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Yang H, Huang Y, Li K, Zhu P, Wang Y, Li X, Meng Q, Niu Q, Wang S, Li Q. Lignocellulosic depolymerization induced by ionic liquids regulating composting habitats based on metagenomics analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:76298-76309. [PMID: 35668255 DOI: 10.1007/s11356-022-21148-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The application of ionic liquids with sawdust and fresh dairy manure was studied in composting. The degradation of organic matter (OM), dissolved organic matter (DOM), and lignocellulose was analyzed. The DOM decreased by 14.25 mg/g and 11.11 mg/g in experimental group (ILs) and control group (CK), respectively. OM decreased by 7.32% (CK) and 8.91% (ILs), respectively. The degradation rates of hemicellulose, lignin, and cellulose in ILs (56.62%, 42.01%, and 23.97%) were higher than in CK (38.39%, 39.82%, and 16.04%). Microbial community and carbohydrate-active enzymes (CAZymes) were analyzed based on metagenomics. Metagenomic analysis results showed that ionic liquids enriched Actinobacteria and Proteobacteria in composting. Compared with CK, the total abundance values of GH11, GH6, AA6, and AA3_2 in ILs increased by 13.98%, 10.12%, 11.21%, and 13.68%, respectively. Ionic liquids can improve the lignocellulosic degradation by regulating the environmental physicochemical parameters (temperature, pH, C/N) to promote the growth of Actinobacteria and Proteobacteria and carbohydrate-active enzymes (CAZymes) abundance. Therefore, ionic liquids are a promising additive in lignocellulosic waste composting.
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Affiliation(s)
- Hongxiang Yang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yite Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Kecheng Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Pengfei Zhu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yiwu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Xiaolan Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qingran Meng
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qiuqi Niu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Susu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
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Wang B, Lu J, Zheng J, Yu Z. iTRAQ-facilitated proteomic analysis of Bacillus cereus via degradation of malachite green. J Microbiol 2021; 59:142-150. [PMID: 33527315 DOI: 10.1007/s12275-021-0441-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/13/2023]
Abstract
The wide use of malachite green (MG) as a dye has caused substantial concern owing to its toxicity. Bacillus cereus can against the toxic effect of MG and efficiently decolourise it. However, detailed information regarding its underlying adaptation and degradation mechanisms based on proteomic data is scarce. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ)-facilitated quantitative method was applied to analyse the molecular mechanisms by which B. cereus degrades MG. Based on this analysis, 209 upregulated proteins and 198 downregulated proteins were identified with a false discovery rate of 1% or less during MG biodegradation. Gene ontology and KEGG analysis determined that the differentially expressed proteins were enriched in metabolic processes, catalytic activity, antioxidant activity, and responses to stimuli. Furthermore, real-time qPCR was utilised to further confirm the regulated proteins involved in benzoate degradation. The proteins BCE_4076 (Acetyl-CoA acetyltransferase), BCE_5143 (Acetyl-CoA acetyltransferase), BCE_5144 (3-hydroxyacyl-CoA dehydrogenase), BCE_4651 (Enoyl-CoA hydratase), and BCE_5474 (3-hydroxyacyl-CoA dehydrogenase) involved in the benzoate degradation pathway may play an important role in the biodegradation of MG by B. cereus. The results of this study not only provide a comprehensive view of proteomic changes in B. cereus upon MG loading but also shed light on the mechanism underlying MG biodegradation by B. cereus.
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Affiliation(s)
- Bobo Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jing Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Junfang Zheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, P. R. China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
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3
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Shiny Matilda C, Madhusudan I, Gaurav Isola R, Shanthi C. Potential of proteomics to probe microbes. J Basic Microbiol 2020; 60:471-483. [PMID: 32212201 DOI: 10.1002/jobm.201900628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 01/05/2023]
Abstract
An organism exposed to a plethora of environmental perturbations undergoes proteomic changes which enable the characterization of total proteins in it. Much of the proteomic information is obtained from genomic data. Additional information on the proteome such as posttranslational modifications, protein-protein interactions, protein localization, metabolic pathways, and so on are deduced using proteomic tools which genomics and transcriptomics fail to offer. The proteomic analysis allows identification of precise changes in proteins, which in turn solve the complexity of microbial population providing insights into the microbial metabolism, cellular pathways, and behavior of microorganisms in new environments. Furthermore, they provide clues for the exploitation of their special features for biotechnological applications. Numerous techniques for the analysis of microbial proteome such as electrophoretic, chromatographic, mass spectrometric-based methods as well as quantitative proteomics are available which facilitate protein separation, expression, identification, and quantification of proteins. An understanding of the potential of each of the proteomic tools has created a significant impact on diverse microbiological aspects and the same has been discussed in this review.
