38025070 PMCID: PMC10663946 DOI: 10.3389/fchem.2023.1273191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Typha domingensis, a medicinal plant with significant traditional importance for curing various human diseases, has potentially bioactive compounds but was less explored previously. Therefore, this study aims to investigate the therapeutic potential of T. domingensis by evaluating the phytochemical profile through high-performance liquid chromatography (HPLC) techniques and its biological activities (in vitro and in vivo) from the methanolic extract derived from the entire plant (TDME). The secondary metabolite profile of TDME regulated by reverse phase ultra-high-performance liquid chromatography-mass spectrometry (RP-UHPLC-MS) revealed some bioactive compounds by -ve and +ve modes of ionization. The HPLC quantification study showed the precise quantity of polyphenols (p-coumaric acid, 207.47; gallic acid, 96.25; and kaempferol, 95.78 μg/g extract). The enzyme inhibition assays revealed the IC50 of TDME as 44.75 ± 0.51, 52.71 ± 0.01, and 67.19 ± 0.68 µgmL-1, which were significant compared to their respective standards (indomethacin, 18.03 ± 0.12; quercetin, 4.11 ± 0.01; and thiourea, 8.97 ± 0.11) for lipoxygenase, α-glucosidase, and urease, respectively. Safety was assessed by in vitro hemolysis (4.25% ± 0.16% compared to triton × 100, 93.51% ± 0.36%), which was further confirmed (up to 10 g/kg) by an in vivo model of rats. TDME demonstrated significant (p < 0.05) potential in analgesic activity by hot plate and tail immersion tests and anti-inflammatory activity by the carrageenan-induced hind paw edema model. Pain latency decreased significantly, and the anti-inflammatory effect increased in a dose-dependent way. Additionally, in silico molecular docking revealed that 1,3,4,5-tetracaffeoylquinic acid and formononetin 7-O-glucoside-6″-O-malonate possibly contribute to enzyme inhibitory activities due to their higher binding affinities compared to standard inhibitors. An in silico absorption, distribution, metabolism, excretion, and toxicological study also predicted the pharmacokinetics and safety of the chosen compounds identified from TDME. To sum up, it was shown that TDME contains bioactive chemicals and has strong biological activities. The current investigations on T. domingensis could be extended to explore its potential applications in nutraceutical industries and encourage the isolation of novel molecules with anti-inflammatory and analgesic effects.
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Affiliation(s)
- Rizwana Dilshad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Kashif-ur-Rehman Khan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Saeed Ahmad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Asmaa E. Sherif
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam bin Abdul Aziz, Al-Khar, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Huma Rao
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Maqsood Ahmad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Bilal Ahmad Ghalloo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - M. Yasmin Begum
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
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Wang Y, Shen J, Meng F, Lu Z, Lv F, Zhou L, Zhao H. Effects of monolauroyl-galactosylglycerol on membrane fatty acids and properties of Bacillus cereus. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12567-4. [PMID: 37204449 DOI: 10.1007/s00253-023-12567-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/28/2023] [Accepted: 04/25/2023] [Indexed: 05/20/2023]
Abstract
The purpose of this study was to provide new ideas for the antibacterial mechanism of monolauroyl-galactosylglycerol (MLGG) from the perspective of cell membranes. The changes in cell membrane properties of Bacillus cereus (B. cereus) CMCC 66,301 exposed to different concentrations (1 × MIC (minimum inhibitory concentration), 2 × MIC, 1 × MBC (minimum bacterial concentration)) of MLGG were evaluated. It was found that the lag phase of B. cereus cells was prolonged at low concentration MLGG (1 × MIC and 2 × MIC), while about 2 log CFU/mL reduction in B. cereus populations were observed when exposed to high concentration MLGG (1 × MBC). MLGG treated B. cereus displayed obvious membrane depolarization, while membrane permeability had no change using PI (propidium iodide) staining. Significant increase in the membrane fluidity in response to MLGG exposure occurred, which was consistent with the modification of membrane fatty acids compositions, where the relative content of straight-chain fatty acids (SCFAs) and unsaturated fatty acids (UFAs) increased, while branched-chain fatty acids (BCFAs) decreased significantly. The decreased transition Tm value and cell surface hydrophobicity was also observed. Additionally, effect of MLGG on bacterial membrane compositions were explored at the submolecular level by infrared spectroscopy. Resistance tests of B. cereus to MLGG had demonstrated the advantages of MLGG as a bacteriostatic agent. Collectively, these studies indicate that modifying the fatty acid composition and properties of cellular membranes through MLGG exposure is crucial for inhibiting bacteria growth, providing new insights into the antimicrobial mechanisms of MLGG. KEY POINTS: • Monolauroyl-galactosylglycerol inserted into B. cereus lipid bilayer membrane • Monolauroyl-galactosylglycerol treatment caused B. cereus membrane depolarization • Monolauroyl-galactosylglycerol resulted in B. cereus membrane fatty acids alteration.
