![]() ![]() ![]() Pseudomonas is a phylogenetically diverse bacterial genus of high interest in clinical, environmental, and molecular sciences. Other authors designed specific primers for their particular purposes based on the gyrB nucleotide sequence of certain bacterial species. For this reason, some authors had to utilize different primer pair combinations to obtain gyrB amplicons for phylogenetic analyses of a whole bacterial genus, such as Pseudomonas. These studies typically used gyrB polymerase chain reaction (PCR) primers that were designed on the basis of the amino acid sequence of GyrB polypeptides from different bacterial species, and therefore, they contain several degenerate bases. In particular, gyrB has been considered a useful housekeeping gene for multilocus sequence analysis (MLSA) in several bacterial genera. Also, the sequences of gyrA and gyrB alleles from quinolone-resistant isolates have been characterized to understand the evolutionary dynamics of antibiotic resistance, and to promote development of novel drugs. Genes encoding the two subunits of this type II topoisomerase, gyrA and gyrB, have been widely used as markers in phylogenetic studies of different prokaryotic taxa. Finally, we demonstrated that a PCR-RFLP (restriction fragment length polymorphism) approach served to differentiate among Pseudomonas species, and even between members of the same species.ĭNA gyrase is an essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of circular double-stranded DNA (dsDNA). Then, we showed that the amplicons produced with this procedure were appropriate for direct sequencing with both primers, obtaining more than 95% of amplicons coverage. We then set up cycling conditions for achieving high specificity and yield of the PCR protocol. Based on the available gyrB sequence from 148 Pseudomonas species, we identified highly conserved regions to design oligonucleotides without fully degenerate positions. As we noticed that there was not a single primer pair available in the literature suitable for direct sequencing of this gene, we decided to design a unique oligonucleotide pair and to set up a polymerase chain reaction (PCR) protocol to obtain a single amplicon for the entire Pseudomonas genus. For that purpose, gyrB is one of the housekeeping genes routinely used for multilocus sequence analysis (MLSA). Many of the program's tools will only be familiar to scientists and academics but there's also a web browser for the direct import of NCBI and EMBL entries.Pseudomonas is a phylogenetically diverse bacterial genus which is broadly distributed in different ecological niches, and whose taxonomy is continuously under revision. Obviously, the main aim of the program is to provide an easy way to clone DNA - a task which it does very well and mainly just using a graphical interface. You can numerically select fragments and carry out calculations of peptides which I have no idea about but certainly look impressive. All the tools you need to analyze and manipulate your DNA sequences are available in a very simple and easy to read all-in-one-window. The program includes a whole host of mapping options such as genetic maps, fragment viewers and a virtual PCR. It is therefore an extremely powerful piece of software that will only be of interests to scientists and science-biology students. Serial Cloner is an application that allows you to read and write files DNA sequences that conform to the FASTA and pDRAW32 format. Until now, it reading and writing it was a very specialised field but this program intends to bring it to the masses. DNA is the complex code that makes up the lifeform in all of us. ![]()
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