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Affiliation(s)
- Chellaiah Shiny Matilda
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Iyengar Madhusudan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Ravi Gaurav Isola
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Chittibabu Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
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Miao J, Wang M, Ma L, Li T, Huang Q, Liu D, Shen Q. Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:4. [PMID: 30622646 PMCID: PMC6318881 DOI: 10.1186/s13068-018-1350-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/26/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND As a ubiquitous filamentous fungal, Aspergillus spp. play a critical role in lignocellulose degradation, which was also defined as considerable cell factories for organic acids and industrially relevant enzymes producer. Nevertheless, the production of various extracellular enzymes can be influenced by different factors including nitrogen source, carbon source, cultivation temperature, and initial pH value. Thus, this study aims to reveal how amino acids affect the decomposition of lignocellulose by Aspergillus fumigatus Z5 through transcriptional and proteomics methods. RESULTS The activities of several lignocellulosic enzymes secreted by A. fumigatus Z5 adding with cysteine, methionine, and ammonium sulfate were determined with the chromatometry method. The peak of endo-glucanase (7.33 ± 0.03 U mL-1), exo-glucanase (10.50 ± 0.07 U mL-1), β-glucosidase (21.50 ± 0.22 U mL-1), and xylanase (76.43 ± 0.71 U mL-1) were all obtained in the Cys treatment. The secretomes of A. fumigatus Z5 under different treatments were also identified by LC-MS/MS, and 227, 256 and 159 different proteins were identified in the treatments of Cys, Met, and CK (Control, treatment with ammonium sulfate as the sole nitrogen source), respectively. Correlation analysis results of transcriptome and proteome data with fermentation profiles showed that most of the cellulose-degrading enzymes including cellulases, hemicellulases and glycoside hydrolases were highly upregulated when cysteine was added to the growth medium. In particular, the enzymes that convert cellulose into cellobiose appear to be upregulated. This study could increase knowledge of lignocellulose bioconversion pathways and fungal genetics. CONCLUSIONS Transcriptome and proteome analyses' results indicated that cysteine could significantly promote the secretion of lignocellulosic enzymes of an efficient lignocellulosic decomposing strain, A. fumigatus Z5. The possible reason for these results is that Z5 preferred to use amino acids such as cysteine to adapt to the external environment through upregulating carbon-related metabolism pathways.
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Affiliation(s)
- Jiaxi Miao
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095 China
| | - Mengmeng Wang
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095 China
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Lei Ma
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095 China
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tuo Li
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095 China
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qiwei Huang
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095 China
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dongyang Liu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095 China
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qirong Shen
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing, 210095 China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095 China
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
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Metabolic Profile of the Cellulolytic Industrial Actinomycete Thermobifida fusca. Metabolites 2017; 7:metabo7040057. [PMID: 29137138 PMCID: PMC5746737 DOI: 10.3390/metabo7040057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 11/17/2022] Open
Abstract
Actinomycetes have a long history of being the source of numerous valuable natural products and medicinals. To expedite product discovery and optimization of biochemical production, high-throughput technologies can now be used to screen the library of compounds present (or produced) at a given time in an organism. This not only facilitates chemical product screening, but also provides a comprehensive methodology to the study cellular metabolic networks to inform cellular engineering. Here, we present some of the first metabolomic data of the industrial cellulolytic actinomycete Thermobifida fusca generated using LC-MS/MS. The underlying objective of conducting global metabolite profiling was to gain better insight on the innate capabilities of T. fusca, with a long-term goal of facilitating T. fusca-based bioprocesses. The T. fusca metabolome was characterized for growth on two cellulose-relevant carbon sources, cellobiose and Avicel. Furthermore, the comprehensive list of measured metabolites was computationally integrated into a metabolic model of T. fusca, to study metabolic shifts in the network flux associated with carbohydrate and amino acid metabolism.
