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Hassan A, Zaib S, Anjum T. Evaluation of antifungal potentials of Albizia kalkora extract as a natural fungicide: In vitro and computational studies. Bioorg Chem 2024; 150:107561. [PMID: 38936050 DOI: 10.1016/j.bioorg.2024.107561] [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: 05/20/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/29/2024]
Abstract
The antifungal bioactivity potential of the organic extract of silk tree (Albizia kalkora) was investigated in the current study. The crude extracts of A. kalkora and methanol, n-hexane, chloroform, and ethyl acetate fractions were prepared. The antifungal activity of obtained fractions of A. kalkora was studied at different concentrations ranging from 0.39-50 µg/mL. Dimethyl sulfoxide (DMSO) was taken as a toxicity control, whereas thiophanate methyl (TM) as a positive control. All the fractions significantly reduced the FOL growth (methanolic: 9.49-94.93 %, n-hexane: 11.12-100 %, chloroform: 20.96-91.41 %, and ethyl acetate: 18.75-96.70 %). The n-hexane fraction showed 6.25 µg/mL MIC as compared to TM with 64 µg/mL MIC. The non-polar (n-hexane) fraction showed maximum antifungal bioactivity against FOL in comparison with chloroform, methanol, and ethyl acetate fractions. GC/MS analysis exhibited that the n-hexane fraction contained hexadecanoic acid, 9,12,15-octadecatrienoic acid, 9,12-octadecadienoic acid, bis(2-ethylhexyl) phthalate, methyl stearate, and [1,2,4]triazolo[1,5-a]pyrimidine-6-carboxylic acid. The results of in vitro antifungal inhibition were further reinforced by molecular docking analysis. Five virulence proteins of FOL i.e., pH-responsive PacC transcription factor (PACC), MeaB, TOR; target of rapamycin (FMK1), Signal transducing MAP kinase kinase (STE-STE7), and High Osmolarity Glycerol 1(HOG1) were docked with identified phytocompounds in the n-hexane fraction by GC/MS analysis. MEAB showed maximum binding affinities with zinnimide (-12.03 kcal/mol), HOG1 and FMK1with α-Tocospiro-B (-11.51 kcal/mol) and (-10.55 kcal/mol) respectively, STE-STE7 with docosanoic acid (-11.31 kcal/mol), and PACC with heptadecanoic acid (-9.88 kcal/mol) respectively with strong hydrophobic or hydrophilic interactions with active pocket residues. In conclusion, the n-hexane fraction of the A. kalkora can be used to manage FOL.
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Affiliation(s)
- Ahmad Hassan
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan.
| | - Tehmina Anjum
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54000, Pakistan
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Okechukwu VO, Kappo AP, Njobeh PB, Mamo MA. Morphed aflaxotin concentration produced by Aspergillus flavus strain VKMN22 on maize grains inoculated on agar culture. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 8:100197. [PMID: 38468716 PMCID: PMC10925925 DOI: 10.1016/j.fochms.2024.100197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/13/2024] [Accepted: 02/25/2024] [Indexed: 03/13/2024]
Abstract
This study identified and monitored the levels of aflatoxins (B1 and B2) produced by Aspergillus flavus isolate VKMN22 (OP355447) in maize samples sourced from a local shop in Johannesburg, South Africa. Maize samples underwent controlled incubation after initial rinsing, and isolates were identified through morphological and molecular methods. In another experiment, autoclaved maize grains were intentionally re-inoculated with the identified fungal isolate using spore suspension (106 spore/mL), after which 1 g of the contaminated maize sample was inoculated on PDA media and cultured for seven days. The aflatoxin concentrations in the A. flavus contaminated maize inoculated on culture media was monitored over seven weeks and then measured using liquid chromatography-mass spectroscopy (LC-MS). Results confirmed the successful isolation of A. flavus strain VKMN22 with accession number OP355447, which consistently produced higher levels of AFB1 compared to AFB2. AF concentrations increased from week one to five, then declined in week six and seven. AFB1 levels ranged from 594.3 to 9295.33 µg/kg (week 1-5) and then reduced from 5719.67 to 2005 µg/kg in week six and seven), while AFB2 levels ranged from 4.92 to 901.67 µg/kg (weeks 1-5) and then degraded to 184 µg/kg in week six then 55.33 µg/kg (weeks 6-7). Levene's tests confirmed significantly higher mean concentrations of AFB1 compared to AFB2 (p ≤ 0.005). The study emphasizes the importance of consistent biomonitoring for a dynamic understanding of AF contamination, informing accurate prevention and control strategies in agricultural commodities thereby safeguarding food safety.
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Affiliation(s)
- Viola O. Okechukwu
- Department of Biochemistry, Auckland Park Kingsway Campus, University of Johannesburg, South Africa
| | - Abidemi P. Kappo
- Department of Biochemistry, Auckland Park Kingsway Campus, University of Johannesburg, South Africa
| | - Patrick B. Njobeh
- Department of Food and Biotechnology, PO Box 17011, Doornfontein Campus, University of Johannesburg, South Africa
| | - Messai A. Mamo
- Department of Chemical Sciences, PO Box 2028, Doornfontein Campus, University of Johannesburg, South Africa
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Panhwar S, Çelikkan H, Evran E, Ekiz E, Ozkan Hukum K, Çetin D, Suludere Z, Hakki Boyaci I, Tamer U. Phage probe on RAFT polymer surface for rapid enumeration of E. coli K12. Bioelectrochemistry 2024; 160:108785. [PMID: 39094446 DOI: 10.1016/j.bioelechem.2024.108785] [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: 03/09/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
This study presents a simple, fast, and sensitive label-free sensing assay for the precise enumeration of modeled pathogenic Escherichia coli K12 (E. coli K12) bacteria for the first time. The method employs the covalent binding bacteriophage technique on the surface of a reversible addition-fragmentation chain transfer (RAFT) polymer film. The Nyquist plots obtained from electrochemical impedance spectroscopy (EIS) identified the charge transfer resistance Rct was calculated from a suitable electrochemical circuit model through an evaluation of the relevant parameter after the immobilization of the bacteriophage and the binding of specific E. coli K12. The impedimetric biosensor reveals specific and reproducible detection with sensitivity in the linear working range of 104.2-107.0 CFU/mL, a limit of detection (LOD) of 101.3 CFU/mL, and a short response time of 15 min. The SERS response validates the surface roughness and interaction of the SERS-tag with E. coli K12-modified electrodes. Furthermore, the covalently immobilized active phage selectivity was proved against various non-targeting bacterial strains in the presence of targeted E.coli K12 with a result of 94 % specificity and 98 % sensitivity. Therefore, the developed phage-based electrode surface can be used as a disposable, label-free impedimetric biosensor for rapid and real-time monitoring of serum samples.
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Affiliation(s)
- Sallahuddin Panhwar
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye; Department of Civil Engineering, National University of Sciences and Technology, Quetta 24090, Balochistan, Pakistan
| | - Hüseyin Çelikkan
- Gazi University, Faculty of Science, Department of Chemistry, Ankara, Türkiye
| | - Eylul Evran
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe 06800 Ankara, Türkiye
| | - Esra Ekiz
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe 06800 Ankara, Türkiye
| | - Kubra Ozkan Hukum
- Gazi University, Faculty of Science, Department of Chemistry, Ankara, Türkiye
| | - Demet Çetin
- Department of Mathematics and Science Education, Gazi Faculty of Education, Gazi University, Besevler, Ankara 06500, Türkiye
| | - Zekiye Suludere
- Faculty of Science, Department of Biology, Gazi University, 06500 Ankara, Türkiye
| | - Ismail Hakki Boyaci
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe 06800 Ankara, Türkiye
| | - Uğur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye; METU MEMS Research and Application Center, Ankara, Türkiye.
