Biology subjects

Felix, P. T.

Publications and source records attributed to Felix, P. T..

8 recordsLinked to original sources

bioRxiv2020

Molecular diversity analysis of the spike glycoprotein (S) gene from Hong Kong - China

In this work, 37 haplotypes of spike glycoprotein of SARS-CoV-2 from Hong Kong, China, were used. All sequences were publicly available on the Platform of the National Center for Biotechnology Information (NCBI) and were analyzed for their Molecular Variance (AMOVA), haplotypic diversity, mismatch, demographic and spatial expansion, molecular diversity and time of evolutionary divergence. The results suggested that there was a low diversity among haplotypes, with very low numbers of transitions, transversions, indels-type mutations and with total absence of population expansion perceived in the neutrality tests. The estimators used in this study supported the uniformity among all the results found and confirm the evolutionary conservation of the gene, as well as its protein product, a fact that stimulates the use of therapies based on neutralizing antibodies, such as vaccines based on protein S.

bioinformatics↗

bioRxiv2020

SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, Sao Paulo, Parana and Tocantins

In this work, 18 sequences of the SARS-CoV-2 virus were used, from four Brazilian states (Rio de Janeiro, Sao Paulo, Parana and Tocantins) with 09, 04, 04, 8 and 01 haplotypes, respectively, with lengths ranging from 234 to 29,903 bp. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform and were previously aligned with the MEGA X software, where all gaps and ambiguous sites were extracted for the construction of the phylogenetic tree. Of the 301 sites analyzed, 68% varied, 131 of which were parsimonium-informative sites. Phylogenetic analyses revealed the presence of two distinct subgroups, corroborated by the high FST (80%). The high degree of polymorphism found among these samples helped to establish a clear pattern of non-genetic structuring, based on the time of divergence between the groups. All molecular variance estimators confirmed that there was no consensus in the conservation of the studied sequences, also indicating a high variation for the protein products of the virus. In a highly miscegenational and diverse population such as the Brazilian population, this observation draws our attention to the need for an urgent increase in public health actions, awareness strategies, hygiene and distancing practices and not the other way around.

bioinformatics↗

bioRxiv2020

Genetic diversity analysis of the D614G mutation in SARS-CoV-2

In this work, we evaluated the levels of genetic diversity in 18 genomes of SARS-CoV-2 carrying the D614G mutation, coming from Malaysia and Venezuela and publicly available at the National Center of Biotechnology and Information (NCBI). These haplotypes were previously used for phylogenetic analysis, following the LaBECom protocols. All gaps and unconserved sites were extracted for the construction of a phylogenetic tree. As specific methodologies for paired FST estimators, Molecular Variance (AMOVA), Genetic Distance, mismatch, demographic and spatial expansion analyses, molecular diversity and evolutionary divergence time analyses, 20,000 random permutations were always used. The results revealed the presence of only 57 sites of polymorphic and parsimonium-informative among the 29,827bp analyzed and the analyses based on FST values confirmed the presence of two distinct genetic entities with fixation index of 22% and with a higher component of population variation (78.14%). Tau variations revealed a significant time of divergence, supported by mismatch analysis of the observed distribution ({tau} = 42%). It is safe to say that the small number of existing polymorphisms should not reflect major changes in the protein products of viral populations in both countries and this consideration provides the safety that, although there are differences in the haplotypes studied, these differences are minimal for both regions analyzed geographically and, therefore, it seems safe to extrapolate the levels of polymorphism and molecular diversity found in the samples for other mutant genomes of SARS-CoV-2 in other countries. This reduces speculation about the possibility of large differences between mutant strains of SARS-CoV-2 (D614G) and wild strains, at least at the level of their protein products, although the mutant form has higher transmission speed and infection. The analyses suggest that possible variations in protein products, of the wild virus in relation to its mutant form, should be minimal, bringing peace of mind as to the increased risk of death from the new form of the virus, as well as possible problems of gradual adjustments in some molecular targets for vaccines.

bioinformatics↗

bioRxiv2020

Levels of genetic diversity of SARS-CoV-2 virus: reducing speculations about the genetic variability of the virus in South America

In this work, we evaluated the levels of genetic diversity in 38 complete Genomes of SARS-CoV-2 from six countries in South America, using specific methodologies for paired FST, AMOVA, mismatch, demographic and spatial expansions, molecular diversity and for the time of evolutionary divergence. The analyses showed non-significant evolutionary divergences within and between the six countries, as well as a significant similarity to the time of genetic evolutionary divergence between all populations. Thus, it seems safe to affirm that we will find similar results for the other Countries of South America, reducing speculation about the existence of rapid and silent mutations that, although there are as we have shown in this work, do not increase, until this moment, the genetic variability of the Virus, a fact that would hinder the work with molecular targets for vaccines and drugs in general.