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Genetics, Molecular, and Proteomics Advances in Filamentous Fungi. Curr Microbiol 2017; 74:1226-1236. [PMID: 28733909 DOI: 10.1007/s00284-017-1308-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Filamentous fungi play a dynamic role in health and the environment. In addition, their unique and complex hyphal structures are involved in their morphogenesis, integrity, synthesis, and degradation, according to environmental and physiological conditions and resource availability. However, in biotechnology, it has a great value in the production of enzymes, pharmaceuticals, and food ingredients. The beginning of nomenclature of overall fungi started in early 1990 after which the categorization, interior and exterior mechanism, function, molecular and genetics study took pace. This mini-review has emphasized some of the important aspects of filamentous fungi, their pattern of life cycle, history, and development of different strategic methods applied to exploit this unique organism. New trends and concepts that have been applied to overcome obstacle because of their basic structure related to genomics and systems biology has been presented. Furthermore, the future aspects and challenges that need to be deciphered to get a bigger and better picture of filamentous fungi have been discussed.
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Yin YR, Meng ZH, Hu QW, Jiang Z, Xian WD, Li LH, Hu W, Zhang F, Zhou EM, Zhi XY, Li WJ. The Hybrid Strategy of Thermoactinospora rubra YIM 77501 T for Utilizing Cellulose as a Carbon Source at Different Temperatures. Front Microbiol 2017; 8:942. [PMID: 28611745 PMCID: PMC5447088 DOI: 10.3389/fmicb.2017.00942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/10/2017] [Indexed: 01/02/2023] Open
Abstract
Thermoactinospora rubra YIM 77501T is an aerobic, Gram-positive, spore-forming and cellulose degrading thermophilic actinomycete isolated from a sandy soil sample of a volcano. Its growth temperature range is 28–60°C. The genomic sequence of this strain revealed that there are 27 cellulase genes belonging to six glycoside hydrolase families. To understand the strategy that this strain uses to utilize carbon sources such as cellulose at different temperatures, comparative transcriptomics analysis of T. rubra YIM 77501T was performed by growing it with cellulose (CMC) and without cellulose (replaced with glucose) at 30, 40, and 50°C, respectively. Transcriptomic analyses showed four cellulase genes (TrBG2, TrBG3, TrBG4, and ThrCel6B) were up-regulated at 30, 40, and 50°C. The rate of gene expression of TrBG2, TrBG3, TrBG4, and ThrCel6B were 50°C > 30°C > 40°C. One cellulase gene (TrBG1) and two cellulase genes (TrBG5 and ThrCel6A) were up-regulated only at 30 and 50°C, respectively. These up-regulated cellulase genes were cloned and expressed in Escherichia coli. The enzymatic properties of up-regulated cellulases showed a variety of responses to temperature. Special up-regulated cellulases TrBG1 and ThrCel6A displayed temperature acclimation for each growth condition. These expression patterns revealed that a hybrid strategy was used by T. rubra to utilize carbon sources at different temperatures. This study provides genomic, transcriptomics, and experimental data useful for understanding how microorganisms respond to environmental changes and their application in enhancing cellulose hydrolysis for animal feed and bioenergy production.