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Karim MJ, Goni MOF, Nahiduzzaman M, Ahsan M, Haider J, Kowalski M. Enhancing agriculture through real-time grape leaf disease classification via an edge device with a lightweight CNN architecture and Grad-CAM. Sci Rep 2024; 14:16022. [PMID: 38992069 PMCID: PMC11239930 DOI: 10.1038/s41598-024-66989-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024] Open
Abstract
Crop diseases can significantly affect various aspects of crop cultivation, including crop yield, quality, production costs, and crop loss. The utilization of modern technologies such as image analysis via machine learning techniques enables early and precise detection of crop diseases, hence empowering farmers to effectively manage and avoid the occurrence of crop diseases. The proposed methodology involves the use of modified MobileNetV3Large model deployed on edge device for real-time monitoring of grape leaf disease while reducing computational memory demands and ensuring satisfactory classification performance. To enhance applicability of MobileNetV3Large, custom layers consisting of two dense layers were added, each followed by a dropout layer, helped mitigate overfitting and ensured that the model remains efficient. Comparisons among other models showed that the proposed model outperformed those with an average train and test accuracy of 99.66% and 99.42%, with a precision, recall, and F1 score of approximately 99.42%. The model was deployed on an edge device (Nvidia Jetson Nano) using a custom developed GUI app and predicted from both saved and real-time data with high confidence values. Grad-CAM visualization was used to identify and represent image areas that affect the convolutional neural network (CNN) classification decision-making process with high accuracy. This research contributes to the development of plant disease classification technologies for edge devices, which have the potential to enhance the ability of autonomous farming for farmers, agronomists, and researchers to monitor and mitigate plant diseases efficiently and effectively, with a positive impact on global food security.
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Affiliation(s)
- Md Jawadul Karim
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi, 6204, Bangladesh
| | - Md Omaer Faruq Goni
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi, 6204, Bangladesh
| | - Md Nahiduzzaman
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi, 6204, Bangladesh
| | - Mominul Ahsan
- Department of Computer Science, University of York, Deramore Lane, Heslington, York, YO10 5GH, UK
| | - Julfikar Haider
- Department of Engineering, Manchester Metropolitan University, Chester Street, Manchester, M1 5GD, UK
| | - Marcin Kowalski
- Institute of Optoelectronics, Military University of Technology, Gen. S. Kaliskiego 2, 00-908, Warsaw, Poland.
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Clark S, Bessin R, Gonthier D, Larson J. Evaluation of Ten Alternative Treatments for the Management of Harlequin Bug ( Murgantia histrionica) on Brassica Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1618. [PMID: 38931050 PMCID: PMC11207866 DOI: 10.3390/plants13121618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Harlequin bug (Murgantia histrionica) poses a significant threat to cruciferous vegetable crops, leading to economic losses and challenges in sustainable agriculture. This 2-year field study evaluated the efficacy of exclusion netting and selected biopesticides in controlling harlequin bug populations in a field-grown broccoli crop. Treatments included an untreated control, industry standards Azera and Entrust, and ProtekNet mesh netting. Additionally, three commercial essential oil treatments including Essentria IC-3, Nature-Cide, and Zero Tolerance were tested along with two bokashi fermented composting products BrewKashi and Oriental Herbal Nutrient (OHN). During both the first and second year of the study, none of the commercially produced essential oil products or bokashi products were effective in controlling harlequin bug or preventing leaf scars. Conversely, ProtekNet consistently provided the highest level of protection against harlequin bugs of all stages as well as leaf damage scars; it also provided the largest broccoli head width and highest yield. Entrust showed similar results compared to ProtekNet, both with the control of harlequin bug life stages and with leaf scars. These findings indicate that both ProtekNet and Entrust are effective organic alternatives for managing harlequin bug on broccoli, while the selected essential oil and bokashi products do not appear to be effective.
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Affiliation(s)
- Sarah Clark
- Department of Entomology, S-225 Ag. Sci. Center North, University of Kentucky, Lexington, KY 40546, USA; (R.B.); (D.G.); (J.L.)
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Majumder A, Bano S. How the Western Diet Thwarts the Epigenetic Efforts of Gut Microbes in Ulcerative Colitis and Its Association with Colorectal Cancer. Biomolecules 2024; 14:633. [PMID: 38927037 PMCID: PMC11201633 DOI: 10.3390/biom14060633] [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: 05/04/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Ulcerative colitis (UC) is an autoimmune disease in which the immune system attacks the colon, leading to ulcer development, loss of colon function, and bloody diarrhea. The human gut ecosystem consists of almost 2000 different species of bacteria, forming a bioreactor fueled by dietary micronutrients to produce bioreactive compounds, which are absorbed by our body and signal to distant organs. Studies have shown that the Western diet, with fewer short-chain fatty acids (SCFAs), can alter the gut microbiome composition and cause the host's epigenetic reprogramming. Additionally, overproduction of H2S from the gut microbiome due to changes in diet patterns can further activate pro-inflammatory signaling pathways in UC. This review discusses how the Western diet affects the microbiome's function and alters the host's physiological homeostasis and susceptibility to UC. This article also covers the epidemiology, prognosis, pathophysiology, and current treatment strategies for UC, and how they are linked to colorectal cancer.
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Affiliation(s)
- Avisek Majumder
- Department of Medicine, University of California, San Francisco, CA 94158, USA
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Chen C, Li SL, Xu YY, Liu J, Graham DW, Zhu YG. Characterising global antimicrobial resistance research explains why One Health solutions are slow in development: An application of AI-based gap analysis. ENVIRONMENT INTERNATIONAL 2024; 187:108680. [PMID: 38723455 DOI: 10.1016/j.envint.2024.108680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
The global health crisis posed by increasing antimicrobial resistance (AMR) implicitly requires solutions based a One Health approach, yet multisectoral, multidisciplinary research on AMR is rare and huge knowledge gaps exist to guide integrated action. This is partly because a comprehensive survey of past research activity has never performed due to the massive scale and diversity of published information. Here we compiled 254,738 articles on AMR using Artificial Intelligence (AI; i.e., Natural Language Processing, NLP) methods to create a database and information retrieval system for knowledge extraction on research perfomed over the last 20 years. Global maps were created that describe regional, methodological, and sectoral AMR research activities that confirm limited intersectoral research has been performed, which is key to guiding science-informed policy solutions to AMR, especially in low-income countries (LICs). Further, we show greater harmonisation in research methods across sectors and regions is urgently needed. For example, differences in analytical methods used among sectors in AMR research, such as employing culture-based versus genomic methods, results in poor communication between sectors and partially explains why One Health-based solutions are not ensuing. Therefore, our analysis suggest that performing culture-based and genomic AMR analysis in tandem in all sectors is crucial for data integration and holistic One Health solutions. Finally, increased investment in capacity development in LICs should be prioritised as they are places where the AMR burden is often greatest. Our open-access database and AI methodology can be used to further develop, disseminate, and create new tools and practices for AMR knowledge and information sharing.
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Affiliation(s)
- Cai Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shu-Le Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jue Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China; Institute for Global Health and Development, Peking University, Beijing 100191, China
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle, UK.
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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8
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Afzal A, Mukhtar T. Revolutionizing nematode management to achieve global food security goals - An overview. Heliyon 2024; 10:e25325. [PMID: 38356601 PMCID: PMC10865254 DOI: 10.1016/j.heliyon.2024.e25325] [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: 08/29/2023] [Revised: 12/07/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Nematodes are soil-dwelling organisms that inflict substantial damage to crops, resulting in significant declines in agricultural productivity. Consequently, they are recognized as one of the primary contributors to global crop damage, with profound implications for food security. Nematology research assumes a pivotal role in tackling this issue and safeguarding food security. The pursuit of nematology research focused on mitigating nematode-induced crop damage and promoting sustainable agriculture represents a fundamental strategy for enhancing food security. Investment in nematology research is crucial to advance food security objectives by identifying and managing nematode species, developing novel technologies, comprehending nematode ecology, and strengthening the capabilities of researchers and farmers. This endeavor constitutes an indispensable step toward addressing one of the most pressing challenges in achieving global food security and promoting sustainable agricultural practices. Primarily, research endeavors facilitate the identification of nematode species responsible for crop damage, leading to the development of effective management strategies. These strategies encompass the utilization of resistant crop varieties, implementation of cultural practices, biological control, and chemical interventions. Secondly, research efforts contribute to the development of innovative technologies aimed at managing nematode populations, such as gene editing techniques that confer resistance to nematode infestations in crops. Additionally, the exploration of beneficial microbes, such as certain fungi and bacteria, as potential biocontrol agents against nematodes, holds promise. The study of nematode ecology represents a foundational research domain that fosters a deeper comprehension of nematode biology and ecological interactions. This knowledge is instrumental in devising precise and efficacious management strategies.
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Affiliation(s)
- Amir Afzal
- Barani Agricultural Research Institute, Chakwal, Pakistan
- Department of Plant Pathology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Tariq Mukhtar
- Department of Plant Pathology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
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Shobade SO, Zabotina OA, Nilsen-Hamilton M. Plant root associated chitinases: structures and functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1344142. [PMID: 38362446 PMCID: PMC10867124 DOI: 10.3389/fpls.2024.1344142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc3. They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5-7 and 30-40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50-60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.
