Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene
Various attempts to amplify an AQP11 cDNA from tissues of the spiny dogfish ( Squalus acanthias ) were made. Two pairs of deoxy-inosine-containing degenerate primers were designed based on conserved amino acid sequences from an AQP11 alignment. These primers yielded some faint bands from gill cDNA t...
Published in: | International Journal of Molecular Sciences |
---|---|
Main Authors: | , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
MDPI AG
2024
|
Subjects: | |
Online Access: | https://doi.org/10.3390/ijms25042028 https://doaj.org/article/c1f21f9eca2b4a8fb45e69b1a9994aff |
id |
ftdoajarticles:oai:doaj.org/article:c1f21f9eca2b4a8fb45e69b1a9994aff |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:c1f21f9eca2b4a8fb45e69b1a9994aff 2024-09-15T18:41:55+00:00 Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene Christopher P. Cutler Meghan E. Canicatti Esosa Omoregie 2024-02-01T00:00:00Z https://doi.org/10.3390/ijms25042028 https://doaj.org/article/c1f21f9eca2b4a8fb45e69b1a9994aff EN eng MDPI AG https://www.mdpi.com/1422-0067/25/4/2028 https://doaj.org/toc/1661-6596 https://doaj.org/toc/1422-0067 doi:10.3390/ijms25042028 1422-0067 1661-6596 https://doaj.org/article/c1f21f9eca2b4a8fb45e69b1a9994aff International Journal of Molecular Sciences, Vol 25, Iss 4, p 2028 (2024) aquaporin spiny dogfish pseudogene degenerate PCR colony PCR 5′ RACE PCR Biology (General) QH301-705.5 Chemistry QD1-999 article 2024 ftdoajarticles https://doi.org/10.3390/ijms25042028 2024-08-05T17:49:58Z Various attempts to amplify an AQP11 cDNA from tissues of the spiny dogfish ( Squalus acanthias ) were made. Two pairs of deoxy-inosine-containing degenerate primers were designed based on conserved amino acid sequences from an AQP11 alignment. These primers yielded some faint bands from gill cDNA that were sequenced. Blast searches with the sequences showed they were not AQP11. An elasmobranch AQP11 nucleotide sequence alignment was produced to identify conserved regions to make further degenerate primers. One primer pair produced a short 148 bp fragment showing particularly strong amplification in gill and intestine. It was sequenced and represented a piece of the AQP11 gene. However, as the fragment may have resulted from contaminating genomic DNA (in total RNA used to make cDNA), 5′ and 3′ RACE were performed to amplify the two ends of the putative cDNA. Furthermore, 5′ and 3′ RACE amplifications depend on the presence of a 5′ cap nucleotide and a poly A tail, respectively on the putative AQP11 mRNA. Hence, successful amplification was only possible from cDNA and not genomic DNA. Nested RACE amplifications were performed using gill and intestinal RACE cDNA, but none of the DNA fragments sequenced were AQP11. Consequently, the spiny dogfish AQP11 gene may represent a pseudogene. Article in Journal/Newspaper spiny dogfish Squalus acanthias Directory of Open Access Journals: DOAJ Articles International Journal of Molecular Sciences 25 4 2028 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
aquaporin spiny dogfish pseudogene degenerate PCR colony PCR 5′ RACE PCR Biology (General) QH301-705.5 Chemistry QD1-999 |
spellingShingle |
aquaporin spiny dogfish pseudogene degenerate PCR colony PCR 5′ RACE PCR Biology (General) QH301-705.5 Chemistry QD1-999 Christopher P. Cutler Meghan E. Canicatti Esosa Omoregie Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene |
topic_facet |
aquaporin spiny dogfish pseudogene degenerate PCR colony PCR 5′ RACE PCR Biology (General) QH301-705.5 Chemistry QD1-999 |
description |
Various attempts to amplify an AQP11 cDNA from tissues of the spiny dogfish ( Squalus acanthias ) were made. Two pairs of deoxy-inosine-containing degenerate primers were designed based on conserved amino acid sequences from an AQP11 alignment. These primers yielded some faint bands from gill cDNA that were sequenced. Blast searches with the sequences showed they were not AQP11. An elasmobranch AQP11 nucleotide sequence alignment was produced to identify conserved regions to make further degenerate primers. One primer pair produced a short 148 bp fragment showing particularly strong amplification in gill and intestine. It was sequenced and represented a piece of the AQP11 gene. However, as the fragment may have resulted from contaminating genomic DNA (in total RNA used to make cDNA), 5′ and 3′ RACE were performed to amplify the two ends of the putative cDNA. Furthermore, 5′ and 3′ RACE amplifications depend on the presence of a 5′ cap nucleotide and a poly A tail, respectively on the putative AQP11 mRNA. Hence, successful amplification was only possible from cDNA and not genomic DNA. Nested RACE amplifications were performed using gill and intestinal RACE cDNA, but none of the DNA fragments sequenced were AQP11. Consequently, the spiny dogfish AQP11 gene may represent a pseudogene. |
format |
Article in Journal/Newspaper |
author |
Christopher P. Cutler Meghan E. Canicatti Esosa Omoregie |
author_facet |
Christopher P. Cutler Meghan E. Canicatti Esosa Omoregie |
author_sort |
Christopher P. Cutler |
title |
Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene |
title_short |
Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene |
title_full |
Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene |
title_fullStr |
Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene |
title_full_unstemmed |
Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias ) May Represent a Pseudogene |
title_sort |
evidence that aquaporin 11 (aqp11) in the spiny dogfish ( squalus acanthias ) may represent a pseudogene |
publisher |
MDPI AG |
publishDate |
2024 |
url |
https://doi.org/10.3390/ijms25042028 https://doaj.org/article/c1f21f9eca2b4a8fb45e69b1a9994aff |
genre |
spiny dogfish Squalus acanthias |
genre_facet |
spiny dogfish Squalus acanthias |
op_source |
International Journal of Molecular Sciences, Vol 25, Iss 4, p 2028 (2024) |
op_relation |
https://www.mdpi.com/1422-0067/25/4/2028 https://doaj.org/toc/1661-6596 https://doaj.org/toc/1422-0067 doi:10.3390/ijms25042028 1422-0067 1661-6596 https://doaj.org/article/c1f21f9eca2b4a8fb45e69b1a9994aff |
op_doi |
https://doi.org/10.3390/ijms25042028 |
container_title |
International Journal of Molecular Sciences |
container_volume |
25 |
container_issue |
4 |
container_start_page |
2028 |
_version_ |
1810486296695537664 |