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Affiliation(s)
- Yi-Rui Yin
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Zhao-Hui Meng
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Qing-Wen Hu
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Zhao Jiang
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Lin-Hua Li
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Wei Hu
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Feng Zhang
- Key Laboratory of Biopesticide and Chemical Biology, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Xiao-Yang Zhi
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Wen-Jun Li
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesÜrümqi, China
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9
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Sharma Ghimire P, Ouyang H, Wang Q, Luo Y, Shi B, Yang J, Lü Y, Jin C. Insight into Enzymatic Degradation of Corn, Wheat, and Soybean Cell Wall Cellulose Using Quantitative Secretome Analysis of Aspergillus fumigatus. J Proteome Res 2016; 15:4387-4402. [PMID: 27618962 DOI: 10.1021/acs.jproteome.6b00465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lignocelluloses contained in animal forage cannot be digested by pigs or poultry with 100% efficiency. On contrary, Aspergillus fumigatus, a saprophytic filamentous fungus, is known to harbor 263 glycoside hydrolase encoding genes, suggesting that A. fumigatus is an efficient lignocellulose degrader. Hence the present study uses corn, wheat, or soybean as a sole carbon source to culture A. fumigatus under animal physiological condition to understand how cellulolytic enzymes work together to achieve an efficient degradation of lignocellulose. Our results showed that A. fumigatus produced different sets of enzymes to degrade lignocelluloses derived from corn, wheat, or soybean cell wall. In addition, the cellulolytic enzymes produced by A. fumigatus were stable under acidic condition or at higher temperatures. Using isobaric tags for a relative and absolute quantification (iTRAQ) approach, a total of ∼600 extracellular proteins were identified and quantified, in which ∼50 proteins were involved in lignocellulolysis, including cellulases, hemicellulases, lignin-degrading enzymes, and some hypothetical proteins. Data are available via ProteomeXchange with identifier PXD004670. On the basis of quantitative iTRAQ results, 14 genes were selected for further confirmation by RT-PCR. Taken together, our results indicated that the expression and regulation of lignocellulolytic proteins in the secretome of A. fumigatus were dependent on both nature and complexity of cellulose, thus suggesting that a different enzyme system is required for degradation of different lignocelluloses derived from plant cells. Although A. fumigatus is a pathogenic fungus and cannot be directly used as an enzyme source, as an efficient lignocellulose degrader its strategy to synergistically degrade various lignocelluloses with different enzymes can be used to design enzyme combination for optimal digestion and absorption of corn, wheat, or soybean that are used as forage of pig and poultry.
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Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100101, China
- Himalayan Environment Research Institute (HERI) , Bouddha-6, Kathmandu, Nepal
| | - Haomiao Ouyang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Qian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Bo Shi
- Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081, China
| | - Jinghua Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Yang Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Cheng Jin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100101, China
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Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH. Proteomics: Technologies and Their Applications. J Chromatogr Sci 2016; 55:182-196. [PMID: 28087761 DOI: 10.1093/chromsci/bmw167] [Citation(s) in RCA: 449] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 07/25/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022]
Abstract
Proteomics involves the applications of technologies for the identification and quantification of overall proteins present content of a cell, tissue or an organism. It supplements the other "omics" technologies such as genomic and transcriptomics to expound the identity of proteins of an organism, and to cognize the structure and functions of a particular protein. Proteomics-based technologies are utilized in various capacities for different research settings such as detection of various diagnostic markers, candidates for vaccine production, understanding pathogenicity mechanisms, alteration of expression patterns in response to different signals and interpretation of functional protein pathways in different diseases. Proteomics is practically intricate because it includes the analysis and categorization of overall protein signatures of a genome. Mass spectrometry with LC-MS-MS and MALDI-TOF/TOF being widely used equipment is the central among current proteomics. However, utilization of proteomics facilities including the software for equipment, databases and the requirement of skilled personnel substantially increase the costs, therefore limit their wider use especially in the developing world. Furthermore, the proteome is highly dynamic because of complex regulatory systems that control the expression levels of proteins. This review efforts to describe the various proteomics approaches, the recent developments and their application in research and analysis.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Madiha Basit
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Muhammad Atif Nisar
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Pakistan .,College of Allied Health Professionals, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
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Qin J, Zhang J, Liu D, Yin C, Wang F, Chen P, Chen H, Ma J, Zhang B, Xu J, Zhang M. iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate. Mol Genet Genomics 2016; 291:1595-605. [PMID: 27048574 DOI: 10.1007/s00438-016-1202-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
Abstract
Photosynthetic rate which acts as a vital limiting factor largely affects the potential of soybean production, especially during the senescence phase. However, the physiological and molecular mechanisms that underlying the change of photosynthetic rate during the developmental process of soybean leaves remain unclear. In this study, we compared the protein dynamics during the developmental process of leaves between the soybean cultivar Hobbit and the high-photosynthetic rate cultivar JD 17 using the iTRAQ (isobaric tags for relative and absolute quantification) method. A total number of 1269 proteins were detected in the leaves of these two cultivars at three different developmental stages. These proteins were classified into nine expression patterns depending on the expression levels at different developmental stages, and the proteins in each pattern were also further classified into three large groups and 20 small groups depending on the protein functions. Only 3.05-6.53 % of the detected proteins presented a differential expression pattern between these two cultivars. Enrichment factor analysis indicated that proteins involved in photosynthesis composed an important category. The expressions of photosynthesis-related proteins were also further confirmed by western blotting. Together, our results suggested that the reduction in photosynthetic rate as well as chloroplast activity and composition during the developmental process was a highly regulated and complex process which involved a serial of proteins that function as potential candidates to be targeted by biotechnological approaches for the improvement of photosynthetic rate and production.