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Affiliation(s)
- Samuel O. Shobade
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A. Zabotina
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Marit Nilsen-Hamilton
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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Silva EC, Quinde CA, Cieza B, Basu A, Vila MMDC, Balcão VM. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes (Basel) 2024; 15:113. [PMID: 38255005 PMCID: PMC10815195 DOI: 10.3390/genes15010113] [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: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses' taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells.
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Affiliation(s)
- Erica C. Silva
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Carlos A. Quinde
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Basilio Cieza
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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Kim DY, Patel SKS, Rasool K, Lone N, Bhatia SK, Seth CS, Ghodake GS. Bioinspired silver nanoparticle-based nanocomposites for effective control of plant pathogens: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168318. [PMID: 37956842 DOI: 10.1016/j.scitotenv.2023.168318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/15/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
Plant pathogens, including bacteria, fungi, and viruses, pose significant challenges to the farming community due to their extensive diversity, the rapidly evolving phenomenon of multi-drug resistance (MDR), and the limited availability of effective control measures. Amid mounting global pressure, particularly from the World Health Organization, to limit the use of antibiotics in agriculture and livestock management, there is increasing consideration of engineered nanomaterials (ENMs) as promising alternatives for antimicrobial applications. Studies focusing on the application of ENMs in the fight against MDR pathogens are receiving increasing attention, driven by significant losses in agriculture and critical knowledge gaps in this crucial field. In this review, we explore the potential contributions of silver nanoparticles (AgNPs) and their nanocomposites in combating plant diseases, within the emerging interdisciplinary arena of nano-phytopathology. AgNPs and their nanocomposites are increasingly acknowledged as promising countermeasures against plant pathogens, owing to their unique physicochemical characteristics and inherent antimicrobial properties. This review explores recent advancements in engineered nanocomposites, highlights their diverse mechanisms for pathogen control, and draws attention to their potential in antibacterial, antifungal, and antiviral applications. In the discussion, we briefly address three crucial dimensions of combating plant pathogens: green synthesis approaches, toxicity-environmental concerns, and factors influencing antimicrobial efficacy. Finally, we outline recent advancements, existing challenges, and prospects in scholarly research to facilitate the integration of nanotechnology across interdisciplinary fields for more effective treatment and prevention of plant diseases.
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Affiliation(s)
- Dae-Young Kim
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea
| | | | - Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Nasreena Lone
- School of Allied Healthcare and Sciences, JAIN Deemed University, Whitefield, Bangalore 560066, India
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | | | - Gajanan Sampatrao Ghodake
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea.
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12
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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Affiliation(s)
- Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain
| | - Jan E Leach
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Pankaj Trivedi
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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13
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Fernández-Pastor I, González-Menéndez V, Martínez Andrade K, Serrano R, Mackenzie TA, Benítez G, Casares-Porcel M, Genilloud O, Reyes F. Xerophytic Lichens from Gypsiferous Outcrops of Arid Areas of Andalusia as a Source of Anti-Phytopathogenic Depsides. J Fungi (Basel) 2023; 9:887. [PMID: 37754995 PMCID: PMC10532656 DOI: 10.3390/jof9090887] [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: 07/26/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
In a survey to evaluate the potential of lichens associated with gypsum areas as sources of new antifungal metabolites, six species of lichens were collected in the gypsum outcrops of the Sorbas Desert (Diploschistes ocellatus and Seirophora lacunosa) and the Tabernas Desert (Cladonia foliacea, Acarospora placodiformis, Squamarina lentigera and Xanthoparmelia pokornyi) in southern Spain. Raw lichen acetone extracts were tested against a panel of seven phytopathogenic fungi, including Botrytis cinerea, Colletotrichum acutatum, Fusarium oxysporum f.sp cubense TR4, Fusarium ploriferaum, Magnaporthe grisea, Verticillium dahliae and Zymoseptoria tritici. Active extracts of Cladonia foliacea, Xanthoparmelia pokornyi and Squamarina lentigera were analyzed by HPLC-MS/MS and Molecular Networking to identify possible metabolites responsible for the antifungal activity. A total of ten depside-like metabolites were identified by MS/MS dereplication and NMR experiments, of which one was a new derivative of fumaroprotocetraric acid. The compounds without previously described biological activity were purified and tested against the panel of fungal phytopathogens. Herein, the antifungal activity against fungal phytopathogens of 4'-O-methylpaludosic acid, divaricatic acid and stenosporic acid is reported for the first time. Stenosporic and divaricatic acids displayed a broad antifungal spectrum against seven relevant fungal phytopathogens in a micromolar range, including the extremely resistant fungus F. oxysporum f. sp. cubense Tropical Race 4 (TR4). 4'-O-methylpaludosic acid exhibited specific antifungal activity against the wheat pathogen Z. tritici, with an IC50 of 38.87 µg/mL (87.1 µM) in the absorbance-based assay and 24.88 µg/mL (55.52 µM) in the fluorescence-based assay.
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Affiliation(s)
- Ignacio Fernández-Pastor
- Fundación MEDINA, Avda. Del Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (I.F.-P.); (K.M.A.); (R.S.); (T.A.M.); (O.G.)
| | - Victor González-Menéndez
- Fundación MEDINA, Avda. Del Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (I.F.-P.); (K.M.A.); (R.S.); (T.A.M.); (O.G.)
| | - Kevin Martínez Andrade
- Fundación MEDINA, Avda. Del Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (I.F.-P.); (K.M.A.); (R.S.); (T.A.M.); (O.G.)
| | - Rachel Serrano
- Fundación MEDINA, Avda. Del Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (I.F.-P.); (K.M.A.); (R.S.); (T.A.M.); (O.G.)
| | - Thomas A. Mackenzie
- Fundación MEDINA, Avda. Del Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (I.F.-P.); (K.M.A.); (R.S.); (T.A.M.); (O.G.)
| | - Guillermo Benítez
- Department of Botany, Faculty of Pharmacy, Cartuja Campus, University of Granada, 18071 Granada, Spain; (G.B.); (M.C.-P.)
| | - Manuel Casares-Porcel
- Department of Botany, Faculty of Pharmacy, Cartuja Campus, University of Granada, 18071 Granada, Spain; (G.B.); (M.C.-P.)
| | - Olga Genilloud
- Fundación MEDINA, Avda. Del Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (I.F.-P.); (K.M.A.); (R.S.); (T.A.M.); (O.G.)
| | - Fernando Reyes
- Fundación MEDINA, Avda. Del Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (I.F.-P.); (K.M.A.); (R.S.); (T.A.M.); (O.G.)
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14
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Hromadová Z, Gálová Z, Mikolášová L, Balážová Ž, Vivodík M, Chňapek M. Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2023; 12:2763. [PMID: 37570917 PMCID: PMC10420954 DOI: 10.3390/plants12152763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023]
Abstract
Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.
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Affiliation(s)
| | | | | | | | | | - Milan Chňapek
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (Z.H.); (Z.G.); (L.M.); (Ž.B.); (M.V.)
