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Mwamula AO, Kwon OG, Kwon C, Kim YS, Kim YH, Lee DW. A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA. Plant Pathol J 2024; 40:171-191. [PMID: 38606447 PMCID: PMC11016563 DOI: 10.5423/ppj.oa.01.2024.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/13/2024]
Abstract
Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.
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Affiliation(s)
- Abraham Okki Mwamula
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
| | - Oh-Gyeong Kwon
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
| | - Chanki Kwon
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| | - Yi Seul Kim
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
| | - Young Ho Kim
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| | - Dong Woon Lee
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
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Sun J, Sun Q, Li X, Li W, Li Y, Zhou Y, Hu Y. Species Identification and Genetic Diversity Analysis of Medicinal Plants Aconitum pendulum Busch and Aconitum flavum Hand.-Mazz. Plants (Basel) 2024; 13:885. [PMID: 38592876 PMCID: PMC10976075 DOI: 10.3390/plants13060885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
The classification system for the genus Aconitum is highly complex. It is also the subject of ongoing debate. Aconitum pendulum Busch and Aconitum flavum Hand.-Mazz. are perennial herbs of the genus Aconitum. Dried roots of these two plants are used in traditional Chinese medicine. In this study, morphological observations and ISSR molecular markers were employed to discriminate between A. flavum and A. pendulum, with the objective of gaining insights into the interspecies classification of Aconitum. The pubescence on the inflorescence of A. flavum was found to be appressed, while that on the inflorescence of A. pendulum was spread. UPGMA (unweighted pair-group method with arithmetic average) cluster analysis, PCoA (principal coordinates analysis), and Bayesian structural analysis divided the 199 individuals (99 individuals from DWM population and 100 individuals from QHL population) into two main branches, which is consistent with the observations of the morphology of pubescence on the inflorescence. These analyses indicated that A. flavum and A. pendulum are distinct species. No diagnostic bands were found between the two species. Two primer combinations (UBC808 and UBC853) were ultimately selected for species identification of A. flavum and A. pendulum. This study revealed high levels of genetic diversity in both A. flavum (He = 0.254, I = 0.395, PPB = 95.85%) and A. pendulum (He = 0.291, I = 0.445, PPB = 94.58%). We may say, therefore, that ISSR molecular markers are useful for distinguishing A. flavum and A. pendulum, and they are also suitable for revealing genetic diversity and population structure.
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Affiliation(s)
- Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (J.S.); (Q.S.); (X.L.); (Y.L.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Sun
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (J.S.); (Q.S.); (X.L.); (Y.L.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Li
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (J.S.); (Q.S.); (X.L.); (Y.L.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Li
- Scientific Research and Popularization Base of Qinghai–Tibet Plateau Biology, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China;
| | - Yi Li
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (J.S.); (Q.S.); (X.L.); (Y.L.); (Y.Z.)
| | - Yubi Zhou
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (J.S.); (Q.S.); (X.L.); (Y.L.); (Y.Z.)
| | - Yanping Hu
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (J.S.); (Q.S.); (X.L.); (Y.L.); (Y.Z.)
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Chudzik A, Jalkanen K, Täubel M, Szponar B, Paściak M. Identification of environmental Actinobacteria in buildings by means of chemotaxonomy, 16S rRNA sequencing, and MALDI-TOF MS. Microbiol Spectr 2024; 12:e0359623. [PMID: 38299830 PMCID: PMC10913483 DOI: 10.1128/spectrum.03596-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
Actinobacteria are abundant in soil and other environmental ecosystems and are also an important part of the human microbiota. Hence, they can also be detected in indoor environments and on building materials, where actinobacterial proliferation on damp materials can indicate moisture damage. The aim of this study was to evaluate the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of 28 environmental strains of Actinobacteria isolated from building materials and indoor and outdoor air samples, mainly collected in the context of moisture damage investigations in buildings in Finland. The 16S rRNA gene sequencing and chemotaxonomic analyses were performed, and results were compared with the MALDI-TOF MS Biotyper identification. Using 16S rRNA gene sequencing, all isolates were identified on the species or genus level and were representatives of Streptomyces, Nocardia, and Pseudonocardia genera. Based on MALDI-TOF MS analysis, initially, 11 isolates were identified as Streptomyces spp. and 1 as Nocardia carnea with a high identification score. After an upgrade in the MALDI-TOF MS in-house database and re-evaluation of mass spectra, 13 additional isolates were identified as Nocardia, Pseudonocardia, and Streptomyces. MALDI-TOF MS has the potential in environmental strain identification; however, the standard database needs to be considerably enriched by environmental Actinobacteria representatives. IMPORTANCE The manuscript addresses the challenges in identifying environmental bacteria using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) Biotyper-based protein profiling. The matter of the studies-actinobacterial strains-has been isolated mostly from building materials that originated from a confirmed moisture-damaged situation. Polyphasic taxonomy, 16S RNA gene sequencing, and MALDI-TOF mass spectrometry were applied for identification purposes. In this experimental paper, a few important facts are highlighted. First, Actinobacteria are abundant in the natural as well as built environment, and their identification on the species and genus levels is difficult and time-consuming. Second, MALDI-TOF MS is an effective tool for identifying bacterial environmental strains, and in parallel, continuous enrichment of the proteomics mass spectral databases is necessary for proper identification. Third, the chemical approach aids in the taxonomical inquiry of Actinobacteria environmental strains.
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Affiliation(s)
- Anna Chudzik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Kaisa Jalkanen
- Environmental Health Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Martin Täubel
- Environmental Health Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Bogumiła Szponar
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Mariola Paściak
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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Cai Q, Feng S, Zheng X. The complete chloroplast genome of Aristolochia fangchi provided insights into the phylogeny and species identification of Aristolochia. Genome 2024; 67:90-98. [PMID: 38091583 DOI: 10.1139/gen-2023-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Aristolochia fangchi is an important species within the family Aristolochiaceae, most of which contain nephrotoxic aristolochic acid. The inadvertent use of Aristolochiaceae plants as raw ingredients in the manufacturing of patent medicine poses a significant risk warranting considerable attention. In this study, we assembled and analyzed the complete chloroplast genome of Aristolochia fangchi, which is a 159 867 bp long circular molecule. Functional annotation of the A. fangchi plastome unveiled a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Subsequently, a series of genome structure and characteristic evaluations were conducted against the A. fangchi plastome. Further phylogenetic analysis suggested that a plausible phylogenetic relationship among Aristolochiaceae derived from the concatenated sequences of shared conserved genes rather than from the entire chloroplast genome with one IR copy. Finally, a DNA polymorphism assessment against a dozen Aristolochia plastomes yielded multiple potential regions for biomarker designation. Six pairs of primers were generated and underwent both in silico and actual PCR validations. In conclusion, this study identified the unique characteristics of the A. fangchi plastome, providing invaluable insights for further investigations on species identification and the phylogeny evolution between A. fangchi and its related species.
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Affiliation(s)
- Qingqun Cai
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou 510405, China
| | - Shiyin Feng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou 510405, China
| | - Xiasheng Zheng
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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Robinson ZL, Stephenson J, Vertacnik K, Willis S, Horn R, McCane J, Coykendall DK, Narum SR. Efficient species identification for Pacific salmon genetic monitoring programs. Evol Appl 2024; 17:e13680. [PMID: 38505217 PMCID: PMC10950091 DOI: 10.1111/eva.13680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.
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Affiliation(s)
- Zachary L. Robinson
- Columbia River Inter‐Tribal Fish Commission, Hagerman Genetics LabHagermanIdahoUSA
| | - Jeff Stephenson
- Columbia River Inter‐Tribal Fish Commission, Hagerman Genetics LabHagermanIdahoUSA
| | - Kim Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | - Stuart Willis
- Columbia River Inter‐Tribal Fish Commission, Hagerman Genetics LabHagermanIdahoUSA
| | - Rebekah Horn
- Columbia River Inter‐Tribal Fish Commission, Hagerman Genetics LabHagermanIdahoUSA
| | - Jesse McCane
- Eagle Fish Genetics Lab, Pacific States Marine Fisheries CommissionEagleIdahoUSA
| | | | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission, Hagerman Genetics LabHagermanIdahoUSA
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Qi G, Hao L, Gan Y, Xin T, Lou Q, Xu W, Song J. Identification of closely related species in Aspergillus through Analysis of Whole-Genome. Front Microbiol 2024; 15:1323572. [PMID: 38450170 PMCID: PMC10915092 DOI: 10.3389/fmicb.2024.1323572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
The challenge of discriminating closely related species persists, notably within clinical diagnostic laboratories for invasive aspergillosis (IA)-related species and food contamination microorganisms with toxin-producing potential. We employed Analysis of the whole-GEnome (AGE) to address the challenges of closely related species within the genus Aspergillus and developed a rapid detection method. First, reliable whole genome data for 77 Aspergillus species were downloaded from the database, and through bioinformatic analysis, specific targets for each species were identified. Subsequently, sequencing was employed to validate these specific targets. Additionally, we developed an on-site detection method targeting a specific target using a genome editing system. Our results indicate that AGE has successfully achieved reliable identification of all IA-related species (Aspergillus fumigatus, Aspergillus niger, Aspergillus nidulans, Aspergillus flavus, and Aspergillus terreus) and three well-known species (A. flavus, Aspergillus parasiticus, and Aspergillus oryzae) within the Aspergillus section. Flavi and AGE have provided species-level-specific targets for 77 species within the genus Aspergillus. Based on these reference targets, the sequencing results targeting specific targets substantiate the efficacy of distinguishing the focal species from its closely related species. Notably, the amalgamation of room-temperature amplification and genome editing techniques demonstrates the capacity for rapid and accurate identification of genomic DNA samples at a concentration as low as 0.1 ng/μl within a concise 30-min timeframe. Importantly, this methodology circumvents the reliance on large specialized instrumentation by presenting a singular tube operational modality and allowing for visualized result assessment. These advancements aptly meet the exigencies of on-site detection requirements for the specified species, facilitating prompt diagnosis and food quality monitoring. Moreover, as an identification method based on species-specific genomic sequences, AGE shows promising potential as an effective tool for epidemiological research and species classification.
