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Xu M, Guo H, Wang Y, Zhou B. Identification of chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes. Genome 2024; 67:64-77. [PMID: 37922519 DOI: 10.1139/gen-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved. Here, we developed 16 oligonucleotide probes for rapid and accurate identification of chromosomes in Gossypium hirsutum: 9 probes, of which each is able to distinguish individually one pair of chromosomes, and seven probes, of which each distinguishes multiple pairs of chromosomes. Besides the identification of Chrs. A09 and D09, we first find Chr. D08, which carries both 45S and 5S rDNA sequences. Interestingly, we also find Chr. A07 has a small 45S rDNA size, suggesting that the size of this site on Chr. A07 may have reduced during evolution. By the combination of 45S and 5S rDNA sequences and oligonucleotide probes developed, 10 chromosomes (Chrs. 3-7, and 9-13) in A subgenome and 7 (Chrs. 1-2, 4-5, and 7-9) in D subgenome of cotton are able to be recognized. This study establishes cotton oligonucleotide fluorescence in situ hybridization technology for discrimination of chromosomes, which supports and guides for sequence assembling, particularly, for tandem repeat sequences in cotton.
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Affiliation(s)
- Min Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyue Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Yingying Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
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Ummarino A, Caputo M, Tucci FA, Pezzicoli G, Piepoli A, Gentile A, Latiano T, Panza A, Calà N, Ceglia AP, Pistoio G, Troiano V, Pucatti M, Latiano A, Andriulli A, Tucci A, Palmieri O. A PCR-based method for the diagnosis of Enterobius vermicularis in stool samples, specifically designed for clinical application. Front Microbiol 2022; 13:1028988. [PMID: 36466657 PMCID: PMC9712443 DOI: 10.3389/fmicb.2022.1028988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/31/2022] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Enterobius vermicularis (E. vermicularis) is a nematode that infects up to 200 million people worldwide, despite effective medications being available. Conventional diagnostic tests are hindered by low sensitivity and poor patient compliance. Furthermore, no biomolecular techniques are available for clinical application. The aim of this study was to develop a procedure specifically designed for clinical application to detect E. vermicularis by means of PCR. MATERIALS AND METHODS Two subject groups were taken into account: a group of 27 infected patients and a control group of 27 healthy subjects. A nested-PCR was performed on fecal samples to detect E. vermicularis. Due to the intrinsic difficulties of the fecal matrix, several countermeasures were adopted to ensure the efficient performance of the method: (a) a large amount of feces for the extraction process (20 g instead of 200 mg); (b) a combination of chemical and physical treatments to grind the fecal matrix; (c) an additional purification process for the negative samples after the first nested-PCR; and (d) the selection of a very specific target region for the PCR. RESULTS Due to the lack of overlap with other organisms, a sequence of the 5S ribosomal DNA (rDNA) spacer region including the tract SL1 was chosen to design appropriate external and internal primers. The first nested-PCR detected E.vermicularis in 19/27 samples from infected patients. After further purification, 5/8 of the negative samples resulted positive at the second PCR. Conversely, all the samples from healthy controls resulted negative to both PCRs. Sensitivity and specificity of the method were, respectively, 88.9% and 100%. CONCLUSION The results prove the high diagnostic accuracy of the proposed method, addressing and overcoming the challenges posed by both conventional tests and PCR-based approaches. Therefore, the method can be proposed for clinical application.
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Affiliation(s)
- Aldo Ummarino
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | - Michele Caputo
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | | | | | - Ada Piepoli
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Annamaria Gentile
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Tiziana Latiano
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Anna Panza
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Nicholas Calà
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | | | | | | | - Michela Pucatti
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | - Anna Latiano
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Angelo Andriulli
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Antonio Tucci
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | - Orazio Palmieri
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
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