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Affiliation(s)
- Jun Qin
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture, Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, People's Republic of China
- Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Jianan Zhang
- National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, People's Republic of China
| | - Duan Liu
- Geochemical Environmental Research Group, Texas A&M University, 833 Graham Road, College Station, TX, 77845, USA
| | - Changcheng Yin
- Beijing Protein Innovation, B-8, Beijing Airport Industrial Zone, Beijing, 101318, People's Republic of China
| | - Fengmin Wang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture, Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, People's Republic of China
| | - Pengyin Chen
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Hao Chen
- Beijing Protein Innovation, B-8, Beijing Airport Industrial Zone, Beijing, 101318, People's Republic of China
| | - Jinbing Ma
- Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Bo Zhang
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jin Xu
- Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, People's Republic of China.
| | - Mengchen Zhang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean Ministry of Agriculture, Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, People's Republic of China.
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12
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Liu D, Li J, Zhao S, Zhang R, Wang M, Miao Y, Shen Y, Shen Q. Secretome diversity and quantitative analysis of cellulolytic Aspergillus fumigatus Z5 in the presence of different carbon sources. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:149. [PMID: 24131596 PMCID: PMC3853031 DOI: 10.1186/1754-6834-6-149] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 10/01/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Aspergillus fumigatus Z5 has a strong ability to decompose lignocellulose biomass, and its extracellular protein secretion has been reported in earlier studies employing traditional techniques. However, a comprehensive analysis of its secretion in the presence of different carbon sources is still lacking. The goal of this work was to identify, quantify and compare the secretome of A. fumigatus Z5 in the presence of different carbon sources to understand in more details the mechanisms of lignocellulose decomposition by Aspergillus fumigatus Z5. RESULTS Cellulolytic A. fumigatus Z5 was grown in the presence of glucose (Gl), Avicel (Av) and rice straw (RS), and the activities of several lignocellulosic enzymes were determined with chromatometry method. The maximum activities of endoglucanase, exoglucanase, β-glucosidase, laminarinase, lichenase, xylanase and pectin lyase were 12.52, 0.59, 2.30, 2.37, 1.68, 15.02 and 11.40 U·ml-1, respectively. A total of 152, 125 and 61 different proteins were identified in the presence of RS, Av and Gl, respectively, and the proteins were functionally divided into glycoside hydrolases, lipases, peptidases, peroxidases, esterases, protein translocating transporters and hypothetical proteins. A total of 49 proteins were iTRAQ-quantified in all the treatments, and the quantification results indicated that most of the cellulases, hemicellulases and glycoside hydrolases were highly upregulated when rice straw and Avicel were used as carbon sources (compared with glucose). CONCLUSIONS The proteins secreted from A. fumigatus Z5 in the present of different carbon source conditions were identified by LC-MS/MS and quantified by iTRAQ-based quantitative proteomics. The results indicated that A. fumigatus Z5 could produce considerable cellulose-, hemicellulose-, pectin- and lignin-degrading enzymes that are valuable for the lignocellulosic bioenergy industry.
