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Wilde THC, Shukla RK, Madden C, Vodovotz Y, Sharma A, McGraw WS, Hale VL. Simian immunodeficiency virus and storage buffer: Field-friendly preservation methods for RNA viral detection in primate feces. mSphere 2023; 8:e0048423. [PMID: 38032220 PMCID: PMC10732032 DOI: 10.1128/msphere.00484-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Simian immunodeficiency virus (SIV), which originated in African monkeys, crossed the species barrier into humans and ultimately gave rise to HIV and the global HIV/AIDS epidemic. While SIV infects over 40 primate species in sub-Saharan Africa, testing for RNA viruses in wild primate populations can be challenging. Optimizing field-friendly methods for assessing viral presence/abundance in non-invasively collected biological samples facilitates the study of viruses, including potentially zoonotic viruses, in wild primate populations. This study compares SIV RNA preservation and recovery from non-human primate feces stored in four different buffers. Our results will inform future fieldwork and facilitate improved approaches to characterizing prevalence, shedding, and transmission of RNA viruses like SIV in natural hosts including wild-living non-human primates.
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Affiliation(s)
- Tessa H. C. Wilde
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | - Rajni Kant Shukla
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Christopher Madden
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Yael Vodovotz
- Department of Food Science and Technology, The Ohio State University, Columbus, Ohio, USA
| | - Amit Sharma
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - W. Scott McGraw
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | - Vanessa L. Hale
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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2
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You Y, Zhou Y, Duan X, Mao X, Li Y. Research progress on the application of different preservation methods for controlling fungi and toxins in fruit and vegetable. Crit Rev Food Sci Nutr 2023; 63:12441-12452. [PMID: 35866524 DOI: 10.1080/10408398.2022.2101982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fruits and vegetables are susceptible to fungal infections during picking, transportation, storage and processing, which have a high potential to produce toxins. Fungi and toxins can cause acute or chronic poisoning after entering the body. In the field of fruit and vegetable preservation, technologies such as temperature control, modified atmosphere, irradiation, application of natural or chemical preservatives, and edible films are commonly used. In practical applications, according to the types, physiological differences and actual needs of fruits and vegetables, suitable preservation methods can be selected to achieve the effect of preservation and control of fungi and toxins. The starting point of fresh-keeping technology is to delay post-harvest senescence of fruits and vegetables, inhibit the respiratory intensity, and control the reproduction of microorganisms, which is important to control the reproduction of fungi and the production of toxins. From the three directions of physical, chemical and biological means, the article analyses and explores the effects of different external factors on the production of toxins and the effects of different preservation techniques on fungal growth and toxin production in fruits and vegetables, in order to provide new ideas for the preservation of fruits and vegetables and the control of harmful substances in food.
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Affiliation(s)
- Yanli You
- Yantai University, Yantai, Shandong, People's Republic of China
| | - Yunna Zhou
- Yantai University, Yantai, Shandong, People's Republic of China
| | - Xuewu Duan
- Department of South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Xin Mao
- Yantai University, Yantai, Shandong, People's Republic of China
| | - Yanshen Li
- Yantai University, Yantai, Shandong, People's Republic of China
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3
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Liu C, Lei J, Zhang M, Wu F, Ren M, Yang J, Wu Q, Shi X. Optimization of Preservation Methods Provides Insights into Photosynthetic Picoeukaryotes in Lakes. Microbiol Spectr 2022; 10:e0255721. [PMID: 35546573 PMCID: PMC9241741 DOI: 10.1128/spectrum.02557-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/18/2022] [Indexed: 11/28/2022] Open
Abstract
