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Zhang Z, Zhang X, Li Y, Su W, Xu Q, Zhang S, Liang H, Ji C, Lin X. Effects of quercetin- and Lactiplantibacillus plantarum-containing bioactive films on physicochemical properties and microbial safety of grass carp. Food Chem 2024; 450:139472. [PMID: 38705103 DOI: 10.1016/j.foodchem.2024.139472] [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: 10/25/2023] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
In this study, the electrospinning technique was used to co-encapsulate Quercetin (Qu) and Lactiplantibacillus plantarum 1-24-LJ in PVA-based nanofibers, and the effect of bioactive films on fish preservation was evaluated at the first time. The findings indicated that both Lpb. plantarum 1-24-LJ and Qu were successfully in the fibers, and co-loaded fibers considerably outperformed single-loaded fiber in terms of bacterial survival and antioxidant activity. Following fish preservation using the loaded fibers, significant reductions were observed in TVB-N, TBARS, and microbial complexity compared to the control group. Additionally, the co-loaded fibers more effectively reduced the counts of H2S-producing bacteria and Pseudomonas. In the future, fibers with both active substances and LAB hold promise as a novel approach for fish preservation.
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Affiliation(s)
- Zuoli Zhang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Construction Corps Key Laboratory of Deep Processing on Featured Agricultural Products in South Xinjiang, College of Food Science and Engineering, Tarim University, Alar 843300, Xinjiang, China
| | - Xianhao Zhang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Yao Li
- Liaoning Province Key Laboratory of Pulp and Papermaking Engineering, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Wentao Su
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Qian Xu
- Construction Corps Key Laboratory of Deep Processing on Featured Agricultural Products in South Xinjiang, College of Food Science and Engineering, Tarim University, Alar 843300, Xinjiang, China
| | - Sufang Zhang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Huipeng Liang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Institute of Technology, China Resources Beer (Holdings) Company Limited, Room 306 China Resources Building No.8 Jianguomen North Avenue, Dongcheng District, Beijing 100005, China
| | - Chaofan Ji
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Xinping Lin
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
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Vega-Heredia S, Giffard-Mena I, Reverter M. Bacterial and viral co-infections in aquaculture under climate warming: co-evolutionary implications, diagnosis, and treatment. DISEASES OF AQUATIC ORGANISMS 2024; 158:1-20. [PMID: 38602294 DOI: 10.3354/dao03778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Climate change and the associated environmental temperature fluctuations are contributing to increases in the frequency and severity of disease outbreaks in both wild and farmed aquatic species. This has a significant impact on biodiversity and also puts global food production systems, such as aquaculture, at risk. Most infections are the result of complex interactions between multiple pathogens, and understanding these interactions and their co-evolutionary mechanisms is crucial for developing effective diagnosis and control strategies. In this review, we discuss current knowledge on bacteria-bacteria, virus-virus, and bacterial and viral co-infections in aquaculture as well as their co-evolution in the context of global warming. We also propose a framework and different novel methods (e.g. advanced molecular tools such as digital PCR and next-generation sequencing) to (1) precisely identify overlooked co-infections, (2) gain an understanding of the co-infection dynamics and mechanisms by knowing species interactions, and (3) facilitate the development multi-pathogen preventive measures such as polyvalent vaccines. As aquaculture disease outbreaks are forecasted to increase both due to the intensification of practices to meet the protein demand of the increasing global population and as a result of global warming, understanding and treating co-infections in aquatic species has important implications for global food security and the economy.
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Affiliation(s)
- Sarahí Vega-Heredia
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México, Egresada del Programa de Ecología Molecular y Biotecnología, carretera transpeninsular Ensenada-Tijuana No. 3917, C.P. 22860, México
| | - Ivone Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México
| | - Miriam Reverter
- School of Biological and Marine Sciences, Plymouth University, Drake Circus, Devon PL4 8AA, UK
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3
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Gross M, Dunthorn M, Mauvisseau Q, Stoeck T. Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers. Environ Microbiol 2024; 26:e16619. [PMID: 38649189 DOI: 10.1111/1462-2920.16619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/16/2024] [Indexed: 04/25/2024]
Abstract
Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour-intensive, time-consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per-cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per-cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.