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Affiliation(s)
- Guihong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lijun Hao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yutong Gan
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qian Lou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wenjie Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
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Zhu Y, Liu Z, Peng L, Liu B, Wu K, Zhang M, Wang X, Pan J. Evaluation of nucleotide MALDI-TOF-MS for the identification of Mycobacterium species. Front Cell Infect Microbiol 2024; 14:1335104. [PMID: 38379773 PMCID: PMC10876993 DOI: 10.3389/fcimb.2024.1335104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Background The accurate identification of the Mycobacterium tuberculosis complex (MTBC) and different nontuberculous mycobacteria (NTM) species is crucial for the timely diagnosis of NTM infections and for reducing poor prognoses. Nucleotide matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been extensively used for microbial identification with high accuracy and throughput. However, its efficacy for Mycobacterium species identification has been less studied. The objective of this study was to evaluate the performance of nucleotide MALDI-TOF-MS for Mycobacterium species identification. Methods A total of 933 clinical Mycobacterium isolates were preliminarily identified as NTM by the MPB64 test. These isolates were identified by nucleotide MALDI-TOF-MS and Sanger sequencing. The performance of nucleotide MALDI-TOF MS for identifying various Mycobacterium species was analyzed based on Sanger sequencing as the gold standard. Results The total correct detection rate of all 933 clinical Mycobacterium isolates using nucleotide MALDI-TOF-MS was 91.64% (855/933), and mixed infections were detected in 18.65% (174/933) of the samples. The correct detection rates for Mycobacterium intracellulare, Mycobacterium abscessus, Mycobacterium kansasii, Mycobacterium avium, MTBC, Mycobacterium gordonae, and Mycobacterium massiliense were 99.32% (585/589), 100% (86/86), 98.46% (64/65), 94.59% (35/37), 100.00% (34/34), 95.65% (22/23), and 100% (19/19), respectively. For the identification of the MTBC, M. intracellulare, M. abscessus, M. kansasii, M. avium, M. gordonae, and M. massiliense, nucleotide MALDI-TOF-MS and Sanger sequencing results were in good agreement (k > 0.7). Conclusion In conclusion, nucleotide MALDI-TOF-MS is a promising approach for identifying MTBC and the most common clinical NTM species.
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Affiliation(s)
- Yelei Zhu
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhengwei Liu
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Lina Peng
- Department of Service and Support, Agena Bioscience, Shanghai, China
| | - Bin Liu
- Department of Service and Support, Agena Bioscience, Shanghai, China
| | - Kunyang Wu
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Mingwu Zhang
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaomeng Wang
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Junhang Pan
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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Duan BL, Chen TY, Shi DD, You CX, Jiang C. [Site-specific PCR identification of animal species and formula particles of Scorpio]. Zhongguo Zhong Yao Za Zhi 2024; 49:942-950. [PMID: 38621901 DOI: 10.19540/j.cnki.cjcmm.20231013.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Scorpio, a commonly used animal medicine in China, is derived from Buthus martensii as recorded in the Chinese Pharmacopoeia. China harbors rich species of Scorpionida and adulterants exist in the raw medicinal material and deep-processed products of Scorpio. The microscopic characteristics of the deep-processed products may be incomplete or lost during processing, which makes the identification difficult. In this study, the maximum likelihood(ML) tree was constructed based on the morphology and cytochrome C oxidase subunit I(COⅠ) to identify the species of Scorpio products. The results showed that the main adulterant of Scorpio was Lychas mucronatus. According to the specific SNP sites in the COⅠ sequence of B. martensii, the stable primers were designed for the identification of the medicinal material and formula granules of Scorpio. The polymerase chain reaction(PCR) at the annealing temperature of 61 ℃ and 30 cycles produced bright specific bands at about 150 bp for both B. martensii and its formula particles and no band for adulterants. The adaptability of the method was investigated, which showed that the bands at about 150 bp were produced for Scorpio medicinal material, lyophilized powder, and formula granules, and commercially available formula granules. The results showed that the established method could be used to identify the adulterants of Scorpio and its formula granules, which could help to improve the quality control system and ensure the safe clinical application of Scorpio formula granules.
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Affiliation(s)
- Bao-Li Duan
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University Tianjin 300392, China
| | - Tian-Yun Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Dan-Dan Shi
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University Tianjin 300392, China
| | - Chun-Xue You
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University Tianjin 300392, China
| | - Chao Jiang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
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Mokhtar NFK, Shun YQ, Raja Nhari RMH, Mohamad NA, Shahidan NM, Warsanah IH, Mohd Hashim A. Nanoplate-based digital PCR for highly sensitive pork DNA detection targeting multi-copy nuclear and mitochondrial genes. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2024; 41:120-133. [PMID: 38190283 DOI: 10.1080/19440049.2023.2298476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
The inclusion of ingredients derived from pigs in highly processed consumer products poses a significant challenge for DNA-targeted analytical enforcement, which could be overcome by using digital PCR. However, most species detection methods use digital PCR to target single-copy nuclear genes, which limits their sensitivity. In this work, we examined the performance of a nanoplate-based digital PCR method that targets multi-copy nuclear (MPRE42) and mitochondrial (Cytb) genes. Poor separation of positive and negative partitions, as well as a 'rain effect' were obtained in the porcine-specific MPRE42 assay. Among the optimization strategies examined, the inclusion of restriction enzymes slightly improved the separation of positive and negative partitions, but a more extensive 'rain effect' was observed. The high copy number of the MPRE42 amplicon is hypothesized to contribute to the saturation of the positive signal. In contrast, the porcine-specific Cytb assay achieved perfect separation of positive and negative partitions with no 'rain effect'. This assay can detect as little as 0.4 pg of pork DNA, with a sensitivity of 0.05% (w/w) in a pork-chicken mixture, proving its applicability for detecting pork in meat and meat-based products. For the MPRE42 assay, potential applications in highly degraded products such as gelatin and lard are anticipated.
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Affiliation(s)
- Nur Fadhilah Khairil Mokhtar
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | | | - Raja Mohd Hafidz Raja Nhari
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nurhidayatul Asma Mohamad
- Laboratory of Halal Services, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nur Maisarah Shahidan
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Irwan Hanish Warsanah
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Amalia Mohd Hashim
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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Blair JD, Gaynor KM, Palmer MS, Marshall KE. A gentle introduction to computer vision-based specimen classification in ecological datasets. J Anim Ecol 2024; 93:147-158. [PMID: 38230868 DOI: 10.1111/1365-2656.14042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 01/18/2024]
Abstract
Classifying specimens is a critical component of ecological research, biodiversity monitoring and conservation. However, manual classification can be prohibitively time-consuming and expensive, limiting how much data a project can afford to process. Computer vision, a form of machine learning, can help overcome these problems by rapidly, automatically and accurately classifying images of specimens. Given the diversity of animal species and contexts in which images are captured, there is no universal classifier for all species and use cases. As such, ecologists often need to train their own models. While numerous software programs exist to support this process, ecologists need a fundamental understanding of how computer vision works to select appropriate model workflows based on their specific use case, data types, computing resources and desired performance capabilities. Ecologists may also face characteristic quirks of ecological datasets, such as long-tail distributions, 'unknown' species, similarity between species and polymorphism within species, which impact the efficacy of computer vision. Despite growing interest in computer vision for ecology, there are few resources available to help ecologists face the challenges they are likely to encounter. Here, we present a gentle introduction for species classification using computer vision. In this manuscript and associated GitHub repository, we demonstrate how to prepare training data, basic model training procedures, and methods for model evaluation and selection. Throughout, we explore specific considerations ecologists should make when training classification models, such as data domains, feature extractors and class imbalances. With these basics, ecologists can adjust their workflows to achieve research goals and/or account for uncertainty in downstream analysis. Our goal is to provide guidance for ecologists for getting started in or improving their use of machine learning for visual classification tasks.
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Affiliation(s)
- Jarrett D Blair
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kaitlyn M Gaynor
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Meredith S Palmer
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Katie E Marshall
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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11
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Harris CM, Kim DY, Jordan CR, Miranda MI, Hellberg RS. DNA barcoding of herbal supplements on the US commercial market associated with the purported treatment of COVID-19. Phytochem Anal 2024. [PMID: 38225696 DOI: 10.1002/pca.3320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/17/2023] [Accepted: 12/17/2023] [Indexed: 01/17/2024]
Abstract
INTRODUCTION The COVID-19 pandemic was associated with an increased global use of traditional medicines, including Ayurvedic herbal preparations. Due to their growing demand, their processed nature, and the complexity of the global supply chain, there is an increased risk of adulteration in these products. OBJECTIVES The objective of this study was to assess the use of DNA barcoding for species identification in herbal supplements on the US market associated with the Ayurvedic treatment of respiratory symptoms. METHODS A total of 54 commercial products containing Ayurvedic herbs were tested with four DNA barcoding regions (i.e., rbcL, matK, ITS2, and mini-ITS2) using two composite samples per product. Nine categories of herbs were targeted: amla, ashwagandha, cinnamon, ginger, guduchi, tribulus, tulsi, turmeric, and vacha. RESULTS At least one species was identified in 64.8% of products and the expected species was detected in 38.9% of products. Undeclared plant species, including other Ayurvedic herbs, rice, and pepper, were detected in 19 products, and fungal species were identified in 12 products. The presence of undeclared plant species may be a result of intentional substitution or contamination during harvest or processing, while fungal DNA was likely associated with the plant material or the growing environment. The greatest sequencing success (42.6-46.3%) was obtained with the matK and rbcL primers. CONCLUSION The results of this study indicate that a combination of genetic loci should be used for DNA barcoding of herbal supplements. Due to the limitations of DNA barcoding in identification of these products, future research should incorporate chemical characterization techniques.
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Affiliation(s)
- Calin M Harris
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Diane Y Kim
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Chevon R Jordan
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Miranda I Miranda
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Rosalee S Hellberg
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
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12
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Wang P, Xie C. Identification and analysis of a clinically isolated strain of Halomonas based on whole-genome sequencing and comparative genomics. Lab Med 2024; 55:80-87. [PMID: 37210212 DOI: 10.1093/labmed/lmad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
OBJECTIVE The aim of this study was to identify the species of a Halomonas strain isolated from a neonatal blood sample and to understand the potential pathogenicity and characteristic genes of the strain. METHODS The genomic DNA of strain 18071143 (identified as Halomonas by matrix-assisted laser desorption-ionization time of flight-mass spectrometry and the 16S ribosomal RNA (rRNA) gene sequence) was sequenced using Nanopore PromethION platforms. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated using the complete genome sequences of the strain. Comparative genomic analyses were performed on strain 18071143 and 3 strains of Halomonas (Halomonas stevensii S18214, Halomonas hamiltonii KCTC 22154, and Halomonas johnsoniae KCTC 22157) that were associated with human infections and had high genomic similarity to strain 18071143. RESULTS Phylogenetic, ANI, and dDDH similarity analyses based on genome sequence indicated that strain 18071143 belonged to the species H stevensii. Similarities exist between strain 18071143 and the other 3 Halomonas strains in terms of gene structure and protein function. Nonetheless, strain 18071143 has greater potential for DNA replication, recombination, repair, and horizontal transfer. CONCLUSION Whole-genome sequencing holds great promise for accurate strain identification in clinical microbiology. In addition, the results of this study provide data for understanding Halomonas from the perspective of pathogenic bacteria.
