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Ghareeb RY, Jaremko M, Abdelsalam NR, Abdelhamid MMA, El-Argawy E, Ghozlan MH. Biocontrol potential of endophytic fungi against phytopathogenic nematodes on potato (Solanum tuberosum L.). Sci Rep 2024; 14:15547. [PMID: 38969662 PMCID: PMC11229511 DOI: 10.1038/s41598-024-64056-x] [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: 09/12/2023] [Accepted: 06/04/2024] [Indexed: 07/07/2024] Open
Abstract
Root-knot nematodes (RKNs) are a vital pest that causes significant yield losses and economic damage to potato plants. The use of chemical pesticides to control these nematodes has led to environmental concerns and the development of resistance in the nematode populations. Endophytic fungi offer an eco-friendly alternative to control these pests and produce secondary metabolites that have nematicidal activity against RKNs. The objective of this study is to assess the efficacy of Aspergillus flavus (ON146363), an entophyte fungus isolated from Trigonella foenum-graecum seeds, against Meloidogyne incognita in filtered culture broth using GC-MS analysis. Among them, various nematicidal secondary metabolites were produced: Gadoleic acid, Oleic acid di-ethanolamide, Oleic acid, and Palmitic acid. In addition, biochemical compounds such as Gallic acid, Catechin, Protocatechuic acid, Esculatin, Vanillic acid, Pyrocatechol, Coumarine, Cinnamic acid, 4, 3-indol butyl acetic acid and Naphthyl acetic acid by HPLC. The fungus was identified through morphological and molecular analysis, including ITS 1-4 regions of ribosomal DNA. In vitro experiments showed that culture filtrate of A. flavus had a variable effect on reducing the number of egg hatchings and larval mortality, with higher concentrations showing greater efficacy than Abamectin. The fungus inhibited the development and multiplication of M. incognita in potato plants, reducing the number of galls and eggs by 90% and 89%, respectively. A. flavus increased the activity of defense-related enzymes Chitinas, Catalyse, and Peroxidase after 15, 45, and 60 days. Leaching of the concentrated culture significantly reduced the second juveniles' stage to 97% /250 g soil and decreased the penetration of nematodes into the roots. A. flavus cultural filtrates via soil spraying improved seedling growth and reduced nematode propagation, resulting in systemic resistance to nematode infection. Therefore, A. flavus can be an effective biological control agent for root-knot nematodes in potato plants. This approach provides a sustainable solution for farmers and minimizes the environmental impact.
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Affiliation(s)
- Rehab Y Ghareeb
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt.
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955, Thuwal, Saudi Arabia
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Mohamed M A Abdelhamid
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Eman El-Argawy
- Department of Plant Pathology, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Mahmoud H Ghozlan
- Department of Plant Pathology, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
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Cho Y, Cho MY, Yoon J, Hong DE, Lee J, Park HS, Lee H, Hong KS, Won‐Kyu L, Saehae C, Song S, Noh Y. Evaluation of unmodified human cell-derived extracellular vesicle mitochondrial deoxyribonucleic acid-based biodistribution in rodents. J Extracell Vesicles 2024; 13:e12489. [PMID: 39016198 PMCID: PMC11253025 DOI: 10.1002/jev2.12489] [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: 10/28/2023] [Revised: 06/10/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024] Open
Abstract
Recently, extracellular vesicles (EVs) have been developed as therapeutic targets for various diseases. Biodistribution is crucial for EVs intended for therapeutic purposes because it can determine the degree of on- and off-target effects. This study aimed to explore techniques to evaluate the biodistribution of unmodified EVs. We devised a novel quantitative polymerase chain reaction (qPCR)-based assay to detect unmodified EVs by targeting mitochondrial deoxyribonucleic acid (mtDNA), a constituent of EVs. We focused on specific mtDNA regions that exhibited homologous variations distinct from their rodent mtDNA counterparts to establish this analytical approach. Herein, we successfully designed primers and probes targeting human and rodent mtDNA sequences and developed a highly specific and sensitive qPCR method. Furthermore, the quantification range of EVs isolated from various cells differed based on the manufacturer and cell source. IRDye 800CW-labelled Expi293F EV mimetics were administered to the animals via the tail vein to compare the imaging test and mtDNA-qPCR results. The results obtained from imaging tests and mtDNA-qPCR to investigate EV biodistribution patterns revealed differences. The results revealed that our newly developed method effectively determined the biodistribution of unmodified EVs with high sensitivity and reproducibility.
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Affiliation(s)
- Young‐Woo Cho
- Division of Drug Safety EvaluationNDDC, Osong Medical Innovation FoundationCheongjuSouth Korea
- College of PharmacyChungbuk National UniversityCheongjuSouth Korea
| | - Mi Young Cho
- Biopharmaceutical Research CenterKorea Basic Science InstituteCheongjuSouth Korea
| | - Jaehyeon Yoon
- Division of Drug Safety EvaluationNDDC, Osong Medical Innovation FoundationCheongjuSouth Korea
| | - Da Eun Hong
- Division of Drug Safety EvaluationNDDC, Osong Medical Innovation FoundationCheongjuSouth Korea
| | - Ju‐young Lee
- Division of Drug Safety EvaluationNDDC, Osong Medical Innovation FoundationCheongjuSouth Korea
- College of PharmacyChungbuk National UniversityCheongjuSouth Korea
| | - Hye Sun Park
- Biopharmaceutical Research CenterKorea Basic Science InstituteCheongjuSouth Korea
| | - Hyunseung Lee
- Biopharmaceutical Research CenterKorea Basic Science InstituteCheongjuSouth Korea
| | - Kwan Soo Hong
- Biopharmaceutical Research CenterKorea Basic Science InstituteCheongjuSouth Korea
- Department of ChemistryChung‐Ang UniversitySeoulSouth Korea
| | - Lee Won‐Kyu
- Division of Drug Safety EvaluationNDDC, Osong Medical Innovation FoundationCheongjuSouth Korea
| | - Choi Saehae
- Division of Drug Safety EvaluationNDDC, Osong Medical Innovation FoundationCheongjuSouth Korea
| | - Suk‐Gil Song
- College of PharmacyChungbuk National UniversityCheongjuSouth Korea
| | - Young‐Woock Noh
- Division of Drug Safety EvaluationNDDC, Osong Medical Innovation FoundationCheongjuSouth Korea
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Akhter G, Ahmed I, Ahmad SM. Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene. Biochem Genet 2024:10.1007/s10528-024-10862-x. [PMID: 38896378 DOI: 10.1007/s10528-024-10862-x] [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: 10/31/2023] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.
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Affiliation(s)
- G Akhter
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - I Ahmed
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India.
| | - S M Ahmad
- Division of Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
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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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Buzan E, Potočnik H, Pokorny B, Potušek S, Iacolina L, Gerič U, Urzi F, Kos I. Molecular analysis of scats revealed diet and prey choice of grey wolves and Eurasian lynx in the contact zone between the Dinaric Mountains and the Alps. Front Zool 2024; 21:9. [PMID: 38500207 PMCID: PMC10949697 DOI: 10.1186/s12983-024-00530-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
A comprehensive understanding of the dietary habits of carnivores is essential to get ecological insights into their role in the ecosystem, potential competition with other carnivorous species, and their effect on prey populations. Genetic analysis of non-invasive samples, such as scats, can supplement behavioural or microscopic diet investigations. The objective of this study was to employ DNA metabarcoding to accurately determine the prey species in grey wolf (Canis lupus) and Eurasian lynx (Lynx lynx) scat samples collected in the Julian Alps and the Dinaric Mountains, Slovenia. The primary prey of wolves were red deer (Cervus elaphus) (detected in 96% scat samples), European roe deer (Capreolus capreolus) (68%), and wild boar (Sus scrofa) (45%). A smaller portion of their diet consisted of mesocarnivores, small mammals, and domestic animals. In contrast, the lynx diet mostly consisted of European roe deer (82%) and red deer (64%). However, small mammals and domestic animals were also present in lynx diet, albeit to a lesser extent. Our findings indicate that the dietary habits of wolves and lynx are influenced by geographical location. Snapshot dietary analyses using metabarcoding are valuable for comprehending the behaviour and ecology of predators, and for devising conservation measures aimed at sustainable management of both their natural habitats and prey populations. However, to gain a more detailed understanding of wolf and lynx dietary habits and ecological impact, it would be essential to conduct long-term genetic monitoring of their diet.