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Affiliation(s)
- Megan Gross
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
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Shahrajabian MH, Sun W. The Significance and Importance of dPCR, qPCR, and SYBR Green PCR Kit in the Detection of Numerous Diseases. Curr Pharm Des 2024; 30:169-179. [PMID: 38243947 DOI: 10.2174/0113816128276560231218090436] [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: 08/31/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 01/22/2024]
Abstract
Digital PCR (dPCR) is the latest technique that has become commercially accessible for various types of research. This method uses Taq polymerase in a standard polymerase chain reaction (PCR) to amplify a target DNA fragment from a complex sample, like quantitative PCR (qPCR) and droplet digital PCR (dd- PCR). ddPCR may facilitate microRNA (miRNA) measurement, particularly in liquid biopsy, because it has been proven to be more effective and sensitive, and in this method, ddPCR can provide an unprecedented chance for deoxyribonucleic acid (DNA) methylation research because of its capability to increase sensitivity and precision over conventional PCR-based methods. qPCR has also been found to be a valuable standard technique to measure both copy DNA (cDNA) and genomic DNA (gDNA) levels, although the finding data can be significantly variable and non-reproducible without relevant validation and verification of both primers and samples. The SYBR green quantitative real-time PCR (qPCR) method has been reported as an appropriate technique for quantitative detection and species discrimination, and has been applied profitably in different experiments to determine, quantify, and discriminate species. Although both TaqMan qRT-PCR and SYBR green qRT-PCR are sensitive and rapid, the SYBR green qRT-PCR assay is easy and the TaqMan qRT-PCR assay is specific but expensive due to the probe required. This review aimed to introduce dPCR, qPCR, SYBR green PCR kit, and digital PCR, compare them, and also introduce their advantages in the detection of different diseases.
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Affiliation(s)
- Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
| | - Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
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Gu Z, Chen L, Zhang W, Su P, Zhang D, Du X, Peng Q, Liu Z, Liao X, Liu Y. A Sensitive Method for Detecting Beauveria bassiana, an Insecticidal Biocontrol Agent, Population Dynamics, and Stability in Different Substrates. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:9933783. [PMID: 37663453 PMCID: PMC10473894 DOI: 10.1155/2023/9933783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023]
Abstract
Beauveria bassiana is a well-known insecticidal biocontrol agent. Despite its broad field applications, its survival, colonization, and stability under field conditions remained unclear, mainly due to the lack of a quick and reliable detection method. In this study, we developed a quantitative real-time PCR technology to monitor the stability and population dynamics of B. bassiana in different substrates (water, soil, and on the cotton leaves surface), different spores of B. bassiana applied on Chinese cabbage leaves surface, and the lethality of Pieris rapae spraying with different spores of B. bassiana. Our results showed a decreased concentration of B. bassiana DNA in all three substrates from the 1st day till 9th day of post inoculation (dpi) period, possibly due to the death of B. bassiana. After this decrease, a quick and significant rebound of B. bassiana DNA concentration was observed, starting from the 11th dpi in all three substrates. The B. bassiana DNA concentration reached the plateau at about 13th dpi in water and 17th dpi in the soil. On cotton leaves surface, the B. bassiana DNA concentration reached the highest level at the 17th dpi followed by a small decline and then stabilized. This increase of DNA concentration suggested recovery of B. bassiana growth in all three substrates. We found that the most suitable killing effectiveness of P. rapae was the 1.0 × 107 spores/mL of B. bassiana. In summary, we have established a detection technology that allows a fast and reliable monitoring for the concentration and stability of B. bassiana under different conditions. This technology can benefit and help us in the development of proper management strategies for the application of this biocontrol agent in the field.