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Affiliation(s)
- Pinjia Wang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Chengbin Xie
- Department of Laboratory Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, China
- Department of Laboratory Medicine, Women's and Children's Hospital Affiliated to Chengdu Medical College, Chengdu, China
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13
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Taniguchi K, Miyaguchi H. COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics. J Proteome Res 2024; 23:377-385. [PMID: 38091499 DOI: 10.1021/acs.jproteome.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.
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Affiliation(s)
- Kei Taniguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
| | - Hajime Miyaguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
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14
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Lindsey RL, Gladney LM, Huang AD, Griswold T, Katz LS, Dinsmore BA, Im MS, Kucerova Z, Smith PA, Lane C, Carleton HA. Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics. Front Microbiol 2023; 14:1225207. [PMID: 38156000 PMCID: PMC10752928 DOI: 10.3389/fmicb.2023.1225207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023] Open
Abstract
Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.
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Affiliation(s)
- Rebecca L. Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, United States
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15
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Krawczyk K, Paukszto Ł, Maździarz M, Sawicki J. The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification. Front Plant Sci 2023; 14:1275377. [PMID: 38143577 PMCID: PMC10739336 DOI: 10.3389/fpls.2023.1275377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023]
Abstract
Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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16
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Wei Z, Chen F, Ding H, Liu W, Yang B, Geng J, Chen S, Guo S. Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera ( Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers. Genes (Basel) 2023; 14:2183. [PMID: 38137004 PMCID: PMC10743295 DOI: 10.3390/genes14122183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Species within the genus Chenopodium hold significant research interest due to their nutritional richness and salt tolerance. However, the morphological similarities among closely related species and a dearth of genomic resources have impeded their comprehensive study and utilization. In the present research, we conduct the sequencing and assembly of chloroplast (cp) genomes from six Chenopodium and related species, five of which were sequenced for the first time. These genomes ranged in length from 151,850 to 152,215 base pairs, showcased typical quadripartite structures, and encoded 85 protein-coding genes (PCGs), 1 pseudogene, 37 tRNA genes, and 8 rRNA genes. Compared with the previously published sequences of related species, these cp genomes are relatively conservative, but there are also some interspecific differences, such as inversion and IR region contraction. We discerned 929 simple sequence repeats (SSRs) and a series of highly variable regions across 16 related species, predominantly situated in the intergenic spacer (IGS) region and introns. The phylogenetic evaluations revealed that Chenopodium is more closely related to genera such as Atriplex, Beta, Dysphania, and Oxybase than to other members of the Amaranthaceae family. These lineages shared a common ancestor approximately 60.80 million years ago, after which they diverged into distinct genera. Based on InDels and SNPs between species, we designed 12 pairs of primers for species identification, and experiments confirmed that they could completely distinguish 10 related species.
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Affiliation(s)
- Zixiang Wei
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Fangjun Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Hongxia Ding
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Wenli Liu
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Bo Yang
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Jiahui Geng
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shihua Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shanli Guo
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Ling MH, Ivorra T, Heo CC, Wardhana AH, Hall MJR, Tan SH, Mohamed Z, Khang TF. Machine learning analysis of wing venation patterns accurately identifies Sarcophagidae, Calliphoridae and Muscidae fly species. Med Vet Entomol 2023; 37:767-781. [PMID: 37477152 DOI: 10.1111/mve.12682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
In medical, veterinary and forensic entomology, the ease and affordability of image data acquisition have resulted in whole-image analysis becoming an invaluable approach for species identification. Krawtchouk moment invariants are a classical mathematical transformation that can extract local features from an image, thus allowing subtle species-specific biological variations to be accentuated for subsequent analyses. We extracted Krawtchouk moment invariant features from binarised wing images of 759 male fly specimens from the Calliphoridae, Sarcophagidae and Muscidae families (13 species and a species variant). Subsequently, we trained the Generalized, Unbiased, Interaction Detection and Estimation random forests classifier using linear discriminants derived from these features and inferred the species identity of specimens from the test samples. Fivefold cross-validation results show a 98.56 ± 0.38% (standard error) mean identification accuracy at the family level and a 91.04 ± 1.33% mean identification accuracy at the species level. The mean F1-score of 0.89 ± 0.02 reflects good balance of precision and recall properties of the model. The present study consolidates findings from previous small pilot studies of the usefulness of wing venation patterns for inferring species identities. Thus, the stage is set for the development of a mature data analytic ecosystem for routine computer image-based identification of fly species that are of medical, veterinary and forensic importance.
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Affiliation(s)
- Min Hao Ling
- Institute of Mathematical Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Tania Ivorra
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh, Selangor, Malaysia
- Department of Environmental Sciences and Natural Resources, University of Alicante, Alicante, Spain
| | - Chong Chin Heo
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh, Selangor, Malaysia
| | - April Hari Wardhana
- Research Center for Veterinary Science, The National Research and Innovation Agency, Bogor, Indonesia
- Faculty of Veterinary Medicine, Airlangga University, Surabaya, Indonesia
| | | | - Siew Hwa Tan
- International Department of Dipterology, Kuala Lumpur Laboratory, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Zulqarnain Mohamed
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Tsung Fei Khang
- Institute of Mathematical Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
- Universiti Malaya Centre for Data Analytics, Universiti Malaya, Kuala Lumpur, Malaysia
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18
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Tadmor‐Levi R, Feldstein‐Farkash T, Milstein D, Golani D, Leader N, Goren M, David L. Revisiting the species list of freshwater fish in Israel based on DNA barcoding. Ecol Evol 2023; 13:e10812. [PMID: 38125953 PMCID: PMC10731390 DOI: 10.1002/ece3.10812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Israel's region forms a continental bridge; hence, the freshwater fish fauna in Israel consists of unique populations of species that originated from Africa, Asia, or Europe and are often endemic or at the edge of their distribution range. Worldwide, fish biodiversity suffers significantly from pressures and disturbances of freshwater habitats, especially in arid regions, such as in parts of Israel. Biodiversity conservation requires efficient tools for monitoring changes in populations. DNA barcoding, by complementing and enhancing species identification, provides such monitoring tools. In this study, over 200 specimens representing over 28 species were DNA barcoded and together with previously available records, a DNA barcoding database for freshwater fish of Israel was established. Of the 71 distinct barcodes generated, 37% were new, attesting to the uniqueness of fish populations in Israel. For most species, morphological and molecular species identifications agreed. However, discrepancies were found for five genera. Based on DNA barcoding, we propose Acanthobrama telavivensis as a junior synonym for Acanthobrama lissneri. In Garra spp., we propose splitting Garra nana into two species and assigning Garra rufa in the region to Garra jordanica, or possibly to two species. Israeli Pseudophoxinus kervillei is not the same species as in Syria and Lebanon. However, Pseudophoxinus syriacus might not be endangered since it is genetically very similar to Pseudophoxinus drusensis. In Israel, instead of five reported Oxynoemacheilus species, combining DNA barcoding with morphology suggests only three. Genetic and geographic separation suggested that Aphanius mento is likely a species complex. The study provides a thorough barcoding database, suggests significant species reconsiderations in the region, and highlights the Sea of Galilee and the Beit She'an valley streams as biodiversity "hotspots." This study will therefore promote further studying of the fish species in the region and their ecology, as well as the monitoring and conservation of freshwater fish biodiversity in Israel and the region.
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Affiliation(s)
- Roni Tadmor‐Levi
- Department of Animal SciencesRobert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovotIsrael
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
| | - Tamar Feldstein‐Farkash
- The Steinhardt Museum of Natural History and School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Dana Milstein
- Science and Conservation DivisionIsrael Nature and Parks AuthorityJerusalemIsrael
| | - Daniel Golani
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
| | - Noam Leader
- Science and Conservation DivisionIsrael Nature and Parks AuthorityJerusalemIsrael
| | - Menachem Goren
- The Steinhardt Museum of Natural History and School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Lior David
- Department of Animal SciencesRobert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovotIsrael
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
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Qu Y, Wang B, Deng J, Feng Y, Pi Z, Ren L, Cai J. Geographical Distribution and Multimethod Species Identification of Forensically Important Necrophagous Flies on Hainan Island. Insects 2023; 14:898. [PMID: 37999097 PMCID: PMC10672153 DOI: 10.3390/insects14110898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Forensic entomology offers unique advantages for the minimum postmortem interval (PMImin) estimation of decomposed corpses in forensic investigations. Accurate species identification and up-to-date locality information are essential. Hainan Island has a tropical rainforest climate and a vast territory. In this study, the community structure of necrophagous flies on Hainan Island was investigated in detail according to geographical environment. The results showed that the dominant species included C. megacephala, S. peregrina, C. rufifacies, S. misera, H. ligurriens, S. sericea, S. cinerea, S. dux, C. pinguis, and M. domestica. Furthermore, C. rufifacies and C. villeneuvi were found only in the high-altitude areas of Wuzhi Mountain, while S. cinerea was distributed only in coastal areas; the latter is a representative species of Hainan Island and has not been reported before. Furthermore, a GenBank database of forensically important flies was established, whilst a high-resolution melt (HRM) curve analysis was applied to identify the common species of Hainan Island for the first time. This study enriches the database of forensically important flies in tropical rainforest regions.
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Affiliation(s)
- Yihong Qu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
- Hainan Equity Judicial Expertise Center, Hainan Vocational College of Political Science and Law, Haikou 570100, China
| | - Bo Wang
- Hainan Provincial Academician Workstation, Haikou 570100, China; (B.W.); (J.D.)
| | - Jianqiang Deng
- Hainan Provincial Academician Workstation, Haikou 570100, China; (B.W.); (J.D.)
| | - Yakai Feng
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi 830011, China;
| | - Zhiyun Pi
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, Academy of Forensic Science, Shanghai 570100, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
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20
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Perkons I, Varunjikar MS, Rasinger JD. Unveiling the potential of proteomics in addressing food and feed safety challenges. EFSA J 2023; 21:e211013. [PMID: 38047126 PMCID: PMC10687763 DOI: 10.2903/j.efsa.2023.e211013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
The food and feed sector in Europe is rapidly evolving to address contemporary challenges, striving for fairer, safer, greener and more sustainable food systems. This includes the exploration of new protein sources for human consumption and animal feed such as protein derived from insects, algae or novel plant-derived proteins, and the re-evaluation of existing sources like processed animal protein (PAP). To generate reliable data on the diverse array of emerging protein sources for future food and feed safety assessments, a growing demand for the development and implementation of advanced analytical techniques exists. New approach methodologies (NAMs) including, mass spectrometry (MS)-based proteomics methods have been emerging as valuable techniques which potentially can be implemented in regulatory laboratory settings to complement conventional approaches in this realm. These MS-driven strategies have already proven their utility in diverse applications, including the detection of prohibited substances in feed, identification of allergens, differentiation of fish species in complex mixtures for fraud detection and the verification of novel foods and alternative protein sources. This EU-FORA programme was focused on three core objectives namely: (i) the training of the fellow in utilising MS-based proteomics for food and feed safety analyses, (ii) the involvement of the fellow in the development of standardised operating procedures (SOP) for targeted and non-targeted proteomic MS-based workflows for species and tissues specific PAP identification in a national reference laboratory (NRL) and (iii) the transfer and implementation of MS-based approaches and standardised protocols for PAP analysis at the fellow's home institution. Altogether, this programme facilitates the broadening and diversification of use of MS-based proteomic methodologies for reinforcing their significance within the domains of food and feed safety research and regulatory science applications.