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Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Hubert Potočnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Boštjan Pokorny
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Laura Iacolina
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Urška Gerič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Felicita Urzi
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia.
| | - Ivan Kos
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
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Bugarski-Stanojević V, Đokić M, Stamenković G, Barišić Klisarić N, Stojković O, Jojić V, Savić I. A Cryptic Subterranean Mammal Species, the Lesser Blind Mole Rat ( Nannospalax leucodon syrmiensis)-Retreated but Not Extinct. Animals (Basel) 2024; 14:774. [PMID: 38473158 DOI: 10.3390/ani14050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Blind mole rats (genus Nannospalax) attract a great deal of attention because of their cancer resistance and longevity. Due to the high rate of chromosome rearrangements, 74 Nannospalax chromosomal forms have been discovered. The convergence of their external morphology complicates their taxonomy, and many cryptic species remain unrecognized. Thus, the European N. leucodon supersp. is listed in the IUCN Red List of Threatened Species with "Data Deficient" status. It is crucial for the conservation of biodiversity to clarify its taxonomy, to recognize each cryptic species, and assign to them the correct conservation status. Of the more than 20 chromosomal forms described within N. leucodon, five cryptic species occur in Serbia. The most threatened among them-N. l. syrmiensis, described and named 50 years ago in the regions of Srem, Belgrade and Mačva-has been declared extinct in the literature, which may have negative consequences for the conservation of wildlife genetic diversity. Through five years of fieldwork and comparison of 16SrRNA and MT-CYTB gene segments between old, archived teeth and recently collected material, we show that N. l. syrmiensis is not extinct. However, its habitat has been fragmented and reduced, owing primarily to anthropogenic impact. Therefore, detailed surveillance, population-structure studies, risk assessment, and appropriate conservation measures are needed.
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Affiliation(s)
- Vanja Bugarski-Stanojević
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Marko Đokić
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Gorana Stamenković
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Nataša Barišić Klisarić
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Oliver Stojković
- Institute of Forensic Medicine, Faculty of Medicine, University of Belgrade, 11060 Belgrade, Serbia
| | - Vida Jojić
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Ivo Savić
- Institute of Zoology, Faculty of Biology, University of Belgrade, 11060 Belgrade, Serbia
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Jafar S, Anjum KM, Zahoor MY, Shehzad W, Naseem A, Imran M. Development and validation of a universal primer pair for the taxonomic and phylogenetic studies of vertebrates. Mol Biol Rep 2024; 51:332. [PMID: 38393511 DOI: 10.1007/s11033-023-09175-w] [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: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 02/25/2024]
Abstract
BACKGROUND Recent studies in the field of molecular identification have described 16S rRNA gene as a highly informative fragment of mitochondrial DNA for species discrimination. This study presents a newly developed universal primer pair yielding an approximately 350 bp fragment of mitochondrial 16S rRNA, variable enough to encompass and identify all vertebrate classes. METHODS AND RESULTS The primers were designed by aligning and analyzing over 1500 16S rRNA sequences downloaded from the NCBI nucleotide database. A total of 93 vertebrate species, spanning 27 orders and 55 families, were PCR-amplified to validate the primers. All the target species were successfully amplified and identified when aligned with reference sequences from the NCBI nucleotide database. Using the Kimura 2-parameter model, low intra-species genetic divergence of the target region was observed - from 0 to 4.63%, whereas relatively higher inter-species genetic divergence was observed, ranging from 4.88% to 69.81%. Moreover, the newly developed primers were successfully applied to a direct PCR protocol, making the workflow very cost-effective, time-saving and less laborious in comparison to conventional PCR. CONCLUSIONS The short length, high variability and conserved priming sites of the target fragment across all vertebrate species make it a highly desirable marker for species identification and discrimination.
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Affiliation(s)
- Sana Jafar
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Khalid Mahmood Anjum
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Kasur, Punjab, Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Wasim Shehzad
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Asif Naseem
- Department of Zoology, Institute of Molecular Biology and Biotechnology, The University of Lahore (Sargodha Campus), Sargodha, Punjab, Pakistan
| | - Muhammad Imran
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan.
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Mejías-Alpízar MJ, Porras-Silesky C, Rodríguez EJ, Quesada J, Alfaro-Segura MP, Robleto-Quesada J, Gutiérrez R, Rojas A. Mitochondrial and ribosomal markers in the identification of nematodes of clinical and veterinary importance. Parasit Vectors 2024; 17:77. [PMID: 38378676 PMCID: PMC10880205 DOI: 10.1186/s13071-023-06113-4] [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: 10/24/2023] [Accepted: 12/26/2023] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Nematodes of the Ascarididae, Ancylostomatidae and Onchocercidae families are parasites of human and veterinary importance causing infections with high prevalence worldwide. Molecular tools have significantly improved the diagnosis of these helminthiases, but the selection of genetic markers for PCR or metabarcoding purposes is often challenging because of the resolution these may show. METHODS Nuclear 18S rRNA, internal transcribed spacers 1 (ITS-1) and 2 (ITS-2), mitochondrial gene cytochrome oxidase 1 (cox1) and mitochondrial rRNA genes 12S and 16S loci were studied for 30 species of the mentioned families. Accordingly, their phylogenetic interspecies resolution, pairwise nucleotide p-distances and sequence availability in GenBank were analyzed. RESULTS The 18S rRNA showed the least interspecies resolution since separate species of the Ascaris, Mansonella, Toxocara or Ancylostoma genus were intermixed in phylogenetic trees as opposed to the ITS-1, ITS-2, cox1, 12S and 16S loci. Moreover, pairwise nucleotide p-distances were significantly different in the 18S compared to the other loci, with an average of 99.1 ± 0.1%, 99.8 ± 0.1% and 98.8 ± 0.9% for the Ascarididae, Ancylostomatidae and Onchocercidae families, respectively. However, ITS-1 and ITS-2 average pairwise nucleotide p-distances in the three families ranged from 72.7% to 87.3%, and the cox1, 12S and 16S ranged from 86.4% to 90.4%. Additionally, 2491 cox1 sequences were retrieved from the 30 analyzed species in GenBank, whereas 212, 1082, 994, 428 and 143 sequences could be obtained from the 18S, ITS-1, ITS-2, 12S and 16S markers, respectively. CONCLUSIONS The use of the cox1 gene is recommended because of the high interspecies resolution and the large number of sequences available in databases. Importantly, confirmation of the identity of an unknown specimen should always be complemented with the careful morphological examination of worms and the analysis of other markers used for specific parasitic groups.
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Affiliation(s)
- María José Mejías-Alpízar
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Catalina Porras-Silesky
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Esteban José Rodríguez
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Joban Quesada
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - María Paula Alfaro-Segura
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Joby Robleto-Quesada
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Ricardo Gutiérrez
- National Reference Center for Bacteriology, Costa Rican Institute for Research and Teaching in Nutrition and Health (INCIENSA), Tres Rios, Costa Rica
- Ross University School of Veterinary Medicine, West Farm, Basseterre, Saint Kitts and Nevis
| | - Alicia Rojas
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica.
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica.
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Tani T. Immortalization of American miniature horse-derived fibroblast by cell cycle regulator with normal karyotype. PeerJ 2024; 12:e16832. [PMID: 38288466 PMCID: PMC10823992 DOI: 10.7717/peerj.16832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Immortalized cells serve as a crucial research tool that capitalizes on their robust proliferative properties for functional investigations of an organism. Establishing an immortalized American miniature horse cell line could yield valuable insights into these animals' genetic and physiological characteristics and susceptibility to health issues. To date, immortalized small horse cells with normal karyotypes have not been established. In this study, we successfully established primary and immortalized fibroblast cell lines through the combined expression of human-derived mutant cyclin-dependent kinase 4 (CDK4R24C), cyclin D1, and Telomerase Reverse Transcriptase (TERT), although CDK4R24C and cyclin D1, SV40T and TERT did not result in successful immortalization. Our comparison of the properties of these immortalized cells demonstrated that K4DT immortalized cells maintain a normal karyotype. Ultimately, our findings could pave the way for the development of targeted interventions to enhance the health and well-being of American miniature horses.
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Affiliation(s)
- Tetsuya Tani
- Department of Advanced Bioscience, Kindai University, Nara, Nara, Japan
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10
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Zeng YP, Huang JY, Tu L, Zhao K. Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota). Mitochondrial DNA B Resour 2024; 9:46-49. [PMID: 38197052 PMCID: PMC10776047 DOI: 10.1080/23802359.2023.2300473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
Butyriboletus hainanensis, a macrofungus belonging to the Boletaceae family, is named after its collection location on Hainan Island, China. However, little is known about its mitochondrial genome and its phylogenetic relationship with other boletes. In this study, we utilized next-generation sequencing technology to sequence the mitochondrial genome of Bu. hainanensis. Our findings revealed that the mitochondrial genome of this species is presumably a circular DNA molecule spanning 36,592 bp. It consists of 15 protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The base composition of the mitochondrial genome is as follows: A (36.64%), C (12.22%), G (11.73%), and T (39.41%), with a GC content of 23.95%. Additionally, a phylogenetic tree was constructed based on 22 mitochondrial genomes, which provided valuable insights into the phylogenetic relationships of Bu. hainanensis with other boletes for the first time.