As the key contributor to plankton biomass and nutrient cycling in aquatic ecosystems, photosynthetic picoeukaryotes (PPEs) have been recently investigated in freshwater ecosystems. However, the limited access to remote areas creates challenges for PPE sample preservation before sorting and counting by flow cytometry (FCM) in the laboratory. Here, we explored the effects of different preservation methods on the PPE community by combining FCM sorting and high-throughput sequencing. Our results showed that dimethyl sulfoxide (DMSO) cryoprotection could destroy the fluorescence and cell structure of the PPEs, making the subsequent FCM analysis and sorting difficult. Aldehyde fixation maintained the PPE fluorescence, and the fixed samples were of sufficient quality for abundance analysis and sorting by FCM. However, the sequencing results showed that, after preservation by aldehydes, the proportion of PPEs dramatically decreased to approximately 10%, in comparison to 90% in the fresh samples, and the sequences of Ascomycota significantly increased. In contrast, preservation with Pluronic F68 (F68) not only could maintain the PPE abundance close to the initial value but also could keep the PPE community similar to that in the fresh samples over a storage time of 6 months. Thus, F68 cryopreservation is a suitable preservation method for PPE communities from freshwater lakes. IMPORTANCE PPEs contribute significantly to primary productivity in freshwater ecosystems. The combination of FCM sorting and high-throughput sequencing has been shown to be a powerful approach and can largely improve our view of the PPE diversity. However, the water samples could not be counted and sorted immediately after sampling from many lakes due to the inaccessibility of FCM in the field. Thus, the comparison of different preservation methods that allow subsequent analysis of the community structure by high-throughput sequencing is an urgent need. Our results indicated that F68 cryopreservation could maintain the PPE abundance close to the initial value and keep the community similar to that in the fresh samples over a storage time of 6 months.
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Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Lei
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingdong Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinsheng Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaiyin, China
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4
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Harder CB, Persson S, Christensen J, Ljubic A, Nielsen EM, Hoorfar J. Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements. AIMS Microbiol 2022; 7:399-414. [PMID: 35071939 PMCID: PMC8712530 DOI: 10.3934/microbiol.2021024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/05/2021] [Indexed: 11/27/2022] Open
Abstract
Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives. This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 106 CFU/mL of both Salmonella and Campylobacter strains stored at −20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.
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Affiliation(s)
- C B Harder
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark.,Molecular Ecology, Microbial Ecology and Evolutionary Genetics, Lund University, Sölvegatan 37, 223 62 Lund
| | - S Persson
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark
| | - J Christensen
- Danish Veterinary and Food Administration, Microbiological department, Søndervang 4, 4100 Ringsted
| | - A Ljubic
- AGC Biologics, Process Transfer, Vandtårnsvej 83, 2860 Søborg, Denmark
| | - E M Nielsen
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark
| | - J Hoorfar
- Technical University of Denmark, National Food Institute, 2800 Kgs. Lyngby, Denmark
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5
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Jensen M, Wippler J, Kleiner M. Evaluation of RNA later as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses. Microbiol Spectr 2021; 9:e0142921. [PMID: 34704828 DOI: 10.1128/Spectrum.01429-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Field studies are central to environmental microbiology and microbial ecology, because they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows investigators to study these communities "in situ," which requires protein preservation directly in the field because protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is nonhazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability under field conditions when targeted for metaproteomic analyses is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNAlater using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNAlater storage after 1 day, 1 week, and 4 weeks at room temperature (22°C to 23°C). We evaluated protein preservation using one-dimensional liquid chromatography-tandem mass spectrometry. We found that RNAlater and flash freezing preserved proteins equally well in terms of total numbers of identified proteins and relative abundances of individual proteins, and none of the test time points was altered, compared to time zero. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomic data and the logistical requirements for field deployment, we recommend RNAlater for protein preservation of field-collected samples targeted for metaproteomic analyses. IMPORTANCE Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provide direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns. In laboratory setups, samples for proteomic analyses are most commonly preserved by flash freezing; however, liquid nitrogen or dry ice is often unavailable at remote field locations, due to their hazardous nature and transport restrictions. Our study shows that RNAlater can serve as a low-hazard, easy-to-transport alternative to flash freezing for field preservation of samples for metaproteomic analyses. We show that RNAlater preserves the metaproteome equally well, compared to flash freezing, and protein abundance patterns remain stable during long-term storage for at least 4 weeks at room temperature.