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Affiliation(s)
- Ingus Perkons
- Institute of Food SafetyAnimal Health and Environment ‘BIOR’, RigaLatvia
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Pascapurnama DN, Zavitri NG, Koesoemadinata RC, Cahyadi AI, Chaidir L. Identification of Significant Pathogenic Nontuberculous Mycobacteria Species from Presumptive TB Patients Using Partial hsp65 Gene Sequencing. Infect Drug Resist 2023; 16:6923-6930. [PMID: 37928609 PMCID: PMC10624186 DOI: 10.2147/idr.s419956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/27/2023] [Indexed: 11/07/2023] Open
Abstract
Purpose To date, the diagnosis of nontuberculous mycobacteria (NTM) disease primarily relies on clinical symptoms and radiological features. Our objective was to apply a sequence-based analysis method by using partial gene sequencing of heat shock protein 65 (hsp65) to identify NTM species. Patients and Methods A total of 32 stored isolates obtained from individuals suspected of having pulmonary NTM infection were subjected to solid Ogawa culture. Genomic DNA from each sample was extracted and used in a conventional polymerase chain reaction (PCR) targeting a specific region of hsp65 gene. Identified amplicons from the PCR were then subjected to targeted sequencing. Analysis of the obtained hsp65 sequence was performed using DNA Baser tool. The consensus sequences obtained were compared to references in the GenBank NCBI database to determine NTM species. Results We identified several important NTM species which posses opportunistic characteristics. M. abscessus and M. chelonae are the most frequent NTM species identified in this study (40.63% and 18.75%, respectively). These two species have the potential to cause significant infections in human, ranging from opportunistic pulmonary infection to localized skin infection. Additionally, pathogenic NTM members of M. fortuitum group (MFG), M. avium, M. intracellulare, M. kansasii, and M. celatum were also found among all identified species. Conclusion Sequence-based analysis is a promising method for identifying species of NTM. The hsp65 gene has a high discriminatory power to identify opportunistic pathogen NTM species in specimens in Indonesia. Consequently, hsp65 partial gene sequencing is considerable as an alternative and reliable approach for NTM speciation.
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Affiliation(s)
| | - Nabilla Ghina Zavitri
- Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | | | - Adi Imam Cahyadi
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Lidya Chaidir
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, Indonesia
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, West Java, Indonesia
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Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. Front Plant Sci 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
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Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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Benyahia H, Parola P, Almeras L. Evolution of MALDI-TOF MS Profiles from Lice and Fleas Preserved in Alcohol over Time. Insects 2023; 14:825. [PMID: 37887837 PMCID: PMC10607003 DOI: 10.3390/insects14100825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023]
Abstract
MALDI-TOF is now considered a relevant tool for the identification of arthropods, including lice and fleas. However, the duration and conditions of storage, such as in ethanol, which is frequently used to preserve these ectoparasites, could impede their classification. The purpose of the present study was to assess the stability of MS profiles from Pediculus humanus corporis lice and Ctenocephalides felis fleas preserved in alcohol from one to four years and kinetically submitted to MALDI-TOF MS. A total of 469 cephalothoraxes from lice (n = 170) and fleas (n = 299) were tested. The reproducibility of the MS profiles was estimated based on the log score values (LSVs) obtained for query profiles compared to the reference profiles included in the MS database. Only MS spectra from P. humanus corporis and C. felis stored in alcohol for less than one year were included in the reference MS database. Approximately 75% of MS spectra from lice (75.2%, 94/125) and fleas (74.4%, 122/164) specimens stored in alcohol for 12 to 48 months, queried against the reference MS database, obtained relevant identification. An accurate analysis revealed a significant decrease in the proportion of identification for both species stored for more than 22 months in alcohol. It was hypothesized that incomplete drying was responsible for MS spectra variations. Then, 45 lice and 60 fleas were subjected to longer drying periods from 12 to 24 h. The increase in the drying period improved the proportion of relevant identification for lice (95%) and fleas (80%). This study highlighted that a correct rate of identification by MS could be obtained for lice and fleas preserved in alcohol for up to four years on the condition that the drying period was sufficiently long for accurate identification.
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Affiliation(s)
- Hanene Benyahia
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France; (H.B.); (P.P.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France; (H.B.); (P.P.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Lionel Almeras
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France; (H.B.); (P.P.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
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Wang WW, Liu ZW, Sun YZ, Liu LF. Comparison of Semen Aesculi species from different geographical origins and horse chestnut based on metabolomics and chemometrics analysis. Phytochem Anal 2023; 34:830-841. [PMID: 36843182 DOI: 10.1002/pca.3212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/20/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Semen Aesculi, a traditional Chinese herbal medicine, has a long history of use for treating chest and abdominal pain with distension. In addition, the horse chestnut (Aesculus hippocastanum L.) is another species of Aesculus in Europe and has notable clinical significance in alleviating chronic venous insufficiency, hemorrhoids, and postoperative edema. Thus, highlighting the comparative study of Semen Aesculi and horse chestnut may broaden clinical applications. OBJECTIVES To conduct a comprehensive comparative analysis on the chemical profiling of these two varieties and determine whether they have equivalent clinical efficacy by integrating plant metabolomics and multivariate statistical methods. METHODS Initially, a comprehensive characterisation was performed using ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UPLC-QTOF-MS/MS) platform, and in total 44 active ingredients were identified. Then, untargeted metabolomics combined with principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) was applied for the discrimination of a German species and three official Chinese species. Next, 24 marker compounds responsible for the discrimination of different species were screened out and used to predict the species of unknown samples by genetic algorithm-optimised support vector machine (GA-SVM) with a high prediction accuracy. Finally, a heatmap visualisation was employed for clarifying the distribution of the identified active ingredients. RESULTS The three species of Chinese Semen Aesculi showed distinct separation from each other, while European horse chestnut and Aesculus chinensis Bunge were similar in chemical composition. CONCLUSIONS This work provided experimental evidence for further expanding the clinical application of Chinese Semen Aesculi and promoted the species identification and quality control of Semen Aesculi.
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Affiliation(s)
- Wei-Wei Wang
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, China Pharmaceutical University, Nanjing, China
| | - Zi-Wei Liu
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, China Pharmaceutical University, Nanjing, China
| | - Ya-Zhe Sun
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, China Pharmaceutical University, Nanjing, China
| | - Li-Fang Liu
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, China Pharmaceutical University, Nanjing, China
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Haddad SF, Lahr BD, Patarroyo SS, Chesdachai S, Kies KD, O’Horo JC, DeSimone DC, Sendi P, Baddour LM. Bloodstream Infection Due to Coagulase-Negative Staphylococci: Impact of Species on Prevalence of Infective Endocarditis. Antibiotics (Basel) 2023; 12:1453. [PMID: 37760749 PMCID: PMC10525567 DOI: 10.3390/antibiotics12091453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Background: Coagulase-negative staphylococci (CoNS) are an important group of organisms that can cause bloodstream infection (BSI) and infective endocarditis (IE). The prevalence of IE in patients with BSI due to different CoNS species, however, has received limited attention; (2) Methods: A retrospective study of adults with monomicrobial CoNS BSI who had undergone echocardiography and a risk factor analysis was done to determine the most common CoNS species that cause definite IE; (3) Results: 247 patients with CoNS BSI were included in the investigation; 49 (19.8%) had definite IE, 124 (50.2%) possible IE, and 74 (30.0%) BSI only. The latter two entities were grouped in one category for further analysis. The most common species in CoNS BSI was Staphylococcus epidermidis (79.4%) and most patients (83.2%) had possible IE/BSI only. 59.1% of patients with BSI due to S. lugdunensis had definite IE. The majority of CoNS were healthcare-associated/nosocomial bacteremia. Multivariable analysis demonstrated that valve disease (p = 0.002) and a foreign cardiovascular material (p < 0.001) were risk factors associated with definite IE. Patients with S. lugdunensis BSI had an 8-fold higher risk of definite IE than did those with S. epidermidis BSI and nearly a 13-fold higher risk than did patients with BSI due to other species of CoNS (p = 0.002); (4) Conclusions: The prevalence of definite IE in patients with BSI due to different CoNS species was significant. CoNS bacteremia, particularly with S. lugdunensis, confers a significant risk of IE, particularly in patients with a valve disease or intravascular foreign body material and should not be immediately dismissed as a contaminant.
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Affiliation(s)
- Sara F. Haddad
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA; (S.S.P.)
| | - Brian D. Lahr
- Division of Clinical Trials and Biostatistics, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Sebastian Santos Patarroyo
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA; (S.S.P.)
| | - Supavit Chesdachai
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA; (S.S.P.)
| | - Kami D. Kies
- Clinical Microbiology Core Laboratory, Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA;
| | - John C. O’Horo
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA; (S.S.P.)
- Division of Pulmonary and Critical Care, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel C. DeSimone
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA; (S.S.P.)
- Department of Cardiovascular Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Larry M. Baddour
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA; (S.S.P.)