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Affiliation(s)
- Zepei Gu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lijie Chen
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Weixing Zhang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Pin Su
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Deyong Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Xiaohua Du
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Qianze Peng
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zhuoxin Liu
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Xiaolan Liao
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yong Liu
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
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Comparison of RT-qPCR and RT-ddPCR with Rift valley fever virus (RVFV) RNA. Sci Rep 2023; 13:3085. [PMID: 36813787 PMCID: PMC9944419 DOI: 10.1038/s41598-023-29023-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Rift valley fever (RVF) is an important zoonotic disease caused by the Rift valley fever virus (RVFV) which can affect ruminants and humans. In this study, a comparison was done of the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription-droplet digital PCR (RT-ddPCR) assays with synthesized RVFV RNA, cultured viral RNA, and mock clinical RVFV RNA samples. The genomic segments (L, M, and S) of three RVFV strains (BIME01, Kenya56, and ZH548) were synthesized and used as templates for in vitro transcription (IVT). Both the RT-qPCR and RT-ddPCR assays for RVFV did not react with any of the negative reference viral genomes. Thus, both the RT-qPCR and RT-ddPCR assays are specific to RVFV. The comparison of both the RT-qPCR and RT-ddPCR assays with serially diluted templates showed that the LoD of both assays are similar, and a concordant of the results was observed. The LoD of both assays reached the practical measurable minimum concentration. Taken altogether, the sensitivity of the RT-qPCR and RT-ddPCR assays is similar, and the material measured by RT-ddPCR can be used as a reference material for RT-qPCR.
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Shen X, Teo TW, Kong TF. A Technique for Rapid Bacterial-Density Enumeration through Membrane Filtration and Differential Pressure Measurements. MICROMACHINES 2022; 13:mi13081198. [PMID: 36014121 PMCID: PMC9415702 DOI: 10.3390/mi13081198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/01/2023]
Abstract
In this article, we present a microfluidic technique for the rapid enumeration of bacterial density with a syringe filter to trap bacteria and the quantification of the bacterial density through pressure difference measurement across the membrane. First, we established the baseline differential pressure and hydraulic resistance for a filtration membrane by fully wetting the filter with DI water. Subsequently, when bacteria were infused and trapped at the pores of the membrane, the differential pressure and hydraulic resistance also increased. We characterized the infusion time required for the bacterial sample to achieve a normalized hydraulic resistance of 1.5. An equivalent electric-circuit model and calibration data sets from parametric studies were used to determine the general form of a calibration curve for the prediction of the bacterial density of a bacterial sample. As a proof of concept, we demonstrated through blind tests with Escherichia coli that the device is capable of determining the bacterial density of a sample ranging from 7.3 × 106 to 2.2 × 108 CFU/mL with mean and median accuracies of 87.21% and 91.33%, respectively. The sample-to-result time is 19 min for a sample with lower detection threshold, while for higher-bacterial-density samples the measurement time is further shortened to merely 8 min.
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Affiliation(s)
- Xinhui Shen
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Ting Wei Teo
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Tian Fook Kong
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore
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von Ammon U, Averink T, Kumanan K, Brosnahan CL, Pochon X, Hutson KS, Symonds JE. An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens. Front Microbiol 2022; 13:885585. [PMID: 35531301 PMCID: PMC9069008 DOI: 10.3389/fmicb.2022.885585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/01/2022] [Indexed: 12/22/2022] Open
Abstract
Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia-like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum, and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10−9 ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10−8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens, respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry.
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Affiliation(s)
- Ulla von Ammon
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- *Correspondence: Ulla von Ammon,
| | - Tessa Averink
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
| | - Karthiga Kumanan
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Cara L. Brosnahan
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | - Xavier Pochon
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Kate S. Hutson
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Jane E. Symonds
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
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