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6
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de Oliveira Filho JG, Miranda M, Ferreira MD, Plotto A. Nanoemulsions as Edible Coatings: A Potential Strategy for Fresh Fruits and Vegetables Preservation. Foods 2021; 10:foods10102438. [PMID: 34681488 PMCID: PMC8535803 DOI: 10.3390/foods10102438] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 01/10/2023] Open
Abstract
Fresh fruits and vegetables are perishable commodities requiring technologies to extend their postharvest shelf life. Edible coatings have been used as a strategy to preserve fresh fruits and vegetables in addition to cold storage and/or controlled atmosphere. In recent years, nanotechnology has emerged as a new strategy for improving coating properties. Coatings based on plant-source nanoemulsions in general have a better water barrier, and better mechanical, optical, and microstructural properties in comparison with coatings based on conventional emulsions. When antimicrobial and antioxidant compounds are incorporated into the coatings, nanocoatings enable the gradual and controlled release of those compounds over the food storage period better than conventional emulsions, hence increasing their bioactivity, extending shelf life, and improving nutritional produce quality. The main goal of this review is to update the available information on the use of nanoemulsions as coatings for preserving fresh fruits and vegetables, pointing to a prospective view and future applications.
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Affiliation(s)
- Josemar Gonçalves de Oliveira Filho
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara—Jaú Km 1, Araraquara 14800-903, SP, Brazil; (J.G.d.O.F.); (M.M.)
| | - Marcela Miranda
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara—Jaú Km 1, Araraquara 14800-903, SP, Brazil; (J.G.d.O.F.); (M.M.)
| | - Marcos David Ferreira
- Embrapa Instrumentação, Rua XV de Novembro, 1452, São Carlos 13560-970, SP, Brazil
- Correspondence: (M.D.F.); (A.P.)
| | - Anne Plotto
- ARS Horticultural Research Laboratory, United States Department of Agriculture, 2001 South Rock Road, Fort Pierce, FL 34945, USA
- Correspondence: (M.D.F.); (A.P.)
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7
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Ortiz T, Argüelles-Arias F, Begines B, García-Montes JM, Pereira A, Victoriano M, Vázquez-Román V, Pérez Bernal JL, Callejón RM, De-Miguel M, Alcudia A. Native Chilean Berries Preservation and In Vitro Studies of a Polyphenol Highly Antioxidant Extract from Maqui as a Potential Agent against Inflammatory Diseases. Antioxidants (Basel) 2021; 10:antiox10060843. [PMID: 34070392 PMCID: PMC8226669 DOI: 10.3390/antiox10060843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 01/26/2023] Open
Abstract
The best conservation method for native Chilean berries has been investigated in combination with an implemented large-scale extract of maqui berry, rich in total polyphenols and anthocyanin to be tested in intestinal epithelial and immune cells. The methanolic extract was obtained from lyophilized and analyzed maqui berries using Folin–Ciocalteu to quantify the total polyphenol content, as well as 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) to measure the antioxidant capacity. Determination of maqui’s anthocyanins profile was performed by ultra-high-performance liquid chromatography (UHPLC-MS/MS). Viability, cytotoxicity, and percent oxidation in epithelial colon cells (HT-29) and macrophages cells (RAW 264.7) were evaluated. In conclusion, preservation studies confirmed that the maqui properties and composition in fresh or frozen conditions are preserved and a more efficient and convenient extraction methodology was achieved. In vitro studies of epithelial cells have shown that this extract has a powerful antioxidant strength exhibiting a dose-dependent behavior. When lipopolysaccharide (LPS)-macrophages were activated, noncytotoxic effects were observed, and a relationship between oxidative stress and inflammation response was demonstrated. The maqui extract along with 5-aminosalicylic acid (5-ASA) have a synergistic effect. All of the compiled data pointed out to the use of this extract as a potential nutraceutical agent with physiological benefits for the treatment of inflammatory bowel disease (IBD).