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Affiliation(s)
- Ying Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Fanqiang Meng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Fengxia Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Libang Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.
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de Albuquerque TL, de Sousa M, Gomes E Silva NC, Girão Neto CAC, Gonçalves LRB, Fernandez-Lafuente R, Rocha MVP. β-Galactosidase from Kluyveromyces lactis: Characterization, production, immobilization and applications - A review. Int J Biol Macromol 2021; 191:881-898. [PMID: 34571129 DOI: 10.1016/j.ijbiomac.2021.09.133] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/30/2021] [Accepted: 09/20/2021] [Indexed: 01/06/2023]
Abstract
A review on the enzyme β-galactosidase from Kluyveromyces lactis is presented, from the perspective of its structure and mechanisms of action, the main catalyzed reactions, the key factors influencing its activity, and selectivity, as well as the main techniques used for improving the biocatalyst functionality. Particular attention was given to the discussion of hydrolysis, transglycosylation, and galactosylation reactions, which are commonly mediated by this enzyme. In addition, the products generated from these processes were highlighted. Finally, biocatalyst improvement techniques are also discussed, such as enzyme immobilization and protein engineering. On these topics, the most recent immobilization strategies are presented, emphasizing processes that not only allow the recovery of the biocatalyst but also deliver enzymes that show better resistance to high temperatures, chemicals, and inhibitors. In addition, genetic engineering techniques to improve the catalytic properties of the β-galactosidases were reported. This review gathers information to allow the development of biocatalysts based on the β-galactosidase enzyme from K. lactis, aiming to improve existing bioprocesses or develop new ones.
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Affiliation(s)
- Tiago Lima de Albuquerque
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Marylane de Sousa
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Natan Câmara Gomes E Silva
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Carlos Alberto Chaves Girão Neto
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Luciana Rocha Barros Gonçalves
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Roberto Fernandez-Lafuente
- Instituto de Catálisis y Petroleoquímica - CSIC, Campus of excellence UAM-CSIC, Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Maria Valderez Ponte Rocha
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil.
