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Amrutha Lakshmi M, B R A, Manyam P, Javeedvali S, Khan AS, Palnam DW, Kandan A. Traditional to technological advancements in Ganoderma detection methods in oil palm. Folia Microbiol (Praha) 2024; 69:953-973. [PMID: 38976188 DOI: 10.1007/s12223-024-01177-w] [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: 09/11/2023] [Accepted: 05/19/2024] [Indexed: 07/09/2024]
Abstract
Ganoderma sp., the fungal agent causing basal stem rot (BSR), poses a severe threat to global oil palm production. Alarming increases in BSR occurrences within oil palm growing zones are attributed to varying effectiveness in its current management strategies. Asymptomatic progression of the disease and the continuous monoculture of oil palm pose challenges for prompt and effective management. Therefore, the development of precise, early, and timely detection techniques is crucial for successful BSR management. Conventional methods such as visual assessments, culture-based assays, and biochemical and physiological approaches prove time-consuming and lack specificity. Serological-based diagnostic methods, unsuitable for fungal diagnostics due to low sensitivity, assay affinity, cross-contamination which further underscores the need for improved techniques. Molecular PCR-based assays, utilizing universal, genus-specific, and species-specific primers, along with functional primers, can overcome the limitations of conventional and serological methods in fungal diagnostics. Recent advancements, including real-time PCR, biosensors, and isothermal amplification methods, facilitate accurate, specific, and sensitive Ganoderma detection. Comparative whole genomic analysis enables high-resolution discrimination of Ganoderma at the strain level. Additionally, omics tools such as transcriptomics, proteomics, and metabolomics can identify potential biomarkers for early detection of Ganoderma infection. Innovative on-field diagnostic techniques, including remote methods like volatile organic compounds profiling, tomography, hyperspectral and multispectral imaging, terrestrial laser scanning, and Red-Green-Blue cameras, contribute to a comprehensive diagnostic approach. Ultimately, the development of point-of-care, early, and cost-effective diagnostic techniques accessible to farmers is vital for the timely management of BSR in oil palm plantations.
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Affiliation(s)
- M Amrutha Lakshmi
- Plant Pathology, ICAR-Indian Institute of Oil Palm Research, India, Andhra Pradesh.
| | - Ajesh B R
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Pradeep Manyam
- Acharya N. G, Ranga Agricultural University, Guntur, Andhra Pradesh, India
| | - Shaik Javeedvali
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Amjada S Khan
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Dauda Wadzani Palnam
- Crop Science Unit, Department of Agronomy, Federal University, Yobe State, Gashua, Nigeria
| | - A Kandan
- ICAR-National Bureau of Agricultural Insect Resources, Bangalore, India
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Karunarathna SC, Patabendige NM, Lu W, Asad S, Hapuarachchi KK. An In-Depth Study of Phytopathogenic Ganoderma: Pathogenicity, Advanced Detection Techniques, Control Strategies, and Sustainable Management. J Fungi (Basel) 2024; 10:414. [PMID: 38921400 PMCID: PMC11204718 DOI: 10.3390/jof10060414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
Phytopathogenic Ganoderma species pose a significant threat to global plant health, resulting in estimated annual economic losses exceeding USD (US Dollars) 68 billion in the agriculture and forestry sectors worldwide. To combat this pervasive menace effectively, a comprehensive understanding of the biology, ecology, and plant infection mechanisms of these pathogens is imperative. This comprehensive review critically examines various aspects of Ganoderma spp., including their intricate life cycle, their disease mechanisms, and the multifaceted environmental factors influencing their spread. Recent studies have quantified the economic impact of Ganoderma infections, revealing staggering yield losses ranging from 20% to 80% across various crops. In particular, oil palm plantations suffer devastating losses, with an estimated annual reduction in yield exceeding 50 million metric tons. Moreover, this review elucidates the dynamic interactions between Ganoderma and host plants, delineating the pathogen's colonization strategies and its elicitation of intricate plant defense responses. This comprehensive analysis underscores the imperative for adopting an integrated approach to Ganoderma disease management. By synergistically harnessing cultural practices, biological control, and chemical treatments and by deploying resistant plant varieties, substantial strides can be made in mitigating Ganoderma infestations. Furthermore, a collaborative effort involving scientists, breeders, and growers is paramount in the development and implementation of sustainable strategies against this pernicious plant pathogen. Through rigorous scientific inquiry and evidence-based practices, we can strive towards safeguarding global plant health and mitigating the dire economic consequences inflicted by Ganoderma infections.