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Affiliation(s)
- Ya-ping Zeng
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Jie-yu Huang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Lei Tu
- Jiulingshan National Nature Reserve Administration of Jiangxi Province, Jing’an, China
| | - Kuan Zhao
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
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Heil AC, de Melo Lima Waterloo M, Guerra JM, Ferreira AMR, da Silva Leite J. Histopathological, immunohistochemical and molecular analyses of foetuses from a female dog naturally infected by Leishmania (Leishmania) infantum - Case report. Vet Med Sci 2023; 9:2443-2446. [PMID: 37669416 PMCID: PMC10650230 DOI: 10.1002/vms3.1254] [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: 06/01/2023] [Revised: 07/19/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023] Open
Abstract
This report presents anatomo-histopathological, immunohistochemical and molecular analyses of an asymptomatic female dog naturally infected with Leishmania (Leishmania) infantum and her four pups. In addition to routine serological tests, the mother's positivity was confirmed by real-time PCR of a bone marrow sample; the placenta and ovaries, however, were negative with the same analysis. The pups presented no positivity in any of the techniques used. It is suggested that the gestational period and factors related to the female's immunological condition cause greater variability in the occurrence of vertical infection.
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Affiliation(s)
- Ana Carina Heil
- Department of Pathology and Veterinary ClinicFederal Fluminense University, NiteróiRio de JaneiroBrazil
| | | | | | - Ana Maria Reis Ferreira
- Department of Pathology and Veterinary ClinicFederal Fluminense University, NiteróiRio de JaneiroBrazil
| | - Juliana da Silva Leite
- Department of Pathology and Veterinary ClinicFederal Fluminense University, NiteróiRio de JaneiroBrazil
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12
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Setiaji A, Lestari DA, Pandupuspitasari NS, Agusetyaningsih I, Khan FA. Genetic characteristics of complete mtDNA genome sequence of Indonesian local rabbit (Oryctolagus cuniculus). J Genet Eng Biotechnol 2023; 21:96. [PMID: 37812313 PMCID: PMC10562326 DOI: 10.1186/s43141-023-00546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Indonesian local rabbit (Oryctolagus cuniculus) is a local breed in Indonesia. We reveal the mitochondrial genome sequence of the Indonesian local Rabbit for the first time. A better understanding of the mechanisms underlying these beneficial aspects of local breeds over imported ones requires detailed genetic investigations, of which mtDNA genome sequencing is of particular importance. Such an investigation will solve the major issues of misidentification with Javanese hares (Lepus nigricollis) and maternal lineage. In addition, this information will guide better statistics on the Indonesian local rabbit breed population and strategies for its conservation and breeding plans. This study aimed to identify and explore the characteristics of the mtDNA genomes of Indonesian local rabbits. RESULT This study observed that the length of the mtDNA genome is 17,469 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), a replication origin, and a noncoding control region (D-loop). CONCLUSIONS mtDNA genome of Indonesian local rabbit was the longest and had the most extended D-loop sequence among the other references of Oryctolagus cuniculus. Other specific differences were also found in the percentage of nucleotides and variation in most of the PCGs when they were aligned with Oryctolagus cuniculus references from GenBank. Indonesian local Rabbits strongly suspected brought from Europe during the colonial period in Indonesia.
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Affiliation(s)
- Asep Setiaji
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, 50275, Indonesia
| | - Dela Ayu Lestari
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, 50275, Indonesia.
| | | | - Ikania Agusetyaningsih
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, 50275, Indonesia
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency (BRIN), South Tangerang, 15314, Indonesia
- Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan
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13
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Long X, Chen W, Liu G, Hu W, Tan Q. Establishment and characterization of a skeletal myoblast cell line of grass carp (Ctenopharyngodon idellus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1043-1061. [PMID: 37782384 DOI: 10.1007/s10695-023-01246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023]
Abstract
Skeletal muscle myoblastic cell lines can provide a valuable new in vitro model for the exploration of the mechanisms that control skeletal muscle development and its associated molecular regulation. In this study, the skeletal muscle tissues of grass carp were digested with trypsin and collagenase I to obtain the primary myoblast cell culture. Myoblast cells were obtained by differential adherence purification and further analyzed by cryopreservation and resuscitation, chromosome analysis, immunohistochemistry, and immunofluorescence. A continuous grass carp myoblast cell line (named CIM) was established from grass carp (Ctenopharyngodon idellus) muscle and has been subcultured > 100 passages in a year and more. The CIM cells revived at 79.78-95.06% viability after 1-6 months of cryopreservation, and shared a population doubling time of 27.24 h. The number of modal chromosomes of CIM cells was 48, and the mitochondrial 12S rRNA sequence of the CIM cell line shared 99% identity with those of grass carp registered in GenBank. No microorganisms (bacteria, fungi, or mycoplasma) were detected during the whole study. The cell type of CIM cells was proven to be myoblast by immunohistochemistry of specific myogenic protein markers, including CD34, desmin, MyoD, and MyHC, as well as relative expression of key genes. And the myogenic rate and fusion index of this cell line after 10 days of induced differentiation were 8.96 ~ 9.42% and 3-24%, respectively. The telomerase activity and transfection efficiency of CIM cell line were 0.027 IU/mgprot and 23 ~ 24%, respectively. These results suggest that a myoblast cell line named CIM with normal biological function has been successfully established, which may provide a valuable tool for related in vitro studies.
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Affiliation(s)
- Xianmei Long
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Wangwang Chen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Guoqing Liu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Wenguang Hu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Qingsong Tan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China.
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14
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Buschi E, Dell’Anno A, Tangherlini M, Stefanni S, Lo Martire M, Núñez-Pons L, Avila C, Corinaldesi C. Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean. Front Microbiol 2023; 14:1234725. [PMID: 37799611 PMCID: PMC10548270 DOI: 10.3389/fmicb.2023.1234725] [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: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.
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Affiliation(s)
- Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat, University of Barcelona, Barcelona, Catalonia, Spain
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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15
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Thamarai Kannan H, Issac PK, Dey N, Guru A, Arockiaraj J. A Review on Mitochondrial Derived Peptide Humanin and Small Humanin-Like Peptides and Their Therapeutic Strategies. Int J Pept Res Ther 2023; 29:86. [DOI: 10.1007/s10989-023-10558-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2023] [Indexed: 10/16/2023]
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16
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Filonzi L, Ardenghi A, Rontani PM, Voccia A, Ferrari C, Papa R, Bellin N, Nonnis Marzano F. Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species. Foods 2023; 12:2420. [PMID: 37372635 DOI: 10.3390/foods12122420] [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: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.
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Affiliation(s)
- Laura Filonzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessia Ardenghi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Pietro Maria Rontani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Voccia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Claudio Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Riccardo Papa
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Nicolò Bellin
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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17
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Bonfigli A, Cesare P, Volpe AR, Colafarina S, Forgione A, Aloisi M, Zarivi O, Poma AMG. Estimation of DNA Degradation in Archaeological Human Remains. Genes (Basel) 2023; 14:1238. [PMID: 37372418 DOI: 10.3390/genes14061238] [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: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.
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Affiliation(s)
- Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Anna Rita Volpe
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Alfonso Forgione
- Department of Human Studies, University of L'Aquila, 67100 L'Aquila, Italy
| | - Massimo Aloisi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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18
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Rana AK, Kumar N. Current wildlife crime (Indian scenario): major challenges and prevention approaches. BIODIVERSITY AND CONSERVATION 2023; 32:1473-1491. [PMID: 37063172 PMCID: PMC10025790 DOI: 10.1007/s10531-023-02577-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/11/2023] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
UNLABELLED The constant depletion of wild flora and fauna in India due to uncontrolled human activities, natural habitat destruction and covert poaching activities is threatening the ecological balance. The poaching and trafficking of wild species in the lure of money as well as fashion has wiped out a range of wildlife species that call for critical attention to tackle this menace. There are many transit routes through the states of Uttar Pradesh, Karnataka, West Bengal, Rajasthan, Madhya Pradesh, and Assam, which are major hubs for wildlife trafficking in India, in both domestic and international markets. The poaching of wild animals and plants slowly erases biodiversity, which in turn affects the survival of humans and other living species. Therefore, there is an urgent need to check ongoing wildlife crimes, raise the number of endangered species, rehabilitate exotic/extinct species and restore natural ecosystems. In this article, we collected wildlife crime data from web portals of various stakeholders, government agencies and authentic news sources, and discuss the current crime trends, challenges, and prevention approaches required to control and restore wildlife biodiversity in India. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10531-023-02577-z.
