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Mousa WK, Abu-Izneid T, Salah-Tantawy A. High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change. FRONTIERS IN PLANT SCIENCE 2024; 15:1294173. [PMID: 38510442 PMCID: PMC10953687 DOI: 10.3389/fpls.2024.1294173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Tareq Abu-Izneid
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Ahmed Salah-Tantawy
- Institute of Analytical and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Zoology, Marine Science Division, College of Science, Al-Azhar University, Assiut, Egypt
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Kuppusamy KM, Selvaraj S, Singaravelu P, John CM, Racheal K, Varghese K, Kaliyamoorthy D, Perumal E, Gunasekaran K. Anti-microbial and anti-cancer efficacy of acetone extract of Rosa chinensis against resistant strain and lung cancer cell line. BMC Complement Med Ther 2023; 23:406. [PMID: 37950173 PMCID: PMC10636979 DOI: 10.1186/s12906-023-04222-2] [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: 05/11/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Screening of herbal plants for various therapeutic properties is the hour as it shows promising activity. Scientific evidence of the pharmacological activity of the plant strengthens the traditional application of plants. METHODS Rose flowers (Rosa chinensis) were procured and grounded into a coarse powder. The DNA was isolated from rose flower and molecular identification was performed by rbcL-BF and rbcL-724R primers. Antibacterial activity was evaluated by using disc and agar diffusion methods and the anti-cancer effect of the rose flower extract (RE) was examined using MTT assay in lung cancer cell line. The mechanism of cell death induced by RE was qualitatively measured using Acridine orange/Ethidium bromide staining and Hoechst staining. GC-MS analysis was performed using GC-MS-5975C. RESULT The RE showed potent antimicrobial activity against various ATCC cultures. The rose extract strongly inhibits the growth of ESBL resistant organism along with inhibition of biofilm formation in the ESBL resistant organism. The extract caused apoptotic and necrotic cell death in lung cancer cells. GC-MS analysis demonstrated the presence of several biologically active compounds such as Clindamycin, Phytol, Octanoic acid, and Stigmasterol which might be the reason for the therapeutic properties of the plant. CONCLUSION This study shows the antimicrobial and biofilm inhibition activity against the clinical isolates of Klebsiella pneumonia. The study shows the cytotoxic and apoptotic activity in A549 cancer cell line. Thus, the plant may act as a potent antimicrobial drug against resistant strains.
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Affiliation(s)
- Kalaivani Madhavaram Kuppusamy
- Research Centre for Cellular Genomics and Cancer Research, Sree Balaji Medical College and Hospital, Chennai, 600044, India
| | - Sivakumar Selvaraj
- Molecular Biology section, Consultant Molecular Biologist, Medall Healthcare Private Limited, Chennai, India
| | - Pujithaa Singaravelu
- Research Centre for Cellular Genomics and Cancer Research, Sree Balaji Medical College and Hospital, Chennai, 600044, India
| | - Cordelia Mano John
- Department of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Kalaiselvan Racheal
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - Keziaann Varghese
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - Dinesh Kaliyamoorthy
- Department of Microbiology, Sree Balaji Medical College and Hospital, Chennai, 600044, India
| | - Elumalai Perumal
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India.
| | - Krishnamoorthy Gunasekaran
- Department of Medical Biochemistry, College of Health Sciences, Dambi Dollo University, KelamWelega Zone, Dembidolo, P.O. Box: 360, Oromia Region, Ethiopia.
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Hlangwani E, Abrahams A, Masenya K, Adebo OA. Analysis of the bacterial and fungal populations in South African sorghum beer (umqombothi) using full-length 16S rRNA amplicon sequencing. World J Microbiol Biotechnol 2023; 39:350. [PMID: 37864040 PMCID: PMC10589195 DOI: 10.1007/s11274-023-03764-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/14/2023] [Indexed: 10/22/2023]
Abstract
There is a need to profile microorganisms which exist pre-and-post-production of umqombothi, to understand its microbial diversity and the interactions which subsequently influence the final product. Thus, this study sought to determine the relative microbial abundance in umqombothi and predict the functional pathways of bacterial and fungal microbiota present. Full-length bacterial 16S rRNA and internal transcribed spacer (ITS) gene sequencing using PacBio single-molecule, real-time (SMRT) technology was used to assess the microbial compositions. PICRUSt2 was adopted to infer microbial functional differences. A mixture of harmful and beneficial microorganisms was observed in all samples. The microbial diversity differed significantly between the mixed raw ingredients (MRI), customary beer brew (CB), and optimised beer brew (OPB). The highest bacterial species diversity was observed in the MRI, while the highest fungal species diversity was observed in the OPB. The dominant bacterial species in the MRI, CB, and OPB were Kosakonia cowanii, Apilactobacillus pseudoficulneus, and Vibrio alginolyticus, respectively, while the dominant fungal species was Apiotrichum laibachii. The predicted functional annotations revealed significant (p < 0.05) differences in the microbial pathways of the fermented and unfermented samples. The most abundant pathways in the MRI were the branched-chain amino acid biosynthesis super pathway and the pentose phosphate pathway. The CB sample was characterised by folate (vitamin B9) transformations III, and mixed acid fermentation. Biotin (vitamin B7) biosynthesis I and L-valine biosynthesis characterised the OPB sample. These findings can assist in identifying potential starter cultures for the commercial production of umqombothi. Specifically, A. pseudoficulneus can be used for controlled fermentation during the production of umqombothi. Likewise, the use of A. laibachii can allow for better control over the fermentation kinetics such as carbohydrate conversion and end-product characteristics, especially esters and aroma compounds.