- Department of Cardiovascular Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
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26
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Yu X, He Y, Gu Y, Zhang T, Huo F, Liang Q, Wu J, Hu Y, Wang X, Tang W, Huang H, Liu G. The Homologous Gene of Chromosomal Virulence D ( chvD) Presents High Resolution as a Novel Biomarker in Mycobacterium Species Identification. Infect Drug Resist 2023; 16:6039-6052. [PMID: 37719646 PMCID: PMC10503549 DOI: 10.2147/idr.s422191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
Objective To evaluate the resolution of chromosomal virulence D (chvD) as a novel marker for mycobacterial species identification. Methods A segment of chvD (652 bp) was amplified by PCR from 63 mycobacterial reference strains, 163 nontuberculous mycobacterial clinical isolates, and 16 M. tuberculosis complex (MTBC) clinical isolates. A phylogenetic tree based on the reference strains was constructed by the neighbor-joining and IQ-tree methods. Comparative sequence analysis of the homologous chvD gene efficiently differentiated the species within the genus Mycobacterium. Slowly growing Mycobacterium (SGM) and rapidly growing Mycobacterium (RGM) were separated in the phylogenetic tree based on the chvD gene. Results The sequence discrepancies were obvious between M. kansasii and M. gastri, M. chelonae and M. abscessus, and M. avium and M. intracellulare, none of which could be achieved by 16S ribosomal RNA (rRNA) homologous gene alignment. Furthermore, chvD manifested larger intraspecies diversity among members of M. intracellulare subspecies. A total of 174 of the 179 (97.21%) clinical isolates, consisting of 12 mycobacterial species, were identified correctly by chvD blast. Four M. abscessus subsp. abscessus were identified as M. abscessus subsp. bolletii by chvD. MTBC isolates were indistinguishable, because they showed 99.84%-100% homology. Conclusion Homologous chvD is a promising gene marker for identifying mycobacterial species, and could be used for highly accurate species identification among mycobacteria.
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Affiliation(s)
- Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Yingxia He
- Wuhan Pulmonary Hospital, Wuhan Institution of Tuberculosis Control, Wuhan, 430030, People’s Republic of China
| | - Yuzhen Gu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Tingting Zhang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Qian Liang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Jing Wu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Yan Hu
- Wuhan Pulmonary Hospital, Wuhan Institution of Tuberculosis Control, Wuhan, 430030, People’s Republic of China
| | - Xuan Wang
- Wuhan Pulmonary Hospital, Wuhan Institution of Tuberculosis Control, Wuhan, 430030, People’s Republic of China
| | - Wei Tang
- Wuhan Pulmonary Hospital, Wuhan Institution of Tuberculosis Control, Wuhan, 430030, People’s Republic of China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Guan Liu
- Wuhan Pulmonary Hospital, Wuhan Institution of Tuberculosis Control, Wuhan, 430030, People’s Republic of China
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Mo ZQ, Wang J, Möller M, Yang JB, Gao LM. Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants. Int J Mol Sci 2023; 24:13216. [PMID: 37686021 PMCID: PMC10487542 DOI: 10.3390/ijms241713216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of Torreya species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in Torreya studies. A total of 38 accessions were included for analyses, representing all nine recognized species of genus Torreya. The plastid phylogeny showed that all 21 wild samples formed species-specific clades, except T. jiulongshanensis. Disregarding this putative hybrid, seven recognized species sampled here were successfully discriminated by the plastid genome. Only the T. nucifera accessions grouped into two grades. The species identification rate of the nrDNA cistron was 62.5%. The Skmer analysis based on nuclear reads from genome skims showed promise for species identification with seven species discriminated. The proportion of misidentified cultivated plants from arboreta/botanical gardens was relatively high with four accessions (23.5%) representing three species. Interspecific relationships within Torreya were fully resolved with maximum support by plastomes, where Torreya jackii was on the earliest diverging branch, though sister to T. grandis in the nrDNA cistron tree, suggesting that this is likely a hybrid species between T. grandis and an extinct Torreya ancestor lineage. The findings here provide quantitative insights into the usage of cultivated samples for phylogenetic study.
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Affiliation(s)
- Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | | | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
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Berinson B, Spenke L, Krivec L, Tanida K, Both A, Keller J, Rolvien T, Christner M, Lütgehetmann M, Aepfelbacher M, Klatte TO, Rohde H. Performance and Hypothetical Impact on Joint Infection Management of the BioFire Joint Infection Panel: a Retrospective Analysis. J Clin Microbiol 2023; 61:e0059223. [PMID: 37439678 PMCID: PMC10446873 DOI: 10.1128/jcm.00592-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is a multiplex PCR panel which detects 31 of the most prevalent bacterial and fungal pathogens causing septic arthritis. Here, 123 cryoconserved contemporary synovial fluid samples from 120 patients underwent BJA analysis. Results were compared to those of culture-based diagnostics (standard of care [SOC]). Clinical data were collected, and the possible impact of the molecular diagnostic application on patient management was evaluated. Fifteen of 123 synovial fluid cultures grew bacterial pathogens. All on-panel pathogens (9/15) were correctly identified by the BJA. The BJA identified four additional bacterial pathogens in four SOC-negative cases. BJA sensitivity and specificity were 100% (95% confidence interval [CI], 69.2% to 100%) and 100% (95% CI, 96.8% to 100%), respectively. Compared to the SOC, the BJA would have resulted in faster provision of species identification and molecular susceptibility data by 49 h and 99 h, respectively. Clinical data analysis indicates that in BJA-positive cases, faster species ID could have led to timelier optimization of antibiotic therapy. This retrospective study demonstrates high sensitivity and specificity of the BJA to detect on-panel organisms in bacterial arthritis. The usefulness of the BJA in prosthetic-joint infections is limited, as important pathogens (i.e., coagulase negative staphylococci and Cutibacterium acnes) are not covered. Evidence from patient data analysis suggests that the assay might prove valuable for optimizing patient management in acute arthritis related to fastidious organisms or for patients who received antibiotics prior to specimen collection.
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Affiliation(s)
- Benjamin Berinson
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Spenke
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas Krivec
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Konstantin Tanida
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Both
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Keller
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Rolvien
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Orla Klatte
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Lin JN, Lai CH, Yang CH, Huang YH. Validation of 16S rRNA and Complete rpoB Gene Sequence Analysis for the Identification of Elizabethkingia Species. Int J Mol Sci 2023; 24:13007. [PMID: 37629190 PMCID: PMC10455528 DOI: 10.3390/ijms241613007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Bacteria in the genus Elizabethkingia have emerged as a cause of life-threatening infections in humans. However, accurate species identification of these pathogens relies on molecular techniques. We aimed to evaluate the accuracy of 16S rRNA and complete RNA polymerase β-subunit (rpoB) gene sequences in identifying Elizabethkingia species. A total of 173 Elizabethkingia strains with whole-genome sequences in GenBank were included. The 16S rRNA gene and rpoB gene sequences from the same Elizabethkingia strains were examined. Of the 41 E. meningoseptica strains, all exhibited >99.5% 16S rRNA similarity to its type strain. Only 83% of the 99 E. anophelis strains shared >99.5% 16S rRNA gene similarity with its type strain. All strains of E. meningoseptica and E. anophelis formed a cluster distinct from the other Elizabethkingia species in the 16S rRNA and rpoB gene phylogenetic trees. The polymorphisms of 16S rRNA gene sequences are not sufficient for constructing a phylogenetic tree to discriminate species in the E. miricola cluster (E. miricola, E. bruuniana, E. occulta, and E. ursingii). The complete rpoB gene phylogenetic tree clearly delineates all strains of Elizabethkingia species. The complete rpoB gene sequencing could be a useful complementary phylogenetic marker for the accurate identification of Elizabethkingia species.
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Affiliation(s)
- Jiun-Nong Lin
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824005, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824005, Taiwan
- Department of Critical Care Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824005, Taiwan
| | - Chung-Hsu Lai
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824005, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824005, Taiwan
| | - Chih-Hui Yang
- Department of Biological Science and Technology, Meiho University, Pingtung 912009, Taiwan
| | - Yi-Han Huang
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824005, Taiwan
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Mai XC, Shen CR, Liu CL, Trinh DM, Nguyen ML. "DNA signaturing" database construction for Tetradesmus species identification and phylogenetic relationships of Scenedesmus-like green microalgae (Scenedesmaceae, Chlorophyta). J Phycol 2023; 59:775-784. [PMID: 37261838 DOI: 10.1111/jpy.13354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Species identification of Scenedesmus-like microalgae, comprising Desmodesmus, Tetradesmus, and Scenedesmus, has been challenging due to their high morphological and genetic similarity. After developing a DNA signaturing tool for Desmodesmus identification, we built a DNA signaturing database for Tetradesmus. The DNA signaturing tool contained species-specific nucleotide sequences of Tetradesmus species or strain groups with high similarity in ITS2 sequences. To construct DNA signaturing, we collected data on ITS2 sequences, aligned the sequences, organized the data by ITS2 sequence homology, and determined signature sequences according to hemi-compensatory base changes (hCBC)/CBC data from previous studies. Four Tetradesmus species and 11 strain groups had DNA signatures. The signature sequence of the genus Tetradesmus, TTA GAG GCT TAA GCA AGG ACCC, recognized 86% (157/183) of the collected Tetradesmus strains. Phylogenetic analysis of Scenedesmus-like species revealed that the Tetradesmus species were monophyletic and closely related to each other based on branch lengths. Desmodesmus was suggested to split into two subgenera due to their genetic and morphological distinction. Scenedesmus must be analyzed along with other genera of the Scenedesmaceae family to determine their genetic relationships. Importantly, DNA signaturing was integrated into a database for identifying Scenedesmus-like species through BLAST.
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Affiliation(s)
- Xuan Cuong Mai
- Department and Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Rui Shen
- Department and Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chao-Lin Liu
- Department of Chemical Engineering and Biochemical Technology R&D Center, Ming Chi University of Technology, New Taipei City, Taiwan
| | - Dang Mau Trinh
- Department of Biotechnology, Faculty of Biology and Environmental Science, The University of Danang - University of Science and Education, Danang, Vietnam
| | - Minh Ly Nguyen
- Department of Biotechnology, Faculty of Biology and Environmental Science, The University of Danang - University of Science and Education, Danang, Vietnam
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Tao G, Li Q, Xu S, Song W, Yang Z, Zhou Y, Gao L, Huang W, Li X, Ye Y. Rapid identification of chemical compositions from three species of Siegesbeckiae Herba by ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-mass spectrometry in combination with deoxyribonucleic acid barcoding. J Sep Sci 2023; 46:e2300160. [PMID: 37269050 DOI: 10.1002/jssc.202300160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023]
Abstract
Siegesbeckiae Herba, a traditional Chinese medicine, originates from Siegesbeckia orientalis, S. glabrescens, and S. pubescens in the Pharmacopoeia of the People's Republic of China. However, accurate identification of decoction pieces from the three plants remains a challenge. In this study, 26 batches of Siegesbeckiae Herba were identified by deoxyribonucleic acid barcoding, and their chemical compositions were determined using ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-mass spectrometry. The results showed that the internal transcribed spacer 2 and internal transcribed spacer 1-5.8 S- internal transcribed spacer 2 sequences could distinguish three species. In total, 48 compounds were identified including 12 marker compounds screened for three species using the partial least square discriminant analysis. Among these, two diterpenoids 16-O-malonylkirenol and 15-O-malonylkirenol, and a novel diterpenoid 15,16-di-O-malonylkirenol were isolated and identified. A convenient method for the identification of Siegesbeckiae Herba was established using kirenol and 16-O-acetlydarutoside as control standards by thin-layer chromatography. Unexpectedly, none of the batches of S. orientalis contained kirenol, which did not meet the quality standards of Siegesbeckiae Herba, suggesting that the rationality of kirenol as a quality marker for S. orientalis should be further investigated. The results of this study will contribute to the quality control of Siegesbeckiae Herba.