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Affiliation(s)
- Dongyang Liu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Li
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuang Zhao
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruifu Zhang
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengmeng Wang
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Youzhi Miao
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifei Shen
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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13
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Ge P, Hao P, Cao M, Guo G, Lv D, Subburaj S, Li X, Yan X, Xiao J, Ma W, Yan Y. iTRAQ-based quantitative proteomic analysis reveals new metabolic pathways of wheat seedling growth under hydrogen peroxide stress. Proteomics 2013; 13:3046-58. [DOI: 10.1002/pmic.201300042] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/16/2013] [Accepted: 06/26/2013] [Indexed: 01/03/2023]
Affiliation(s)
- Pei Ge
- College of Life Sciences; Capital Normal University; Beijing China
| | - Pengchao Hao
- College of Life Sciences; Capital Normal University; Beijing China
| | - Min Cao
- College of Life Sciences; Capital Normal University; Beijing China
| | - Guangfang Guo
- College of Life Sciences; Capital Normal University; Beijing China
| | - Dongwen Lv
- College of Life Sciences; Capital Normal University; Beijing China
| | | | - Xiaohui Li
- College of Life Sciences; Capital Normal University; Beijing China
| | - Xing Yan
- College of Life Sciences; Capital Normal University; Beijing China
| | - Jitian Xiao
- School of Computer and Security Science; Edith Cowan University; Perth WA Australia
| | - Wujun Ma
- State Agriculture Biotechnology Centre; Murdoch University; Perth WA Australia
- Western Australian Department of Agriculture and Food; Perth WA Australia
| | - Yueming Yan
- College of Life Sciences; Capital Normal University; Beijing China
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14
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Adav SS, Chao LT, Sze SK. Protein abundance in multiplexed samples (PAMUS) for quantitation of Trichoderma reesei secretome. J Proteomics 2013; 83:180-96. [DOI: 10.1016/j.jprot.2013.03.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/20/2013] [Accepted: 03/23/2013] [Indexed: 11/27/2022]
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15
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Gomez del Pulgar EM, Saadeddin A. The cellulolytic system ofThermobifida fusca. Crit Rev Microbiol 2013; 40:236-47. [DOI: 10.3109/1040841x.2013.776512] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Qin J, Gu F, Liu D, Yin C, Zhao S, Chen H, Zhang J, Yang C, Zhan X, Zhang M. Proteomic analysis of elite soybean Jidou17 and its parents using iTRAQ-based quantitative approaches. Proteome Sci 2013; 11:12. [PMID: 23531047 PMCID: PMC3622570 DOI: 10.1186/1477-5956-11-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/16/2013] [Indexed: 01/15/2023] Open
Abstract
Background Derived from Hobbit as the female parent and Zao5241 as the male parent, the elite soybean cultivar Jidou17 is significantly higher yielding and shows enhanced qualities and stronger resistance to non-biological stress than its parents. The purpose of this study is to understand the difference in protein expression patterns between Jidou17 and its parental strains and to evaluate the parental contributions to its elite traits. Results Leaves (14 days old) from Jidou17 and its parental cultivars were analysed for differential expressed proteins using an iTRAQ-based (isobaric tags for relative and absolute quantitation) method. A total of 1269 proteins was detected, with 141 and 181 proteins in Jidou17 differing from its female and male parent, respectively. Functional classification and an enrichment analysis based on biological functions, biological processes, and cellular components revealed that all the differential proteins fell into many functional categories but that the number of proteins varied greatly for the different categories, with enrichment in specific categories. A pathway analysis indicated that the differentiated proteins were mainly classified into the ribosome assembly pathway. Protein expression clustering results showed that the expression profiles between Jidou17 and its female parent Hobbit were more similar than those between Jidou17 and its male parent Zao5241 and between the two parental strains. Therefore, the female parent Hobbit contributed more to the Jidou17 genotype. Conclusions This study applied a proven technique to study proteomics in 14-day-old soybean leaves and explored the depth and breadth of soybean protein research. The results provide new data for further understanding the mechanisms of elite cultivar development.
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Affiliation(s)
- Jun Qin
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Soybean Biology and Genetic Improvement, Ministry of Agriculture, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050031, P,R, China.