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Affiliation(s)
- Ajay Kumar Rana
- Division of Biology, Central Forensic Science Laboratory Hyderabad, Ministry of Home Affairs, Government of India, Amberpet post, Ramanthapur, Hyderabad, Telangana 500013 India
| | - Nishant Kumar
- Quality Control, Bihar, Patna, Department of Agriculture, Government of Bihar, Patna, 800001 India
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19
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Jeon GT, Kim HR, Kim JM, Baek JS, Shin YK, Kwon OK, Kang HE, Cho HS, Cheon DS, Park CK. Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples. Animals (Basel) 2023; 13:ani13040602. [PMID: 36830388 PMCID: PMC9951688 DOI: 10.3390/ani13040602] [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: 12/24/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been frequently reported in companion dogs and cats worldwide during the ongoing coronavirus disease. However, RT-qPCR methods developed for humans have been used for the diagnosis of SARS-CoV-2 infections in suspected companion dogs and cats owing to the lack of the companion animal-tailored methods. Therefore, we developed a multiplex RT-qPCR (mRT-qPCR) using newly designed primers and probes targeting RdRp and N genes of all currently circulating SARS-CoV-2 variants as well as the canine or feline 16S rRNA gene as an endogenous internal positive control (EIPC) for reliable diagnosis of SARS-CoV-2 infection from suspected dogs and cats. The developed mRT-qPCR assay specifically detected the target genes of SARS-CoV-2 but no other canine or feline pathogens. Furthermore, canine and feline EIPCs were stably amplified by mRT-qPCR in samples containing canine- or feline-origin cellular materials. This assay has high repeatability and reproducibility, with an optimal limit of detection (<10 RNA copies per reaction) and coefficients of variation (<1.0%). The detection rate of SARS-CoV-2 of the developed mRT-qPCR was 6.6% for canine and feline nasopharyngeal samples, which was consistent with that of a commercial mRT-qPCR kit for humans. Collectively, the newly developed mRT-qPCR with canine and feline EIPC can efficiently diagnose and evaluate the viral load in field specimens and will be a valuable tool for etiological diagnosis, epidemiological study, and controlling SARS-CoV-2 infections in canine and feline populations.
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Affiliation(s)
- Gyu-Tae Jeon
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hye-Ryung Kim
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Min Kim
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ji-Su Baek
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeun-Kyung Shin
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Oh-Kyu Kwon
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Hae-Eun Kang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Ho-Seong Cho
- Bio-Safety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | | | - Choi-Kyu Park
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
- Correspondence: ; Tel.: +82-53-950-5973
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20
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Ghemrawi M, Tejero NF, Duncan G, McCord B. Pyrosequencing: Current forensic methodology and future applications-a review. Electrophoresis 2023; 44:298-312. [PMID: 36168852 DOI: 10.1002/elps.202200177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Nicole Fernandez Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - George Duncan
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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21
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In silico identification of multiple conserved motifs within the control region of Culicidae mitogenomes. Sci Rep 2022; 12:21920. [PMID: 36536037 PMCID: PMC9763401 DOI: 10.1038/s41598-022-26236-5] [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: 08/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Mosquitoes are important vectors for human and animal diseases. Genetic markers, like the mitochondrial COI gene, can facilitate the taxonomic classification of disease vectors, vector-borne disease surveillance, and prevention. Within the control region (CR) of the mitochondrial genome, there exists a highly variable and poorly studied non-coding AT-rich area that contains the origin of replication. Although the CR hypervariable region has been used for species differentiation of some animals, few studies have investigated the mosquito CR. In this study, we analyze the mosquito mitogenome CR sequences from 125 species and 17 genera. We discovered four conserved motifs located 80 to 230 bp upstream of the 12S rRNA gene. Two of these motifs were found within all 392 Anopheles (An.) CR sequences while the other two motifs were identified in all 37 Culex (Cx.) CR sequences. However, only 3 of the 304 non-Culicidae Dipteran mitogenome CR sequences contained these motifs. Interestingly, the short motif found in all 37 Culex sequences had poly-A and poly-T stretch of similar length that is predicted to form a stable hairpin. We show that supervised learning using the frequency chaos game representation of the CR can be used to differentiate mosquito genera from their dipteran relatives.
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22
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Andaman local goat: mitochondrial genome characterization and lineage analysis. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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23
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Hulting KA, Mason SD, Story CM, Keller GS. Wetland cohesion is associated with increased probability of infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis. DISEASES OF AQUATIC ORGANISMS 2022; 151:97-109. [PMID: 36226838 DOI: 10.3354/dao03692] [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: 06/16/2023]
Abstract
The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) poses a substantial threat to amphibian populations. Understanding the landscape conditions that facilitate Bd transmission and persistence is crucial for predicting Bd trends in amphibian populations. Here, we investigated the interactions between land use, wetland connectivity, and Bd occurrence and infection intensity. In northeastern Massachusetts, we sampled Pseudacris crucifer, Lithobates sylvaticus, L. clamitans, and L. pipiens from 24 sites. We found an overall 30.6% Bd prevalence at our sites, with prevalence differing among species. Bd occurrence increased with wetland-patch cohesion, potentially due to microclimate shifts from decreased forest or changes in host movement. Bd infection intensity was not mediated by landscape context. Overall, our results highlight the importance of landscape structure for Bd dynamics, suggesting that certain landscapes may facilitate transmission and harbor Bd more than others. To mitigate the impacts of Bd on amphibian populations, conservation efforts should account for interactions between Bd and landscape variables.
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Affiliation(s)
- Katherine A Hulting
- Landscape Ecology Lab, Department of Life, Health, and Physical Sciences, Gordon College, Wenham, MA 01984, USA
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24
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Zyrianova IM, Zaripov OG. 18S ribosomal DNA-based PCR test for avian and mammalian DNA identification in meat products. Vet Anim Sci 2022; 15:100234. [PMID: 35112013 PMCID: PMC8790660 DOI: 10.1016/j.vas.2022.100234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/13/2021] [Accepted: 01/19/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Irina M. Zyrianova
- Institute for Innovative Biotechnologies in Animal Husbandry, The branch of L.K. Ernst Federal Research Center for Animal Husbandry, 12/4 Kostyakov Street, Moscow, 127422, Russian Federation
- Corresponding author.
| | - Oleg G. Zaripov
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, 60, Podolsk district, Moscow region, 142132, Russian Federation
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Kumar S, Singh A, Shanker A. pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites. Life Sci Alliance 2022; 5:5/6/e202101307. [PMID: 35181599 PMCID: PMC8860089 DOI: 10.26508/lsa.202101307] [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: 11/19/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/02/2022] Open
Abstract
The polymorphic microSATellites database (pSATdb) provides information on common, polymorphic, and unique mitochondrial microsatellites. Microsatellites, also termed as simple sequence repeats, are repetitive tracts in a DNA sequence, typically consisting of one to six nucleotides. These repeats are found in all genomes and play key roles in phylogeny and species identification. Microsatellites are highly polymorphic, and their length may differ from species to species. There are several online resources dedicated to mitochondria; however, comprehensive information is not available about the length variation of mitochondrial microsatellites. Therefore, to explore it between species among a genus, we have developed a database named pSATdb (polymorphic microSATellites database; https://lms.snu.edu.in/pSATdb/). pSATdb contains 28,710 perfect microsatellites identified across 5,976 mitochondrial genome (mt-genome) sequences from 1,576 genera which includes 1,535 (5,846 mt-genome) and 41 (130 mt-genome) genera of Metazoa and Viridiplantae, respectively. pSATdb is the only database which provides genus-wise information about the length variation of mitochondrial microsatellites. Because of the emerging role of microsatellites in genomics studies, the identified common, polymorphic, and unique microsatellites stored in pSATdb will be effectively useful in various studies including genetic diversity, mapping, marker-assisted selection, and comparative population studies.
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Affiliation(s)
- Sonu Kumar
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Ashutosh Singh
- Translational Bioinformatics Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Asheesh Shanker
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
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Chaora NS, Khanyile KS, Magwedere K, Pierneef R, Tabit FT, Muchadeyi FC. A 16S Next Generation Sequencing Based Molecular and Bioinformatics Pipeline to Identify Processed Meat Products Contamination and Mislabelling. Animals (Basel) 2022; 12:ani12040416. [PMID: 35203124 PMCID: PMC8868451 DOI: 10.3390/ani12040416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Meat adulteration and fraud encompasses the deliberate fraudulent addition or substitution of proteins of animal or plant origin in edible products primarily for economic gain. The mitochondrial 16S ribosomal (rRNA) gene was used to identify species that are present in pure and processed meat samples. The meat samples were sequenced using an Illumina sequencing platform, and bioinformatics analysis was carried out for species identification. The results indicated that pork was the major contaminant in most of the meat samples. The bioinformatics pipeline demonstrated its specificity through identification of species specific and quantification of the contamination levels across all samples. Food business operators and regulatory sectors can validate this method for food fraud checks and manage any form of mislabeling in the animal or plant protein food ecosystem. Abstract Processed meat is a target in meat adulteration for economic gain. This study demonstrates a molecular and bioinformatics diagnostic pipeline, utilizing the mitochondrial 16S ribosomal RNA (rRNA) gene, to determine processed meat product mislabeling through Next-Generation Sequencing. Nine pure meat samples were collected and artificially mixed at different ratios to verify the specificity and sensitivity of the pipeline. Processed meat products (n = 155), namely, minced meat, biltong, burger patties, and sausages, were collected across South Africa. Sequencing was performed using the Illumina MiSeq sequencing platform. Each sample had paired-end reads with a length of ±300 bp. Quality control and filtering was performed using BBDuk (version 37.90a). Each sample had an average of 134,000 reads aligned to the mitochondrial genomes using BBMap v37.90. All species in the artificial DNA mixtures were detected. Processed meat samples had reads that mapped to the Bos (90% and above) genus, with traces of reads mapping to Sus and Ovis (2–5%) genus. Sausage samples showed the highest level of contamination with 46% of the samples having mixtures of beef, pork, or mutton in one sample. This method can be used to authenticate meat products, investigate, and manage any form of mislabeling.
