Limits...
Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order Primates.

Devor EJ - Genome Biol. (2001)

Bottom Line: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates.The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Genetics and Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA. rdevor@idtdna.com

ABSTRACT

Background: The serine hydroxymethyltransferase processed pseudogene SHMT-ps1 has been suggested to be unique to the order Primates because of the failure to amplify this sequence by PCR from genomic DNAs of any non-primate mammal species. Here, 'molecular beacon' probes specific to SHMT-ps1 were used in an attempt to verify this suggestion.

Results: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates. The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.

Conclusions: These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

Show MeSH
Results of molecular beacon end-point assays using the E8/E9 and E9/E10 probes on a representative genomic DNA panel. There is no difficulty in distinguishing a positive from a negative result in this assay. Note that the ruffed lemur sample (V. variegata) is clearly negative for both probes.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC25776&req=5

Figure 1: Results of molecular beacon end-point assays using the E8/E9 and E9/E10 probes on a representative genomic DNA panel. There is no difficulty in distinguishing a positive from a negative result in this assay. Note that the ruffed lemur sample (V. variegata) is clearly negative for both probes.

Mentions: End-point molecular beacon assays (see Materials and methods) were carried out on 19 primate and 12 non-primate mammalian genomic DNAs. The results of those assays confirmed the previous conclusion that SHMT-ps1 is not found outside members of the order Primates. There was, however, one notable departure from expectation among the primate DNA samples. In previous studies, genomic DNA from Lemur catta had given a 292 base pair (bp) SHMT-ps1 amplicon from which sequence had been obtained [7]. In the present study, the genomic DNA sample from the ruffed lemur, Varecia variegata, gave no evidence of the pseudogene with either molecular beacon probe, E8/E9 or E9/E10 (Figure 1). To establish which of these results was reliable, genomic DNAs from an additional 17 lemurs covering nine living species were examined by PCR using the C1/B6 primer pair under the amplification conditions given in the Materials and methods. In no case did the lemur samples yield the expected SHMT-ps1 amplicon, whereas the other primate controls succeeded each time they were used. On the basis of these new data, it now appears that the original L. catta sample did not contain pure lemur genomic DNA, and that the SHMT-ps1 locus is not present in the prosimians as previously thought.


Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order Primates.

Devor EJ - Genome Biol. (2001)

Results of molecular beacon end-point assays using the E8/E9 and E9/E10 probes on a representative genomic DNA panel. There is no difficulty in distinguishing a positive from a negative result in this assay. Note that the ruffed lemur sample (V. variegata) is clearly negative for both probes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC25776&req=5

Figure 1: Results of molecular beacon end-point assays using the E8/E9 and E9/E10 probes on a representative genomic DNA panel. There is no difficulty in distinguishing a positive from a negative result in this assay. Note that the ruffed lemur sample (V. variegata) is clearly negative for both probes.
Mentions: End-point molecular beacon assays (see Materials and methods) were carried out on 19 primate and 12 non-primate mammalian genomic DNAs. The results of those assays confirmed the previous conclusion that SHMT-ps1 is not found outside members of the order Primates. There was, however, one notable departure from expectation among the primate DNA samples. In previous studies, genomic DNA from Lemur catta had given a 292 base pair (bp) SHMT-ps1 amplicon from which sequence had been obtained [7]. In the present study, the genomic DNA sample from the ruffed lemur, Varecia variegata, gave no evidence of the pseudogene with either molecular beacon probe, E8/E9 or E9/E10 (Figure 1). To establish which of these results was reliable, genomic DNAs from an additional 17 lemurs covering nine living species were examined by PCR using the C1/B6 primer pair under the amplification conditions given in the Materials and methods. In no case did the lemur samples yield the expected SHMT-ps1 amplicon, whereas the other primate controls succeeded each time they were used. On the basis of these new data, it now appears that the original L. catta sample did not contain pure lemur genomic DNA, and that the SHMT-ps1 locus is not present in the prosimians as previously thought.

Bottom Line: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates.The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Genetics and Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA. rdevor@idtdna.com

ABSTRACT

Background: The serine hydroxymethyltransferase processed pseudogene SHMT-ps1 has been suggested to be unique to the order Primates because of the failure to amplify this sequence by PCR from genomic DNAs of any non-primate mammal species. Here, 'molecular beacon' probes specific to SHMT-ps1 were used in an attempt to verify this suggestion.

Results: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates. The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.

Conclusions: These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

Show MeSH