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Affiliation(s)
- Samantha C. Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China;
- National Institute of Fundamental Studies, Hantane Road, Kandy 20000, Sri Lanka
| | | | - Wenhua Lu
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Suhail Asad
- School of Biology and Chemistry, Pu’er University, Pu’er 665000, China;
| | - Kalani K. Hapuarachchi
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
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3
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Dakheel KH, Abdul Rahim R, Al-Obaidi JR, Neela VK, Hun TG, Mat Isa MN, Razali N, Yusoff K. Proteomic analysis revealed the biofilm-degradation abilities of the bacteriophage UPMK_1 and UPMK_2 against Methicillin-resistant Staphylococcus aureus. Biotechnol Lett 2022; 44:513-522. [PMID: 35122191 DOI: 10.1007/s10529-022-03229-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/26/2022] [Indexed: 11/02/2022]
Abstract
OBJECTIVE The degradation activity of two bacteriophages UPMK_1 and UPMK_2 against methicillin-resistant Staphylococcus aureus phages were examined using gel zymography. METHODS The analysis was done using BLASTP to detect peptides catalytic domains. Many peptides that are related to several phage proteins were revealed. RESULTS UPMK_1 and UPMK_2 custom sequence database were used for peptide identification. The biofilm-degrading proteins in the bacteriophage UPMK_2 revealed the same lytic activity towards polysaccharide intercellular adhesin-dependent and independent of Methicillin-resistant Staphylococcus aureus (MRSA) biofilm producers in comparison to UPMK_1, which had lytic activity restricted solely to its host. CONCLUSION Both bacteriophage enzymes were involved in MRSA biofilm degradation during phage infection and they have promising enzybiotics properties against MRSA biofilm formation.
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Affiliation(s)
- Khulood Hamid Dakheel
- Department of Biology, College of Science, Mustansiriyah University, Palestine Street, PO Box 14022, Baghdad, Iraq
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jameel R Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia.
| | - Vasantha Kumari Neela
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Tan Geok Hun
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute (MGI), Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Nurhanani Razali
- Membranology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Tancha, Onna-son, Kunigami-kun, Okinawa, 904-0495, Japan
| | - Khatijah Yusoff
- Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology & Biomolecular Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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4
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Fisol AFBC, Saidi NB, Al-Obaidi JR, Lamasudin DU, Atan S, Razali N, Sajari R, Rahmad N, Hussin SNIS, Mr NH. Differential Analysis of Mycelial Proteins and Metabolites From Rigidoporus Microporus During In Vitro Interaction With Hevea Brasiliensis. MICROBIAL ECOLOGY 2022; 83:363-379. [PMID: 33890145 DOI: 10.1007/s00248-021-01757-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Rigidoporus microporus is the fungus accountable for the white root rot disease that is detrimental to the rubber tree, Hevea brasiliensis. The pathogenicity mechanism of R. microporus and the identity of the fungal proteins and metabolites involved during the infection process remain unclear. In this study, the protein and metabolite profiles of two R. microporus isolates, Segamat (SEG) and Ayer Molek (AM), were investigated during an in vitro interaction with H. brasiliensis. The isolates were used to inoculate H. brasiliensis clone RRIM 2025, and mycelia adhering to the roots of the plant were collected for analysis. Transmission electron microscope (TEM) images acquired confirms the hyphae attachment and colonization of the mycelia on the root of the H. brasiliensis clones after 4 days of inoculation. The protein samples were subjected to 2-DE analysis and analyzed using MALDI-ToF MS/MS, while the metabolites were extracted using methanol and analyzed using LC/MS-QTOF. Based on the differential analyses, upregulation of proteins that are essential for fungal evolution such as malate dehydrogenase, fructose 1,6-biphosphate aldolase, and glyceraldehyde-3-phosphate dehydrogenase hints an indirect role in fungal pathogenicity, while metabolomic analysis suggests an increase in acidic compounds which may lead to increased cell wall degrading enzyme activity. Bioinformatics analyses revealed that the carbohydrate and amino acid metabolisms were prominently affected in response to the fungal pathogenicity. In addition to that, other pathways that were significantly affected include "Protein Ubiquitination Pathway," Unfolded Protein Response," "HIFα Signaling," and "Sirtuin Signaling Pathway." The identification of responsive proteins and metabolites from this study promotes a better understanding of mechanisms underlying R. microporus pathogenesis and provides a list of potential biological markers for early recognition of the white root rot disease.