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Affiliation(s)
- Nyaradzo Stella Chaora
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Rooderpoort 1709, South Africa; (N.S.C.); (F.T.T.)
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
| | - Khulekani Sedwell Khanyile
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria 0001, South Africa;
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
| | - Frederick Tawi Tabit
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Rooderpoort 1709, South Africa; (N.S.C.); (F.T.T.)
| | - Farai Catherine Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
- Correspondence:
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McDermott JH, Wolf J, Hoshitsuki K, Huddart R, Caudle KE, Whirl-Carrillo M, Steyger PS, Smith RJH, Cody N, Rodriguez-Antona C, Klein TE, Newman WG. Clinical Pharmacogenetics Implementation Consortium Guideline for the Use of Aminoglycosides Based on MT-RNR1 Genotype. Clin Pharmacol Ther 2022; 111:366-372. [PMID: 34032273 PMCID: PMC8613315 DOI: 10.1002/cpt.2309] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 02/03/2023]
Abstract
Aminoglycosides are widely used antibiotics with notable side effects, such as nephrotoxicity, vestibulotoxicity, and sensorineural hearing loss (cochleotoxicity). MT-RNR1 is a gene that encodes the 12s rRNA subunit and is the mitochondrial homologue of the prokaryotic 16s rRNA. Some MT-RNR1 variants (i.e., m.1095T>C; m.1494C>T; m.1555A>G) more closely resemble the bacterial 16s rRNA subunit and result in increased risk of aminoglycoside-induced hearing loss. Use of aminoglycosides should be avoided in individuals with an MT-RNR1 variant associated with an increased risk of aminoglycoside-induced hearing loss unless the high risk of permanent hearing loss is outweighed by the severity of infection and safe or effective alternative therapies are not available. We summarize evidence from the literature supporting this association and provide therapeutic recommendations for the use of aminoglycosides based on MT-RNR1 genotype (updates at https://cpicpgx.org/guidelines/ and www.pharmgkb.org).
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Affiliation(s)
- John Henry McDermott
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Kelly E. Caudle
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Peter S. Steyger
- Translational Hearing Center, Biomedical Sciences, Creighton University, National Center for Rehabilitative Auditory Research, VA Portland Health Care System, Portland, Oregon, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Internal Medicine (Nephrology), Pediatrics and Molecular Physiology & Biophysics, University of Iowa, Iowa City, Iowa, USA
| | - Neal Cody
- Department of Genetics and Genomic Sciences, Ichan School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Medicine, Stanford University, Stanford, California, USA
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
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Allam M, Mahrous NS. Molecular genetic diversity of some rabbit breeds based on mitochondrial 16S rRNA sequences. WORLD RABBIT SCIENCE 2021. [DOI: 10.4995/wrs.2021.15110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
<p>The present study was performed to assess the genetic variations among six rabbit breeds in Egypt based on mitochondrial 16S rRNA sequences. The length of partial mitochondrial 16S rRNA in the six rabbit breeds ranged from 546 bp to 558 bp. The sequenced regions were submitted to GenBank/NCBI under accession numbers (MW052052 - MW052057). The average content of A+T was 57% in all breeds. Among breeds, the percentages of genetic distance values were ranged from 0.000 to 0.004. The highest P-distance (0.004) was found between the New Zealand White breed and all other breeds. The results support the suitability of mitochondrial 16S rRNA for genetic diversity analysis of rabbit breeds and the applicability for future research on genetic relationships and the phylogeny of rabbit breeds.</p>
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Choi J, Kim W, Yoon H, Lee J, Jun JH. Dynamic Oxygen Conditions Promote the Translocation of HIF-1 α to the Nucleus in Mouse Blastocysts. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5050527. [PMID: 34608438 PMCID: PMC8487385 DOI: 10.1155/2021/5050527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022]
Abstract
Oxygen tension is one of the most critical factors for mammalian embryo development and its survival. The HIF protein is an essential transcription factor that activated under hypoxic conditions. In this study, we evaluated the effect of dynamic oxygen conditions on the expression of embryonic genes and translocation of hypoxia-inducible factor-1α (HIF-1α) in cultured mouse blastocysts. Two-pronuclear (2PN) zygotes harvested from ICR mice were subjected to either high oxygen (HO; 20%), low oxygen (LO; 5%), or dynamic oxygen (DO; 5% to 2%) conditions. In the DO group, PN zygotes were cultured in 5% O2 from days 1 to 3 and then in 2% O2 till day 5 after hCG injection. On day 5, the percentage of blastocysts in the cultured embryos from each group was estimated, and the embryos were also subjected to immunocytochemical and gene expression analysis. We found that the percentage of blastocysts was similar among the experimental groups; however, the percentage of hatching blastocysts in the DO and LO groups was significantly higher than that in the HO group. The total cell number of blastocysts in the DO group was significantly higher than that of both the HO and LO groups. Further, gene expression analysis revealed that the expression of genes related to the embryonic development was significantly higher in the DO group than that in the HO and LO groups. Interestingly, HIF-1α mRNA expression did not significantly differ; however, HIF-1α protein translocation from the cytoplasm to the nucleus was significantly higher in the DO group than in the HO and LO groups. Our study suggests that dynamic oxygen concentrations increase the developmental capacity in mouse preimplantation embryos through activation of the potent transcription factor HIF-1α.
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Affiliation(s)
- Jungwon Choi
- Department of Senior Healthcare BK21 Plus Program, Graduate School, Eulji University, Seongnam, Republic of Korea
- Department of Biomedical Laboratory Science, Eulji University, Seongnam, Republic of Korea
| | - Wontae Kim
- Department of Biomedical Laboratory Science, Eulji University, Seongnam, Republic of Korea
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Seongnam, Republic of Korea
| | - Hyejin Yoon
- Department of Senior Healthcare BK21 Plus Program, Graduate School, Eulji University, Seongnam, Republic of Korea
- Department of Biomedical Laboratory Science, Eulji University, Seongnam, Republic of Korea
| | - Jaewang Lee
- Department of Biomedical Laboratory Science, Eulji University, Seongnam, Republic of Korea
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Seongnam, Republic of Korea
| | - Jin Hyun Jun
- Department of Senior Healthcare BK21 Plus Program, Graduate School, Eulji University, Seongnam, Republic of Korea
- Department of Biomedical Laboratory Science, Eulji University, Seongnam, Republic of Korea
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Seongnam, Republic of Korea
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Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation. PLoS One 2021; 16:e0256961. [PMID: 34473778 PMCID: PMC8412288 DOI: 10.1371/journal.pone.0256961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.
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Di Bernardi C, Wikenros C, Hedmark E, Boitani L, Ciucci P, Sand H, Åkesson M. Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats. Ecol Evol 2021; 11:11739-11748. [PMID: 34522337 PMCID: PMC8427573 DOI: 10.1002/ece3.7918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/07/2023] Open
Abstract
Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.
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Affiliation(s)
- Cecilia Di Bernardi
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Camilla Wikenros
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Eva Hedmark
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Håkan Sand
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Mikael Åkesson
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
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Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths. Parasit Vectors 2021; 14:233. [PMID: 33933158 PMCID: PMC8088577 DOI: 10.1186/s13071-021-04737-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic markers are employed widely in molecular studies, and their utility depends on the degree of sequence variation, which dictates the type of application for which they are suited. Consequently, the suitability of a genetic marker for any specific application is complicated by its properties and usage across studies. To provide a yardstick for future users, in this study we assess the suitability of genetic markers for molecular systematics and species identification in helminths and provide an estimate of the cut-off genetic distances per taxonomic level. METHODS We assessed four classes of genetic markers, namely nuclear ribosomal internal transcribed spacers, nuclear rRNA, mitochondrial rRNA and mitochondrial protein-coding genes, based on certain properties that are important for species identification and molecular systematics. For molecular identification, these properties are inter-species sequence variation; length of reference sequences; easy alignment of sequences; and easy to design universal primers. For molecular systematics, the properties are: average genetic distance from order/suborder to species level; the number of monophyletic clades at the order/suborder level; length of reference sequences; easy alignment of sequences; easy to design universal primers; and absence of nucleotide substitution saturation. Estimation of the cut-off genetic distances was performed using the 'K-means' clustering algorithm. RESULTS The nuclear rRNA genes exhibited the lowest sequence variation, whereas the mitochondrial genes exhibited relatively higher variation across the three groups of helminths. Also, the nuclear and mitochondrial rRNA genes were the best possible genetic markers for helminth molecular systematics, whereas the mitochondrial protein-coding and rRNA genes were suitable for molecular identification. We also revealed that a general gauge of genetic distances might not be adequate, using evidence from the wide range of genetic distances among nematodes. CONCLUSION This study assessed the suitability of DNA genetic markers for application in molecular systematics and molecular identification of helminths. We provide a novel way of analyzing genetic distances to generate suitable cut-off values for each taxonomic level using the 'K-means' clustering algorithm. The estimated cut-off genetic distance values, together with the summary of the utility and limitations of each class of genetic markers, are useful information that can benefit researchers conducting molecular studies on helminths.