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Wang J, Cao X, Chen W, Xu J, Wu B. Identification and Characterization of a Thermostable GH36 α-Galactosidase from Anoxybacillusvitaminiphilus WMF1 and Its Application in Synthesizing Isofloridoside by Reverse Hydrolysis. Int J Mol Sci 2021; 22:10778. [PMID: 34639118 PMCID: PMC8509150 DOI: 10.3390/ijms221910778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
An α-galactosidase-producing strain named Anoxybacillus vitaminiphilus WMF1, which catalyzed the reverse hydrolysis of d-galactose and glycerol to produce isofloridoside, was isolated from soil. The α-galactosidase (galV) gene was cloned and expressed in Escherichia coli. The galV was classified into the GH36 family with a molecular mass of 80 kDa. The optimum pH and temperature of galV was pH 7.5 and 60 °C, respectively, and it was highly stable at alkaline pH (6.0-9.0) and temperature below 65 °C. The specificity for p-nitrophenyl α-d-galactopyranoside was 70 U/mg, much higher than that for raffinose and stachyose. Among the metals and reagents tested, galV showed tolerance in the presence of various organic solvents. The kinetic parameters of the enzyme towards p-nitrophenyl α-d-galactopyranoside were obtained as Km (0.12 mM), Vmax (1.10 × 10-3 mM s-1), and Kcat/Km (763.92 mM-1 s-1). During the reaction of reverse hydrolysis, the enzyme exhibited high specificity towards the glycosyl donor galactose and acceptors glycerol, ethanol and ethylene glycol. Finally, the isofloridoside was synthesized using galactose as the donor and glycerol as the acceptor with a 26.6% conversion rate of galactose. This study indicated that galV might provide a potential enzyme source in producing isofloridoside because of its high thermal stability and activity.
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Affiliation(s)
- Jialing Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan Road, Nanjing 211816, China; (J.W.); (X.C.); (W.C.)
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan Road, Nanjing 211816, China
| | - Xuefei Cao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan Road, Nanjing 211816, China; (J.W.); (X.C.); (W.C.)
| | - Weihao Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan Road, Nanjing 211816, China; (J.W.); (X.C.); (W.C.)
| | - Jiaxing Xu
- College of Chemistry and Chemical Engineering, Huaiyin Normal University, 111 Jiangxi Road, Huai’an 223300, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan Road, Nanjing 211816, China; (J.W.); (X.C.); (W.C.)
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Lyu J, Gao R, Guo Z. Galactosyldiacylglycerols: From a Photosynthesis-Associated Apparatus to Structure-Defined In Vitro Assembling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8910-8928. [PMID: 33793221 DOI: 10.1021/acs.jafc.1c00204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Being ubiquitously present in plants, microalgae, and cyanobacteria and as the major constituents of thylakoid membranes, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) make up approximately 52 and 26%, respectively, of chloroplast lipids. Thylakoid membranes harbor the photosynthetic complexes and numerous essential biochemical pathways where MGDG and DGDG play a central role in facilitating photosynthesis light reaction, maintaining chloroplast morphology, and responding to abiotic stresses. Furthermore, these galactolipids are also bioactive compounds with antitumor, antimicrobial, antiviral, immunosuppressive, and anti-inflammatory activities and important nutritional value. These characteristics are strictly dependent upon their fatty acyl chain length, olefinic nature, and stereoconfiguration. However, their application potentials are practically untapped, largely as a result of the fact that their availability in large quantity and high purity (structured galactolipids) is challenging. In addition to laborious extraction from natural sources, in vitro assembling of these molecules could be a promising alternative. Thus, this review updates the latest advances in elucidating biosynthesis paths of MGDG and DGDG and related enzyme systems, which present invaluable inspiration to design approaches for a retrosynthesis of galactolipids. More critically, this work summarizes recent developments in the biological and enzymatic syntheses of galactolipids, especially the strategic scenarios for the construction of in vitro enzymatic and/or chemoenzymatic synthesis routes. Protein engineering of enzymes involved in the synthesis of MGDG and DGDG to improve their properties is highlighted, and the applications of galactolipids in foods and medicine are also discussed.