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Affiliation(s)
- Ahmad Faiz Bin Che Fisol
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Noor Baity Saidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jameel R Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia.
| | - Dhilia Udie Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Safiah Atan
- Malaysian Rubber Board, 47000, Sungai Buloh, Selangor, Malaysia
| | - Nurhanani Razali
- Membranology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Tancha, Onna-son, Kunigami-kun, Okinawa, 904-0495, Japan
- Department of Hygienic Sciences, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Roslinda Sajari
- Malaysian Rubber Board, 47000, Sungai Buloh, Selangor, Malaysia
| | - Norasfaliza Rahmad
- Agro-Biotechnology Institute Malaysia (ABI), National Institutes of Biotechnology Malaysia (NIBM), c/o MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Siti Nahdatul Isnaini Said Hussin
- Agro-Biotechnology Institute Malaysia (ABI), National Institutes of Biotechnology Malaysia (NIBM), c/o MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Nurul Hafiza Mr
- Agro-Biotechnology Institute Malaysia (ABI), National Institutes of Biotechnology Malaysia (NIBM), c/o MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
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Growth performance of Ganoderma lucidum using billet method in Garhwal Himalaya, India. Saudi J Biol Sci 2021; 28:2709-2717. [PMID: 34025157 PMCID: PMC8117109 DOI: 10.1016/j.sjbs.2021.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
Medicinal mushrooms have been used in various treatments from a very long time, among which, Ganoderma lucidum is one of the most important medicinal mushroom. It is cultivated worldwide to meet its ever-increasing demand in the market. It is generally cultivated by bed log (Sawdust) and wood log (billet) method. This study was an attempt to observe the growth performance of G. lucidum on poplar billets (Populus deltoides) in the Sherpur Village (Dehradun) and Manjgaun village (Tehri Garhwal) of Garhwal Himalaya, India. The farmers’ field with empty house/ rooms having proper growing conditions especially humidity and light were used for the cultivation of G. lucidum. The G. lucidum spawn was inoculated in poplar wood billets and these billets were installed in well prepared soil. The results demonstrated that cropping cycle of G. lucidum was shorter (132–136 days) in Sherpur Village (Dehradun) as compared to Manjgaun village (141–145 days) in Tehri Garhwal. Further the results also revealed that yield was decreased in the subsequent flushes. In Village Sherpur, the fruiting bodies of G. lucidum were harvested between 64-66 days, 100-101 days and 135-136 days during first, second and third flush after the installation of billets, respectively. However; in village Manjgaun, the fruiting bodies of G. lucidum were harvested between 69 and 71 days, 107-108 days and 144-145 days in first, second and third after the installation of billets respectively. Warmer temperature in Village Sherpur resulted in the early emergence and development of the fruiting bodies as compared to village Manjgaun where pinhead and fruiting body development was delayed due to the lower temperature during cropping cycle.