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Garibian PG, Karabanov DP, Neretina AN, Taylor DJ, Kotov AA. Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 2021; 9:e11310. [PMID: 33981506 PMCID: PMC8074845 DOI: 10.7717/peerj.11310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
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Affiliation(s)
- Petr G. Garibian
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Fish Ecology, I.D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Anna N. Neretina
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Derek J. Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, New York, United States
| | - Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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Jaafar F, Na-Nakorn U, Srisapoome P, Amornsakun T, Duong TY, Gonzales-Plasus MM, Hoang DH, Parhar IS. A Current Update on the Distribution, Morphological Features, and Genetic Identity of the Southeast Asian Mahseers, Tor Species. BIOLOGY 2021; 10:biology10040286. [PMID: 33915909 PMCID: PMC8065745 DOI: 10.3390/biology10040286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The mahseer, particularly the Tor species, is of significant cultural and economic importance as a high-value freshwater food fish in the Southeast (SE) Asian region. However, overexploitation of natural stocks because of high demand and their deteriorating habitat has resulted in a marked decline of Tor species in the wild. There are 13 Tor species that inhabit SE Asian rivers. All these species share distinct morphology, which is the presence of the median lobe. The unique characteristics, including body color, mouth position, and number of lateral scales, distinguish one species from another. Nonetheless, the taxonomy of the Tor species remains unstable and confusing, with contradictory data presented by different authors from different countries for a single Tor species. Therefore, in this review, we have gathered data for the SE Asian Tor species, outlining their distribution, morphology, and genetic identification. In addition, the present review also proposes a list of valid Tor species in the SE Asian region. The proposed list will serve as a standard and template for improving SE Asia’s Tor taxonomy, enhancing the study’s continuity, and a better understanding of specific Tor species. Abstract The king of rivers or mahseer comprises three genera: Tor, Neolissochilus, and Naziritor, under the Cyprinidae family. The Tor genus has been classified as the true mahseer due to the presence of a median lobe among the three genera. The Tor species are widely distributed across Southeast (SE) Asia, and 13 Tor species have been reported previously: Tor ater, Tor dongnaiensis, Tor douronensis, Tor laterivittatus, Tor mosal, Tor mekongensis, Tor putitora, Tor sinensis, Tor soro, Tor tambra, Tor tambroides, Tor tor and Tor yingjiangensis. However, the exact number of valid Tor species remains debatable. Different and unstandardized approaches of applying genetic markers in taxonomic identification and morphology variation within the same species have further widened the gap and ameliorated the instability of Tor species taxonomy. Therefore, synchronized and strategized research among Tor species researchers is urgently required to improve and fill the knowledge gap. This review is a current update of SE Asia’s Tor species, outlining their distribution, morphology, and genetic identification. In addition, the present review proposes that there are ten valid Tor species in the SE Asian region. This list will serve as a template and standard to improve the taxonomy of the SE Asian Tor species, which could serve as a basis to open new directions in Tor research.
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Affiliation(s)
- Faizul Jaafar
- Brain Research Institute Monash Sunway (BRIMS), Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; (U.N.-N.); (P.S.)
| | - Prapansak Srisapoome
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; (U.N.-N.); (P.S.)
| | - Thumronk Amornsakun
- Department of Technology and Industries, Prince of Songkla University Pattani Campus, Pattani 94000, Thailand;
| | - Thuy-Yen Duong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City 94000, Vietnam;
| | - Maria Mojena Gonzales-Plasus
- College of Fisheries and Aquatic Science, Puerto Princesa Campus, Western Philippines University, Puerto Princesa City 5300, Philippines;
| | - Duc-Huy Hoang
- Department of Ecology and Evolutionary, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City 700000, Vietnam;
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Ishwar S. Parhar
- Brain Research Institute Monash Sunway (BRIMS), Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
- Correspondence: ; Tel.: +60-3-5514-6304
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Widayanti R, Kusumaastuti KA, Novi JM, Adani FK, Gultom CRP, Prastiti AD, Nugroho HA, Pakpahan S. Genetic variation and phylogenetic analysis of Indonesian indigenous catfish (baung fish) based on mitochondrial 12S rRNA gene. Vet World 2021; 14:751-757. [PMID: 33935423 PMCID: PMC8076454 DOI: 10.14202/vetworld.2021.751-757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Baung fish is an essential commodity in Indonesia; however, few studies have explored the genetic diversity of Indonesian catfish. Thus, this study aimed to analyze the genetic variation and phylogenetic relationships among Indonesian catfish based on the mitochondrial 12S ribosomal RNA (rRNA) gene. Materials and Methods: In total, 28 catfish were collected from nine rivers in seven provinces and from the Indian Ocean. Catfish genomes were obtained from epaxial and hepaxial muscle samples. The mitochondrial 12S rRNA gene was amplified by polymerase chain reaction using a pair of primers (Baung12SF and Baung12SR). The 12S rRNA sequences were analyzed using MEGA X to determine genetic variation and phylogenetic relationships. Results: In total, 178 variation sites in the 12S rRNA gene were substituted among Indonesian catfish. The genetic distance between all Indonesian catfish samples was 0.1-16.0%. The closest genetic distance was between MP and PM catfish, whereas the farthest genetic distances were between BF and EM and PD and EM. For the entire population, based on mean diversity calculations, the number of base substitutions per site was 0.08. Conclusion: Indonesian catfish were divided into four clades based on the 12S rRNA gene. The catfish MP, KR, PM, MS, BB, and KS were grouped with Hemibagrus nemurus, the catfish EM was grouped with Mystus vittatus, the catfish BSBJ was grouped with Pangasius pangasius, and the catfish PD and BF were grouped with Netuma thalassina.
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Affiliation(s)
- Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ken Ayik Kusumaastuti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Joana Martha Novi
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Khairuna Adani
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Catrine Relia Patrecia Gultom
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayuning Devina Prastiti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Herjuno Ari Nugroho
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Jakarta-Bogor KM 46, Cibinong, West Java, Indonesia
| | - Suhendra Pakpahan
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Jakarta-Bogor KM 46, Cibinong, West Java, Indonesia
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Analysis of Matched Skin and Gut Microbiome of Patients with Vitiligo Reveals Deep Skin Dysbiosis: Link with Mitochondrial and Immune Changes. J Invest Dermatol 2021; 141:2280-2290. [PMID: 33771527 DOI: 10.1016/j.jid.2021.01.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022]
Abstract
Vitiligo is an autoimmune disease characterized by patchy, white skin owing to melanocyte loss. Commensal cutaneous or gut dysbiosis has been linked to various dermatological disorders. In this study, we studied the skin and gut microbiota of patients with vitiligo compared with those of healthy controls. We obtained swabs and biopsies from both lesional and nonlesional skin as well as stool and blood samples from each individual. We detected reduced richness and diversity of microbiota in the stools of subjects with vitiligo compared with the stools of the controls (P < 0.01). Skin swabs had greater α-diversity than biopsies (P < 0.001); swabs from lesional sites were primarily depleted of Staphylococcus compared with those from nonlesional sites (P < 0.02). Sampling deeper layers from the same patients showed differences in both α- and β-diversity between samples with decreased richness and distribution of species (P < 0.01) in the lesional site. Biopsy microbiota from the lesional skin had distinct microbiota composition, which was depleted of protective Bifidobacterium and Bacteroides but was enriched in Proteobacteria, Streptococcus, Mycoplasma, and mtDNA (P < 0.001); the latter increased in the same patients with heightened innate immunity and stress markers in their blood (P < 0.05). These data describe vitiligo-specific cutaneous and gut microbiota and a link between skin dysbiosis, mitochondrial damage, and immunity in patients with vitiligo.
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Li Y, Gordon E, Shean RC, Idle A, Deng X, Greninger AL, Delwart E. CrAssphage and its bacterial host in cat feces. Sci Rep 2021; 11:815. [PMID: 33436756 PMCID: PMC7804022 DOI: 10.1038/s41598-020-80076-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022] Open
Abstract
CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages' cellular host has been identified as the anaerobic Bacteroides intestinalis. CrAssphage has also been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. Here we describe crAssphage DNA in a feline fecal sample. 95% of the ~ 100 Kb genome could be assembled and classified in genus 1 of the recently proposed Alphacrassvirinae subfamily. The cat origin of the fecal sample was confirmed by partial mitochondrial DNA sequencing. High levels of Bacteroides intestinalis DNA could also be detected in this cat's feces. Fecal samples longitudinally collected over a 4-week period showed the continuous shedding of crAssphage DNA. We therefore report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal.