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Affiliation(s)
- Jiabao Lyu
- Department of Engineering, Faculty of Technical Science, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus, Denmark
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life Science, Jilin University, Changchun, Jilin 130012, People's Republic of China
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life Science, Jilin University, Changchun, Jilin 130012, People's Republic of China
| | - Zheng Guo
- Department of Engineering, Faculty of Technical Science, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus, Denmark
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Glycosyl hydrolase catalyzed glycosylation in unconventional media. Appl Microbiol Biotechnol 2020; 104:9523-9534. [PMID: 33034701 DOI: 10.1007/s00253-020-10924-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023]
Abstract
The reversible hydrolytic property of glycosyl hydrolases (GHs) as well as their acceptance of aglycones other than water has provided the abilities of GHs in synthesizing glycosides. Together with desirable physiochemical properties of glycosides and their high commercial values, research interests have been aroused to investigate the synthetic other than the hydrolytic properties of GHs. On the other hand, just like the esterification processes catalyzed by lipases, GH synthetic effectiveness is strongly obstructed by water both thermodynamically and kinetically. Medium engineering by involving organic solvents can be a viable approach to alleviate the obstacles caused by water. However, as native hydrolyases function in water-enriched environments, most GHs display poor catalytic performance in the presence of organic solvents. Some GHs from thermophiles are more tolerant to organic solvents due to their robust folded structures with strong residue interactions. Other than native sources, immobilization, protein engineering, employment of surfactant, and lyophilization have been proved to enhance the GH stability from the native state, which opens up the possibilities for GHs to be employed in unconventional media as synthases. KEY POINTS: • Unconventional media enhance the synthetic ability but destabilize GHs. • Viable approaches are discussed to improve GH stability from the native state. • GHs robust in unconventional media can be valuable industrial synthases.
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Production of isofloridoside from galactose and glycerol using α-galactosidase from Alicyclobacillus hesperidum. Enzyme Microb Technol 2020; 134:109480. [DOI: 10.1016/j.enzmictec.2019.109480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 11/23/2022]
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Vera C, Guerrero C, Aburto C, Cordova A, Illanes A. Conventional and non-conventional applications of β-galactosidases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140271. [DOI: 10.1016/j.bbapap.2019.140271] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/15/2019] [Accepted: 08/30/2019] [Indexed: 02/04/2023]
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Stanfill B, Reehl S, Bramer L, Nakayasu ES, Rich SS, Metz TO, Rewers M, Webb-Robertson BJ. Extending Classification Algorithms to Case-Control Studies. Biomed Eng Comput Biol 2019; 10:1179597219858954. [PMID: 31320812 PMCID: PMC6630079 DOI: 10.1177/1179597219858954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/26/2019] [Indexed: 12/16/2022] Open
Abstract
Classification is a common technique applied to 'omics data to build predictive models and identify potential markers of biomedical outcomes. Despite the prevalence of case-control studies, the number of classification methods available to analyze data generated by such studies is extremely limited. Conditional logistic regression is the most commonly used technique, but the associated modeling assumptions limit its ability to identify a large class of sufficiently complicated 'omic signatures. We propose a data preprocessing step which generalizes and makes any linear or nonlinear classification algorithm, even those typically not appropriate for matched design data, available to be used to model case-control data and identify relevant biomarkers in these study designs. We demonstrate on simulated case-control data that both the classification and variable selection accuracy of each method is improved after applying this processing step and that the proposed methods are comparable to or outperform existing variable selection methods. Finally, we demonstrate the impact of conditional classification algorithms on a large cohort study of children with islet autoimmunity.