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Affiliation(s)
- Edwin Hlangwani
- Food Innovation Research Group, Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg, South Africa
| | - Adrian Abrahams
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg, South Africa
| | - Kedibone Masenya
- Neuroscience Institute, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
| | - Oluwafemi Ayodeji Adebo
- Food Innovation Research Group, Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg, South Africa.
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Zhang X, Zhang X, Wang L, Liu Q, Liang Y, Zhang J, Xue Y, Tian Y, Zhang H, Li N, Sheng C, Nie P, Feng S, Liao B, Bai D. Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut ( Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1153293. [PMID: 37223785 PMCID: PMC10200878 DOI: 10.3389/fpls.2023.1153293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/28/2023] [Indexed: 05/25/2023]
Abstract
Low temperatures significantly affect the growth and yield of peanuts. Temperatures lower than 12 °C are generally detrimental for the germination of peanuts. To date, there has been no report on precise information on the quantitative trait loci (QTL) for cold tolerance during the germination in peanuts. In this study, we developed a recombinant inbred line (RIL) population comprising 807 RILs by tolerant and sensitive parents. Phenotypic frequencies of germination rate low-temperature conditions among RIL population showed normally distributed in five environments. Then, we constructed a high density SNP-based genetic linkage map through whole genome re-sequencing (WGRS) technique and identified a major quantitative trait locus (QTL), qRGRB09, on chromosome B09. The cold tolerance-related QTLs were repeatedly detected in all five environments, and the genetic distance was 6.01 cM (46.74 cM - 61.75 cM) after taking a union set. To further confirm that qRGRB09 was located on chromosome B09, we developed Kompetitive Allele Specific PCR (KASP) markers for the corresponding QTL regions. A regional QTL mapping analysis, which was conducted after taking the intersection of QTL intervals of all environments into account, confirmed that qRGRB09 was between the KASP markers, G22096 and G220967 (chrB09:155637831-155854093), and this region was 216.26 kb in size, wherein a total of 15 annotated genes were detected. This study illustrates the relevance of WGRS-based genetic maps for QTL mapping and KASP genotyping that facilitated QTL fine mapping of peanuts. The results of our study also provided useful information on the genetic architecture underlying cold tolerance during germination in peanuts, which in turn may be useful for those engaged in molecular studies as well as crop improvement in the cold-stressed environment.
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Affiliation(s)
- Xin Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
- State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Xiaoji Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Luhuan Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Qimei Liu
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Yuying Liang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Jiayu Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Yunyun Xue
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Yuexia Tian
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Huiqi Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Na Li
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Cong Sheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Pingping Nie
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Suping Feng
- College of Food Science and Engineering, Hainan Tropical Ocean College, Hainan, China
| | - Boshou Liao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dongmei Bai
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
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Zhou GD, He P, Tian L, Xu S, Yang B, Liu L, Wang Y, Bai T, Li X, Li S, Zheng SJ. Disentangling the resistant mechanism of Fusarium wilt TR4 interactions with different cultivars and its elicitor application. FRONTIERS IN PLANT SCIENCE 2023; 14:1145837. [PMID: 36938065 PMCID: PMC10018200 DOI: 10.3389/fpls.2023.1145837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Fusarium wilt of banana, especially Tropical Race 4 (TR4) is a major factor restricting banana production. Developing a resistant cultivar and inducing plant defenses by elicitor application are currently two of the best options to control this disease. Isotianil is a monocarboxylic acid amide that has been used as a fungicide to control rice blast and could potentially induce systemic acquired resistance in plants. To determine the control effect of elicitor isotianil on TR4 in different resistant cultivars, a greenhouse pot experiment was conducted and its results showed that isotianil could significantly alleviate the symptoms of TR4, provide enhanced disease control on the cultivars 'Baxi' and 'Yunjiao No.1' with control effect 50.14% and 56.14%, respectively. We compared the infection processes in 'Baxi' (susceptible cultivars) and 'Yunjiao No.1' (resistant cultivars) two cultivars inoculated with pathogen TR4. The results showed that TR4 hyphae could rapidly penetrate the cortex into the root vascular bundle for colonization, and the colonization capacity in 'Baxi' was significantly higher than that in 'Yunjiao No.1'. The accumulation of a large number of starch grains was observed in corms cells, and further analysis showed that the starch content in 'Yunjiao No. 1' as resistant cultivar was significantly higher than that in 'Baxi' as susceptible cultivar, and isotianil application could significantly increase the starch content in 'Baxi'. Besides, a mass of tyloses were observed in the roots and corms and these tyloses increased after application with isotianil. Furthermore, the total starch and tyloses contents and the control effect in the corms of 'Yunjiao No.1' was higher than that in the 'Baxi'. Moreover, the expression levels of key genes for plant resistance induction and starch synthesis were analyzed, and the results suggested that these genes were significantly upregulated at different time points after the application of isotianil. These results suggest that there are significant differences between cultivars in response to TR4 invasion and plant reactions with respect to starch accumulation, tyloses formation and the expression of plant resistance induction and starch synthesis related genes. Results also indicate that isotianil application may contribute to disease control by inducing host plant defense against TR4 infection and could be potentially used together with resistant cultivar as integrated approach to manage this destructive disease. Further research under field conditions should be included in the next phases of study.