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17
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Huang XF, Santhanam N, Badri DV, Hunter WJ, Manter DK, Decker SR, Vivanco JM, Reardon KF. Isolation and characterization of lignin-degrading bacteria from rainforest soils. Biotechnol Bioeng 2013; 110:1616-26. [PMID: 23297115 DOI: 10.1002/bit.24833] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 11/21/2012] [Accepted: 12/17/2012] [Indexed: 11/09/2022]
Abstract
The deconstruction of lignin to enhance the release of fermentable sugars from plant cell walls presents a challenge for biofuels production from lignocellulosic biomass. The discovery of novel lignin-degrading enzymes from bacteria could provide advantages over fungal enzymes in terms of their production and relative ease of protein engineering. In this study, 140 bacterial strains isolated from soils of a biodiversity-rich rainforest in Peru were screened based on their oxidative activity on ABTS, a laccase substrate. Strain C6 (Bacillus pumilus) and strain B7 (Bacillus atrophaeus) were selected for their high laccase activity and identified by 16S rDNA analysis. Strains B7 and C6 degraded fragments of Kraft lignin and the lignin model dimer guaiacylglycerol-β-guaiacyl ether, the most abundant linkage in lignin. Finally, LC-MS analysis of incubations of strains B7 and C6 with poplar biomass in rich and minimal media revealed that a higher number of compounds were released in the minimal medium than in the rich one. These findings provide important evidence that bacterial enzymes can degrade and/or modify lignin and contribute to the release of fermentable sugars from lignocellulose.
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Affiliation(s)
- Xing-Feng Huang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, USA
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18
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Characterization of extracellular lignocellulolytic enzymes of Coniochaeta sp. during corn stover bioconversion. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Quantitative proteomic analysis of secretome of microbial consortium during saw dust utilization. J Proteomics 2012; 75:5590-603. [DOI: 10.1016/j.jprot.2012.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/28/2012] [Accepted: 08/13/2012] [Indexed: 11/23/2022]
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20
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Adav SS, Cheow ESH, Ravindran A, Dutta B, Sze SK. Label free quantitative proteomic analysis of secretome by Thermobifida fusca on different lignocellulosic biomass. J Proteomics 2012; 75:3694-706. [DOI: 10.1016/j.jprot.2012.04.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/25/2012] [Accepted: 04/22/2012] [Indexed: 11/27/2022]
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21
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Adav SS, Chao LT, Sze SK. Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Mol Cell Proteomics 2012; 11:M111.012419. [PMID: 22355001 DOI: 10.1074/mcp.m111.012419] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Trichoderma reesei is a mesophilic, filamentous fungus, and it is a major industrial source of cellulases, but its lignocellulolytic protein expressions on lignocellulosic biomass are poorly explored at present. The extracellular proteins secreted by T. reesei QM6a wild-type and hypercellulolytic mutant Rut C30 grown on natural lignocellulosic biomasses were explored using a quantitative proteomic approach with 8-plex high throughput isobaric tags for relative and absolute quantification (iTRAQ) and analyzed by liquid chromatography tandem mass spectrometry. We quantified 230 extracellular proteins, including cellulases, hemicellulases, lignin-degrading enzymes, proteases, protein-translocating transporter, and hypothetical proteins. Quantitative iTRAQ results suggested that the expressions and regulations of these lignocellulolytic proteins in the secretome of T. reesei wild-type and mutant Rut C30 were dependent on both nature and complexity of different lignocellulosic carbon sources. Therefore, we discuss here the essential lignocellulolytic proteins for designing an enzyme mixture for optimal lignocellulosic biomass hydrolysis.
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Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, Singapore
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22
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Quantitative proteomic analysis of lignocellulolytic enzymes by Phanerochaete chrysosporium on different lignocellulosic biomass. J Proteomics 2012; 75:1493-504. [DOI: 10.1016/j.jprot.2011.11.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 10/29/2011] [Accepted: 11/17/2011] [Indexed: 11/23/2022]
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23
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Manavalan A, Adav SS, Sze SK. iTRAQ-based quantitative secretome analysis of Phanerochaete chrysosporium. J Proteomics 2011; 75:642-54. [DOI: 10.1016/j.jprot.2011.09.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/11/2011] [Accepted: 09/03/2011] [Indexed: 10/17/2022]
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24
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Adav SS, Ravindran A, Chao LT, Tan L, Singh S, Sze SK. Proteomic Analysis of pH and Strains Dependent Protein Secretion of Trichoderma reesei. J Proteome Res 2011; 10:4579-96. [DOI: 10.1021/pr200416t] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Anita Ravindran
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Lim Tze Chao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Lynette Tan
- Temasek Engineering School, Temasek Polytechnic, 21 Tampines Avenue 1, Singapore 529757
| | - Sunil Singh
- Temasek Engineering School, Temasek Polytechnic, 21 Tampines Avenue 1, Singapore 529757
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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