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Optimization of Protein Extraction Method for 2DE Proteomics of Goat's Milk. Molecules 2020; 25:molecules25112625. [PMID: 32516945 PMCID: PMC7321142 DOI: 10.3390/molecules25112625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/17/2022] Open
Abstract
Two-dimensional electrophoretic (2DE)-based proteomics remains a powerful tool for allergenomic analysis of goat’s milk but requires effective extraction of proteins to accurately profile the overall causative allergens. However, there are several current issues with goat’s milk allergenomic analysis, and among these are the absence of established standardized extraction method for goat’s milk proteomes and the complexity of goat’s milk matrix that may hamper the efficacy of protein extraction. This study aimed to evaluate the efficacies of three different protein extraction methods, qualitatively and quantitatively, for the 2DE-proteomics, using milk from two commercial dairy goats in Malaysia, Saanen, and Jamnapari. Goat’s milk samples from both breeds were extracted by using three different methods: a milk dilution in urea/thiourea based buffer (Method A), a triphasic separation protocol in methanol/chloroform solution (Method B), and a dilution in sulfite-based buffer (Method C). The efficacies of the extraction methods were assessed further by performing the protein concentration assay and 1D and 2D SDS-PAGE profiling, as well as identifying proteins by MALDI-TOF/TOF MS/MS. The results showed that method A recovered the highest amount of proteins (72.68% for Saanen and 71.25% for Jamnapari) and produced the highest number of protein spots (199 ± 16.1 and 267 ± 10.6 total spots for Saanen and Jamnapari, respectively) with superior gel resolution and minimal streaking. Six milk protein spots from both breeds were identified based on the positive peptide mass fingerprinting matches with ruminant milk proteins from public databases, using the Mascot software. These results attest to the fitness of the optimized protein extraction protocol, method A, for 2DE proteomic and future allergenomic analysis of the goat’s milk.
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Integrated Proteomics and Metabolomics Analysis Provides Insights into Ganoderic Acid Biosynthesis in Response to Methyl Jasmonate in Ganoderma Lucidum. Int J Mol Sci 2019; 20:ijms20246116. [PMID: 31817230 PMCID: PMC6941157 DOI: 10.3390/ijms20246116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
Ganoderma lucidum is widely recognized as a medicinal basidiomycete. It was previously reported that the plant hormone methyl jasmonate (MeJA) could induce the biosynthesis of ganoderic acids (GAs), which are the main active ingredients of G. lucidum. However, the regulatory mechanism is still unclear. In this study, integrated proteomics and metabolomics were employed on G. lucidum to globally identify differences in proteins and metabolites under MeJA treatment for 15 min (M15) and 24 h (M24). Our study successfully identified 209 differential abundance proteins (DAPs) in M15 and 202 DAPs in M24. We also identified 154 metabolites by GC-MS and 70 metabolites by LC-MS in M24 that are involved in several metabolic pathways. With an in-depth analysis, we found some DAPs and metabolites that are involved in the oxidoreduction process, secondary metabolism, energy metabolism, transcriptional and translational regulation, and protein synthesis. In particular, our results reveal that MeJA treatment leads to metabolic rearrangement that inhibited the normal glucose metabolism, energy supply, and protein synthesis of cells but promoted secondary metabolites, including GAs. In conclusion, our proteomics and metabolomics data further confirm the promoting effect of MeJA on the biosynthesis of GAs in G. lucidum and will provide a valuable resource for further investigation of the molecular mechanisms of MeJA signal response and GA biosynthesis in G. lucidum and other related species.