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15
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Jeger MJ, Fielder H, Beale T, Szyniszewska AM, Parnell S, Cunniffe NJ. What Can Be Learned by a Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021? PHYTOPATHOLOGY 2023; 113:1141-1158. [PMID: 36935375 DOI: 10.1094/phyto-02-23-0069-ia] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A synoptic review of plant disease epidemics and outbreaks was made using two complementary approaches. The first approach involved reviewing scientific literature published in 2021, in which quantitative data related to new plant disease epidemics or outbreaks were obtained via surveys or similar methodologies. The second approach involved retrieving new records added in 2021 to the CABI Distribution Database, which contains over a million global geographic records of organisms from over 50,000 species. The literature review retrieved 186 articles, describing studies in 62 categories (pathogen species/species complexes) across more than 40 host species on six continents. Pathogen species with more than five articles were Bursaphelenchus xylophilus, 'Candidatus Liberibacter asiaticus', cassava mosaic viruses, citrus tristeza virus, Erwinia amylovora, Fusarium spp. complexes, F. oxysporum f. sp. cubense, Magnaporthe oryzae, maize lethal necrosis co-infecting viruses, Meloidogyne spp. complexes, Pseudomonas syringae pvs., Puccinia striiformis f. sp. tritici, Xylella fastidiosa, and Zymoseptoria tritici. Automated searches of the CABI Distribution Database identified 617 distribution records new in 2021 of 283 plant pathogens. A further manual review of these records confirmed 15 pathogens reported in new locations: apple hammerhead viroid, apple rubbery wood viruses, Aphelenchoides besseyi, Biscogniauxia mediterranea, 'Ca. Liberibacter asiaticus', citrus tristeza virus, Colletotrichum siamense, cucurbit chlorotic yellows virus, Erwinia rhapontici, Erysiphe corylacearum, F. oxysporum f. sp. cubense Tropical race 4, Globodera rostochiensis, Nothophoma quercina, potato spindle tuber viroid, and tomato brown rugose fruit virus. Of these, four pathogens had at least 25% of all records reported in 2021. We assessed two of these pathogens-tomato brown rugose fruit virus and cucurbit chlorotic yellows virus-to be actively emerging in/spreading to new locations. Although three important pathogens-'Ca. Liberibacter asiaticus', citrus tristeza virus, and F. oxysporum f. sp. cubense-were represented in the results of both our literature review and our interrogation of the CABI Distribution Database, in general, our dual approaches revealed distinct sets of plant disease outbreaks and new records, with little overlap. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Michael J Jeger
- Department of Life Sciences, Imperial College London, Ascot, U.K
| | | | | | | | - Stephen Parnell
- Warwick Crop Centre, University of Warwick, Wellesbourne Campus, Warwick, U.K
| | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge, U.K
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16
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Khan S, Zahoor M, Sher Khan R, Ikram M, Islam NU. The impact of silver nanoparticles on the growth of plants: The agriculture applications. Heliyon 2023; 9:e16928. [PMID: 37346326 PMCID: PMC10279825 DOI: 10.1016/j.heliyon.2023.e16928] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Nanotechnology is the most advanced and rapidly progressing field of science and technology. It primarily deals with developing novelty in nanomaterials by understanding and controlling matter at the nanoscale level. Silver nanoparticles (AgNPs) are the most prominent nanoparticles incorporated with wide-ranging applications, owing to their distinct characteristics. Different methods have been employed for nanoparticles synthesis like chemical method, physical method, photochemical method, top-down/bottom-up approach and biological methods. The positive impacts of silver nanoparticles have been observed in various economy-based sectors, including agriculture. The scientific curiosity about AgNPs in agriculture and plant biotechnology has shown optimum efficacy over the last few years. It not only enhances seed germination and plant growth, but also improves the quantum efficiency of the photosynthetic process. AgNPs play a vital role in agriculture by having several applications that are crucial for ensuring food security and improving crop production. Moreover, they also act as nano-pesticides, providing sufficient dose to the target plants without releasing unnecessary pesticides into the environment. Nano-fertilizers slowly release nutrients to the plants, thereby preventing excessive nutrient loss. AgNPs are utilized for effective and non-toxic pest management, making them an excellent tool for combating pests safely. They combine either edible or non-biodegradable polymers for active food packaging. In addition, AgNPs also possess diverse biological properties such as antiviral, antibacterial and antifungal activities, which protect plants from hazardous microbes. The aim of this review is to comprehensively survey and summarize recent literature regarding the positive and negative impacts of AgNPs on plant growth, as well as their agricultural applications.
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Affiliation(s)
- Sajad Khan
- Center for Biotechnology and Microbiology Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Zahoor
- Department of Biochemistry, University of Malakand at Chakdara, Dir Lower, Khyber Pakhtunkhwa, Pakistan
| | - Raham Sher Khan
- Center for Biotechnology and Microbiology Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ikram
- Department of Chemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Noor Ul Islam
- Department of Chemistry, University of Malakand at Chakdara, Dir Lower, Khyber Pakhtunkhwa, Pakistan
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17
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Watts D, Palombo EA, Jaimes Castillo A, Zaferanloo B. Endophytes in Agriculture: Potential to Improve Yields and Tolerances of Agricultural Crops. Microorganisms 2023; 11:1276. [PMID: 37317250 DOI: 10.3390/microorganisms11051276] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
Endophytic fungi and bacteria live asymptomatically within plant tissues. In recent decades, research on endophytes has revealed that their significant role in promoting plants as endophytes has been shown to enhance nutrient uptake, stress tolerance, and disease resistance in the host plants, resulting in improved crop yields. Evidence shows that endophytes can provide improved tolerances to salinity, moisture, and drought conditions, highlighting the capacity to farm them in marginal land with the use of endophyte-based strategies. Furthermore, endophytes offer a sustainable alternative to traditional agricultural practices, reducing the need for synthetic fertilizers and pesticides, and in turn reducing the risks associated with chemical treatments. In this review, we summarise the current knowledge on endophytes in agriculture, highlighting their potential as a sustainable solution for improving crop productivity and general plant health. This review outlines key nutrient, environmental, and biotic stressors, providing examples of endophytes mitigating the effects of stress. We also discuss the challenges associated with the use of endophytes in agriculture and the need for further research to fully realise their potential.
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Affiliation(s)
- Declan Watts
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Alex Jaimes Castillo
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Bita Zaferanloo
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
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18
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Xie X, Xia F, Wu Y, Liu S, Yan K, Xu H, Ji Z. A Novel Feature Selection Strategy Based on Salp Swarm Algorithm for Plant Disease Detection. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0039. [PMID: 37228513 PMCID: PMC10204742 DOI: 10.34133/plantphenomics.0039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/28/2023] [Indexed: 05/27/2023]
Abstract
Deep learning has been widely used for plant disease recognition in smart agriculture and has proven to be a powerful tool for image classification and pattern recognition. However, it has limited interpretability for deep features. With the transfer of expert knowledge, handcrafted features provide a new way for personalized diagnosis of plant diseases. However, irrelevant and redundant features lead to high dimensionality. In this study, we proposed a swarm intelligence algorithm for feature selection [salp swarm algorithm for feature selection (SSAFS)] in image-based plant disease detection. SSAFS is employed to determine the ideal combination of handcrafted features to maximize classification success while minimizing the number of features. To verify the effectiveness of the developed SSAFS algorithm, we conducted experimental studies using SSAFS and 5 metaheuristic algorithms. Several evaluation metrics were used to evaluate and analyze the performance of these methods on 4 datasets from the UCI machine learning repository and 6 plant phenomics datasets from PlantVillage. Experimental results and statistical analyses validated the outstanding performance of SSAFS compared to existing state-of-the-art algorithms, confirming the superiority of SSAFS in exploring the feature space and identifying the most valuable features for diseased plant image classification. This computational tool will allow us to explore an optimal combination of handcrafted features to improve plant disease recognition accuracy and processing time.
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Affiliation(s)
- Xiaojun Xie
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Center for Data Science and Intelligent Computing, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Fei Xia
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shouyang Liu
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ke Yan
- Department of the Built Environment, College of Design and Engineering, National University of Singapore, 4 Architecture Drive, Singapore 117566, Singapore
| | - Huanliang Xu
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhiwei Ji
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Center for Data Science and Intelligent Computing, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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19
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Yang P, Zhao L, Gao YG, Xia Y. Detection, Diagnosis, and Preventive Management of the Bacterial Plant Pathogen Pseudomonas syringae. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091765. [PMID: 37176823 PMCID: PMC10181079 DOI: 10.3390/plants12091765] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
Plant diseases caused by the pathogen Pseudomonas syringae are serious problems for various plant species worldwide. Accurate detection and diagnosis of P. syringae infections are critical for the effective management of these plant diseases. In this review, we summarize the current methods for the detection and diagnosis of P. syringae, including traditional techniques such as culture isolation and microscopy, and relatively newer techniques such as PCR and ELISA. It should be noted that each method has its advantages and disadvantages, and the choice of each method depends on the specific requirements, resources of each laboratory, and field settings. We also discuss the future trends in this field, such as the need for more sensitive and specific methods to detect the pathogens at low concentrations and the methods that can be used to diagnose P. syringae infections that are co-existing with other pathogens. Modern technologies such as genomics and proteomics could lead to the development of new methods of highly accurate detection and diagnosis based on the analysis of genetic and protein markers of the pathogens. Furthermore, using machine learning algorithms to analyze large data sets could yield new insights into the biology of P. syringae and novel diagnostic strategies. This review could enhance our understanding of P. syringae and help foster the development of more effective management techniques of the diseases caused by related pathogens.
