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Salam LB. Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil. Folia Microbiol (Praha) 2024; 69:59-80. [PMID: 37450270 DOI: 10.1007/s12223-023-01077-5] [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: 05/13/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Elizade University, Ilara-Mokin, Ondo State, Nigeria.
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Aregbesola OA, Kumar A, Mokoena MP, Olaniran AO. Role of tetrachloro-1,4-benzoquinone reductase in phenylalanine hydroxylation system and pentachlorophenol degradation in Bacillus cereus AOA-CPS1. Int J Biol Macromol 2020; 161:875-890. [PMID: 32535205 DOI: 10.1016/j.ijbiomac.2020.06.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022]
Abstract
This study reports a ≅12.5 kDa protein tetrachloro-1,4-benzoquinone reductase (CpsD) from Bacillus cereus strain AOA-CPS1 (BcAOA). CpsD is purified to homogeneity with a total yield of 35% and specific activity of 160 U·mg-1 of protein. CpsD showed optimal activity at pH 7.5 and 40 °C. The enzyme was found to be functionally stable between pH 7.0-7.5 and temperature between 30 °C and 35 °C. CpsD activity was enhanced by Fe2+ and inhibited by sodium azide and SDS. CpsD followed Michaelis-Menten kinetic exhibiting an apparent vmax, Km, kcat and kcat/Km values of 0.071 μmol·s-1, 94 μmol, 0.029 s-1 and 3.13 × 10-4 s-1·μmol-1, respectively, for substrate tetrachloro-1,4-benzoquinone. The bioinformatics analysis indicated that CpsD belongs to the PCD/DCoH superfamily, with specific conserved protein domains of pterin-4α-carbinolamine dehydratase (PCD). This study proposed that CpsD catalysed the reduction of tetrachloro-1,4-benzoquinone to tetrachloro-p-hydroquinone and released the products found in phenylalanine hydroxylation system (PheOHS) via a Ping-Pong or atypical ternary mechanism; and regulate expression of phenylalanine 4-monooxygenase by blocking reverse flux in BcAOA PheOHS using a probable Yin-Yang mechanism. The study also concluded that CpsD may play a catalytic and regulatory role in BcAOA PheOHS and pentachlorophenol degradation pathway.
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Affiliation(s)
- Oladipupo A Aregbesola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
| | - Ajit Kumar
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
| | - Mduduzi P Mokoena
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa.
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Cloning, overexpression, purification, characterization and structural modelling of a metabolically active Fe 2+ dependent 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (CpsA) from Bacillus cereus strain AOA-CPS_1. Int J Biol Macromol 2020; 161:247-257. [PMID: 32512093 DOI: 10.1016/j.ijbiomac.2020.05.268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 05/24/2020] [Accepted: 05/30/2020] [Indexed: 11/23/2022]
Abstract
2,6-Dichloro-p-hydroquinone (DiCHQ) aromatic-ring cleavage by DiCHQ 1,2-dioxygenase (CpsA) is very crucial for complete transformation of pentachlorophenol (PCP) to 2-chloromaleylacetate in Bacillus cereus AOA-CPS_1 (BcAOA). The 978 bp gene (cpsA) was detected and amplified in the genome of BcAOA; cloned, overexpressed and purified to homogeneity. CpsA showed a single ≅36.9 kDa protein band on SDS-PAGE and exhibited optimum activity at 30 °C and pH 9.0. CpsA was stable between 20 °C and 40 °C, and also retained about 90% of its activity at 60 °C for 120 min. The enzyme retained about 90% activity between pH 9.0 and 11.5 and 60% activity at pH 13.0. CpsA was found to be Fe2+ dependent as about 90% increased activity was observed in the presence of FeSO4. CpsA showed apparent vmax, Km, kcat and kcat/Km of 27.77 ± 0.9 μMs-1, 0.990 ± 0.03 mM, 4.20 ± 0.04 s-1 and 4.24 ± 0.03 s-1 mM-1, respectively at pH 9.0. Analysis of the reaction products via GC-MS confirmed 2-chloromaleylacetate as the ring-cleavage product. CpsA 3D structure revealed a conserved 2-His-1-carboxylate facial triad motif (His 9, His 244 and Thr 11), with Fe3+ at the centre. Findings from this study provide new insights into the involvement of this enzyme in PCP degradation and suggests alternate possible mechanism of ring-cleavage by dioxygenases.