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Affiliation(s)
- Guang-Dong Zhou
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- Center For Potato Research, Resource Plant Research Institute, Yunnan University, Kunming, Yunnan, China
| | - Ping He
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Libo Tian
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- Center For Potato Research, Resource Plant Research Institute, Yunnan University, Kunming, Yunnan, China
| | - Shengtao Xu
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Baoming Yang
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Lina Liu
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Yongfen Wang
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- Institute of Tropical and Subtropical Industry Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China
| | - Tingting Bai
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Xundong Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Shu Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Si-Jun Zheng
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- Bioversity International, Kunming, Yunnan, China
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Tan SW, Gooran N, Lim HM, Yoon BK, Jackman JA. Tethered Bilayer Lipid Membrane Platform for Screening Triton X-100 Detergent Replacements by Electrochemical Impedance Spectroscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:874. [PMID: 36903751 PMCID: PMC10005542 DOI: 10.3390/nano13050874] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
In light of regulatory considerations, there are ongoing efforts to identify Triton X-100 (TX-100) detergent alternatives for use in the biological manufacturing industry to mitigate membrane-enveloped pathogen contamination. Until now, the efficacy of antimicrobial detergent candidates to replace TX-100 has been tested regarding pathogen inhibition in endpoint biological assays or probing lipid membrane disruption in real-time biophysical testing platforms. The latter approach has proven especially useful to test compound potency and mechanism of action, however, existing analytical approaches have been limited to studying indirect effects of lipid membrane disruption such as membrane morphological changes. A direct readout of lipid membrane disruption by TX-100 detergent alternatives would be more practical to obtain biologically relevant information to guide compound discovery and optimization. Herein, we report the use of electrochemical impedance spectroscopy (EIS) to investigate how TX-100 and selected replacement candidates-Simulsol SL 11W (Simulsol) and cetyltrimethyl ammonium bromide (CTAB)-affect the ionic permeability of tethered bilayer lipid membrane (tBLM) platforms. The EIS results revealed that all three detergents exhibited dose-dependent effects mainly above their respective critical micelle concentration (CMC) values while displaying distinct membrane-disruptive behaviors. TX-100 caused irreversible membrane disruption leading to complete solubilization, whereas Simulsol caused reversible membrane disruption and CTAB induced irreversible, partial membrane defect formation. These findings establish that the EIS technique is useful for screening the membrane-disruptive behaviors of TX-100 detergent alternatives with multiplex formatting possibilities, rapid response, and quantitative readouts relevant to antimicrobial functions.
