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Lee CJ, Shin W, Song M, Shin SS, Park Y, Srikulnath K, Kim DH, Han K. Comparison of digital PCR platforms using the molecular marker. Genomics Inform 2023; 21:e24. [PMID: 37704210 PMCID: PMC10326530 DOI: 10.5808/gi.23008] [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: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 07/08/2023] Open
Abstract
Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.
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Affiliation(s)
- Cherl-Joon Lee
- Department of Bio-Convergence Engineering, Dankook University, Yongin 16890, Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan 31116, Korea
| | | | | | - Yujun Park
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Facult y of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Kyudong Han
- Department of Bio-Convergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- HuNBiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Bio-Medical Engineering Research Center, Dankook University, Cheonan 31116, Korea
- DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 31116, Korea
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Wong CH, Tsai MA, Ko FC, Wang JH, Xue YJ, Yang WC. Skin Cortisol and Acoustic Activity: Potential Tools to Evaluate Stress and Welfare in Captive Cetaceans. Animals (Basel) 2023; 13:ani13091521. [PMID: 37174558 PMCID: PMC10177183 DOI: 10.3390/ani13091521] [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: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
As people's focus broadens from animals on farms to zoos and aquaria, the field of welfare science and the public's concern for animal welfare continue to grow. In captive animals, stress and its causes are topics of interest in welfare issues, and the identification of an objective method that can be used to assess animals' stress as a physiological state is essential. Both behavioral and physiological parameters can be used as indicators in order to assess animal stress quantitatively. To validate this approach, acoustic activity and the sloughed scrape skin cortisol concentration were used to evaluate the animal welfare of captive beluga whales (Delphinapterus leucas). The acoustic activity (5 min at 10:00 am) of three captive D. leucas was routinely recorded by a transducer and analyzed using audio editing software. The calls were separated into three main categories: whistles, pulses, and combo calls. The sloughed scrape skin samples were collected non-invasively once a week from all three animals' fluke and/or flipper. Cortisol was extracted using a modified skin steroid extraction technique, and detected via commercially available enzyme immunoassays. The results showed that the cortisol concentration increased by varying levels when the whales encountered the same event. In addition, the number and distribution of the calls changed along with the events. This indicated that the changes in the cortisol concentration and acoustic behavior may have reflected the fluctuations in the environment and body condition. Therefore, the scrape cortisol measurement and acoustic recordings could be used to monitor stress levels in captive beluga whales. We recommend that aquaria consider incorporating skin scrape cortisol and acoustic activity monitoring into their standards for animal welfare.
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Affiliation(s)
- Chung-Hei Wong
- School of Veterinary Medicine, National Taiwan University, Taipei 106, Taiwan
| | - Ming-An Tsai
- Collage of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan
| | - Fung-Chi Ko
- National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan
- Institute of Marine Biology, National Dong-Hwa University, Pingtung 944, Taiwan
| | - Jiann-Hsiung Wang
- College of Veterinary Medicine, National Chiayi University, Chiayi 600, Taiwan
| | - Yi-Jing Xue
- College of Veterinary Medicine, National Chiayi University, Chiayi 600, Taiwan
| | - Wei-Cheng Yang
- School of Veterinary Medicine, National Taiwan University, Taipei 106, Taiwan
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Of Whales and Genes: Unraveling the Physiological Response to Stressors in Belugas (Delphinapterus leucas) at the Molecular Level. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2021. [DOI: 10.3390/jzbg2040040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marine mammals, now more than ever, are exposed to environmental and anthropogenic stressors. A better understanding of stress physiology in marine mammals is warranted in order to assist in conservation efforts. This study screened gene expression profiles (cytokines, stress-response markers) in blood samples collected opportunistically under controlled conditions from aquarium belugas during transport and introduction to a novel environment (T/NEnv), participation in out-of-water examinations (OWE) and from wild belugas during live capture–release health assessments (WLCR). Quantitative-PCR was used to measure gene expression involved in physiological and immune responses at different time scales. Linear mixed models with repeated measures and pairwise comparisons were used for analysis. Overall, a generalized down-regulation of relative gene expression when compared to samples collected under behavioral control from aquarium whales or to pre-assessment samples of wild whales was observed, with genes IFNγ, IL2, TGFβ and Nr3c1 displaying the largest significant (p < 0.05) changes. Significant (p < 0.05) negative associations of inflammatory gene expression with norepinephrine suggest inhibitory effects of catecholamines on the inflammatory response. Overall, this study contributes to our understanding of the physiological response to stressors at the molecular level in belugas, and the genes suggested here can further be utilized as additional tools in beluga health assessments and monitoring.