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Affiliation(s)
- Bryan Stanfill
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah Reehl
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lisa Bramer
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Bobbie-Jo Webb-Robertson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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12
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Alhudhud M, Sadiq S, Ngo HN, Hidalgo-Cantabrana C, Ruas-Madiedo P, van Sinderen D, Humphreys PN, Laws AP. Extraction of the same novel homoglycan mixture from two different strains of Bifidobacterium animalis and three strains of Bifidobacterium breve. Benef Microbes 2018; 9:663-674. [PMID: 29695179 DOI: 10.3920/bm2017.0145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Three strains of Bifidobacterium breve (JCM 7017, JCM 7019 and JCM 2258) and two strains of Bifidobacterium animalis subsp. lactis (AD011 and A1dOxR) were grown in broth cultures or on plates, and a standard exopolysaccharide extraction method was used in an attempt to recover exocellular polysaccharides. When the extracted materials were analysed by NMR it was clear that mixtures of polysaccharides were being isolated including exopolysaccharides (EPS) cell wall polysaccharides and intracellular polysaccharides. Treatment of the cell biomass from the B. breve strains, or the B. animalis subsp. lactis AD011 strain, with aqueous sodium hydroxide provided a very similar mixture of polysaccharides but without the EPS. The different polysaccharides were partially fractionated by selective precipitation from an aqueous solution upon the addition of increasing percentages of ethanol. The polysaccharides extracted from B. breve JCM 7017 grown in HBM media supplemented with glucose (or isotopically labelled D-glucose-1-13C) were characterised using 1D and 2D-NMR spectroscopy. Addition of one volume of ethanol generated a medium molecular weight glycogen (Mw=1×105 Da, yield 200 mg/l). The addition of two volumes of ethanol precipitated an intimate mixture of a low molecular weight β-(1→6)-glucan and a low molecular weight β-(1→6)-galactofuranan which could not be separated (combined yield 46 mg/l). When labelled D-glucose-1-13C was used as a carbon supplement, the label was incorporated into >95% of the anomeric carbons of each polysaccharide confirming they were being synthesised in situ. Similar 1H NMR profiles were obtained for polysaccharides recovered from the cells of B. animalis subsp. lactis AD011and A1dOxR (in combination with an EPS), B. breve JCM 7017, B. breve JCM 7019, B. breve JCM 2258 and from an EPS (-ve) mutant of B. breve 7017 (a non-EPS producer).
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Affiliation(s)
- M Alhudhud
- 1 Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom
| | - S Sadiq
- 1 Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom
| | - H N Ngo
- 1 Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom
| | - C Hidalgo-Cantabrana
- 2 Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - P Ruas-Madiedo
- 2 Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - D van Sinderen
- 3 School of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - P N Humphreys
- 4 Department of Biological Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom
| | - A P Laws
- 1 Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom
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Xiong Y, Yang R, Sun X, Yang H, Chen H. Effect of the epiphytic bacterium Bacillus sp. WPySW2 on the metabolism of Pyropia haitanensis. JOURNAL OF APPLIED PHYCOLOGY 2017; 30:1225-1237. [PMID: 29755207 PMCID: PMC5928181 DOI: 10.1007/s10811-017-1279-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 06/08/2023]
Abstract
A variety of different symbiotic microbial communities are harbored on the surface of seaweeds, the interactions of which depend upon nutritional exchanges between the microbes and the hosts. Metabolomic profiling is able to provide a comprehensive and unbiased snapshot of the metabolites associated with seaweed-microbe interactions. In this study, the relationships between phycosphere bacteria and the red alga Pyropia haitanensis were investigated on a metabolomic basis using gas chromatography-mass spectrometry, and the pathways of the interactions between the seaweed and its associated phycospheric microbes were revealed. Bacillus sp. WPySW2, one bacterial species isolated from the phycosphere of Pyropia species, had a significant influence on the metabolomic profile of the algae. Some of the intracellular metabolites such as phenylalanine, leucine, isoleucine, valine, proline, tyrosine, threonine, octadecanoic acid, hexadecanoic acid, and citric acid were downregulated in the thalli of P. haitanensis when it was co-cultured with Bacillus sp. WPySW2, while several special metabolites including melibiose, serine, glycerol-3-phosphate, galactosylglycerol, and alanine were upregulated. The results demonstrated that P. haitanensis grew better when it was co-cultured with Bacillus sp. WPySW2 at 20 °C. In conclusion, several main intracellular metabolites were downregulated and upregulated, which might have facilitated bacterial colonization.