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Affiliation(s)
- Sue Woon Tan
- School of Chemical Engineering and Translational Nanobioscience Research Center, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Negin Gooran
- School of Chemical Engineering and Translational Nanobioscience Research Center, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hye Min Lim
- School of Healthcare and Biomedical Engineering, Chonnam National University, Yeosu 59626, Republic of Korea
- Interdisciplinary Program of Biomedical Engineering, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Bo Kyeong Yoon
- School of Healthcare and Biomedical Engineering, Chonnam National University, Yeosu 59626, Republic of Korea
- Interdisciplinary Program of Biomedical Engineering, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Joshua A. Jackman
- School of Chemical Engineering and Translational Nanobioscience Research Center, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Valeeva LR, Dzhabrailova SM, Sharipova MR. cis-Prenyltransferases of Marchantia polymorpha: Phylogenetic Analysis and Perspectives for Use as Regulators of Antimicrobial Agent Synthesis. Mol Biol 2022. [DOI: 10.1134/s002689332206019x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Dhahi TS, Adam T, Gopinath SCB, Hashim U. Gold nanogap impedimetric biosensor for precise and selective Ganoderma boninense detection. 3 Biotech 2022; 12:299. [PMID: 36276457 PMCID: PMC9522946 DOI: 10.1007/s13205-022-03368-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/17/2022] [Indexed: 11/01/2022] Open
Abstract
Ganoderma species are common wood-rotting fungi that cause root and stem rot in most monocots, dicots, and gymnosperms. It influences plantation crops such as oil palm and rubber in Malaysia, but the effects vary greatly within the genus. Because of the complex chemistry of Ganoderma, extracting and identifying the physiologically active chemicals is often time-consuming and necessitates extensive bioassays. This study investigated the specific identification of the most infectious Ganoderma species using a sub-20-nm gold electrode. Three electrodes were created using chemically controlled etching (2, 10, and 20 nm). An AutoCAD mask containing nanogap pad electrodes was used to create a chrome glass surface, which was then translated and built. Following the successful construction of the device, the sensor was evaluated using a combination of conventional photolithography and a size reduction technique to imprint the nanogap design onto the gold surface. Ganoderma boninense target DNA was synthesised and surface-modified to enable interaction at extremely low molecular concentrations. The proposed device has a detection limit of 0.001 mol/L, which is seven times lower than the detection limits of currently available devices. The capacitance, conductivity, and permittivity of complementary, non-complementary, single mismatched, and targeted biomolecules changed during hybridization. This sensor correctly differentiated between all samples. The sensor's performance is further validated by comparing experimental data from the sensor to theoretical data from the sensor's corresponding circuit model. The two data sets are very similar.
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Affiliation(s)
- Thikra S. Dhahi
- Electronics Technical Department, Southern Technical University, Basra, Iraq
- Faculty of Electronic Engineering & Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
| | - Tijjani Adam
- Faculty of Electronic Engineering & Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
| | - Subash C. B. Gopinath
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
- Centre of Excellence for Nanobiotechnology and Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, Semeling, 08100 Kedah, Malaysia
| | - U. Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
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Zhou X, Liu S, Gao W, Hu B, Zhu B, Sun L. Monoterpenoids Evolution and MEP Pathway Gene Expression Profiles in Seven Table Grape Varieties. PLANTS 2022; 11:plants11162143. [PMID: 36015445 PMCID: PMC9413098 DOI: 10.3390/plants11162143] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022]
Abstract
This research investigated the evolution of both monoterpenoids and expression profiles of related biosynthesis genes in the MEP pathway in seven different table grape varieties from veraison to maturity stage in two seasons, and the correlation was further evaluated between monoterpenoid accumulation and expression of these genes studied in these varieties. Results showed that linalool, trans-furan linalool oxide, geraniol, and cis-furan linalool oxide were the main compounds in the five Muscat varieties two seasons. ‘Zaomeiguixiang’ had the highest contents of geraniol and β-Citronellol. ‘Xiangfei’ had the most abundant of linalool and cis-furan linalool oxide, whereas the neutral varieties of ‘Moldova’ and ‘Christmas Rose’ had the least amount. Monoterpenoid volatiles have been grouped in three evolutionary patterns in the berry development of these varieties. ‘Zaomeiguixiang’ and ‘Xiangfei’ had distinct different pattern of terpenoids evolution profiles. Pearson’s correlation analysis showed that in the MEP pathway, the first biosynthesis gene VvDXS3 was significantly correlated to the accumulation of monoterpenoids, and appeared to be an important candidate gene for synthesis of the monoterpenoids.
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Affiliation(s)
- Xiaomiao Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Department of Food Science and Engineering, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100093, China
| | - Songyu Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Department of Food Science and Engineering, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100093, China
| | - Wengping Gao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Department of Food Science and Engineering, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Binfang Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Department of Food Science and Engineering, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Baoqing Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Department of Food Science and Engineering, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Correspondence: (B.Z.); (L.S.)
| | - Lei Sun
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100093, China
- Correspondence: (B.Z.); (L.S.)