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IMMUNOMEDIATOR GENE TRANSCRIPTION PROFILING IN BELUGA WHALE ( DELPHINAPTERUS LEUCAS) CLINICAL CASES. J Zoo Wildl Med 2020; 51:334-349. [PMID: 32549563 DOI: 10.1638/2018-0225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2019] [Indexed: 11/21/2022] Open
Abstract
There is an unmet need for specific diagnostics of immune perturbations and inflammation in beluga whale (Delphinapterus leucas) clinical care. Quantitative real-time polymerase chain reaction (qPCR) has been used to measure immunomediator gene transcription in beluga whales. The study hypothesis was that a qPCR-based immunomediator assay would supplement routine clinical data with specific and sensitive information on immune status. Two beluga whale clinical cases provided an opportunity to test this hypothesis: a whale with a skin laceration and a whale with gastrointestinal inflammation. Mitogen-stimulated immunomediator gene transcription (MSIGT) was compared between the cases and healthy contact whales. In both case studies, mitogens increased transcription of IL1B, PTGS2 (Cox-2), TNF, HIF1A, and IL2 but decreased IL10 transcription in peripheral blood mononuclear cells (PBMC) from the abnormal whale over the control. Correlations were identified between most immunomediators tested and one or more standard blood clinical values. Considering all 15 immunomediators tested, the whale with gastrointestinal inflammation had a more unique MSIGT signature than the whale with a laceration. These results support further elucidation of beluga whale PBMC cytokine profiles for use as immune biomarkers.
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Sassu EL, Kangethe RT, Settypalli TBK, Chibssa TR, Cattoli G, Wijewardana V. Development and evaluation of a real-time PCR panel for the detection of 20 immune markers in cattle and sheep. Vet Immunol Immunopathol 2020; 227:110092. [PMID: 32673891 DOI: 10.1016/j.vetimm.2020.110092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/05/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
Abstract
The establishment of a panel of immune markers is of paramount importance to understand the different transcription patterns of infectious diseases in livestock. The array of commercially available immunological assays for cattle and sheep is currently limited, due to the lack of antibodies for these species. Even though SYBR Green based real time quantitative PCR (qPCR) is the most commonly used method to study cytokine transcription in ruminants, a lack of standardization impairs its implementation in the study of different ruminant diseases. In order to obtain reliable qPCR results, several variables need to be considered: choice of reference genes for optimal normalization, variation of annealing temperature among primer sets, and assay specificity and sensitivity. In this study, we developed and validated a panel of immune markers in bovine and ovine samples using SYBR Green based qPCR in a cost-effective way with multiple primer sets optimised to amplify at a common thermal cycling temperature. Twenty primer sets were designed to quantify immune markers (IL-1b, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-13, IL-15, IL-18, IL-23, TNF-α, IFN-γ, IFN-α, Ki-67, NFkB-65, TLR-3, TLR-4, TLR-8 and Rig-1) in ovine and bovine templates. For optimal normalization and selection of suitable reference genes, primer sets that measure the transcription of five reference genes were also included in the panel. The amplification efficiency, linearity and specificity was validated for all target genes. Optimal amplification conditions were achieved in both ovine and bovine samples for all gene targets, with the exception of Ki67. Relative quantification studies were performed on ovine and bovine mRNA obtained from sheep peripheral blood mononuclear cells (PBMCs) stimulated with three different treatments (PMA/Ionomycin, Concanavalin A (Con A) and pokeweed mitogen (PWM)). Pokeweed and ConA efficiently induced gene transcription of most of the targeted genes, while PMA/Ionomycin showed a weaker induction. Finally, we further assessed usability of our panel by running it on bovine monocyte derived dendritic cells (MoDCs) stimulated with different vaccines. Results confirmed the induction of a specific pro-inflammatory gene transcription pattern by rabies vaccine, which resembles the one occurring during viral infection. Altogether, we validated the efficiency and usability of an extended real-time PCR panel that gives the possibility to rapidly measure a broad spectrum of ovine and bovine immune markers by using a single set of reagents and protocol thus representing a valid and cost-effective tool for research purposes.