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8
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Development of Ganoderma lucidum spore powder based proteoglycan and its application in hyperglycemic, antitumor and antioxidant function. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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Jin X, Zhu L, Tao C, Xie Q, Xu X, Chang L, Tan Y, Ding G, Li H, Wang X. An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS. BMC Genomics 2019; 20:285. [PMID: 30975097 PMCID: PMC6458646 DOI: 10.1186/s12864-019-5658-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are widely used in plant proteomics research. However, these two techniques cannot be simultaneously satisfied by traditional protein extraction methods when investigate cotton leaf proteome. Results Here, we evaluated the efficiency of three different protein extraction methods for 2-DE and LC-MS/MS analyses of total proteins obtained from cotton leaves. The protein yield of the borax/PVPP/phenol (BPP) method (0.14%) was significantly lower than the yields of the trichloroacetic acid/acetone (TCA) precipitation method (1.42%) and optimized TCA combined with BPP (TCA-B) method (0.47%). The BPP method was failed to get a clear 2-DE electrophoretogram. Fifty pairs of protein spots were randomly selected from the 2-DE gels of TCA- and TCA-B-extracted proteins for identification by MALDI TOF/TOF, and the results of 42 pairs were consistent. High-throughput proteomic analysis showed that 6339, 9282 and 9697 unique proteins were identified from the total cotton leaf proteins extracted by the TCA, BPP and TCA-B methods, respectively. Gene Ontology (GO) analysis revealed that the proteins specifically identified by TCA method were primarily distributed in the plasma membrane, while BPP and TCA-B methods specific proteins distributed in the cytosol, indicating the sub-cellular preference of different protein extraction methods. Further, ATP-dependent zinc metalloprotease FTSH 8 could be observed in the 2-DE gels of TCA and TCA-B methods, and could only be detected in the LC-MS/MS results of the BPP and TCA-B methods, showing that TCA-B method might be the optimized choice for both 2-DE and LC-MS/MS. Conclusion Our data provided an improved TCA-B method for protein extraction that is compatible with 2-DE and LC-MS/MS for cotton leaves and similar plant tissues which is rich in polysaccharides and polyphenols. Electronic supplementary material The online version of this article (10.1186/s12864-019-5658-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.,College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Liping Zhu
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Chengcheng Tao
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Xinyang Xu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Lili Chang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yanhua Tan
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Guohua Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China.
| | - Xuchu Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China. .,College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China. .,Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
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10
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Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Qiao M, Tu M, Wang Z, Mao F, Chen H, Qin L, Du M. Identification and Antithrombotic Activity of Peptides from Blue Mussel (Mytilus edulis) Protein. Int J Mol Sci 2018; 19:E138. [PMID: 29300301 PMCID: PMC5796087 DOI: 10.3390/ijms19010138] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022] Open
Abstract
The blue mussel (Mytilus edulis) reportedly contains many bioactive components of nutritional value. Water-, salt- and acid-soluble M. edulis protein fractions were obtained and the proteins were trypsinized. The resultant peptides were analyzed by ultra-performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS). 387 unique peptides were identified that matched 81 precursor proteins. Molecular mass distributions of the proteins and peptides were analyzed by sodium dodecyl sulfate-polyacryl amide gel electrophoresis (SDS-PAGE). The differences between the three protein samples were studied by Venn diagram of peptide and protein compositions. Toxicity, allergic and antithrombotic activity of peptides was predicted using database website and molecular docking respectively. The antithrombotic activity of enzymatic hydrolysate from water-, salt- and acid-soluble M. edulis protein were 40.17%, 85.74%, 82.00% at 5 mg/mL, respectively. Active mechanism of antithrombotic peptide (ELEDSLDSER) was also research about amino acid binding sites and interaction, simultaneously.
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Affiliation(s)
- Meiling Qiao
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Maolin Tu
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Zhenyu Wang
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Fengjiao Mao
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Hui Chen
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Lei Qin
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Ming Du
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
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12
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Schulte F, Hardt M, Niehaus K. A robust protocol for the isolation of cellular proteins from Xanthomonas campestris to analyze the methionine effect in 2D-gel experiments. Electrophoresis 2017; 38:2603-2609. [PMID: 28605028 DOI: 10.1002/elps.201700064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 11/06/2022]
Abstract
Two-dimensional PAGE (2D-PAGE) is a key technique for the separation of complex protein samples to survey the protein inventory of prokaryotic microorganisms. Although the preparation of proteins is a critical step in 2D gel experiments, its effect on the outcome of proteome data is often underestimated. In this work, we show that the choice of protein isolation method can have a profound impact on the quality of 2D gels of protein extracts from prokaryotes. Based on Xanthomonas campestris, a commercially relevant producer of the thickening agent xanthan, we validated a phenol extraction protocol for the purification of bacterial proteins that provides excellent 2D gel separation. As a proof of concept, this method was used to study the effect of methionine-a medium compound that reduces the xanthan output of industrial fermentations-on the cellular proteome of Xanthomonas. The detection of nine regulated proteins associated with sulfur metabolism (Cgl, CysI, CysJ, CysK, MetH1, MetY) and sugar nucleotide biosynthesis (Pgi, Ugd, XanA) proved the efficiency of phenol extraction for the screening of statistically significant abundance changes in 2D gel spots and MALDI-TOF-MS based identification in bacteria. Since this method is very robust, it may be useful for the study of other prokaryotes that are relevant in industrial biotechnology.