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Zhao Y, Vlasselaer L, Ribeiro B, Terzoudis K, Van den Ende W, Hertog M, Nicolaï B, De Coninck B. Constitutive Defense Mechanisms Have a Major Role in the Resistance of Woodland Strawberry Leaves Against Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2022; 13:912667. [PMID: 35874021 PMCID: PMC9298464 DOI: 10.3389/fpls.2022.912667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
The necrotrophic fungus Botrytis cinerea is a major threat to strawberry cultivation worldwide. By screening different Fragaria vesca genotypes for susceptibility to B. cinerea, we identified two genotypes with different resistance levels, a susceptible genotype F. vesca ssp. vesca Tenno 3 (T3) and a moderately resistant genotype F. vesca ssp. vesca Kreuzkogel 1 (K1). These two genotypes were used to identify the molecular basis for the increased resistance of K1 compared to T3. Fungal DNA quantification and microscopic observation of fungal growth in woodland strawberry leaves confirmed that the growth of B. cinerea was restricted during early stages of infection in K1 compared to T3. Gene expression analysis in both genotypes upon B. cinerea inoculation suggested that the restricted growth of B. cinerea was rather due to the constitutive resistance mechanisms of K1 instead of the induction of defense responses. Furthermore, we observed that the amount of total phenolics, total flavonoids, glucose, galactose, citric acid and ascorbic acid correlated positively with higher resistance, while H2O2 and sucrose correlated negatively. Therefore, we propose that K1 leaves are more resistant against B. cinerea compared to T3 leaves, prior to B. cinerea inoculation, due to a lower amount of innate H2O2, which is attributed to a higher level of antioxidants and antioxidant enzymes in K1. To conclude, this study provides important insights into the resistance mechanisms against B. cinerea, which highly depend on the innate antioxidative profile and specialized metabolites of woodland strawberry leaves.
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Affiliation(s)
- Yijie Zhao
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Heverlee, Belgium
| | - Liese Vlasselaer
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Heverlee, Belgium
| | - Bianca Ribeiro
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Heverlee, Belgium
| | - Konstantinos Terzoudis
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Heverlee, Belgium
| | - Wim Van den Ende
- KU Leuven Plant Institute, Heverlee, Belgium
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Maarten Hertog
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Heverlee, Belgium
| | - Bart Nicolaï
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Heverlee, Belgium
- Flanders Centre of Postharvest Technology, Leuven, Belgium
| | - Barbara De Coninck
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Heverlee, Belgium
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11
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Genetic Diversity of Ancient Camellia sinensis (L.) O.Kuntze in Sandu County of Guizhou Province in China. DIVERSITY 2021. [DOI: 10.3390/d13060276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The ancient tea plant germplasm is an important resource for breeding new tea plant varieties and has great economic value. However, due to man-made and natural disturbances, it has become endangered. In order to have a better management of the conserved tea plant germplasm, it is a requirement to understand the genetic and phenotypic diversity. The aim of this study was to evaluate the genetic and phenotypic diversity of 145 ancient tea plant germplasm resources from five populations in Sandu County of Guizhou province in China. To explore the population genetics of tea plant, we successfully identified 15 simple sequence repeat (SSR) markers, which were highly polymorphic. Additionally, we applied traditional phenotypic methods to evaluate the tea plant diversity. The results suggested that the genetic and phenotypic diversity were relatively high. A total of 96 alleles were identified, and the mean polymorphic information content (PIC) value was found to be 0.66. The analysis of molecular variance (AMOVA) showed that genetic variation within the populations was greater than among the populations. Overall, our results are the valuable baseline data in developing more efficient management and breeding plans for one of the most popular non-alcoholic beverage crops, the tea plant species.
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12
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Sevestre F, Facon M, Wattebled F, Szydlowski N. Facilitating gene editing in potato: a Single-Nucleotide Polymorphism (SNP) map of the Solanum tuberosum L. cv. Desiree genome. Sci Rep 2020; 10:2045. [PMID: 32029861 PMCID: PMC7005264 DOI: 10.1038/s41598-020-58985-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 01/21/2020] [Indexed: 11/09/2022] Open
Abstract
Genome editing is a powerful tool for plant functional genomics allowing for multiallelic targeted mutagenesis. The recent development of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated protein 9 (Cas9) systems for gene editing in plants allows for simple, cost-effective introduction of site-specific double-stranded DNA breaks. The nuclear genomes of a homozygous doubled-monoploid potato clone (DM) and a heterozygous diploid clone (RH) have been sequenced in 2011. However, common potato cultivars display a highly heterozygous autotetraploid genome thus complicating target design for tetra-allelic gene editing. Here, we report on the SNP physical map of the widely used Solanum tuberosum L. cv. Desiree and on the position of the diverse indels providing an essential tool for target design in genome editing approaches. We used this tool for designing a specific gRNA and successfully knocking-out a newly discovered starch synthase gene (SS6) in potato. Resequencing data are publicly available at the Sequence Read Archive of the NCBI (accession number: PRJNA507597) and will represent a valuable resource for functional genomic studies of various metabolic pathways, cell and plant physiology as well as high-throughput reverse genetics in potato.