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Biotransformation of pentachlorophenol by an indigenous Bacillus cereus AOA-CPS1 isolated from wastewater effluent in Durban, South Africa. Biodegradation 2020; 31:369-383. [DOI: 10.1007/s10532-020-09915-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 09/23/2020] [Indexed: 01/10/2023]
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Chen L, Krol ES, Sakharkar MK, Khan HA, Alhomida AS, Yang J. Residues His172 and Lys238 are Essential for the Catalytic Activity of the Maleylacetate Reductase from Sphingobium chlorophenolicum Strain L-1. Sci Rep 2017; 7:18097. [PMID: 29273747 PMCID: PMC5741723 DOI: 10.1038/s41598-017-18475-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/12/2017] [Indexed: 02/08/2023] Open
Abstract
Maleylacetate reductase (PcpE), the last enzyme in the pentachlorophenol biodegradation pathway in Sphingobium chlorophenolicum L-1, catalyzes two consecutive reductive reactions, reductive dehalogenation of 2-chloromaleylacetate (2-CMA) to maleylacetate (MA) and subsequent reduction of MA to 3-oxoadipate (3-OXO). In each reaction, one molecule of NADH is consumed. To better understand its catalytic function, we undertook a structural model-based site-directed mutagenesis and steady-state kinetics study of PcpE. Our results showed that the putative catalytic site of PcpE is located in a positively charged solvent channel at the interface of the two domains and the binding of 2-CMA/MA involves seven basic amino acids, His172, His236, His237, His241 and His251, Lys140 and Lys238. Mutagenesis studies showed that His172 and Lys238 are essential for the catalytic activity of PcpE. However, the mutation of His236 to an alanine can increase the catalytic efficiency (k cat /K m ) of PcpE by more than 2-fold, implying that PcpE is still in an early stage of molecular evolution. Similar to tetrachlorobenzoquinone reductase (PcpD), PcpE is also inhibited by pentachlorophenol in a concentration-dependent manner. Furthermore, our studies showed that PcpE exhibits an extremely low but detectable level of alcohol dehalogenase activity toward ethanol and supports the notion that it is evolved from an iron-containing alcohol dehydrogenase.
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Affiliation(s)
- Lifeng Chen
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
- Agrisoma Biosciences Inc., 4410-110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Ed S Krol
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Meena K Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Haseeb A Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah S Alhomida
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jian Yang
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
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Yadid I, Rudolph J, Hlouchova K, Copley SD. Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol. Proc Natl Acad Sci U S A 2013; 110:E2182-90. [PMID: 23676275 PMCID: PMC3683723 DOI: 10.1073/pnas.1214052110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbes in contaminated environments often evolve new metabolic pathways for detoxification or degradation of pollutants. In some cases, intermediates in newly evolved pathways are more toxic than the initial compound. The initial step in the degradation of pentachlorophenol by Sphingobium chlorophenolicum generates a particularly reactive intermediate; tetrachlorobenzoquinone (TCBQ) is a potent alkylating agent that reacts with cellular thiols at a diffusion-controlled rate. TCBQ reductase (PcpD), an FMN- and NADH-dependent reductase, catalyzes the reduction of TCBQ to tetrachlorohydroquinone. In the presence of PcpD, TCBQ formed by pentachlorophenol hydroxylase (PcpB) is sequestered until it is reduced to the less toxic tetrachlorohydroquinone, protecting the bacterium from the toxic effects of TCBQ and maintaining flux through the pathway. The toxicity of TCBQ may have exerted selective pressure to maintain slow turnover of PcpB (0.02 s(-1)) so that a transient interaction between PcpB and PcpD can occur before TCBQ is released from the active site of PcpB.