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Affiliation(s)
- Tamara Ortiz
- Departamento de Citología e Histología Normal y Patológica, Universidad de Sevilla, Avda. Sánchez-Pizjuán s/n, 41009 Sevilla, Spain; (T.O.); (V.V.-R.)
| | - Federico Argüelles-Arias
- Departamento de Medicina, Universidad de Sevilla, Avda. Sánchez-Pizjuán s/n, 41009 Sevilla, Spain; (F.A.-A.); (J.-M.G.-M.)
- Departamento de Gastroenterología, Hospital Universitario Virgen Macarena, c/Dr. Fedriani nº 3, 41009 Sevilla, Spain
| | - Belén Begines
- Departamento de Química Orgánica y Farmacéutica, Universidad de Sevilla, c/Prof García González nº 2, 41012 Sevilla, Spain;
| | - Josefa-María García-Montes
- Departamento de Medicina, Universidad de Sevilla, Avda. Sánchez-Pizjuán s/n, 41009 Sevilla, Spain; (F.A.-A.); (J.-M.G.-M.)
| | - Alejandra Pereira
- Departamento de Nutrición y Dietética, Escuela de Ciencias de la Salud, Universidad de Desarrollo Concepción Barrios Arana1735, Concepción 4070146, Chile;
| | - Montserrat Victoriano
- Departamento de Nutricion y Dietetica, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile. Barrio Universitario s/n, Concepción 4070146, Chile;
| | - Victoria Vázquez-Román
- Departamento de Citología e Histología Normal y Patológica, Universidad de Sevilla, Avda. Sánchez-Pizjuán s/n, 41009 Sevilla, Spain; (T.O.); (V.V.-R.)
| | - Juan Luis Pérez Bernal
- Departamento de Química Analítica, Universidad de Sevilla, c/Prof García González nº 2, 41012 Sevilla, Spain;
| | - Raquel M. Callejón
- Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Universidad de Sevilla, c/Prof García González nº 2, 41012 Sevilla, Spain;
| | - Manuel De-Miguel
- Departamento de Citología e Histología Normal y Patológica, Universidad de Sevilla, Avda. Sánchez-Pizjuán s/n, 41009 Sevilla, Spain; (T.O.); (V.V.-R.)
- Correspondence: (M.D.-M.); (A.A.); Tel.: +34-955-421-025 (M.D.-M.); +34-954-556-740 (A.A.)
| | - Ana Alcudia
- Departamento de Química Orgánica y Farmacéutica, Universidad de Sevilla, c/Prof García González nº 2, 41012 Sevilla, Spain;
- Correspondence: (M.D.-M.); (A.A.); Tel.: +34-955-421-025 (M.D.-M.); +34-954-556-740 (A.A.)
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8
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Hayar S, Zeitoun R, Maestroni BM. Validation of a Rapid Multiresidue Method for the Determination of Pesticide Residues in Vine Leaves. Comparison of the Results According to the Different Conservation Methods. Molecules 2021; 26:molecules26041176. [PMID: 33671830 PMCID: PMC7927040 DOI: 10.3390/molecules26041176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/16/2022] Open
Abstract
The QuEChERS method was applied to the determination of pesticide residues in vine (Vitis vinifera) leaves by LC-MSMS. The method was validated in-house for 33 pesticides representing 17 different chemical groups, that are most commonly used in grape production. Recoveries for the pesticides tested ranged from 75 to 104%, and repeatability and reproducibility relative standard deviations (RSDr% and RSDRw%) were less than 20%. The method was applied to the analysis of pesticide residues in 17 market brands of vine leaves processed according to three different preservation methods and sampled from the Lebanese market. Dried vine leaves were more contaminated with pesticide residues than those preserved in brine or stuffed vine leaves. The systemic fungicides were the most frequently detected among all the phytosanitary compounds usually applied to grape production. Brine-preserved and stuffed vine leaves contained lower concentrations of the residues but still contained a cocktail of different pesticides.