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Affiliation(s)
- François Sevestre
- Univ. Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Maud Facon
- Univ. Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Fabrice Wattebled
- Univ. Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Nicolas Szydlowski
- Univ. Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
- Univ. Lille, CNRS, USR 3290 - MSAP - Miniaturisation pour la Synthèse l'Analyse et la Protéomique, F-59000, Lille, France.
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13
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Diversity of Onygenalean Fungi in Keratin-Rich Habitats of Maharashtra (India) and Description of Three Novel Taxa. Mycopathologia 2019; 185:67-85. [PMID: 31187339 DOI: 10.1007/s11046-019-00346-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
Abstract
Extensive survey was carried out in the state of Maharashtra, India, as part of a 3-year project to explore keratinophilic fungal diversity for conservation and biotechnological potential. A total of 578 soil samples were collected from keratin-rich habitats across 24 districts of Maharashtra State. Hair-baiting technique and micro-dilution drop-trail method were employed for isolation and purification of keratinophilic fungi from soil. A total of 66 species belonging to 17 genera of order Onygenales were recorded in hair baits. Eleven taxa were found to be new to science, most of which were rare as they were recorded in only one sample out of the > 500 samples analyzed. Three novel taxa have been characterized at morphological and molecular level and described here as new to science. These taxa include Currahmyces indicus gen. et sp. nov., Canomyces reticulatus gen. et sp. nov., Ctenomyces indicus sp. nov. All these novel taxa are morphologically and phylogenetically distinct from known taxa of order Onygenales. The study indicates that systematic sampling of a larger area is needed to uncover the hidden (unknown) diversity of keratinophilic fungi which is overlooked in sporadic samplings as evident from previous studies.
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A simple and effective method to obtain high DNA quality and quantity from Cerrado plant species. Mol Biol Rep 2019; 46:4611-4615. [PMID: 31073915 DOI: 10.1007/s11033-019-04845-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/30/2019] [Indexed: 02/03/2023]
Abstract
Despite the importance in conservation and breeding purposes, molecular studies using Cerrado plant species are still rare, mainly because of their high amounts of secondary compounds, impeding DNA extraction to downstream applications, such as PCR amplification. To date, the DNA extraction methods described are sometimes inadequate for these species, expensive, time-intensive and/or use very toxic reagents. Here, we present a simple and effective method, based on SDS and Triton X-100, to obtain high DNA quality and quantity from Cerrado plant species for molecular biological techniques. The DNA obtained by our protocol was free of contaminants and excellent for enzymatic restriction and PCR amplification. The concentration of extracted DNA across all tested species ranged from 156 to 1166 ng µL-1 (1.56-11.66 µg g-1 of dry tissue), with an A260/A280 ratio from 1.78 to 1.92. The new DNA extraction protocol described here provides high DNA quality and quantity from Cerrado plant species in a fast, simple and less toxic way. Thus, the use of our method will allow ecologists, geneticists and breeders to rapidly obtain high-quality and -quantity DNA from Cerrado plant species for any molecular biology study.
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15
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Zhang X, Yu Y, Jiang S, Yu H, Xiang Y, Liu D, Qu Y, Cui X, Ge F. Oleanane-Type Saponins Biosynthesis in Panax notoginseng via Transformation of β-Amyrin Synthase Gene from Panax japonicus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1982-1989. [PMID: 30742432 DOI: 10.1021/acs.jafc.8b07183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Oleanane-type saponins considered as the main medicinal ingredients in Panax japonicus are not found in Panax notoginseng. β-Amyrin synthase (βAS) was recognized as the first key enzyme in the biosynthetic branch of oleanane-type saponins. In this study, βAS gene from P. japonicus ( PjβAS) was transferred into P. notoginseng cells. Along with PjβAS expression in the transgenic cells, the expression levels of several key enzyme genes related to triterpenoid saponins biosynthesis and the content of P. notoginseng saponins were also increased. Two oleanane-type saponins, chikusetsusaponin IV and chikusetsusaponin IVa, contained in P. japonicus were first discovered in transgenic P. notoginseng cells. This study successfully constructed a biosynthetic pathway of oleanane-type saponins in P. notoginseng by introducing just one gene into the species. On the basis of this discovery and previous studies, the common biosynthetic pathway of triterpenoid saponins in Panax genus may be unified to some extent.
