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The compositional landscape of minicircle sequences isolated from active lesions and scars of American cutaneous leishmaniasis.

Rodrigues EH, Soares FC, Werkhäuser RP, de Brito ME, Fernandes O, Abath FG, Brandão A - Parasit Vectors (2013)

Bottom Line: Additionally, we built a nucleotide dictionary with words of 7, 8, 9 and 10 nucleotides.With regard to the most frequent nucleotide words above length 6, there is also a distinct pattern for 7, 8, 9 and 10mer.It might be useful as a molecular tool in research concerning the evolution of infecting Leishmania in both vector and vertebrate hosts.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: American cutaneous leishmaniasis (ACL) is characterized by cutaneous lesions that heal spontaneously or after specific treatment. This paper reports on the analysis of kDNA minicircle sequences from clinical samples (typical lesions and scars) that were PCR-amplified with specific primers for Leishmania species of the subgenus Viannia.

Methods: From 56 clinical isolates we obtained a single amplified fragment (ca. 790 bp), which after cloning and sequencing resulted in 290 minicircle sequences from both active lesions and scars. We aimed to get a compositional profile of these sequences in clinical samples and evaluate the corresponding compositional changes. Sequences were analyzed with the compseq and wordcount (Emboss package) to get the composition of di-, tri-, tetra-, penta- and hexanucleotides. Additionally, we built a nucleotide dictionary with words of 7, 8, 9 and 10 nucleotides.

Results: This compositional analysis showed that minicircles amplified from active cutaneous lesions and scars have a distinct compositional profile as viewed by nucleotide composition of words up to 10mer. With regard to the most frequent nucleotide words above length 6, there is also a distinct pattern for 7, 8, 9 and 10mer.

Conclusion: These results indicate that minicircle sequences can be monitored upon direct exposure to a selection/stressing environment (e.g. chemical action) by evaluating their nucleotide compositional profile. It might be useful as a molecular tool in research concerning the evolution of infecting Leishmania in both vector and vertebrate hosts.

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Related in: MedlinePlus

Word cloud of nucleotide words found in minicircles from Leishmania (Viannia) braziliensis obtained from clinical samples of patients before and after treatment (typical lesions and scars, respectively) of the ACL. Graphics represent the most frequent words composed of seven, eight, nine and ten nucleotides. A) active lesions; B) scars.
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Figure 3: Word cloud of nucleotide words found in minicircles from Leishmania (Viannia) braziliensis obtained from clinical samples of patients before and after treatment (typical lesions and scars, respectively) of the ACL. Graphics represent the most frequent words composed of seven, eight, nine and ten nucleotides. A) active lesions; B) scars.

Mentions: We analyzed the nucleotide words at the range 7- to 10mer in a population composed of kDNA minicircle sequences from Leishmania (V.) spp. The most frequent nucleotide words are graphically displayed using word cloud software, which allows a prompt visual grasping of the outstanding words for each set of sequences (Figure 3). The choice of this display method is based on the assumption that the partial set of sequences may represent the whole set of minicircles from this population (which we actually do not know). Thus, we expect that the most frequent nucleotide words might be a nucleotide sequence signature for all minicircles in each group. It is worth noting the relative dispersion of word frequency in both groups (Figure 3). The most frequent words from scar sequences are concentrated in a few words, in contrast to active sequences, which exhibit a higher number of words. The clouds show that the outstanding words (highest frequency) differ between active lesion and scar sequences. For example, the outstanding words for all lengths of the scar sequences are based on the core motif ATTT. In contrast, active sequences display a core motif (AATA) for 7- and 8mer and other motifs for words of 9- and 10mer. Though the most frequent words from both sets are composed mainly of A and T, in the composition of active sequences for 9- and 10mer words there is an increase of GT motifs. This is probably influenced by the presence of the universal minicircle sequence, GGGGTTGGTGTA, but we cannot discard the selection bias introduced by the PCR and subsequent molecular cloning. Regardless of the sequence being extracted, either from an active lesion or scar, the base T is the predominant one for the most frequent words in Leishmania (V.) spp. minicircles.