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Affiliation(s)
- Salem Hayar
- Doctoral School of Science and Technology, Research Platform for Environmental Sciences (EDST-PRASE), Lebanese University, Rafic Hariri Campus, Hadath-Mount Lebanon, Lebanon
- Department of Plant Protection, Faculty of Agricultural Engineering and Veterinary Medicine, Lebanese University, Dekweneh-Beirut, Lebanon
- Environmental Health Research Lab (EHRL), Faculty of Sciences, Section V, Lebanese University, Nabatieh, Lebanon;
- Correspondence: ; Tel.: +961-3-416364
| | - Rawan Zeitoun
- Environmental Health Research Lab (EHRL), Faculty of Sciences, Section V, Lebanese University, Nabatieh, Lebanon;
- Department of Chemistry and Biochemistry, Faculty of Sciences, Section V, Lebanese University, Nabatieh, Lebanon
| | - Britt Marianna Maestroni
- Food and Environmental Protection Laboratory, Joint FAO/IAEA Division of Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramerstrasse 5, A-1400 Vienna, Austria;
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9
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Qiu Z, Wang J, Delgado-Baquerizo M, Trivedi P, Egidi E, Chen YM, Zhang H, Singh BK. Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition? Front Plant Sci 2020; 11:993. [PMID: 32714361 PMCID: PMC7351510 DOI: 10.3389/fpls.2020.00993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes.
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Affiliation(s)
- Zhiguang Qiu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
| | - Pankaj Trivedi
- Microbiome Cluster and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Yi-Min Chen
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Haiyang Zhang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
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10
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Agger P, Lass T, Smerup M, Frandsen J, Pedersen M. Optimal preservation of porcine cardiac tissue prior to diffusion tensor magnetic resonance imaging. J Anat 2015; 227:695-701. [PMID: 26391195 DOI: 10.1111/joa.12377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2015] [Indexed: 11/26/2022] Open
Abstract
The effects of ex vivo preservation techniques on the quality of diffusion tensor magnetic resonance imaging in hearts are poorly understood, and the optimal handling procedure prior to investigation remains to be determined. Therefore, 24 porcine hearts were examined in six groups treated with different preservation techniques, including chemical fixation and freezing. Diffusion properties of each heart were assessed with diffusion tensor imaging in terms of fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (Da) and radial diffusivity (Dr). Tractography was performed to visualize the course of the cardiomyocytes, assuming greater diffusivity in the longitudinal than the transverse axis of individual cardiomyocytes. Significant differences in MD, Da and Dr were found, as well as in FA between groups (P < 0.001). Freezing of specimens resulted in the lowest mean FA of 0.21 (0.06) and highest Dr of 8.92 (1.5) mm2 s(-1) . The highest mean FA was found to be 0.43 (0.11) in hearts perfusion-fixed with formalin. Calculated tractographies were indistinguishable among groups except in frozen specimens, where no fibres could be tracked. Perfusion fixation with formalin provided the best tractography, but immersion fixation yielded diffusion data most similar to fresh hearts. These findings suggest that parameters derived from diffusion tensor imaging in ex vivo hearts are sensitive to fixation and storage methods. In particular, freezing of specimens should be avoided prior to diffusion tensor imaging investigation due to significant changes in diffusion parameters and subsequent image deteriorations.
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Affiliation(s)
- Peter Agger
- Department of Cardiothoracic & Vascular Surgery, Aarhus University Hospital, Aarhus, Denmark.,Comparative Medicine Lab, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas Lass
- Department of Cardiothoracic & Vascular Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - Morten Smerup
- Department of Cardiothoracic & Vascular Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - Jesper Frandsen
- Center for Functionally Integrative Neuroscience, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Pedersen
- Comparative Medicine Lab, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark.,MR Research Center, Aarhus University Hospital, Aarhus, Denmark
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