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Affiliation(s)
- Guanqi Tao
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
| | - Qin Li
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
| | - Shifang Xu
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
| | - Wenying Song
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
| | - Zonghan Yang
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
| | - Yinjuan Zhou
- Department of Pharmacy, The First People's Hospital of Xiaoshan District, Hangzhou, Zhejiang, P. R. China
| | - Lijuan Gao
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
| | - Wenkang Huang
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
| | - Xiaoyu Li
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
| | - Yiping Ye
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, P. R. China
- Research Institute, Zhejiang NHU Company Ltd, Xinchang, Zhejiang, P. R. China
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32
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Yao L, Gui X, Wu X, Yang J, Fang Y, Sun Q, Gu J, Sha W. Rapid Identification of Nontuberculous Mycobacterium Species from Respiratory Specimens Using Nucleotide MALDI-TOF MS. Microorganisms 2023; 11:1975. [PMID: 37630537 PMCID: PMC10458091 DOI: 10.3390/microorganisms11081975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
We performed a prospective study to evaluate the diagnostic accuracy of nucleotide matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying nontuberculous mycobacterium (NTM) from clinical respiratory samples. A total of 175 eligible patients were prospectively enrolled, including 108 patients diagnosed with NTM pulmonary disease (NTM-PD) and 67 control patients with other diseases. All specimens were subjected to acid-fast staining, liquid culture combined with MPT64 antigen detection, and a nucleotide MALDI-TOF MS assay. NTM cultures were also subjected to the MeltPro Myco assay for species identification. Altogether, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of nucleotide MALDI-TOF MS were 77.8% (95% CI: 68.6-85.0%), 92.5% (82.8-97.2%), 94.4% (86.8-97.9%), and 72.1% (61.2-81.0%), respectively; these results were not statistically different from the results of culture + MPT64 antigen testing (75.0% [65.6-82.6%], 95.5% [86.6-98.8%], 96.4% [89.2-99.1%], and 70.3% [59.7-79.2%], respectively). In the identification of NTM species, of the 84 nucleotide MALDI-TOF MS positive samples, 77 samples (91.7%) were identified at the species level. Using culture + MeltPro Myco assay as the reference standard, nucleotide MALDI-TOF MS correctly identified 77.8% (63/81) of NTM species. Our results demonstrated that the nucleotide MALDI-TOF MS assay was a rapid single-step method that provided the reliable detection of NTM and identification of NTM species. This new method had the same sensitivity and specificity as the culture + MPT64 antigen method, but was much more rapid.
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Affiliation(s)
| | | | | | | | | | | | - Jin Gu
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (L.Y.); (X.G.)
| | - Wei Sha
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (L.Y.); (X.G.)
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Ivanova T, Bosseva Y, Chervenkov M, Dimitrova D. Sweet Basil between the Soul and the Table-Transformation of Traditional Knowledge on Ocimum basilicum L. in Bulgaria. Plants (Basel) 2023; 12:2771. [PMID: 37570924 PMCID: PMC10420671 DOI: 10.3390/plants12152771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023]
Abstract
The study tracks the utilization of Ocimum basilicum L. (sweet basil)-a garden plant popular for its ritual and ornamental value in the past, that is currently applied in various forms and ways as medicine, food, insect repellent, etc.-in Bulgaria. Previous data for Bulgarian rural home gardens showed a significant number of preserved local landraces; however, it remained unclear how people perceive the large varietal diversity of this species and how the traditions related to its use are preserved. We combined a literature review on the cultural value of sweet basil and the breeding of local genetic resources with an online questionnaire, directed to adult laypeople, that sought to access different aspects of past (recalled) and present use and related knowledge. The identification skills of the participants were tested using images of local plant landraces and foreign varieties. Responses from 220 participants showed that potted "Genovese"-type individual was most frequently identified as sweet basil (89.9%), followed by two examples of local landraces in flower. Participants who grow sweet basil or used it in more varied ways had significantly better identification skills. Ocimum basilicum was most frequently reported as food, while ritual/symbolic use was preserved while devalued during the Communism regime (1945-1989). Food and religious uses were negatively associated in the past, but presently, the tendency is completely reversed. Preferences for the informal exchange of seeds and seed-saving practices were discussed.
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Affiliation(s)
- Teodora Ivanova
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (Y.B.); (M.C.); (D.D.)
| | - Yulia Bosseva
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (Y.B.); (M.C.); (D.D.)
| | - Mihail Chervenkov
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (Y.B.); (M.C.); (D.D.)
- Faculty of Veterinary Medicine, University of Forestry, 1797 Sofia, Bulgaria
| | - Dessislava Dimitrova
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (Y.B.); (M.C.); (D.D.)
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Kyrkjeeide MO, Meleshko O, Flatberg KI, Hassel K. Short stories from Sphagnum of rare species, taxonomy, and speciation. Ecol Evol 2023; 13:e10356. [PMID: 37484930 PMCID: PMC10361360 DOI: 10.1002/ece3.10356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023] Open
Abstract
Conserving species and their genetic variation are a global priority to safeguard evolutionary potential in a rapidly changing world. Species are fundamental units in research and nature management, but taxonomic work is increasingly undermined. Increasing knowledge on the species genetic diversity would aid in prioritizing conservation efforts. Sphagnum is a diverse, well-known bryophyte genus, which makes the genus suited to study speciation and cryptic variation. The species share specific characteristics and can be difficult to separate in the field. By combining molecular data with thorough morphological examination, new species have recently been discovered. Still, there are taxonomic uncertainties, even for species assessed on the IUCN Red List of threatened species. Here, we use molecular data to examine three rare species within the subgenus Acutifolia described based on morphological characters. All species have narrow distributions and limited dispersability. First, we confirm the genetic origin of S. skyense. Second, we show that S. venustum is a haploid species genetically distinct from morphologically similar species. Lastly, S. nitidulum was found to have a distinct haplotype, but cannot be genetically separated from other red Acutifolia species. We also found high genetic variation within red Acutifolia specimens, indicating the need of further morphological examination and possibly taxonomic revision. Until then, our results have shown that genetic data can aid in prioritizing targets of conservation efforts when taxonomy is unresolved. All three taxa should be further searched for by field biologists to increase knowledge about their distribution ranges.
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Affiliation(s)
| | - Olena Meleshko
- Department of Natural HistoryNorwegian University of Science and TechnologyTrondheimNorway
| | - Kjell Ivar Flatberg
- Department of Natural HistoryNorwegian University of Science and TechnologyTrondheimNorway
| | - Kristian Hassel
- Department of Natural HistoryNorwegian University of Science and TechnologyTrondheimNorway
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Hu Q, Pan Y, Xia H, Yu K, Yao Y, Guan F. Species Identification of Caviar Based on Multiple DNA Barcoding. Molecules 2023; 28:5046. [PMID: 37446706 DOI: 10.3390/molecules28135046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/11/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
This study aimed to explore the applicability of DNA barcoding for assessing the authenticity of caviar on the Chinese market. A set of universal COI primers and two sets of designed primers based on COI and D-loop genes were used to identify maternal species of samples from 21 batches of caviar. The results showed that the PCR products from three sets of primers had more than 98% similarity to the sequences in database. The COI gene could not distinguish sturgeons with closed genetic relationships, while D-loop gene could effectively improve the accuracy of DNA barcoding and was more suitable to the identification of interspecific sturgeon than the COI gene. The neighbor-joining dendrogram further confirmed the applicability and accuracy of COI and D-loop genes in identifying maternal relatives of caviar (Acipenser baerii/Acipenser gueldenstaedtii/Acipenser schrenckii/Huso dauricus/Huso huso). Despite the limitations of mitochondrial DNA in identifying hybrid sturgeon species, the presence of counterfeit caviar of non-sturgeon ingredients could be excluded. All the caviar samples were identified successfully as sturgeon species, but the mislabeling rate of species was 33.4%, indicating that there were illegal phenomena such as disorderly labeling, mislabeling, and adulteration on the market.
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Affiliation(s)
- Qingqing Hu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yingqiu Pan
- Taizhou Food and Drug Inspection and Research Institute, Taizhou 318000, China
| | - Huili Xia
- Taizhou Food and Drug Inspection and Research Institute, Taizhou 318000, China
| | - Kexin Yu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yian Yao
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Feng Guan
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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Wu Y, Sun XR, Pritchard HW, Shen YB, Wu XQ, Peng CY. The metagenomics of soil bacteria and fungi and the release of mechanical dormancy in hard seeds. Front Plant Sci 2023; 14:1187614. [PMID: 37441178 PMCID: PMC10335401 DOI: 10.3389/fpls.2023.1187614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/19/2023] [Indexed: 07/15/2023]
Abstract
Persistence in the soil is a function of seed physiology, particularly non-germination and inherent lifespan. However, for seeds with mechanical dormancy, non-germination is also a function of the composition and activity of the soil microbiota. We attempted to screen out microorganisms in the soil that can specifically and rapidly decompose the hard fruit pericarps of Tilia miqueliana Maxim., a unique native tree species in China. Using the classical replica plating method, more than 100 different culturable microorganisms that could rapidly erode the pericarp were collected from the surface of pericarps under different culture conditions. At the same time, we successfully extended the concept of metagenomics and applied it to the identification of mixed artificial cultures. The decomposition process of the pericarps in soil was also simulated artificially. The physical and chemical data suggested a potential mechanism of microbial scarification and cracking in pericarp, whilst the embryos inside the eroded fruits retained good viability. Our discoveries could pave the way for the removal of physical and mechanical obstacles that prevent hard coat seeds from germinating. We anticipate that the use of this technology will improve the germination of other hard coat seeds. More research is needed to investigate the impacts on other seeds. The findings of this research can inform the design of experiments on the seed ecology of persistence.