The compositional landscape of minicircle sequences isolated from active lesions and scars of American cutaneous leishmaniasis.

Rodrigues EH, Soares FC, Werkhäuser RP, de Brito ME, Fernandes O, Abath FG, Brandão A - Parasit Vectors (2013)

Word cloud of nucleotide words found in minicircles from Leishmania (Viannia) braziliensis obtained from clinical samples of patients before and after treatment (typical lesions and scars, respectively) of the ACL. Graphics represent the most frequent words composed of seven, eight, nine and ten nucleotides. A) active lesions; B) scars.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750493&req=5

Figure 3: Word cloud of nucleotide words found in minicircles from Leishmania (Viannia) braziliensis obtained from clinical samples of patients before and after treatment (typical lesions and scars, respectively) of the ACL. Graphics represent the most frequent words composed of seven, eight, nine and ten nucleotides. A) active lesions; B) scars.
Mentions: We analyzed the nucleotide words at the range 7- to 10mer in a population composed of kDNA minicircle sequences from Leishmania (V.) spp. The most frequent nucleotide words are graphically displayed using word cloud software, which allows a prompt visual grasping of the outstanding words for each set of sequences (Figure 3). The choice of this display method is based on the assumption that the partial set of sequences may represent the whole set of minicircles from this population (which we actually do not know). Thus, we expect that the most frequent nucleotide words might be a nucleotide sequence signature for all minicircles in each group. It is worth noting the relative dispersion of word frequency in both groups (Figure 3). The most frequent words from scar sequences are concentrated in a few words, in contrast to active sequences, which exhibit a higher number of words. The clouds show that the outstanding words (highest frequency) differ between active lesion and scar sequences. For example, the outstanding words for all lengths of the scar sequences are based on the core motif ATTT. In contrast, active sequences display a core motif (AATA) for 7- and 8mer and other motifs for words of 9- and 10mer. Though the most frequent words from both sets are composed mainly of A and T, in the composition of active sequences for 9- and 10mer words there is an increase of GT motifs. This is probably influenced by the presence of the universal minicircle sequence, GGGGTTGGTGTA, but we cannot discard the selection bias introduced by the PCR and subsequent molecular cloning. Regardless of the sequence being extracted, either from an active lesion or scar, the base T is the predominant one for the most frequent words in Leishmania (V.) spp. minicircles.

Bottom Line: Additionally, we built a nucleotide dictionary with words of 7, 8, 9 and 10 nucleotides.With regard to the most frequent nucleotide words above length 6, there is also a distinct pattern for 7, 8, 9 and 10mer.It might be useful as a molecular tool in research concerning the evolution of infecting Leishmania in both vector and vertebrate hosts.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: American cutaneous leishmaniasis (ACL) is characterized by cutaneous lesions that heal spontaneously or after specific treatment. This paper reports on the analysis of kDNA minicircle sequences from clinical samples (typical lesions and scars) that were PCR-amplified with specific primers for Leishmania species of the subgenus Viannia.

Methods: From 56 clinical isolates we obtained a single amplified fragment (ca. 790 bp), which after cloning and sequencing resulted in 290 minicircle sequences from both active lesions and scars. We aimed to get a compositional profile of these sequences in clinical samples and evaluate the corresponding compositional changes. Sequences were analyzed with the compseq and wordcount (Emboss package) to get the composition of di-, tri-, tetra-, penta- and hexanucleotides. Additionally, we built a nucleotide dictionary with words of 7, 8, 9 and 10 nucleotides.

Results: This compositional analysis showed that minicircles amplified from active cutaneous lesions and scars have a distinct compositional profile as viewed by nucleotide composition of words up to 10mer. With regard to the most frequent nucleotide words above length 6, there is also a distinct pattern for 7, 8, 9 and 10mer.

Conclusion: These results indicate that minicircle sequences can be monitored upon direct exposure to a selection/stressing environment (e.g. chemical action) by evaluating their nucleotide compositional profile. It might be useful as a molecular tool in research concerning the evolution of infecting Leishmania in both vector and vertebrate hosts.

Show MeSH
Related in: MedlinePlus