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Affiliation(s)
- Elena L Sassu
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Richard T Kangethe
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Tirumala Bharani K Settypalli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Tesfaye Rufael Chibssa
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Viskam Wijewardana
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
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Chen IH, Chou LS, Chou SJ, Wang JH, Stott J, Blanchard M, Jen IF, Yang WC. Sound exposure-induced cytokine gene transcript profile changes in captive bottlenose dolphin (Tursiops truncatus) blood identified by a probe-based qRT-PCR. J Vet Med Sci 2018; 80:601-605. [PMID: 29479043 PMCID: PMC5938186 DOI: 10.1292/jvms.17-0548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cetacean health may be potentially affected by anthropogenic sound. We have initiated investigations on the effect of low-frequency underwater sound on immunological gene transcript profiles of captive bottlenose dolphins (Tursiops truncatus) using a probe-based quantitative gene expression assay. Six immunologic genes (IL-2Rα, -4, -10, -12, TNFα and IFNγ) were selected for analysis using two validated housekeeping genes (PGK1 and HPRT1) as reference genes. Twenty-four blood samples from six clinically healthy individuals and six blood samples from individuals after sound exposures were available. The gene transcript profile of sound-exposed dolphins was consistent with a stress-induced TH2 shift profile as compared to controls. This study may lead to better understanding of the effects of anthropogenic sound on immune responses of cetaceans.
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Affiliation(s)
- I-Hua Chen
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Lien-Siang Chou
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan (R.O.C.)
| | - Shih-Jen Chou
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Jiann-Hsiung Wang
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Jeffrey Stott
- School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A
| | - Myra Blanchard
- School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A
| | - I-Fan Jen
- Farglory Ocean Park, No.189, Yenliao Village, Shoufong, Hualien, Taiwan (R.O.C.)
| | - Wei-Cheng Yang
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
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Hofstetter AR, Eberle KC, Venn-Watson SK, Jensen ED, Porter TJ, Waters TE, Sacco RE. Monitoring bottlenose dolphin leukocyte cytokine mRNA responsiveness by qPCR. PLoS One 2017; 12:e0189437. [PMID: 29272269 PMCID: PMC5741220 DOI: 10.1371/journal.pone.0189437] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/24/2017] [Indexed: 11/26/2022] Open
Abstract
Both veterinarians caring for dolphins in managed populations and researchers monitoring wild populations use blood-based diagnostics to monitor bottlenose dolphin (Tursiops truncatus) health. Quantitative PCR (qPCR) can be used to assess cytokine transcription patterns of peripheral blood mononuclear cells (PBMC). This can supplement currently available blood tests with information on immune status. Full realization of this potential requires establishment of normal ranges of cytokine gene transcription levels in bottlenose dolphins. We surveyed four dolphins over the span of seven months by serial bleeds. PBMC were stimulated with phytohaemagglutinin (1, 5, and 10 μg/mL) and concanavalin A (1 μg/mL) for 48 H in vitro. RNA from these cultures was probed by qPCR using Tursiops truncatus-specific primers (IL-1α, IL-1β, IL-1RA, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p40, IL-13, IL-18, IFN-γ and TNF-α). Two blood samples from an additional bottlenose dolphin diagnosed with acute pulmonary disease add further perspective to the data. We observed that mitogen choice made a significant difference in the magnitude of gene transcription observed. On the other hand, most cytokines tested exhibited limited intra-animal variation. However, IL-6 and IL-12p40 differed between older and younger dolphins. Furthermore, the magnitude of mitogenic response clusters the tested cytokines into three groups. The data provide a reference for the selection of target cytokine mRNAs and their expected range of mitogen-stimulated cytokine gene transcription for future studies.
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Affiliation(s)
- Amelia Ruth Hofstetter
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, United States of America
- * E-mail:
| | - Kirsten C. Eberle
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, United States of America
| | - Stephanie K. Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California, United States of America
| | - Eric D. Jensen
- United States Navy Marine Mammal Program, San Diego, California, United States of America
| | - Tracy J. Porter
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, United States of America
| | - Theresa E. Waters
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, United States of America
| | - Randy E. Sacco
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, United States of America
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