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Affiliation(s)
- Yuqin Xiong
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, No. 818 Fenghua Road, Post Box 71, Ningbo, Zhejiang 315211 China
| | - Rui Yang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, No. 818 Fenghua Road, Post Box 71, Ningbo, Zhejiang 315211 China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, Zhejiang 315211 China
| | - Xiaoxiao Sun
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, No. 818 Fenghua Road, Post Box 71, Ningbo, Zhejiang 315211 China
| | - Huatian Yang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, No. 818 Fenghua Road, Post Box 71, Ningbo, Zhejiang 315211 China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, Zhejiang 315211 China
| | - Haimin Chen
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, No. 818 Fenghua Road, Post Box 71, Ningbo, Zhejiang 315211 China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, Zhejiang 315211 China
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14
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Wojciechowska A, Klewicki R, Sójka M, Grzelak-Błaszczyk K. Application of Transgalactosylation Activity of β-Galactosidase from Kluyveromyces lactis for the Synthesis of Ascorbic Acid Galactoside. Appl Biochem Biotechnol 2017; 184:386-400. [PMID: 28707051 PMCID: PMC5756576 DOI: 10.1007/s12010-017-2551-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/25/2017] [Indexed: 11/29/2022]
Abstract
In view of a commonly known beneficial role and low stability of ascorbic acid, many efforts are constantly undertaken to produce its improved derivatives. This paper presents results on the synthesis of ascorbic acid galactoside using transgalactosylation properties of β-galactosidase from Kluyveromyces lactis and lactose as a donor of galactosyl moiety. The purpose of this study was to determine the influence of selected factors (concentration and molar ratio of substrates, amount of the enzyme preparation, pH of the solution, presence of different ions) on the course of transgalactosylation reaction. Research has shown that approx. 2.5% dry matter (d.m.; 12.7 g/L) of ascorbic acid galactoside is formed under favourable conditions (50% (w/v) substrates, sodium ascorbate and lactose at the molar ratio of 1.9:1, enzyme dose of 28,600 U/100 g lactose, pH = 7.0). The addition of Mg2+ or K+ ions to the reaction medium caused an increase in the final product content (even up to approx. 3.4% d.m., 17.2 g/L), while Na+ or Mn2+ had an adverse impact on the yield. The gathered data may be valuable for cosmetic or food industry.
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Affiliation(s)
- Aleksandra Wojciechowska
- Institute of Food Technology and Analysis, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Łódź, Poland.
| | - Robert Klewicki
- Institute of Food Technology and Analysis, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Łódź, Poland
| | - Michał Sójka
- Institute of Food Technology and Analysis, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Łódź, Poland
| | - Katarzyna Grzelak-Błaszczyk
- Institute of Food Technology and Analysis, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Łódź, Poland
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15
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Wojciechowska A, Klewicki R, Sójka M, Klewicka E. Synthesis of the Galactosyl Derivative of Gluconic Acid With the Transglycosylation Activity of β-Galactosidase. Food Technol Biotechnol 2017; 55:258-265. [PMID: 28867957 PMCID: PMC5569345 DOI: 10.17113/ftb.55.02.17.4732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 11/29/2016] [Indexed: 11/12/2022] Open
Abstract
Bionic acids are bioactive compounds demonstrating numerous interesting properties. They are widely produced by chemical or enzymatic oxidation of disaccharides. This paper focuses on the galactosyl derivative of gluconic acid as a result of a new method of bionic acid synthesis which utilises the transglycosylation properties of β-galactosidase and introduces lactose as a substrate. Products obtained in such a process are characterised by different structures (and, potentially, properties) than those resulting from traditional oxidation of disaccharides. The aim of this study is to determine the effect of selected parameters (concentration and ratio of substrates, dose of the enzyme, time, pH, presence of salts) on the course of the reaction carried out with the enzymatic preparation Lactozym, containing β-galactosidase from Kluyveromyces lactis. Research has shown that increased dry matter content in the baseline solution (up to 50%, by mass per volume) and an addition of NaCl contribute to higher yield. On the other hand, reduced content of the derivative is a result of increased pH from 7.0 to 9.0 and an addition of magnesium and manganese salts. Moreover, exceeding the β-galactosidase dose over approx. 35 000 U per 100 g of lactose also leads to reduced yield of the process. The most favourable molar ratio of sodium gluconate to lactose is 2.225:0.675. Depending on the conditions of the synthesis, the product concentration ranged between 17.3 and 118.3 g/L of the reaction mixture, which corresponded to the mass fraction of 6.64-23.7% of dry matter. The data obtained as a result of the present study may be useful for designing an industrial process.