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Affiliation(s)
- Piao Yang
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH 43210, USA
| | - Lijing Zhao
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH 43210, USA
| | - Yu Gary Gao
- OSU South Centers, The Ohio State University, 1864 Shyville Road, Piketon, OH 45661, USA
- Department of Extension, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Ye Xia
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH 43210, USA
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20
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Narware J, Singh SP, Manzar N, Kashyap AS. Biogenic synthesis, characterization, and evaluation of synthesized nanoparticles against the pathogenic fungus Alternaria solani. Front Microbiol 2023; 14:1159251. [PMID: 37138620 PMCID: PMC10149959 DOI: 10.3389/fmicb.2023.1159251] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
In the present study, Trichoderma harzianum culture filtrate (CF) was used as a reducing and capping agent to synthesize silver nanoparticles (Ag NPs) in a quick, simple, cost-effective, and eco-friendly manner. The effects of different ratios (silver nitrate (AgNO3): CF), pH, and incubation time on the synthesis of Ag NPs were also examined. Ultraviolet-visible (UV-Vis) spectra of the synthesized Ag NPs showed a distinct surface plasmon resonance (SPR) peak at 420 nm. Spherical and monodisperse NPs were observed using scanning electron microscopy (SEM). Elemental silver (Ag) was identified in the Ag area peak indicated by energy dispersive x-ray (EDX) spectroscopy. The crystallinity of Ag NPs was confirmed by x-ray diffraction (XRD), and Fourier transform infrared (FTIR) was used to examine the functional groups present in the CF. Dynamic light scattering (DLS) revealed an average size (43.68 nm), which was reported to be stable for 4 months. Atomic force microscopy (AFM) was used to confirm surface morphology. We also investigated the in vitro antifungal efficacy of biosynthesized Ag NPs against Alternaria solani, which demonstrated a significant inhibitory effect on mycelial growth and spore germination. Additionally, microscopic investigation revealed that Ag NP-treated mycelia exhibited defects and collapsed. Apart from this investigation, Ag NPs were also tested in an epiphytic environment against A. solani. Ag NPs were found to be capable of managing early blight disease based on field trial findings. The maximum percentage of early blight disease inhibition by NPs was observed at 40 parts per million (ppm) (60.27%), followed by 20 ppm (58.68%), whereas in the case of the fungicide mancozeb (1,000 ppm), the inhibition was recorded at 61.54%.
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Affiliation(s)
- Jeetu Narware
- Department of Mycology and Plant Pathology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Satyendra P. Singh
- Department of Mycology and Plant Pathology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Nazia Manzar
- Molecular Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganism, Mau, Uttar Pradesh, India
| | - Abhijeet Shankar Kashyap
- Molecular Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganism, Mau, Uttar Pradesh, India
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21
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Miranda-Calixto A, Loera-Corral O, López-Pérez M, Figueroa-Martínez F. Improvement of Akanthomyces lecanii resistance to tebuconazole through UV-C radiation and selective pressure on microbial evolution and growth arenas. J Invertebr Pathol 2023; 198:107914. [PMID: 36958641 DOI: 10.1016/j.jip.2023.107914] [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: 08/12/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Tebuconazole (TEB) is a fungicide widely used in agriculture; however, its constant application has increased the emergence of resistant plant pathogenic fungal strains and reduced the effectiveness of fungi as biological control agents; for instance, the entomopathogenic and hyperparasitic fungus Akanthomyces lecanii, suitable for simultaneous biological control of insect pest and plant pathogenic fungi, is highly sensitive to fungicides. We carried out the induction of resistance to TEB in two wild type strains of A. lecanii by UV radiation and selective pressure in increasing fungicide gradients using a modified Microbial Evolution and Growth Arena (MEGA), to produce A. lecanii strains that can be used as biological control agent in the presence of tebuconazole. Nine UV-induced and three naturally adapted A. lecanii strains were resistant to TEB at the agriculturally recommended dose, and three irradiated strains were resistant to TEB concentration ten times higher; moreover, growth, sporulation rates, production of hydrolytic enzymes, and virulence against the hemipteran Coccus viridis, a major pest of coffee crops, were not affected in the TEB-resistant strains. These A. lecanii TEB-resistant strains would have a greater opportunity to develop and to establish themselves in fields where the fungicide is present and can be used in a combined biological-chemical strategy to improve insect and plant pathogenic fungal control in agriculture. Also, the selective pressure through modified MEGA plate methodology can be used for the adaptation of entomopathogenic filamentous fungi to withstand other chemical or abiotic stresses that limits its effectiveness for pest control.
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Affiliation(s)
- Arturo Miranda-Calixto
- Universidad Autónoma Metropolitana-Iztapalapa, Departamento de Biotecnología, San Rafael Atlixco 186, Col. Vicentina, C. P. 09340 CDMX, Mexico
| | - Octavio Loera-Corral
- Universidad Autónoma Metropolitana-Iztapalapa, Departamento de Biotecnología, San Rafael Atlixco 186, Col. Vicentina, C. P. 09340 CDMX, Mexico
| | - Marcos López-Pérez
- Universidad Autónoma Metropolitana-Lerma Departamento de Ciencias Ambientales, Av. de las Garzas 10, El panteón, C. P. 52005 Lerma de Villada, Mexico
| | - Francisco Figueroa-Martínez
- CONACyT Research Fellow - Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, C. P. 09340 CDMX, Mexico.
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22
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Mostaffa NH, Suhaimi AH, Al-Idrus A. Interactomics in plant defence: progress and opportunities. Mol Biol Rep 2023; 50:4605-4618. [PMID: 36920596 DOI: 10.1007/s11033-023-08345-0] [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: 12/28/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023]
Abstract
Interactomics is a branch of systems biology that deals with the study of protein-protein interactions and how these interactions influence phenotypes. Identifying the interactomes involved during host-pathogen interaction events may bring us a step closer to deciphering the molecular mechanisms underlying plant defence. Here, we conducted a systematic review of plant interactomics studies over the last two decades and found that while a substantial progress has been made in the field, plant-pathogen interactomics remains a less-travelled route. As an effort to facilitate the progress in this field, we provide here a comprehensive research pipeline for an in planta plant-pathogen interactomics study that encompasses the in silico prediction step to the validation step, unconfined to model plants. We also highlight four challenges in plant-pathogen interactomics with plausible solution(s) for each.
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Affiliation(s)
- Nur Hikmah Mostaffa
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ahmad Husaini Suhaimi
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Aisyafaznim Al-Idrus
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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23
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Mumford EL, Martinez DJ, Tyance-Hassell K, Cook A, Hansen GR, Labonté R, Mazet JAK, Mumford EC, Rizzo DM, Togami E, Vreedzaam A, Parrish-Sprowl J. Evolution and expansion of the One Health approach to promote sustainable and resilient health and well-being: A call to action. Front Public Health 2023; 10:1056459. [PMID: 36711411 PMCID: PMC9880335 DOI: 10.3389/fpubh.2022.1056459] [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: 09/28/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
One Health is a transdisciplinary approach used to address complex concerns related to human, animal, plant, and ecosystem health. One Health frameworks and operational tools are available to support countries and communities, particularly for the prevention and control of zoonotic diseases and antimicrobial resistance and the protection of food safety. However, One Health has yet to be implemented in a manner that fully considers the complexities and interconnectedness of the diverse influences that have impacts at a larger system level. This lack of consideration can undermine the sustainability of any positive outcomes. To ensure the One Health approach can function effectively within the new global context of converging and escalating health, social, economic, and ecological crises, it must evolve and expand in three overlapping dimensions: (1) Scope: the partners, knowledge, and knowledge systems included, (2) Approach: the techniques, methodologies, and scholarship considered, and (3) Worldview inclusivity: the interweaving of other worldviews together with the mainstream scientific worldview that currently predominates. Diverse partners and knowledge from outside the mainstream health and scientific sectors, including Indigenous peoples and representatives of local communities, and traditionally generated knowledge, must be included. These systems of knowledge can then be braided together with mainstream science to comprise a holistic framework for decision-making. Scholarship and methodologies being applied in other fields and contexts to solve complex challenges and manage uncertainty, such as collaborative governance, social-ecologic systems theory, and complexity science, must be recognized and incorporated. The spectrum of considered worldviews must also expand to authentically integrate the expanded scope and approach into action and sustainable impact. By increasing community and social engagement and by recognizing and entwining different worldviews, the plurality of disciplines, and traditional and scientific ways of knowing to address community concerns in the contexts in which they exist, we can ensure that One Health remains effective and true to its paradigm in our rapidly changing and complex world.