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Affiliation(s)
- Yanpeng Li
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Emilia Gordon
- The British Columbia Society for the Prevention of Cruelty to Animals, Vancouver, BC, V5T 1R1, Canada
| | - Ryan C Shean
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - Amanda Idle
- The British Columbia Society for the Prevention of Cruelty to Animals, Vancouver, BC, V5T 1R1, Canada
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA.
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Iyiola OA. Genetic Diversity and Molecular Characterization of Mosquitoes (Diptera: Culicidae) In North-Central Nigeria Using Ribosomal DNA ITS2 and Mitochondrial 16S-DNA Sequences. THE IRAQI JOURNAL OF VETERINARY MEDICINE 2020. [DOI: 10.30539/ijvm.v44i2.985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Mosquitoes are vectors of various life-threatening diseases like malaria, yellow fever, dengue fever etc. Their close proximity to human habitations allows ease for disease transmission. They have been identified by key morphological tools like their wings, legs, bristles etc. but closely related species are difficult to identify based on morphology. Molecular tools have, therefore, been employed to help with the more accurate identification. This study was aimed at identifying and characterizing different mosquito species in five different states in North-Central Nigeria using internal transcribed spacer 2 (ITS2) and mitochondrial 16S rDNA regions. Mosquito larvae were collected from stagnant water in breeding places at each collection site in North-central Nigeria. Morphological identification was carried out using standard keys. DNA extraction was performed using EZNA extraction kit. PCR amplification of ribosomal ITS2 and mitochondrial 16S-rDNA gene regions were carried out. The PCR amplicons were sequenced using primers initially used for the PCR. Sequence data were aligned in MEGA 6.0 using ClustalW multiple alignment feature and then compared with GenBank databases for similarity. Phylogenetic analysis of DNA sequences from the ITS2 region was able to distinguish two mosquito subfamilies; Anophelinae and Culicinae as well as differentiate between and amongst Culex and Aedes species. However, it was unable to effectively distinguish between the two different species of Anopheles sequenced. Mitochondrial 16S rRNA marker was also able to distinguish the two mosquito subfamilies. It efficiently identified and differentiated Culex, Aedes and Anopheles mosquito species sequenced in this study. This study concludes that heterogeneity among Nigerian populations of Anopheles mosquitoes of may likely impact malaria vector control programs. We recommend the combination of nuclear and mitochondrial markers for effective and reliable phylogenetic study and determination of evolutionary relationship among mosquito species.
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Jaiswal KS, Khanna S, Ghosh A, Padhan P, Raghav SK, Gupta B. Differential mitochondrial genome in patients with Rheumatoid Arthritis. Autoimmunity 2020; 54:1-12. [PMID: 33191792 DOI: 10.1080/08916934.2020.1846182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Mitochondria play an important role in cell survival, function and lineage differentiation. Changes in mitochondrial DNA (mtDNA) may control mitochondrial functions and thus may impart an alternative cellular state thereby leading to a disease condition in the body. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease wherein immune cells become self-reactive causing joint inflammation, swelling and pain in patients. The changes in mtDNA may alter cellular functions thereby directing the immune cells towards an inflammatory phenotype in RA. Therefore, it becomes pertinent to identify changes in mtDNA sequence in immune cells of RA patients to understand the pathogenesis and progression of RA. METHODS mtDNA from peripheral blood mono-nuclear cells (PBMCs) of 23 RA patients and 17 healthy controls (HCs) were sequenced using next-generation sequencing (NGS). Further, single nucleotide polymorphisms (SNPs) and other variable changes in mtDNA hypervariable and coding regions, amino acid changes with a putative impact on disease, levels of heteroplasmy, copy number variations and haplogroup analysis in RA patients and HCs were analysed and compared to identify any association of mtDNA changes and RA disease. RESULTS A total of 382 single nucleotide mtDNA variants were observed, 91 (23.82%) were present in hypervariable region and 291 (76.18%) in coding region of patients and HC. The variant 513 GCA > ACA, with G present in HVR-III, known to control the mitochondrial translation function, was significantly present in RA patients. The CYTB gene had larger number of SNPs in HC samples while RNR2 was more variable in RA patients. A non-synonymous heteroplasmy in ND1 gene was found at a single nucleotide position 3533 in an increased number of RA patients as compared to the controls. A significant increase in mtDNA duplication and a higher frequency of the haplogroup U was also characteristic of RA. Also, the presence of SNPs in mitochondrial tRNA genes at two positions 12308 A > G and 15924 A > G were found to be pathogenic. CONCLUSION We herein observed an altered mtDNA sequence in immune cells of RA patients and thus a possible role of mitochondrial genome in the development of RA. The observed nucleotide changes in mtDNA control region, RNR2 gene, increased heteroplasmy and mtDNA duplication in RA patients may alter sites for transcription factor binding thereby influencing mtDNA gene expression, as well as copy numbers thereby affecting the mitochondrial proteins and their functions. These changes in mtDNA could be one of the probable reasons among many leading to the progression of RA.
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Affiliation(s)
- Kumar Sagar Jaiswal
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Shweta Khanna
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Arup Ghosh
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Prasanta Padhan
- Department of Rheumatology, Kalinga Institute of Medical Sciences, Bhubaneswar, India
| | - Sunil Kumar Raghav
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Bhawna Gupta
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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Fadhil IA, Al-Shuhaib MBS. Phylogenetic differentiation between Awassi and Hamdani sheep using the mitochondrial 12S rRNA. Anim Biotechnol 2020; 33:801-809. [PMID: 33108945 DOI: 10.1080/10495398.2020.1837146] [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] [Indexed: 12/25/2022]
Abstract
This study was conducted to assess the role of the mitochondrial 12S rRNA variations in the phylogenetic discrimination between two Iraqi breeds of sheep that differ in geographical distribution. A total of 122 animals (68 Awassi and 54 Hamdani) were included in the study. Direct sequencing of amplicons followed by the construction of a median-joining network and several trees were performed to identify the possible phylogenetic differences between both involved breeds. Genetic diversity, relative frequencies, and analysis of molecular variance (AMOVA) were performed to assess the genetic correlation between both populations. The median-joining network and minimized tree values showed that all observed haplotypes were separated into two groups according to their breed. Comprehensive phylogenetic data revealed only one Asian ancestor for all observed haplotypes. As indicated by AMOVA, the observed diversity was mostly due to between-population variation (1.24836%), while within-population variation (0.91221%) accounted for much less. The currently investigated rRNA amplicons exhibited different mitochondrial manifestations between Awassi and Hamdani breeds. Due to the ability of these 12S rRNA amplicons to mimic the geographical diversity for the currently investigated breeds, it is highly recommended to be used as potent mitochondrial genetic markers among broader ovine sequences.
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Affiliation(s)
- Israa A Fadhil
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, Iraq
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Sreekumar PG, Kannan R. Mechanisms of protection of retinal pigment epithelial cells from oxidant injury by humanin and other mitochondrial-derived peptides: Implications for age-related macular degeneration. Redox Biol 2020; 37:101663. [PMID: 32768357 PMCID: PMC7767738 DOI: 10.1016/j.redox.2020.101663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/18/2020] [Accepted: 07/26/2020] [Indexed: 02/06/2023] Open
Abstract
The mitochondrial-derived peptides (MDPs) are a new class of small open reading frame encoded polypeptides with pleiotropic properties. The prominent members are Humanin (HN) and small HN-like peptide (SHLP) 2, which encode 16S rRNA, while mitochondrial open reading frame of the twelve S c (MOTS-c) encodes 12S rRNA of the mitochondrial genome. While the multifunctional properties of HN and its analog 14-HNG have been well documented, their protective role in the retinal pigment epithelium (RPE)/retina has been investigated only recently. In this review, we have summarized the multiple effects of HN and its analogs, SHLP2 and MOTS-c in oxidatively stressed human RPE and the regulatory pathways of signaling, mitochondrial function, senescence, and inter-organelle crosstalk. Emphasis is given to the mitochondrial functions such as biogenesis, bioenergetics, and autophagy in RPE undergoing oxidative stress. Further, the potential use of HN and its analogs in the prevention of age-related macular degeneration (AMD) are also presented. In addition, the role of novel, long-acting HN elastin-like polypeptides in nanotherapy of AMD and other ocular diseases stemming from oxidative damage is discussed. It is expected MDPs will become a promising group of mitochondrial peptides with valuable therapeutic applications in the treatment of retinal diseases.
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Affiliation(s)
- Parameswaran G Sreekumar
- The Stephen J. Ryan Initiative for Macular Research (RIMR), Doheny Eye Institute, Los Angeles, CA, 90033, USA
| | - Ram Kannan
- The Stephen J. Ryan Initiative for Macular Research (RIMR), Doheny Eye Institute, Los Angeles, CA, 90033, USA; Stein Eye Institute, Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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Chan AHE, Chaisiri K, Morand S, Saralamba N, Thaenkham U. Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes. Parasit Vectors 2020; 13:364. [PMID: 32690073 PMCID: PMC7372814 DOI: 10.1186/s13071-020-04242-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/15/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics. METHODS To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms. RESULTS The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers. CONCLUSIONS This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.