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Affiliation(s)
- Aleksandra Wojciechowska
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences,
Lodz University of Technology, Stefanowskiego 4/10, PL-90-924 Łódź, Poland
| | - Robert Klewicki
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences,
Lodz University of Technology, Stefanowskiego 4/10, PL-90-924 Łódź, Poland
| | - Michał Sójka
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences,
Lodz University of Technology, Stefanowskiego 4/10, PL-90-924 Łódź, Poland
| | - Elżbieta Klewicka
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, PL-90-924 Łódź, Poland
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16
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Martinez-Garcia M, van der Maarel MJEC. Floridoside production by the red microalga Galdieria sulphuraria under different conditions of growth and osmotic stress. AMB Express 2016; 6:71. [PMID: 27620735 PMCID: PMC5020028 DOI: 10.1186/s13568-016-0244-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 12/04/2022] Open
Abstract
Floridoside is a compatible solute synthesized by red algae that has attracted considerable attention due to its promising antifouling and therapeutic properties. However, research on industrial applications of floridoside is hampered by limited compound availability and the development of a production process yielding high amounts of this glycoside has not been explored yet. In the present work, floridoside accumulation by the red microalgae Galdieria sulphuraria under different conditions was investigated in order to optimize the production of this glycoside in this microalgae. G. sulphuraria shows consider advantages over other red algae as potential industrial producer of floridoside due to its unicellular nature, its ability to grow heterotrophically in complete darkness and its acidophilic lifestyle. The main compatible solute accumulated by G. sulphuraria under salt stress was purified, identified as floridoside by 1H-NMR and used as standard for quantification. Our results showed that applying the osmotic stress after the cells had grown first in medium with no salt resulted in higher floridoside yields compared to those obtained in cells growing under osmotic stress from the beginning. Among several parameters tested, the use of glycerol as carbon source for cell growth showed the most significant impact on floridoside accumulation, which reached a maximum of 56.8 mg/g dry biomass.
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17
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Qi D, Wei W, Diao M, Lv F, Lu Z, Bie X, Zhao H. Enzymatic synthesis and antitumor evaluation of mono- and diesters of 3-O-β-D-galactopyranosyl-sn-glycerol. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1247821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Danping Qi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Wei Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Mingming Diao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Fengxia Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
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18
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Wei W, Qi D, Diao M, Zhaoxin L, Lv F, Zhao H. β-galactosidase-catalyzed synthesis of 3-O-β-D-galactopyranosyl-sn-glycerol: Optimization by response surface methodology. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1247815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Wei Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Danping Qi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Mingming Diao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Lu Zhaoxin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Fengxia Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
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Xu L, Liu X, Yin Z, Liu Q, Lu L, Xiao M. Site-directed mutagenesis of α-l-rhamnosidase from Alternaria sp. L1 to enhance synthesis yield of reverse hydrolysis based on rational design. Appl Microbiol Biotechnol 2016; 100:10385-10394. [DOI: 10.1007/s00253-016-7676-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/06/2016] [Accepted: 06/11/2016] [Indexed: 12/19/2022]
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20
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Jeong JW, Seo DH, Jung JH, Park JH, Baek NI, Kim MJ, Park CS. Biosynthesis of Glucosyl Glycerol, a Compatible Solute, Using Intermolecular Transglycosylation Activity of Amylosucrase from Methylobacillus flagellatus KT. Appl Biochem Biotechnol 2014; 173:904-17. [DOI: 10.1007/s12010-014-0889-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
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