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Affiliation(s)
- Elizabeth L. Mumford
- School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom,*Correspondence: Elizabeth L. Mumford ✉
| | - Deniss J. Martinez
- Graduate Group in Ecology, University of California, Davis, Davis, CA, United States
| | - Karli Tyance-Hassell
- (Anishinaabe) Office of Research and Community Engagement, Alaska Pacific University, Anchorage, AK, United States
| | - Alasdair Cook
- Department of Veterinary Epidemiology and Public Health, University of Surrey, Guildford, United Kingdom
| | | | - Ronald Labonté
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
| | - Jonna A. K. Mazet
- Grand Challenges, University of California, Davis, Davis, CA, United States
| | | | - David M. Rizzo
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Eri Togami
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | | | - John Parrish-Sprowl
- Department of Communication Studies, Indiana University, Indianapolis, IN, United States
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24
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Togami E, Behravesh CB, Dutcher TV, Hansen GR, King LJ, Pelican KM, Mazet JAK. Characterizing the One Health workforce to promote interdisciplinary, multisectoral approaches in global health problem-solving. PLoS One 2023; 18:e0285705. [PMID: 37192188 DOI: 10.1371/journal.pone.0285705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND In recognition of the interconnected nature of complex challenges such as COVID-19, a collaborative, multisectoral, and transdisciplinary approach, referred to as One Health, has been employed to address sustainable development and strengthen global health security. Although significant investments have been made to build global health capacity, characterization of the One Health is absent from the literature. METHODS AND FINDINGS We collected and analyzed perspectives from students, graduates, workers, and employers in One Health through a multinational online survey across health disciplines and sectors. Respondents were recruited through professional networks. A total of 828 respondents from 66 countries participated, representing governmental and academic institutions and students, among others; 57% were female, and 56% had completed professional health degrees. Interpersonal communication, communication with non-scientific audiences, and the ability to work in transdisciplinary teams were valued in the workplace and were considered essential competencies to build an interdisciplinary health workforce. Employers indicated difficulty recruiting workers, while workers indicated limited availability of positions. Employers identified limited funding and ill-defined career pathways as prominent challenges for retaining One Health workers. CONCLUSIONS Successful One Health workers use interpersonal skills and scientific knowledge to address complex health challenges. Aligning the definition of One Health will likely improve the matching of job seekers and employers. Encouraging the employment of the One Health approach for a diverse range of positions, even if they do not explicitly include "One Health" in the job title, and clarifying the expectations, roles and responsibilities within a transdisciplinary team will lead to building a stronger workforce. As One Health has evolved to address food insecurity, emerging diseases, and antimicrobial resistance, it holds promise for supporting an interdisciplinary global health workforce that can make substantial progress on Sustainable Development Goals and improve global health security for all.
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Affiliation(s)
- Eri Togami
- One Health Institute, University of California, Davis, Davis, CA, United States of America
| | - Casey Barton Behravesh
- National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Tracey V Dutcher
- Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Riverdale, MD, United States of America
| | - Gail R Hansen
- Hansen Consulting LLC, Washington, DC, United States of America
| | - Lonnie J King
- College of Veterinary Medicine, Ohio State University, Columbus, OH, United States of America
| | - Katharine M Pelican
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Jonna A K Mazet
- One Health Institute, University of California, Davis, Davis, CA, United States of America
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25
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Bacha SAS, Li Y, Nie J, Xu G, Han L, Farooq S. Comprehensive review on patulin and Alternaria toxins in fruit and derived products. FRONTIERS IN PLANT SCIENCE 2023; 14:1139757. [PMID: 37077634 PMCID: PMC10108681 DOI: 10.3389/fpls.2023.1139757] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Mycotoxins are toxic secondary metabolites produced by certain fungi, which can contaminate various food commodities, including fruits and their derived products. Patulin and Alternaria toxins are among the most commonly encountered mycotoxins in fruit and their derived products. In this review, the sources, toxicity, and regulations related to these mycotoxins, as well as their detection and mitigation strategies are widely discussed. Patulin is a mycotoxin produced mainly by the fungal genera Penicillium, Aspergillus, and Byssochlamys. Alternaria toxins, produced by fungi in the Alternaria genus, are another common group of mycotoxins found in fruits and fruit products. The most prevalent Alternaria toxins are alternariol (AOH) and alternariol monomethyl ether (AME). These mycotoxins are of concern due to their potential negative effects on human health. Ingesting fruits contaminated with these mycotoxins can cause acute and chronic health problems. Detection of patulin and Alternaria toxins in fruit and their derived products can be challenging due to their low concentrations and the complexity of the food matrices. Common analytical methods, good agricultural practices, and contamination monitoring of these mycotoxins are important for safe consumption of fruits and derived products. And Future research will continue to explore new methods for detecting and managing these mycotoxins, with the ultimate goal of ensuring the safety and quality of fruits and derived product supply.
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Affiliation(s)
- Syed Asim Shah Bacha
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Yinping Li
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Jiyun Nie, ; Yinping Li,
| | - Jiyun Nie
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, China
- *Correspondence: Jiyun Nie, ; Yinping Li,
| | - Guofeng Xu
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Lingxi Han
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Saqib Farooq
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
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26
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Jeger MJ. Tolerance of plant virus disease: Its genetic, physiological, and epidemiological significance. Food Energy Secur 2022. [DOI: 10.1002/fes3.440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Michael John Jeger
- Department of Life Sciences, Silwood Park Imperial College London Ascot UK
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27
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Lappe RR, Elmore MG, Lozier ZR, Jander G, Miller WA, Whitham SA. Metagenomic identification of novel viruses of maize and teosinte in North America. BMC Genomics 2022; 23:767. [DOI: 10.1186/s12864-022-09001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America.
Results
Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize.
Conclusions
Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.
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28
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Falkenberg T, Ekesi S, Borgemeister C. Integrated Pest Management (IPM) and One Health - a call for action to integrate. CURRENT OPINION IN INSECT SCIENCE 2022; 53:100960. [PMID: 35963579 DOI: 10.1016/j.cois.2022.100960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
One Health (OH) has gained considerable prominence since the beginning of the 21st century, among others, driven by the recent epidemics and the increasing importance of zoonotic diseases. Yet, despite the holistic and multidimensional nature of OH, to date, most emphasis has been on the interactions between animal and human health, with considerably less attention to environmental and plant health. However, there is growing evidence that the challenges of climate change, growing food and nutritional insecurity, and biodiversity loss can best be addressed within the context of the OH framework. Conceptionally, Integrated Pest Management (IPM) could perfectly fit into such an approach, but historically, IPM has been practiced very much in a compartmentalized manner. New approaches such as Regenerative Agriculture and Sustainable Intensification offer solutions to how to successfully embed IPM into a OH framework.
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Affiliation(s)
- Timo Falkenberg
- Center for Development Research (ZEF), University of Bonn, Germany; Institute for Hygiene and Public Health, University Hospital Bonn, Germany
| | - Sunday Ekesi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
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29
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Complete Genome Sequence of Dickeya chrysanthemi Bacteriophage DchS19. Microbiol Resour Announc 2022; 11:e0080022. [PMID: 36102644 PMCID: PMC9583810 DOI: 10.1128/mra.00800-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the complete genome of a lytic Dickeya chrysanthemi bacteriophage, DchS19, which was isolated from a soil sample in Sungai Petani, Kedah, Malaysia. The phage, from the Autographviridae family, has a 39,149-bp double-stranded DNA genome containing 49 protein-coding genes and shares 94.65% average nucleotide identity with Erwinia phage pEp_SNUABM_12.