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Affiliation(s)
- Xiang Zhang
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
| | - Yilin Yu
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
| | - Sen Jiang
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
| | - Hong Yu
- School of Life Science , Yunnan University , Kunming 650500 , China
| | - Yingying Xiang
- Department of Stomatology , Yan'an Hospital Affiliated to Kunming Medical University , Kunming 650031 , China
| | - Diqiu Liu
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
| | - Yuan Qu
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
| | - Xiuming Cui
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
| | - Feng Ge
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
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16
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Watanabe K, Nozawa S, Hsiang T, Callan B. The cup fungus Pestalopezia brunneopruinosa is Pestalotiopsis gibbosa and belongs to Sordariomycetes. PLoS One 2018; 13:e0197025. [PMID: 29949577 PMCID: PMC6021046 DOI: 10.1371/journal.pone.0197025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/24/2018] [Indexed: 01/09/2023] Open
Abstract
Pestalopezia brunneopruinosa, the type species of Pestalopezia in Leotiomycetes, produces typical cup-shaped ascomata. Because its asexual morph has conidia comprised of five cells including apical and basal appendages and three pigmented median cells, it was first described as Pestalotia gibbosa, which belongs to Sordariomycetes. This contradiction has not been resolved due to the difficulty in isolating this fungus in culture. In this study, we isolated separate strains from the sexual morph and the asexual morph for molecular analysis. Phylogenetic trees of Sporocadaceae based on internal transcribed spacer, partial β-tubulin, and partial translation elongation factor 1-alpha sequence datasets revealed that both strains fall into the same taxon, in a clade in Pestalotiopsis sensu stricto alongside P. gaultheriae and P. spathulata. We provide the first evidence that fungi producing cup-shaped ascomata in Pestalotiopsis belong to Sordariomycetes, and we have proposed the transfer of Pestalopezia brunneopruinosa to Pestalotiopsis gibbosa.
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Affiliation(s)
- Kyoko Watanabe
- Graduate School of Agriculture, Tamagawa University, Machida, Tokyo, Japan
| | - Shunsuke Nozawa
- Graduate School of Agriculture, Tamagawa University, Machida, Tokyo, Japan
| | - Tom Hsiang
- Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Brenda Callan
- Pacific Forestry Centre, Natural Resources Canada, Victoria, British Columbia, Canada
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17
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Mohammed Abubakar B, Mohd Salleh F, Shamsir Omar MS, Wagiran A. Review: DNA Barcoding and Chromatography Fingerprints for the Authentication of Botanicals in Herbal Medicinal Products. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2017; 2017:1352948. [PMID: 28536641 PMCID: PMC5425840 DOI: 10.1155/2017/1352948] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/11/2017] [Accepted: 03/16/2017] [Indexed: 01/28/2023]
Abstract
In the last two decades, there has been a tremendous increase in the global use of herbal medicinal products (HMPs) due to their claimed health benefits. This has led to increase in their demand and consequently, also, resulted in massive adulteration. This is due to the fact that most of the traditional methods cannot identify closely related species in a process product form. Therefore the urgent need for simple and rapid identification methods resulted in the discovery of a novel technique. DNA barcoding is a process that uses short DNA sequence from the standard genome for species identification. This technique is reliable and is not affected by external factors such as climates, age, or plant part. The difficulties in isolation of DNA of high quality in addition to other factors are among the challenges encountered using the DNA barcoding in the authentication of HMP. These limitations indicated that using DNA barcoding alone may ineffectively authenticate the HMP. Therefore, the combination of DNA barcoding with chromatographic fingerprint, a popular and generally accepted technique for the assessment and quality control of HMP, will offer an efficient solution to effectively evaluate the authenticity and quality consistency of HMP. Detailed and quality information about the main composition of the HMPs will help to ascertain their efficacy and safety as these are very important for quality control.
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Affiliation(s)
- Bashir Mohammed Abubakar
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
- Department of Biological Sciences, Bauchi State University Gadau, PMB 065, Bauchi, Nigeria
| | - Faezah Mohd Salleh
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir Omar
- Department of Biosciences & Health Sciences, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
| | - Alina Wagiran
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
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18
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Selection of efficient Taq DNA polymerase to optimize T-DNA genotyping method for rapid detection of mutant Arabidopsis thaliana plants. BIONANOSCIENCE 2017; 6:407-410. [PMID: 28191385 DOI: 10.1007/s12668-016-0253-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Plants harbor homologues of various animal genes involved in phosphorus metabolism, telomere biology and other cellular processes. Compared to experiments with many other multicellular organisms, research in the model plant Arabidopsis thaliana takes advantage of short generation time and an ever increasing arsenal of genetic and transgenic tools, including large collections of T-DNA knockout and activation lines. The availability of thousands of publicly available transgenic Arabidopsis lines provides a unique opportunity to address a number of important biological questions. However, identification of individual T-DNA mutant plants from a pool of seeds provided by a biological stock distribution center remains a laborious and time-consuming procedure. Here we compared a number of commercial Taq DNA polymerases commonly used for routine PCR genotyping to identify a single polymerase most suitable for genotyping T-DNA mutant plants. Our data indicate that Emerald Amp GT PCR Master Mix provides the most reliable, quick and simple DNA genotyping tool to determine the presence of a T-DNA insertion and to establish whether an individual A. thaliana plant is heterozygous or homozygous for the mutant allele.