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Affiliation(s)
- Fabian Schulte
- Department of Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, USA
| | - Markus Hardt
- Department of Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, USA.,Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA.,Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
| | - Karsten Niehaus
- Fakultät für Biologie, Proteom- und Metabolomforschung, Universität Bielefeld, Bielefeld, Germany
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Fan X, Zhu L, Wang K, Wang B, Wu Y, Xie W, Huang C, Chan BP, Du Y. Stiffness-Controlled Thermoresponsive Hydrogels for Cell Harvesting with Sustained Mechanical Memory. Adv Healthc Mater 2017; 6. [PMID: 28105774 DOI: 10.1002/adhm.201601152] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/23/2016] [Indexed: 01/17/2023]
Abstract
Most mechanobiological investigations focused on in situ mechanical regulation of cells on stiffness-controlled substrates with few downstream applications, as it is still challenging to harvest and expand mechanically primed cells by enzymatic digestion (e.g., trypsin) without interrupting cellular mechanical memory between passages. This study develops thermoresponsive hydrogels with controllable stiffness to generate mechanically primed cells with intact mechanical memory for augmented wound healing. No significant cellular property alteration of the fibroblasts primed on thermoresponsive hydrogels with varied stiffness has been observed through thermoresponsive harvesting. When reseeding the harvested cells for further evaluation, softer hydrogels are proven to better sustain the mechanical priming effects compared to rigid tissue culture plate, which indicates that both the stiffness-controlled substrate and thermoresponsive harvesting are required to sustain cellular mechanical memory between passages. Moreover, epigenetics analysis reveals that thermoresponsive harvesting could reduce the rearrangement and loss of chromatin proteins compared to that of trypsinization. In vivo wound healing using mechanically primed fibroblasts shows featured epithelium and sebaceous glands, which indicates augmented skin recovery compared with trypsinized fibroblasts. Thus, the thermoresponsive hydrogel-based cell harvesting system offers a powerful tool to investigate mechanobiology between cell passages and produces abundant cells with tailored mechanical priming properties for cell-based applications.
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Affiliation(s)
- Xingliang Fan
- Department of Biomedical Engineering; School of Medicine; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; Tsinghua University; Beijing 100084 China
- Joint Center for Life Sciences; Tsinghua University-Peking University; Beijing 100084 China
| | - Lu Zhu
- Department of Biomedical Engineering; School of Medicine; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; Tsinghua University; Beijing 100084 China
- Institute of Medical Equipment; Academy of Military Medical Sciences; Tianjin 300161 China
| | - Ke Wang
- Department of Chemistry; School of Science; Tsinghua University; Beijing 100084 China
| | - Bingjie Wang
- Department of Biomedical Engineering; School of Medicine; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; Tsinghua University; Beijing 100084 China
- School of Life Science; Tsinghua University; Beijing 100084 China
| | - Yaozu Wu
- Department of Biomedical Engineering; School of Medicine; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; Tsinghua University; Beijing 100084 China
| | - Wei Xie
- Joint Center for Life Sciences; Tsinghua University-Peking University; Beijing 100084 China
- School of Life Science; Tsinghua University; Beijing 100084 China
| | - Chengyu Huang
- Department of Plastic; Reconstructive and Aesthetic Surgery; Beijing Tsinghua Changgung Hospital; Tsinghua University; Beijing 102218 China
| | - Barbara Pui Chan
- Tissue Engineering Laboratory; Department of Mechanical Engineering; The University of Hong Kong; Pokfulam Road Hong Kong Special Administrative Region China
| | - Yanan Du
- Department of Biomedical Engineering; School of Medicine; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; Tsinghua University; Beijing 100084 China
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