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30
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Ali MR, Bacchu MS, Al-Mamun MR, Hossain MI, Khaleque A, Khatun A, Ridoy DD, Aly MAS, Khan MZH. Recent Advanced in MXene Research toward Biosensor Development. Crit Rev Anal Chem 2022:1-18. [PMID: 36068703 DOI: 10.1080/10408347.2022.2115286] [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: 10/14/2022]
Abstract
MXene is a rapidly emerging group of two-dimensional (2D) multifunctional nanomaterials, drawing huge attention from researchers of a broad scientific field. Reporting the synthesis of MXene was the following breakthrough in 2D materials following the discovery of graphene. MXene is considered the most recent developments of materials, including transition metal carbonitrides, nitrides, and carbides synthesized by etching or mechanical-based exfoliation of selective MAX phases. MXene has a plethora of prodigious properties such as unique interlayer spacing, high ion and electron transport, large surface area, excellent thermal and electrical conductivity, exceptional volumetric capacitance, thermal shock, and oxidation resistance, easily machinable and inherently hydrophilic, and biocompatibility. Owing to the abundance of tailorable surface function groups, these properties can be further enhanced by surface functionalization with covalent and non-covalent modifications via numerous surface functionalization methods. Therefore, MXene finds their way to a plethora of applications in numerous fields including catalysis, membrane separation, energy storage, sensing, and biomedicine. Here, the focus is on reviewing the structure, synthesis techniques, and functionalization methods of MXene. Furthermore, MXene-based detection platforms in different sensing applications are survived. Great attention is given to reviewing the applications of MXene in the detection of biomolecules, pathogenic bacteria and viruses, cancer biomarkers food contaminants and mycotoxins, and hazardous pollutants. Lastly, the future perspective of MXene-based biosensors as a next-generation diagnostics tool is discussed. Crucial visions are introduced for materials science and sensing communities to better route while investigating the potential of MXene for creating innovative detection mechanisms.
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Affiliation(s)
- Md Romzan Ali
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
| | - Md Sadek Bacchu
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
| | - Md Rashid Al-Mamun
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
| | - Md Ikram Hossain
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
| | - Abdul Khaleque
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
| | - Anowara Khatun
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
| | - Dipto Debnath Ridoy
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
| | - Mohamed Aly Saad Aly
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Md Zaved Hossain Khan
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Nano-bio and Advanced Materials Engineering (NAME), Jashore University of Science and technology, Jashore, Bangladesh
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31
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Maximiano MR, Rios TB, Campos ML, Prado GS, Dias SC, Franco OL. Nanoparticles in association with antimicrobial peptides (NanoAMPs) as a promising combination for agriculture development. Front Mol Biosci 2022; 9:890654. [PMID: 36081849 PMCID: PMC9447862 DOI: 10.3389/fmolb.2022.890654] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial peptides are small molecules, up to 10 kDa, present in all kingdoms of life, including in plants. Several studies report that these molecules have a broad spectrum of activity, including antibacterial, antifungal, antiviral, and insecticidal activity. Thus, they can be employed in agriculture as alternative tools for phytopathogen and pest control. However, the application of peptides in agriculture can present challenges, such as loss of activity due to degradation of these molecules, off-target effects, and others. In this context, nanotechnology can offer versatile structures, including metallic nanoparticles, liposomes, polymeric nanoparticles, nanofibers, and others, which might act both in protection and in release of AMPs. Several polymers and biomaterials can be employed for the development of nanostructures, such as inorganic metals, natural or synthetic lipids, synthetic and hybrid polymers, and others. This review addresses the versatility of NanoAMPs (Nanoparticles in association with antimicrobial peptides), and their potential applications in agribusiness, as an alternative for the control of phytopathogens in crops.
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Affiliation(s)
- Mariana Rocha Maximiano
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Thuanny Borba Rios
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Marcelo Lattarulo Campos
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de MT, Cuiabá, Brazil
| | | | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- Pós-graduação em Biologia Animal, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- *Correspondence: Octávio Luiz Franco,
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32
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Nehra M, Kumar V, Kumar R, Dilbaghi N, Kumar S. Current Scenario of Pathogen Detection Techniques in Agro-Food Sector. BIOSENSORS 2022; 12:bios12070489. [PMID: 35884292 PMCID: PMC9313409 DOI: 10.3390/bios12070489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 05/05/2023]
Abstract
Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.
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Affiliation(s)
- Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Virendra Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Rajesh Kumar
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Correspondence:
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Artificial Intelligence Potential in Higher Education Institutions Enhanced Learning Environment in Romania and Serbia. SUSTAINABILITY 2022. [DOI: 10.3390/su14105842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In their struggle to offer a sustainable educational system and transversal competencies for market requests, significant transformations characterise the higher education system in Serbia and Romania. According to EU policy, these transformations are related to educational reforms and the introduction of new technology and methodologies in teaching and learning. They are expected to answer to the PISA requirements and to increase the DESI (Digital Economy and Society Index). They are also likely to mitigate the inequity of HEIs (higher education institutions), empowered by a structured, goal-oriented strategy towards agile management in HEIs that is also appropriate for new market demands. Our study is based on an exploratory survey applied to 139 Romanian and Serbian teachers from the Information Technology School—ITS, Belgrade, and Spiru Haret University, Romania. The survey let them provide their knowledge of AI or their perceptions of the difficulties and opportunities of these technologies in HEIs. Our study discovered how difficulties and opportunities associated with AI impact HEIs. This study aims to see how AI might assist higher education in Romania and Serbia. We also considered how they might be integrated with the educational system, and if instructors would utilise them. Developing creative and transversal skills is required to anticipate future breakthroughs and technological possibilitiesThe new methods of education focuses on ethics, values, problem-solving, and daily activities. Students’ learning material, how they might achieve critical abilities, and their educational changes must be addressed in the future. In this environment, colleges must create new digital skills in IA, machine learning, IoT, 5G, the cloud, big data, blockchain, data analysis, using MS Office and other applications, MOOCs, simulation applications, VR/AR, and gamification. They must also develop cross-disciplinary skills and a long-term mindset.
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34
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Hui F. Research on the Construction of Emergency Network Public Opinion Emotional Dictionary Based on Emotional Feature Extraction Algorithm. Front Psychol 2022; 13:857769. [PMID: 35529545 PMCID: PMC9072777 DOI: 10.3389/fpsyg.2022.857769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
How to strengthen emergency management and improve the ability to prevent and respond to emergencies is an important part of building a harmonious socialist society. This paper proposes a domain emotion dictionary construction method for network public opinion analysis of public emergencies. Using the advantages of corpus and semantic knowledge base, this paper extracts the seed words based on the large-scale network public opinion corpus and combined with the existing emotion dictionary, trains the word vector through the word2vec model in deep learning, expands the emotion words, and obtains the candidate emotion words according to the semantic similarity calculation, So as to generate a domain emotion dictionary. The accuracy rate of emotion discrimination by the emotion dictionary constructed in this paper is 0.86, the recall rate is 0.92. Through the verification of accuracy and recall rate, the construction method proposed in this paper has good accuracy and reliability. Because of the great differences in different experiences and situations of different groups, there will be great differences in views and perspectives on the same event. The key to prevent the public from blindly following the crowd should be to reach groups close to emotional distance, and targeted prevention and control of public opinion can be conducted according to different characteristics of different groups.
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Affiliation(s)
- Fang Hui
- Northwestern Polytechnical University, Xi'an, China
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McNeil C, Verlander S, Divi N, Smolinski M. Straight from the source: Landscape of Participatory Surveillance Systems across the One Health Spectrum (Preprint). JMIR Public Health Surveill 2022; 8:e38551. [PMID: 35930345 PMCID: PMC9391976 DOI: 10.2196/38551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/11/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - Nomita Divi
- Ending Pandemics, San Francisco, CA, United States
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In Vitro Screening of New Biological Limiters against Some of the Main Soil-Borne Phytopathogens. SUSTAINABILITY 2022. [DOI: 10.3390/su14052693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This study explored the role of Aphanocladium album (strain MX95), Pleurotus ostreatus (strain ALPO) and Pleurotus eryngii (strain AL142PE) as potential biological limiters. MX95, ALPO and AL142PE were screened under laboratory studies against Phytophthora nicotianae (PN), Fusarium oxysporum f. sp. radicis-lycopersici (FORL), Fusarium oxysporum f. sp. lycopersici (FOL), Fusarium solani (FS), Sclerotinia minor (SM), Sclerotinia sclerotiorum (SS), Athelia (Sclerotium) rolfsii (AR) and Verticillium dahliae (VD). The radial growth inhibition and the over-growth of potential antagonists on the target organisms were used to assess the interactions in the in vitro dual culture plate assay. The antagonistic ability of each challenge isolate was evaluated by calculating an index of the antagonism (AI) based on the interaction type in the dual cultures. MX95, reducing the growth of SS (20%) and FS (40%), displayed deadlock at mycelial contact against FOL and FORL, deadlock at distance versus VD and completely over-grew PN and SM. ALPO reduced (43 to 88%) the mycelial growth of tested pathogens except FORL and replaced PN and VD. AL142PE reducing (53 to 67%) SS, VD, FS and FOL mycelial growth and completely over-grew PN. AR showed combative ability against all the experienced biological limiters. Based on the results of the AI values, MX95 (AI = 16.5) was considered an active antagonist, while ALPO (AI = 11.5) and AL142PE (AI = 12.0) were moderately active antagonists. Strains MX95, ALPO and AL142PE were suitable as environment-friendly potential biocontrol agents to manage some of the main soil-borne agents of foot, root, soft rot and wilt diseases. These results are the first step in the assessment of the potential capacity of these organisms as biological limiters. Nevertheless, additional experiments should be performed for the translation to the field conditions in plant protection against soil-borne plant pathogens. In particular, the optimisation of dose and application time validation should be performed for a solid conclusion about the competitive ability of MX95, ALPO and AL142PE and the usefulness of potential biological limiters.