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Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Serge Morand
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- CNRS ISEM-CIRAD ASTRE, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Mahidol University, Bangkok, Thailand
| | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Kotov AA, Garibian PG, Bekker EI, Taylor DJ, Karabanov DP. A new species group from the Daphnia curvirostris species complex (Cladocera: Anomopoda) from the eastern Palaearctic: taxonomy, phylogeny and phylogeography. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The eastern Palaearctic is a centre of diversity for freshwater cladocerans (Crustacea), but little is known about the evolution and taxonomy of this diversity. Daphnia curvirostris is a Holarctic species complex that has most of its diversity in the eastern Palaearctic. We examined the phylogeography, rates of evolution and taxonomic status for each clade of the D. curvirostris complex using morphological and genetic evidence from four genes. The cybertaxonomical and morphological evidence supported an eastern Palaearctic clade, with at least four species (described here as the Daphnia korovchinskyi sp. nov. group) having diagnostic morphological characters. We also detected convergent morphological characters in the D. curvirostris complex that provided information about species boundaries. Two of the new species (Daphnia koreana sp. nov. and Daphnia ishidai sp. nov.) are known from single ponds and are threatened by human activity. Divergence time estimates suggested an ancient origin (12–28 Mya) for the D. korovchinskyi group, but these estimates are complicated by the small number of calibration points.
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Affiliation(s)
- Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Petr G Garibian
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Eugeniya I Bekker
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, NY, USA
| | - Dmitry P Karabanov
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
- I. D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Russia
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Divya PR, Jency PME, Joy L, Kathirvelpandian A, Singh RK, Basheer VS. Population connectivity and genetic structure of Asian green mussel, Perna viridis along Indian waters assessed using mitochondrial markers. Mol Biol Rep 2020; 47:5061-5072. [PMID: 32524388 DOI: 10.1007/s11033-020-05575-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/05/2020] [Indexed: 11/24/2022]
Abstract
Perna viridis (Linnaeus, 1758), the Asian green mussel, belonging to the family Mytilidae is widely distributed along the Indian coast. The species is majorly found in southeastern countries and is considered an ideal candidate for aquaculture due to its high nutritional value and growth rate. Obtaining their genetic information is essential for their sustainable capture-based production. In the present study, genetic variation, population structure, and demographic processes of the populations across the distribution of this species were assessed using the mitochondrial DNA ATPase6 and cytb gene. In total, we selected 170 samples from five localities across the Indian subcontinent including Andaman Sea. Sequence analysis of partial cytb (885 bp) and ATPase6 (714 bp) genes revealed 45 and 58 haplotypes, respectively. The significant coefficient of genetic differentiation (FST: 0.255 for cytb and 0.252 for ATPase6) and analyses of molecular variance indicated three varieties of stocks, namely Arabian Sea, Bay of Bengal, and Andaman Sea. All the populations showed low nucleotide diversity, suggesting severe historical bottleneck events and high haplotype diversity, indicating population expansion. The genetic variation and demographic process reported in this study will form the baseline information for framing policies, which can be adopted while planning stock specific ranching and relaying programmes in the Indian subcontinent with view to enhance and manage the fishery.
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Affiliation(s)
- P R Divya
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India.
| | - P M Elizabeth Jency
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
| | - Linu Joy
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
| | - A Kathirvelpandian
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
| | - Rajeev Kumar Singh
- ICAR National Bureau of Fish Genetic Resources, Dilkusha Post, Canal ring Road, Lucknow, 226002, India
| | - V S Basheer
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
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Effects of Mitochondrial-Derived Peptides (MDPs) on Mitochondrial and Cellular Health in AMD. Cells 2020; 9:cells9051102. [PMID: 32365540 PMCID: PMC7290668 DOI: 10.3390/cells9051102] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
Substantive evidence demonstrates the contribution of mitochondrial dysfunction in the etiology and pathogenesis of Age-related Macular Degeneration (AMD). Recently, extensive characterization of Mitochondrial-Derived Peptides (MDPs) has revealed their cytoprotective role in several diseases, including AMD. Here we summarize the varied effects of MDPs on cellular and mitochondrial health, which establish the merit of MDPs as therapeutic targets for AMD. We argue that further research to delve into the mechanisms of action and delivery of MDPs may advance the field of AMD therapy.
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Bugarski-Stanojević V, Stamenković G, Ćirović D, Ćirić D, Stojković O, Veličković J, Kataranovski D, Savić I. 16S rRNA gene polymorphism supports cryptic speciation within the lesser blind mole rat Nannospalax leucodon superspecies (Rodentia: Spalacidae). Mamm Biol 2020. [DOI: 10.1007/s42991-020-00019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Hsieh CH, Huang CG, Wu WJ, Wang HY. A rapid insect species identification system using mini-barcode pyrosequencing. PEST MANAGEMENT SCIENCE 2020; 76:1222-1227. [PMID: 31696604 DOI: 10.1002/ps.5674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Rapid and accurate species identification is not only important for biodiversity studies and pest quarantine and management, but in some cases may also influence the results of international trade negotiations. In this study, we developed a rapid species identification system for insects. RESULTS A universal DNA mini-barcode primer pair was designed to target ∼ 120 bp of the mitochondrial 16S rDNA gene. This primer set can amplify the targeted region from all 300 species of 26 insect orders tested as well as other classes of Arthropoda. Although we found no within-species variation in this region, it provided enough information to separate closely related species or species complexes, in particular Thrips spp. and Bemisia spp. By combining a quick DNA extraction method with pyrosequencing, we were able to generate DNA sequences and complete species identification within 5 h. CONCLUSION Mini-barcode pyrosequencing of 16S rDNA coupled with the GenBank database provides a rapid, accurate, and efficient species identification system. This system is therefore useful for biodiversity discovery, forensic identification, and quarantine control and management. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Chia-Hung Hsieh
- Department of Forestry and Nature Conservation, Chinese Culture University, Taipei, Taiwan
| | - Chin-Gi Huang
- Department of Earth and Life Science, University of Taipei, Taipei, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Miaoli, Taiwan
| | - Wen-Jer Wu
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
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Khachatryan L, de Leeuw RH, Kraakman MEM, Pappas N, Te Raa M, Mei H, de Knijff P, Laros JFJ. Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples. Forensic Sci Int Genet 2020; 46:102257. [PMID: 32058299 DOI: 10.1016/j.fsigen.2020.102257] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 12/30/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022]
Abstract
The assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed using different state of the art techniques and reference databases, can produce widely different results. In light of the fact that most forensic metagenomic analysis are still performed using 16S data, our results are especially important.
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Affiliation(s)
- Lusine Khachatryan
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Rick H de Leeuw
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Margriet E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Nikos Pappas
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Marije Te Raa
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Tafur-Culqui J, Calderon MS, Bustamante DE. Identification of commercial meats from Amazonas, Peru using PCR-RFLP of mitochondrial 12S rRNA gene. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2020. [DOI: 10.1590/1981-6723.27419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract The use of analytical methodologies based on DNA (e.g. PCR-RFLP) to determine the authenticity of different types of meat products after the initial labeling is pivotal to avoid fraudulent practices due to the increased rates of meat consumption. Our PCR-RFLP of mitochondrial 12S rRNA gene using restriction enzymes (AluI and ApoI) aimed to confirm the accuracy of the meat species labeling, based on fresh and processed meat collected in central markets along the main cities in the Amazonas Region (Bagua, Bagua Grande, Chachapoyas, Luya, Pedro Ruiz, Rodriguez de Mendoza). Our analyses qualitatively identified and differentiated three commercial species of fresh meat (bovine, porcine, ovine) and also found the substitution of goat by sheep meat. Regarding processed meat, its composition was uncertain and further analyses should be addressed to determine the meat origin. Monitoring using DNA-based analytical methods of meat trade is suggested to determine fraudulent practices, such as species substitution in markets along regions of Peru.
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50
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Arisuryanti T, Ulin Nikmah B, Kasayev T, Hakim L. Determination of species boundaries of Selais fish from Arut River, Central Kalimantan based on 16S mitochondrial gene using Bayesian approach. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202801003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Selais fish is difficult to discriminate with other Silurid fish species based on morphological characters. As a result, the valid species of selais fish is uncertain. Therefore, a molecular phylogenetic study was needed to clarify species boundaries and to addresses genetic relationships of the selais fish. In this study, 16S mitochondrial gene of ten selais samples collected from Arut River (Central Kalimantan) were sequenced, from which a Bayesian trees was generated. Result revealed monophyletic of selais fish which is revealed as a single species. The Bayesian inference showed that the selais fish clade is distinguished with two other genus, Kryptopterus and Ompok, by its sequence differences. This finding can address species boundaries of selais fish using Bayesian approach, but the name of the selais species has not been clarified.
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