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Affiliation(s)
- Yu Wu
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-innovation Center for Sustainable Forestry in Southern China, Southern Tree Inspection Center National Forestry Administration, Nanjing, Jiangsu, China
| | - Xiao-Rui Sun
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hugh W. Pritchard
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex, United Kingdom
| | - Yong-Bao Shen
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-innovation Center for Sustainable Forestry in Southern China, Southern Tree Inspection Center National Forestry Administration, Nanjing, Jiangsu, China
| | - Xiao-Qin Wu
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Chen-Yin Peng
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-innovation Center for Sustainable Forestry in Southern China, Southern Tree Inspection Center National Forestry Administration, Nanjing, Jiangsu, China
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Wang X, Tian S, Wang H, Yang L, Zou X, Baskaran XR, Li Q, Xing H, Li HL. The complete chloroplast genome sequence of Zingiber teres S. Q. Tong & Y. M. Xia (Zingiberaceae). Mitochondrial DNA B Resour 2023; 8:699-703. [PMID: 37383606 PMCID: PMC10294729 DOI: 10.1080/23802359.2023.2226256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Here, the complete chloroplast genome sequence of Zingiber teres is described using MGI paired-end sequencing. The genome is 163,428 bp in length and contains a small single-copy region (SSC) of 15,782 bp, a large single-copy region (LSC) of 88,142 bp, and two inverted repeat (IR) regions of 29,752 bp. The overall GC content is 36.1%, and the GC content of the IR regions is 41.1%, which is higher than that of both the LSC region (33.8%) and SSC region (29.5%). The genome of Z. teres contains 133 complete genes, including 88 protein-coding genes (79 protein-coding gene species), 38 tRNA genes (28 tRNA species), and 8 rRNA genes (four rRNA species). Maximum likelihood phylogenetic analysis yielded a well-resolved tree of the genus Zingiber, and Z. teres and Zingiber mioga were sister species in this tree. The development of DNA barcodes could aid the identification of Zingiber species.
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Affiliation(s)
- Xiao Wang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Shuming Tian
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Hao Wang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Lin Yang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xiaoling Zou
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | | | - Qiang Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Haitao Xing
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gorini T, Mezzasalma V, Deligia M, De Mattia F, Campone L, Labra M, Frigerio J. Check Your Shopping Cart: DNA Barcoding and Mini-Barcoding for Food Authentication. Foods 2023; 12:2392. [PMID: 37372604 DOI: 10.3390/foods12122392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The molecular approach of DNA barcoding for the characterization and traceability of food products has come into common use in many European countries. However, it is important to address and solve technical and scientific issues such as the efficiency of the barcode sequences and DNA extraction methods to be able to analyze all the products that the food sector offers. The goal of this study is to collect the most defrauded and common food products and identify better workflows for species identification. A total of 212 specimens were collected in collaboration with 38 companies belonging to 5 different fields: seafood, botanicals, agrifood, spices, and probiotics. For all the typologies of specimens, the most suitable workflow was defined, and three species-specific primer pairs for fish were also designed. Results showed that 21.2% of the analyzed products were defrauded. A total of 88.2% of specimens were correctly identified by DNA barcoding analysis. Botanicals (28.8%) have the highest number of non-conformances, followed by spices (28.5%), agrifood (23.5%), seafood (11.4%), and probiotics (7.7%). DNA barcoding and mini-barcoding are confirmed as fast and reliable methods for ensuring quality and safety in the food field.
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Affiliation(s)
- Tommaso Gorini
- FEM2-Ambiente, Piazza della Scienza 2, 20126 Milano, Italy
| | | | - Marta Deligia
- Department of Scienze Agrarie, Forestali e Alimentari, University of Turin, Via Verdi 8, 10124 Torino, Italy
| | | | - Luca Campone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Massimo Labra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Jessica Frigerio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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Guo L, Wang X, Wang R, Li P. Characterization and Comparative Analysis of Chloroplast Genomes of Medicinal Herb Scrophularia ningpoensis and Its Common Adulterants (Scrophulariaceae). Int J Mol Sci 2023; 24:10034. [PMID: 37373180 DOI: 10.3390/ijms241210034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Scrophularia ningpoensis, a perennial medicinal plant from the Scrophulariaceae family, is the original species of Scrophulariae Radix (SR) in the Chinese Pharmacopoeia. This medicine is usually deliberately substituted or accidentally contaminated with other closely related species including S. kakudensis, S. buergeriana, and S. yoshimurae. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete chloroplast genomes of the four mentioned Scrophularia species were sequenced and characterized. Comparative genomic studies revealed a high degree of conservation in genomic structure, gene arrangement, and content within the species, with the entire chloroplast genome spanning 153,016-153,631 bp in full length, encoding 132 genes, including 80 protein-coding genes, 4 rRNA genes, 30 tRNA genes, and 18 duplicated genes. We identified 8 highly variable plastid regions and 39-44 SSRs as potential molecular markers for further species identification in the genus. The consistent and robust phylogenetic relationships of S. ningpoensis and its common adulterants were firstly established using a total of 28 plastid genomes from the Scrophulariaceae family. In the monophyletic group, S. kakudensis was determined to be the earliest diverging species, succeeded by S. ningpoensis. Meanwhile, S. yoshimurae and S. buergeriana were clustered together as sister clades. Our research manifestly illustrates the efficacy of plastid genomes in identifying S. ningpoensis and its counterfeits and will also contribute to a deeper understanding of the evolutionary processes within Scrophularia.
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Affiliation(s)
- Lei Guo
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xia Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ruihong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Oh SY. A useful species identification and quality control using volatile patterns of ssajuari-ssuk and sajabal-ssuk (Artemisia princeps Pamp. cv. ssajuari and Artemisia princeps Pamp. cv. sajabal; Korean mugwort) according to air-drying term by fast gas chromatography with uncoated surface acoustic wave sensor. Phytochem Anal 2023. [PMID: 37282799 DOI: 10.1002/pca.3240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]
Abstract
INTRODUCTION Ssajuari-ssuk and sajabal-ssuk have many clinical benefits. It is difficult to discriminate between these two species based on general characteristics aside from the shapes of the leaves. Thus, species identification and quality control between ssajuari-ssuk and sajabal-ssuk are of great concern in plant science and clinical therapy. OBJECTIVE The aim of this study is to determine whether fast gas chromatography with uncoated surface acoustic wave sensor (GC-SAW) can be a useful technique for performing species identification and quality control using volatile patterns of ssajuari-ssuk and sajabal-ssuk air-dried for 4 months and 2 years and 4 months. METHODOLOGY Fast GC-SAW sensor provides second unit analysis, simple, on-line measurements that do not require pretreatment of the sample and rapid sensory information. Headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) was employed to confirm the identification of the volatiles and compared to fast GC-SAW sensor. RESULTS In air-dried sajabal-ssuk, the concentration of 1,8-cineole was higher than that in air-dried ssajuari-ssuk, while the level of α-thujone was considerably lower than that of air-dried ssajuari-ssuk. Each of ssajuari-ssuk and sajabal-ssuk air-dried for 4 months and 2 years and 4 months has its own characteristic volatile pattern owing to its individual chemotypes or chemical compositions. CONCLUSION Consequently, the fast GC-SAW sensor can be a useful technique for species identification and quality control using volatile patterns of ssajuari-ssuk and sajabal-ssuk air-dried for 4 months and 2 years and 4 months. This method can be used for the standardisation of quality control using volatile patterns of herbal medicines.
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Affiliation(s)
- Se Yeon Oh
- Department of Food Science and Technology, Keimyung University, Daegu, South Korea
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Wang YS, Jin YX, Liu KJ, Guo C, Wang YH, Xu C, Zhang ZX, Dong WP. [ Species identification of Ligustrum lucidum]. Zhongguo Zhong Yao Za Zhi 2023; 48:2940-2948. [PMID: 37381954 DOI: 10.19540/j.cnki.cjcmm.20230315.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Ligustrum lucidum is a woody perennial plant of genus Ligustrum in family Oleaceae. Its dried fruit has high medicinal value. In this study, the authors evaluated the variability and species identification efficiency of three specific DAN barcodes(rbcL-accD, ycf1a, ycf1b) and four general DAN barcodes(matK, rbcL, trnH-psbA, ITS2) for a rapid and accurate molecular identification of Ligustrum species. The results revealed that matK, rbcL, trnH-psbA, ITS2 and ycf1a were inefficient for identifying the Ligustrum species, and a large number of insertions and deletions were observed in rbcL-accD sequence, which was thus unsuitable for development as specific barcode. The ycf1b-2 barcode had DNA barcoding gap and high success rate of PCR amplification and DNA sequencing, which was the most suitable DNA barcode for L. lucidum identification and achieved an accurate result. In addition, to optimize the DNA extraction experiment, the authors extracted and analyzed the DNA of the exocarp, mesocarp, endocarp and seed of L. lucidum fruit. It was found that seed was the most effective part for DNA extraction, where DNAs of high concentration and quality were obtained, meeting the needs of species identification. In this study, the experimental method for DNA extraction of L. lucidum was optimized, and the seed was determined as the optimal part for DNA extraction and ycf1b-2 was the specific DNA barcode for L. lucidum identification. This study laid a foundation for the market regulation of L. lucidum.
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Affiliation(s)
- Yu-Shuang Wang
- School of Ecology and Nature Conservation, Beijing Forestry University Beijing 100083, China
| | - Yuan-Xi Jin
- School of Ecology and Nature Conservation, Beijing Forestry University Beijing 100083, China
| | - Kang-Jia Liu
- School of Ecology and Nature Conservation, Beijing Forestry University Beijing 100083, China
| | - Chang Guo
- School of Ecology and Nature Conservation, Beijing Forestry University Beijing 100083, China
| | - Yi-Heng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany,Chinese Academy of Sciences Beijing 100093, China
| | - Zhi-Xiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University Beijing 100083, China
| | - Wen-Pan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University Beijing 100083, China
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Razuvaeva AV, Ulyanova EG, Skolotneva ES, Andreeva IV. Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods. Vavilovskii Zhurnal Genet Selektsii 2023; 27:240-249. [PMID: 37293445 PMCID: PMC10244583 DOI: 10.18699/vjgb-23-30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/25/2022] [Accepted: 01/07/2022] [Indexed: 06/10/2023] Open
Abstract
Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agro- and biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed - from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region.
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Affiliation(s)
- A V Razuvaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Ulyanova
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
| | - E S Skolotneva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Andreeva
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
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Ortega-Lasuen U, Pedrera O, Telletxea E, Barrutia O, Díez JR. Secondary Students' Knowledge on Birds and Attitudes towards Conservation: Evaluation of an Environmental Education Program. Int J Environ Res Public Health 2023; 20:5769. [PMID: 37239496 PMCID: PMC10218049 DOI: 10.3390/ijerph20105769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023]
Abstract
Urdaibai Biosphere Reserve holds a diversity of habitats and resources that are essential for migratory bird species' conservation, and at the same time provides a rich milieu for the development of environmental education programs. This study evaluates the impact of a daylong and place-based environmental education program, performed at the Urdaibai Bird Center (UBC), on secondary education students' environmental attitudes and knowledge. Students (n = 908) completed a written questionnaire where their perceptions on the Urdaibai Biosphere Reserve and marshes, together with their interest in biodiversity, knowledge about bird migration and bird species identification skills, and attitudes towards conservation were assessed. Results show that students' knowledge regarding Biosphere Reserves, marshes, and bird migration is limited, and that their bird identification skills are scarce. Although they scored high on environmental attitudes, a significant number of them feel that conservation efforts are excessive and hinder economic development. Students living within the Biosphere Reserve, as well as from rural milieus or who underwent primary education through a bird-centered curriculum hold a better knowledge of the local biodiversity. To adapt the environmental education program at the UBC, its integration in formal teaching/learning contexts via meaningful hands-on and/or project-based activities could be considered, together with the systematic evaluation of the outcomes.