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Paguirigan JA, Liu R, Im SM, Hur JS, Kim W. Evaluation of Antimicrobial Properties of Lichen Substances against Plant Pathogens. THE PLANT PATHOLOGY JOURNAL 2022; 38:25-32. [PMID: 35144359 PMCID: PMC8831355 DOI: 10.5423/ppj.oa.12.2021.0176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Plant pathogens pose major threats on agriculture and horticulture, causing significant economic loss worldwide. Due to the continuous and excessive use of synthetic pesticides, emergence of pesticide resistant pathogens has become more frequent. Thus, there is a growing needs for environmentally-friendly and selective antimicrobial agents with a novel mode of action, which may be used in combination with conventional pesticides to delay development of pesticide resistance. In this study, we evaluated the potentials of lichen substances as novel biopesticides against eight bacterial and twelve fungal plant pathogens that have historically caused significant phytopathological problems in South Korea. Eight lichen substances of diverse chemical origins were extracted from axenic culture or dried specimen, and further purified for comparative analysis of their antimicrobial properties. Usnic acid and vulpinic acid exhibited strong antibacterial activities against Clavibacter michiganensis subsp. michiganensis. In addition, usnic acid and vulpinic acid were highly effective in the growth inhibition of fungal pathogens, such as Diaporthe eres, D. actinidiae, and Sclerotinia sclerotiorum. Intriguingly, the growth of Rhizoctonia solani was specifically inhibited by lecanoric acid, indicating that lichen substances exhibit some degrees of selectivity to plant pathogens. These results suggested that lichen substance can be used as a selective biopesticide for controlling plant disease of agricultural and horticultural significance, minimizing possible emergence of pesticide resistant pathogens in fields.
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Affiliation(s)
- Jaycee A. Paguirigan
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922,
Korea
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Boulevard, Manila 1008,
Philippines
| | - Rundong Liu
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922,
Korea
| | - Seong Mi Im
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922,
Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922,
Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922,
Korea
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Identification and Functional Characterization of Toxoneuron nigriceps Ovarian Proteins Involved in the Early Suppression of Host Immune Response. INSECTS 2022; 13:insects13020144. [PMID: 35206718 PMCID: PMC8876978 DOI: 10.3390/insects13020144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022]
Abstract
The endophagous parasitoid Toxoneuron nigriceps (Viereck) (Hymenoptera, Braconidae) of the larval stages of the tobacco budworm Heliothis virescens (Fabricius) (Lepidoptera, Noctuidae) injects the egg, the venom, the calyx fluid, which includes a Polydnavirus (T. nigriceps BracoVirus: TnBV) and the Ovarian Proteins (OPs) into the host body during oviposition. The host metabolism and immune system are disrupted prematurely shortly after parasitization by the combined action of the TnBV, venom, and OPs. OPs are involved in the early suppression of host immune response, before TnBV infects and expresses its genes in the host tissues. In this work, we evaluated the effect of HPLC fractions deriving from in toto OPs. Two fractions caused a reduction in hemocyte viability and were subsequently tested to detect changes in hemocyte morphology and functionality. The two fractions provoked severe oxidative stress and actin cytoskeleton disruption, which might explain the high rate of hemocyte mortality, loss of hemocyte functioning, and hence the host’s reduced hemocyte encapsulation ability. Moreover, through a transcriptome and proteomic approach we identify the proteins of the two fractions: eight proteins were identified that might be involved in the observed host hemocyte changes. Our findings will contribute to a better understanding of the secreted ovarian components and their role in parasitoid wasp strategy for evading host immune responses.
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Gangurde SS, Xavier A, Naik YD, Jha UC, Rangari SK, Kumar R, Reddy MSS, Channale S, Elango D, Mir RR, Zwart R, Laxuman C, Sudini HK, Pandey MK, Punnuri S, Mendu V, Reddy UK, Guo B, Gangarao NVPR, Sharma VK, Wang X, Zhao C, Thudi M. Two decades of association mapping: Insights on disease resistance in major crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1064059. [PMID: 37082513 PMCID: PMC10112529 DOI: 10.3389/fpls.2022.1064059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.
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Affiliation(s)
- Sunil S. Gangurde
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | | | - Raj Kumar
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - M. S. Sai Reddy
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Sonal Channale
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Rebecca Zwart
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - C. Laxuman
- Zonal Agricultural Research Station (ZARS), Kalaburagi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish K. Pandey
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Somashekhar Punnuri
- College of Agriculture, Family Sciences and Technology, Dr. Fort Valley State University, Fort Valley, GA, United States
| | - Venugopal Mendu
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, West Virginia, WV, United States
| | - Baozhu Guo
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
| | | | - Vinay K. Sharma
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
| | - Mahendar Thudi
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
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Lo Presti D, Cimini S, Massaroni C, D’Amato R, Caponero MA, De Gara L, Schena E. Plant Wearable Sensors Based on FBG Technology for Growth and Microclimate Monitoring. SENSORS 2021; 21:s21196327. [PMID: 34640649 PMCID: PMC8512323 DOI: 10.3390/s21196327] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022]
Abstract
Plants are primary resources for oxygen and foods whose production is fundamental for our life. However, diseases and pests may interfere with plant growth and cause a significant reduction of both the quality and quantity of agriculture products. Increasing agricultural productivity is crucial for poverty reduction and food security improvements. For this reason, the 2030 Agenda for Sustainable Development gives a central role to agriculture by promoting a strong technological innovation for advancing sustainable practices at the plant level. To accomplish this aim, recently, wearable sensors and flexible electronics have been extended from humans to plants for measuring elongation, microclimate, and stressing factors that may affect the plant’s healthy growth. Unexpectedly, fiber Bragg gratings (FBGs), which are very popular in health monitoring applications ranging from civil infrastructures to the human body, are still overlooked for the agriculture sector. In this work, for the first time, plant wearables based on FBG technology are proposed for the continuous and simultaneous monitoring of plant growth and environmental parameters (i.e., temperature and humidity) in real settings. The promising results demonstrated the feasibility of FBG-based sensors to work in real situations by holding the promise to advance continuous and accurate plant health growth monitoring techniques.
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Affiliation(s)
- Daniela Lo Presti
- Unit of Measurement and Biomedical Instrumentations, Departmental Faculty of Engineering, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy; (C.M.); (E.S.)
- Correspondence: ; Tel.: +39-06225419650
| | - Sara Cimini
- Unit of Food Science and Nutrition, Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy; (S.C.); (L.D.G.)
| | - Carlo Massaroni
- Unit of Measurement and Biomedical Instrumentations, Departmental Faculty of Engineering, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy; (C.M.); (E.S.)
| | - Rosaria D’Amato
- Photonics Micro and Nanostructures Laboratory, Fusion and Technologies for Nuclear Safety and Security Department, FSN-TECFIS-MNF, ENEA C.R. Frascati, Via E. Fermi, 45, 00044 Frascati, Italy; (R.D.); (M.A.C.)
| | - Michele Arturo Caponero
- Photonics Micro and Nanostructures Laboratory, Fusion and Technologies for Nuclear Safety and Security Department, FSN-TECFIS-MNF, ENEA C.R. Frascati, Via E. Fermi, 45, 00044 Frascati, Italy; (R.D.); (M.A.C.)
| | - Laura De Gara
- Unit of Food Science and Nutrition, Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy; (S.C.); (L.D.G.)
| | - Emiliano Schena
- Unit of Measurement and Biomedical Instrumentations, Departmental Faculty of Engineering, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy; (C.M.); (E.S.)
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