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19
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Soffritti G, Busconi M, Sánchez RA, Thiercelin JM, Polissiou M, Roldán M, Fernández JA. Genetic and Epigenetic Approaches for the Possible Detection of Adulteration and Auto-Adulteration in Saffron (Crocus sativus L.) Spice. Molecules 2016; 21:343. [PMID: 26978342 PMCID: PMC6273936 DOI: 10.3390/molecules21030343] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/05/2016] [Accepted: 03/04/2016] [Indexed: 11/16/2022] Open
Abstract
Saffron (Crocus sativus L.) is very expensive and, because of this, often subject to adulteration. Modern genetic fingerprinting techniques are an alternative low cost technology to the existing chemical techniques, which are used to control the purity of food products. Buddleja officinalis Maxim, Gardenia jasminoides Ellis, Curcuma longa L., Carthamus tinctorius L. and Calendula officinalis L. are among the most frequently-used adulterants in saffron spice. Three commercial kits were compared concerning the ability to recover PCR-grade DNA from saffron, truly adulterated samples and possible adulterants, with a clear difference among them, mainly with the processed samples. Only one of the three kits was able to obtain amplifiable DNA from almost all of the samples, with the exception of extracts. On the recovered DNA, new markers were developed based on the sequence of the plastid genes matK and rbcL. These primers, mainly those developed on matK, were able to recognize saffron and the adulterant species and also in mixtures with very low percentages of adulterant. Finally, considering that the addition of different parts of saffron flowers is one of the most widespread adulterations, by analyzing the DNA of the different parts of the flower (styles, stamens and tepals) at the genetic and epigenetic level, we succeeded in finding differences between the three tissues that can be further evaluated for a possible detection of the kind of fraud.
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Affiliation(s)
- Giovanna Soffritti
- Department of Sustainable Crop Production, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, Piacenza 29122, Italy.
| | - Matteo Busconi
- Department of Sustainable Crop Production, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, Piacenza 29122, Italy.
- BioDNA, Centro di Ricerca sulla biodiversità e sul DNA antico, Università Cattolica del Sacro Cuore, Piacenza 29122, Italy.
| | - Rosa Ana Sánchez
- Laboratory of Biotechnology and Natural Resources, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, IDR-Biotecnología, Campus Universitario s/n, Albacete 02071, Spain.
| | - Jean-Marie Thiercelin
- Tradimpex Jm Thiercelin sas, Parc de l'Ecopôle 3 Rue Pierre et Marie Curie, Combs La Ville 77380, France.
| | - Moschos Polissiou
- Laboratory of Chemistry, Department of Food Science and Human Nutrition, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos, Athens 11855, Greece.
| | - Marta Roldán
- Laboratory of Biotechnology and Natural Resources, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, IDR-Biotecnología, Campus Universitario s/n, Albacete 02071, Spain.
| | - José Antonio Fernández
- Laboratory of Biotechnology and Natural Resources, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, IDR-Biotecnología, Campus Universitario s/n, Albacete 02071, Spain.
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Abstract
Variability of leaf structure and presence of secondary metabolites in mature leaf tissue present a challenge for reliable DNA extraction from Osmanthus species and cultivars. The objective of this study was to develop a universal rapid, effective, and cost-efficient method of DNA isolation for Osmanthus mature leaf tissue. Four different methods were used to isolate DNA from 8 cultivars of Osmanthus. Absorbance spectra, DNA concentration, appearance on agarose gel, and performance in PCR were used to analyze quality, quantity, and integrity of isolated DNA. Methods were ranked in order, based on total quantity, quality, and performance points as the following: 1) solid-phase extraction (SPE), 2) modified alkaline lysis (SDS), 3) cetyltrimethylammonium bromide (CTAB) with chloroform (CHL), and 4) CTAB with phenol/chloroform (PHE). Total DNA, isolated via SPE, showed the least contamination but the lowest mean quantity (9.6 ± 3.4 μg) and highest cost. The highest quantity of DNA was isolated via SDS (117 ± 54.1 μg). SPE and SDS resolved the most individuals on agarose gel, whereas the 2 CTAB methods had poorly resolved gels. All methods except PHE performed well in PCR. Additions to the modified alkaline lysis method increased A260:A230 by up to 59% without affecting yield. With the use of SDS, an average of 1000 μg/g DNA was isolated from fresh leaf tissue of 18 samples in ∼1.5 h at a cost of 0.74 U.S. dollars (USD)/sample. We recommend improved alkaline lysis as a rapid, effective, and cost-efficient method of isolating DNA from Osmanthus species.
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Affiliation(s)
- Lisa Alexander
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Otis L. Floyd Nursery Research Center, McMinnville, Tennessee, USA
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