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Affiliation(s)
- Unai Ortega-Lasuen
- Department of Didactics of Mathematics, Experimental and Social Sciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (E.T.)
| | - Oier Pedrera
- Department of Didactics of Mathematics, Experimental and Social Sciences, University of the Basque Country (UPV/EHU), 20018 Donostia San Sebastian, Spain; (O.P.); (O.B.)
| | - Erin Telletxea
- Department of Didactics of Mathematics, Experimental and Social Sciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (E.T.)
| | - Oihana Barrutia
- Department of Didactics of Mathematics, Experimental and Social Sciences, University of the Basque Country (UPV/EHU), 20018 Donostia San Sebastian, Spain; (O.P.); (O.B.)
| | - José Ramón Díez
- Department of Didactics of Mathematics, Experimental and Social Sciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (E.T.)
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Ghelardi E, Mazzantini D, Celandroni F, Calvigioni M, Panattoni A, Lupetti A, Bois De Fer B, Perez M. Analysis of the microbial content of probiotic products commercialized worldwide and survivability in conditions mimicking the human gut environment. Front Microbiol 2023; 14:1127321. [PMID: 37234535 PMCID: PMC10208119 DOI: 10.3389/fmicb.2023.1127321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/23/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction Probiotics are living microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Adequate number of living microbes, the presence of specific microorganisms, and their survival in the gastrointestinal (GI) environment are important to achieve desired health benefits of probiotic products. In this in vitro study, 21 leading probiotic formulations commercialized worldwide were evaluated for their microbial content and survivability in simulated GI conditions. Methods Plate-count method was used to determine the amount of living microbes contained in the products. Culture-dependent Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry and culture-independent metagenomic analysis through 16S and 18S rDNA sequencing were applied in combination for species identification. To estimate the potential survivability of the microorganisms contained in the products in the harsh GI environment, an in vitro model composed of different simulated gastric and intestinal fluids was adopted. Results The majority of the tested probiotic products were concordant with the labels in terms of number of viable microbes and contained probiotic species. However, one product included fewer viable microbes than those displayed on the label, one product contained two species that were not declared, and another product lacked one of the labeled probiotic strains. Survivability in simulated acidic and alkaline GI fluids was highly variable depending on the composition of the products. The microorganisms contained in four products survived in both acidic and alkaline environments. For one of these products, microorganisms also appeared to grow in the alkaline environment. Conclusion This in vitro study demonstrates that most globally commercialized probiotic products are consistent with the claims described on their labels with respect to the number and species of the contained microbes. Evaluated probiotics generally performed well in survivability tests, although viability of microbes in simulated gastric and intestinal environments showed large variability. Although the results obtained in this study indicate a good quality of the tested formulations, it is important to stress that stringent quality controls of probiotic products should always be performed to provide optimal health benefits for the host.
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Affiliation(s)
- Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marco Calvigioni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Adelaide Panattoni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Liu H, Wang D, Zhang C, Pu T, Xiong L, Wei F, Hu Y. Development of short-target primers for species identification in biological studies of Carnivora. Ecol Evol 2023; 13:e10135. [PMID: 37250442 PMCID: PMC10212699 DOI: 10.1002/ece3.10135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.
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Affiliation(s)
- Huiwen Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dan Wang
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | | | | | - Lijuan Xiong
- School of Life SciencesGuizhou Normal UniversityGuiyangChina
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Robillard AJ, Trizna MG, Ruiz‐Tafur M, Dávila Panduro EL, de Santana CD, White AE, Dikow RB, Deichmann JL. Application of a deep learning image classifier for identification of Amazonian fishes. Ecol Evol 2023; 13:e9987. [PMID: 37143991 PMCID: PMC10151603 DOI: 10.1002/ece3.9987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/10/2023] [Accepted: 03/24/2023] [Indexed: 05/06/2023] Open
Abstract
Given the sharp increase in agricultural and infrastructure development and the paucity of widespread data available to support conservation management decisions, a more rapid and accurate tool for identifying fish fauna in the world's largest freshwater ecosystem, the Amazon, is needed. Current strategies for identification of freshwater fishes require high levels of training and taxonomic expertise for morphological identification or genetic testing for species recognition at a molecular level. To overcome these challenges, we built an image masking model (U-Net) and a convolutional neural net (CNN) to classify Amazonian fish in photographs. Fish used to generate training data were collected and photographed in tributaries in seasonally flooded forests of the upper Morona River valley in Loreto, Peru in 2018 and 2019. Species identifications in the training images (n = 3068) were verified by expert ichthyologists. These images were supplemented with photographs taken of additional Amazonian fish specimens housed in the ichthyological collection of the Smithsonian's National Museum of Natural History. We generated a CNN model that identified 33 genera of fishes with a mean accuracy of 97.9%. Wider availability of accurate freshwater fish image recognition tools, such as the one described here, will enable fishermen, local communities, and citizen scientists to more effectively participate in collecting and sharing data from their territories to inform policy and management decisions that impact them directly.
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Affiliation(s)
- Alexander J. Robillard
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
- Chesapeake Biological LaboratoryUniversity of Maryland Center for Environmental ScienceSolomonsMarylandUSA
| | - Michael G. Trizna
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Morgan Ruiz‐Tafur
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
- Laboratorio de Taxonomía de PecesInstituto de Investigaciones de la Amazonía Peruana (IIAP)San Juan BautistaPeru
| | - Edgard Leonardo Dávila Panduro
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
| | - C. David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Alexander E. White
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Rebecca B. Dikow
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Jessica L. Deichmann
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
- Working Land and Seascapes, Conservation CommonsSmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
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Lin L, Cheng H, Li W, Li M, Zou H, Wang G. Limnotrachelobdella hypophthalmichthysa n. sp. (Hirudinida: Piscicolidae) on Gills of Bighead Carp Hypophthalmichthys nobilis in China. Pathogens 2023; 12:pathogens12040562. [PMID: 37111447 PMCID: PMC10141120 DOI: 10.3390/pathogens12040562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
We describe the characterization of a novel fish leech species found on the gills of bighead carp (Hypophthalmichthys nobilis) from lakes and reservoirs in China. This leech is morphologically similar to Limnotrachelobdella sinensis recorded on goldfish and common carp. However, there are 0-2 pairs of symmetrical or asymmetrical eyes and 10 pairs of pulsatile vesicles in the newly discovered leech, in remarkable contrast to L. sinensis. Except for bighead carp, where it demonstrated a higher than 90% prevalence, and silver carp (H. molitrix), where there was low infection, this leech was not detected on any other fish from the Qiandao reservoir in China that were examined during this investigation. Molecular analyses indicated 87.8% ITS sequence identity with L. sinensis and 85.0 and 86.1% COX1 sequence identity with L. sinensis and L. okae, respectively. The uncorrected p-distance based on the COX1 sequence was found to be 15.1 and 14.0% for L. sinensis and L. okae, respectively, suggesting interspecific variation. Phylogenetic analyses based on the combination of 18S and COX1 sequences showed that the newly discovered leech groups with Limnotrachelobdella species. Histopathological observation indicated that attachment of the leech on the gill rakers and gill arches causes a loss of connective tissue, hemorrhage, and ulceration. Based on the morphology, molecular analyses, and host specificity, we conclude that this leech is a new species of Limnotrachelobdella and named it Limnotrachelobdella hypophthalmichthysa n. sp.
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Affiliation(s)
- Lin Lin
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Houda Cheng
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guitang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
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Byadgi OV, Rahmawaty A, Wang PC, Chen SC. Comparative genomics of Edwardsiella anguillarum and Edwardsiella piscicida isolated in Taiwan enables the identification of distinctive features and potential virulence factors using Oxford-Nanopore MinION® sequencing. J Fish Dis 2023; 46:287-297. [PMID: 36571326 DOI: 10.1111/jfd.13743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Edwardsiella tarda (ET) and Edwardsiella anguillarum (EA) are the most harmful bacterial fish pathogens in Taiwan. However, there is confusion regarding the genotypic identification of E. tarda and E. piscicida (EP). Therefore, we used a novel Nanopore MinION MK1C platform to sequence and compare the complete genomes of E. piscicida and E. anguillarum. The number of coding genes, rRNA, and tRNA recorded for E. anguillarum and E. piscicida were 8322, 25, and 98, and 5458, 25, and 98, respectively. Ribosomal multilocus sequence typing (rMLST) for E. piscicida indicated 35 rps. The shared clusters between E. anguillarum and E. piscicida indicated several unique clusters for the individual genomes. The phylogenetic tree analysis for all complete genomes indicated that E. anguillarum and E. piscicida were placed into two species-specific genotypes. Distribution of subsystems for annotated genomes found that genes related to virulence, defence, and disease for E. anguillarum were 103 and those for E. piscicida were 60 and pathogenic islands (PI) were 498 and 225, respectively. Vaccine candidates were identified in silico from the core genes using high antigenic, solubility, and secretion probabilities. Altogether, the genome data revealed distinctive features between E. anguillarum and E. piscicida, which suggest different pathogenicity and thus the need for separate preventive strategies.
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Affiliation(s)
- Omkar Vijay Byadgi
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Atiek Rahmawaty
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Teklemariam DM, Gailing O, Siregar IZ, Amandita FY, Moura CCM. Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae. Ecol Evol 2023; 13:e9935. [PMID: 37038522 PMCID: PMC10082172 DOI: 10.1002/ece3.9935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 04/12/2023] Open
Abstract
The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short-lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.
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Affiliation(s)
- Daniel M. Teklemariam
- Department of Forest Genetics and Forest Tree BreedingUniversity of Göttingen37077GöttingenGermany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree BreedingUniversity of Göttingen37077GöttingenGermany
- Centre of Biodiversity and Sustainable Land UseUniversity of GöttingenGöttingenGermany
| | | | | | - Carina C. M. Moura
- Department of Forest Genetics and Forest Tree BreedingUniversity of Göttingen37077GöttingenGermany
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