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Cho YW, Yoon J, Song SG, Noh YW. Mitochondrial DNA as a target for analyzing the biodistribution of cell therapy products. Sci Rep 2024; 14:7934. [PMID: 38575614 PMCID: PMC10995129 DOI: 10.1038/s41598-024-56591-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Biodistribution tests are crucial for evaluating the safety of cell therapy (CT) products in order to prevent unwanted organ homing of these products in patients. Quantitative polymerase chain reaction (qPCR) using intronic Alu is a popular method for biodistribution testing owing to its ability to detect donor cells without modifying CT products and low detection limit. However, Alu-qPCR may generate inaccurate information owing to background signals caused by the mixing of human genomic DNA with that of experimental animals. The aim of this study was to develop a test method that is more specific and sensitive than Alu-qPCR, targeting the mitochondrial DNA (mtDNA) sequence that varies substantially between humans and experimental animals. We designed primers for 12S, 16S, and cytochrome B in mtDNA regions, assessed their specificity and sensitivity, and selected primers and probes for the 12S region. Human adipose-derived stem cells, used as CT products, were injected into the tail vein of athymic NCr-nu/nu mice and detected, 7 d after administration, in their lungs at an average concentration of 2.22 ± 0.69 pg/μg mouse DNA, whereas Alu was not detected. Therefore, mtDNA is more specific and sensitive than Alu and is a useful target for evaluating CT product biodistribution.
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Affiliation(s)
- Young-Woo Cho
- College of Pharmacy, Chungbuk National University, Cheongju, 28644, Republic of Korea
- Division of Drug Screening Evaluation, NDDC, Osong Medical Innovation Foundation, Cheongju, 28160, Republic of Korea
| | - Jaehyeon Yoon
- Division of Drug Screening Evaluation, NDDC, Osong Medical Innovation Foundation, Cheongju, 28160, Republic of Korea
| | - Suk-Gil Song
- College of Pharmacy, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Young-Woock Noh
- Division of Drug Screening Evaluation, NDDC, Osong Medical Innovation Foundation, Cheongju, 28160, Republic of Korea.
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Li W, Ren Q, Feng J, Lee SY, Liu Y. DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China. PLoS One 2024; 19:e0297164. [PMID: 38241246 PMCID: PMC10798443 DOI: 10.1371/journal.pone.0297164] [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: 05/14/2023] [Accepted: 12/30/2023] [Indexed: 01/21/2024] Open
Abstract
Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.
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Affiliation(s)
- Wenlan Li
- School of Pharmacy, Harbin University of Commerce, Harbin, China
| | - Qiqi Ren
- School of Pharmacy, Harbin University of Commerce, Harbin, China
- Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Haikou, China
| | - Jian Feng
- Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Haikou, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai, Malaysia
| | - Yangyang Liu
- Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Haikou, China
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Chan AHE, Thaenkham U, Poodeepiyasawat A, Boonserm S, Namjad P, Laoungbua P, Tawan T, Bun NP, Ratnarathorn N, Charoennitiwat V. Discovery of Encyclometra bungara (Digenea: Encyclometridae) in a new host ( Enhydris enhydris) from Thailand and Cambodia through morphological and molecular identification. Parasitology 2024; 151:77-83. [PMID: 38229575 PMCID: PMC10941033 DOI: 10.1017/s0031182023001166] [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: 09/25/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The genus Encyclometra is one of the two genera in family Encyclometridae, known for parasitising the oesophagus, stomach and intestine of snakes. Among Encyclometra, the species present are: Encyclometra colubrimurorum, Encyclometra japonica, Encyclometra asymmetrica and Encyclometra bungara. Species discrimination within Encyclometra has predominantly relied on morphological differences, such as the length of the caeca and the position of the testes. Morphological overlaps exist among these species making species discrimination challenging. Additionally, the use of molecular information has been limited for Encyclometra. To determine the Encyclometra species infecting Enhydris enhydris from Thailand and Cambodia, morphological and molecular identification was conducted. Morphological characters and measurements were obtained from 30 Encyclometra adults, and they were compared with previous studies of other Encyclometra species. Novel sequences of E. bungara were generated using the nuclear 18S and 28S ribosomal RNA genes, and the mitochondrial cytochrome c oxidase subunit 1 gene. Our results revealed that the specimens could be morphologically identified as E. bungara, with support from molecular information obtained from the phylogenies of the 3 genetic markers employed. Molecular analysis showed that the Encyclometra specimens were distinct from E. colubrimurorum and E. japonica. Through morphological and molecular identification of the Encyclometra specimens found in E. enhydris from Thailand and Cambodia, we describe and provide a record of E. bungara in a new host and new locality. Additionally, novel molecular sequences were generated, revealing the phylogenetic position of E. bungara within the superfamily Gorgoderoidea.