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Affiliation(s)
| | | | | | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
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Verma T, Singh N. Isolation and process parameter optimization ofBrevibacterium caseifor simultaneous bioremediation of hexavalent chromium and pentachlorophenol. J Basic Microbiol 2012; 53:277-90. [DOI: 10.1002/jobm.201100542] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Tuhina Verma
- Department of Microbiology; Dr. R.M.L. Avadh University; Faizabad; India
| | - Neha Singh
- Department of Microbiology; Dr. R.M.L. Avadh University; Faizabad; India
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Treviño-Quintanilla LG, Freyre-González JA, Guillén-Garcés RA, Olvera C. Molecular characterization of chloranilic acid degradation in Pseudomonas putida TQ07. J Microbiol 2011; 49:974-80. [PMID: 22203561 DOI: 10.1007/s12275-011-1507-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 11/24/2011] [Indexed: 11/25/2022]
Abstract
Pentachlorophenol is the most toxic and recalcitrant chlorophenol because both aspects are directly proportional to the halogenation degree. Biological and abiotic pentachlorophenol degradation generates p-chloranil, which in neutral to lightly alkaline environmental conditions is hydrolyzed to chloranilic acid that present a violet-reddish coloration in aqueous solution. Several genes of the degradation pathway, cadR-cadCDX, as well as other uncharacterized genes (ORF5 and 6), were isolated from a chloranilic acid degrading bacterium, Pseudomonas putida strain TQ07. The disruption by random mutagenesis of the cadR and cadC genes in TQ07 resulted in a growth deficiency in the presence of chloranilic acid, indicating that these genes are essential for TQ07 growth with chloranilic acid as the sole carbon source. Complementation assays demonstrated that a transposon insertion in mutant CAD82 (cadC) had a polar effect on other genes contained in cosmid pLG3562. These results suggest that at least one of these genes, cadD and cadX, also takes part in chloranilic acid degradation. Based on molecular modeling and function prediction, we strongly suggest that CadC is a pyrone dicarboxylic acid hydrolase and CadD is an aldolase enzyme like dihydrodipicolinate synthase. The results of this study allowed us to propose a novel pathway that offers hypotheses on chloranilic acid degradation (an abiotic by-product of pentachlorophenol) by means of a very clear phenotype that is narrowly related to the capability of Pseudomonas putida strain TQ07 to degrade this benzoquinone.
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Affiliation(s)
- Luis G Treviño-Quintanilla
- Departamento de Tecnología Ambiental, Universidad Politécnica del Estado de Morelos, Blvd. Cuauhnáhuac 566, Col. Lomas del Texcal, 62550 Jiutepec, Morelos, México.
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Sun W, Sammynaiken R, Chen L, Maley J, Schatte G, Zhou Y, Yang J. Sphingobium chlorophenolicum dichlorohydroquinone dioxygenase (PcpA) is alkaline resistant and thermally stable. Int J Biol Sci 2011; 7:1171-9. [PMID: 22043174 PMCID: PMC3204407 DOI: 10.7150/ijbs.7.1171] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/17/2011] [Indexed: 11/27/2022] Open
Abstract
Dichlorohydroquinone dioxygenase (PcpA) is the ring-cleavage enzyme in the PCP biodegradation pathway in Sphingobium chlorophenolicum strain ATCC 39723. PcpA dehalogenates and oxidizes 2,6-dichlorohydroquinone to form 2-chloromaleylacetate, which is subsequently converted to succinyl coenzyme A and acetyl coenzyme A via 3-oxoadipate. Previous studies have shown that PcpA is highly substrate-specific and only uses 2,6-dichlorohydroquinone as its substrate. In the current study, we overexpressed and purified recombinant PcpA and showed that PcpA was highly alkaline resistant and thermally stable. PcpA exhibited two activity peaks at pH 7.0 and 10.0, respectively. The apparent kcat and Km were measured as 0.19 ± 0.01 s-1 and 0.24 ± 0.08 mM, respectively at pH 7.0, and 0.17 ± 0.01 s-1 and 0.77 ± 0.29 mM, respectively at pH 10.0. Electron paramagnetic resonance studies showed rapid oxidation of Fe(II) to Fe(III) in PcpA and the formation of a stable radical intermediate during the enzyme catalysis. The stable radical was predicted to be an epoxide type dichloro radical with the unpaired electron density localized on C3.
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Affiliation(s)
- Wanpeng Sun
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Edwards R, Dixon DP, Cummins I, Brazier-Hicks M, Skipsey M. New Perspectives on the Metabolism and Detoxification of Synthetic Compounds in Plants. PLANT ECOPHYSIOLOGY 2011. [DOI: 10.1007/978-90-481-9852-8_7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Cloning, overexpression, purification, and characterization of the maleylacetate reductase from Sphingobium chlorophenolicum strain ATCC 53874. Curr Microbiol 2009; 58:599-603. [PMID: 19242755 DOI: 10.1007/s00284-009-9377-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 01/26/2009] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
Abstract
The final enzyme in the pentachlorophenol (PCP) biodegradation pathway in Sphingobium chlorophenolicum is maleylacetate reductase (PcpE), which catalyzes the reductive dehalogenation of 2-chloromaleylacetate to maleylacetate and the subsequent reduction of malyelacetate to 3-oxoadipate. In this study, the pcpE gene was cloned from S. chlorophenolicum strain ATCC 53874 and overexpressed in Escherichia coli BL21-AI cells. The recombinant PcpE, purified to higher than 95% purity using affinity chromatography, exhibited optimal activity at pH 7.0. The kinetic parameters k(cat) and K(m) were 1.2 +/- 0.3 s(-1) and 0.09 +/- 0.04 mM, respectively, against maleylacetate under the optimal pH. In addition, the purified PcpE was able to restore PCP-degrading capability to S. chlorophenolicum strain ATCC 39723, implicating that there was no functional PcpE in the ATCC 39723 strain.
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Sharma A, Thakur IS, Dureja P. Enrichment, isolation and characterization of pentachlorophenol degrading bacterium Acinetobacter sp. ISTPCP-3 from effluent discharge site. Biodegradation 2009; 20:643-50. [DOI: 10.1007/s10532-009-9251-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 01/28/2009] [Indexed: 11/30/2022]
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Su Y, Chen L, Bandy B, Yang J. The Catalytic Product of Pentachlorophenol 4-Monooxygenase is Tetra-chlorohydroquinone rather than Tetrachlorobenzoquinone. Open Microbiol J 2008; 2:100-6. [PMID: 19088919 PMCID: PMC2593034 DOI: 10.2174/1874285800802010100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 07/23/2006] [Accepted: 07/23/2008] [Indexed: 11/22/2022] Open
Abstract
Pentachlorophenol 4-monooxygenase (PcpB) catalyzes the hydroxylation of pentachlorophenol in the pentachlorophenol biodegradation pathway in Sphingobium chlorophenolicum. Previous studies from two different research groups proposed oppositely that the catalytic product of PcpB was tetrachlorohydroquinone (TCHQ) and tetrachlorobenzoquinone (TCBQ). We re-examined the identity of the catalytic product of PcpB, because TCHQ and TCBQ are present in a redox-equilibrium in aqueous solutions and the chemical reagents NADPH, ethyl acetate and glutathione used for the product detection in the previous studies may shift the redox-equilibrium. In this study, we investigated the effects of NADPH, ethyl acetate and glutathione on the redox-equilibrium and product distribution. Under newly designed experimental conditions, we confirmed unambiguously that the catalytic product of PcpB is TCHQ instead of TCBQ. We also propose that TCBQ may be produced non-specifically by peroxidases within the bacterial cells and that TCBQ reductase (PcpD) might act as a self-protective rather than a PCP-degradation enzyme.
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Affiliation(s)
- Yunyou Su
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9, Canada
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