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Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Akkarin Poodeepiyasawat
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Somusa Boonserm
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pakteema Namjad
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Panithi Laoungbua
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Tanapong Tawan
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Ngor Peng Bun
- Faculty of Fisheries, Royal University of Agriculture, Phnom Penh, Cambodia
| | - Napat Ratnarathorn
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
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Cutmore SC, Corner RD, Cribb TH. Morphological constraint obscures richness: a mitochondrial exploration of cryptic richness in Transversotrema (Trematoda: Transversotrematidae). Int J Parasitol 2023; 53:595-635. [PMID: 37488048 DOI: 10.1016/j.ijpara.2023.06.006] [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: 03/22/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/26/2023]
Abstract
Species of Transversotrema Witenberg, 1944 (Transversotrematidae) occupy a unique ecological niche for the Trematoda, living externally under the scales of their teleost hosts. Previous studies of the genus have been impeded partly by limited variation in ribosomal DNA sequence data between closely related species and partly by a lack of morphometrically informative characters. Here, we assess richness of the tropical Indo-west Pacific species through parallel phylogenetic and morphometric analyses, generating cytochrome c oxidase subunit 1 mitochondrial sequence data and morphometric data for hologenophore specimens from Australia, French Polynesia, Japan and Palau. These analyses demonstrate that molecular data provide the only reliable basis for species identification; host distribution, and to a lesser extent morphology, are useful for identifying just a few species of Transversotrema. We infer that a combination of morphological simplicity and infection site constraint has led to the group displaying exceptionally low morphological diversification. Phylogenetic analyses of the mitochondrial data broadly support previous systematic interpretations based on ribosomal data, but also demonstrate the presence of several morphologically and ecologically cryptic species. Ten new species are described, eight from the Great Barrier Reef, Australia (Transversotrema chrysallis n. sp., Transversotrema daphnidis n. sp., Transversotrema enceladi n. sp., Transversotrema hyperionis n. sp., Transversotrema iapeti n. sp., Transversotrema rheae n. sp., Transversotrema tethyos n. sp., and Transversotrema titanis n. sp.) and two from off Japan (Transversotrema methones n. sp. and Transversotrema panos n. sp.). There are now 26 Transversotrema species known from Australian marine fishes, making it the richest trematode genus for the fauna.
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Affiliation(s)
- Scott C Cutmore
- Queensland Museum, Biodiversity and Geosciences Program, South Brisbane, Queensland 4101, Australia.
| | - Richard D Corner
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
| | - Thomas H Cribb
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
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Khairulmunir M, Gani M, Karuppannan KV, Mohd-Ridwan AR, Md-Zain BM. High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger ( Pantheratigrisjacksoni) during fasting. Biodivers Data J 2023; 11:e104757. [PMID: 37711366 PMCID: PMC10498273 DOI: 10.3897/bdj.11.e104757] [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: 04/09/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.
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Affiliation(s)
- Mohamad Khairulmunir
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota SamarahanMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
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Chan AHE, Saralamba N, Saralamba S, Ruangsittichai J, Chaisiri K, Limpanont Y, Charoennitiwat V, Thaenkham U. Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes. Sci Rep 2022; 12:9947. [PMID: 35705676 PMCID: PMC9200835 DOI: 10.1038/s41598-022-14176-z] [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] [Received: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies.
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Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sompob Saralamba
- Mathematical and Economic Modelling (MAEMOD), Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Cháves-González LE, Morales-Calvo F, Mora J, Solano-Barquero A, Verocai GG, Rojas A. What lies behind the curtain: Cryptic diversity in helminth parasites of human and veterinary importance. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2022; 2:100094. [PMID: 35800064 PMCID: PMC9253710 DOI: 10.1016/j.crpvbd.2022.100094] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Parasite cryptic species are morphologically indistinguishable but genetically distinct organisms, leading to taxa with unclear species boundaries. Speciation mechanisms such as cospeciation, host colonization, taxon pulse, and oscillation may lead to the emergence of cryptic species, influencing host-parasite interactions, parasite ecology, distribution, and biodiversity. The study of cryptic species diversity in helminth parasites of human and veterinary importance has gained relevance, since their distribution may affect clinical and epidemiological features such as pathogenicity, virulence, drug resistance and susceptibility, mortality, and morbidity, ultimately affecting patient management, course, and outcome of treatment. At the same time, the need for recognition of cryptic species diversity has implied a transition from morphological to molecular diagnostic methods, which are becoming more available and accessible in parasitology. Here, we discuss the general approaches for cryptic species delineation and summarize some examples found in nematodes, trematodes and cestodes of medical and veterinary importance, along with the clinical implications of their taxonomic status. Lastly, we highlight the need for the correct interpretation of molecular information, and the correct use of definitions when reporting or describing new cryptic species in parasitology, since molecular and morphological data should be integrated whenever possible. Cryptic diversity has been described in helminths of human and animal importance. Cryptic species are morphologically indistinguishable but genetically distinct organisms. These entities emerge by different evolutionary and speciation mechanisms. Analysis of molecular and morphological data is needed for cryptic species delimitation. Cryptic diversity may affect pathogenicity, virulence and drug resistance of helminths.
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Affiliation(s)
- Luis Enrique Cháves-González
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Fernando Morales-Calvo
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Javier Mora
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Alberto Solano-Barquero
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Guilherme G. Verocai
- Department of Veterinary Pathobiology, Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
| | - Alicia Rojas
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
- Corresponding author. Twitter icon
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