genetics↗

bioRxiv2020

Photomap of the polythenic chromosomes of Drosophila malerkotliana and in situ mapping of the Hsp83 locus

A photomap of the polythenic chromosomes of D. malerkotliana was constructed to facilitate the identification of the chromosomal arms and their sections, in order to allow the identification of the breaking points of inversions and the location of the bands marked by in situ hybridization. The photomap included the six chromosome arms corresponding to pairs I (chromosome X), II and III, excluding pair IV and Y chromosome, because they were not visualized in the material examined, probably due to their small size. Through the in situ hybridization technique with the use of a biotined probe of a fragment of the D. melanogaster gene, the Hsp83 locus of D. malerkotliana was mapped. The probe hybridized with a frequency of 70% in section 98 of the IIIR chromosome. This is the first mapped gene in the species, and indicates that possibly the IIIR arm of D. malerkotliana corresponds to the IIIL arm of D. melanogaster, where the Hsp83 gene was located.

genomics↗

bioRxiv2020

Occurrence of Drosophilids in the Pernambuco's coastal region (years 2000-2001) and the frequency of chromosomal inversions found in Drosophila malerkotliana

Drosophilids were collected in the campus of UFPE (Recife), Rio Doce (Olinda), Vila Velha (Itamaraca), Parque de dois Irmaos (Recife) and Charles Darwin Ecological Refuge (Igarassu), in the years 2000 and 2001, seeking to establish the frequency of occurrence of the various species of the genus Drosophila. In these collections, D. malerkotliana occurred in an average frequency of 64%, followed by D. melanogaster, with an average frequency of 23%. The frequency of D. malerkotliana was higher than that of D. melanogaster in localities with high and medium degree of urbanization. Despite the great distance from the distribution center of the species (Africa), D. malerkotliana presented high polymorphism of chromosomal inversions. In the locality of Rio Doce, inversions In(IIL)24B-39A and In(IIL)21-25, occurred with frequencies of 18.5% and 100%, respectively, while inversion In(IIIR)84-88B occurred with a frequency of 100%. In the population of campus UFPE (Recife), also with high urbanization, two inversions were found, In(IIIR)93C-94A and In(IIIL)64A-72A with frequencies of 37.1 and 60%, respectively. In the population of The Parque de Dois Irmaos (Recife), with medium urbanization, four inversions were visualized: In(IIIL)70C-73B (66%); In(IIIR)93C-94A (52%); In(IIL)24B-39A (33%); and In(IIR)50B-51A (33%). In the population of the Charles Darwin Ecological Refuge (Igarassu), of low urbanization, only the inversion In(IIIR)100A-98B(?) was found. -88(?), with 100% frequency. These data suggest that the polymorphism of inversions is higher in localities with greater urbanization, possibly due to the longer colonization time, which allowed the accumulation of genetic variations.

ecology↗

bioRxiv2020

Phylogenetics analysis of TP53 gene in humans and its use in biosensors for breast cancer diagnosis

Biosensors are small devices that use biological reactions to detect target analytes. Such devices combine a biological component with a physical transducer, which converts bio-recognition processes into measurable signals. Its use brings a number of advantages, as they are highly sensitive and selective, relatively easy in terms of development, as well as accessible and ready to use. Biosensors can be of direct detection, using a non-catalytic ligand, such as cell receptors and antibodies, or indirect detection, in which there is the use of fluorescently marked antibodies or catalytic elements, such as enzymes. They also appear as bio-affinity devices, depending only on the selective binding of the target analyte to the ligative attached to the surface (e.g., oligonucleotide probe). The objectives were to evaluate the levels of genetic diversity existing in fragments of the TP53 gene deposited in molecular databases and to study its viability as a biosensor in the detection of breast cancer. The methodology used was to recover and analyze 301 sequences of a fragment of the TP53 gene of humans from GENBANK, which, after being aligned with the MEGA software version 6.06, were tested for the phylogenetic signal using TREE-PUZZLE 5.2. Trees of maximum likelihood were generated through PAUP version 4.0b10 and the consistency of the branches was verified with the bootstrap test with 1000 pseudo-replications. After aligning, 783 of the 791 sites remained conserved. The maximum likelihood had a slight manifestation since the gamma distribution used 05 categories + G for the evolutionary rates between sites with (0.90 0.96, 1.00, 1.04 and 1.10 substitutions per site). To estimate ML values, a tree topology was automatically computed with a maximum Log of -1058,195 for this calculation. All positions containing missing gaps or data were deleted, leaving a total of 755 sites in the final dataset. The evolutionary history was represented by consensus trees generated by 500 replications, which according to neighbor-join and BioNJ algorithms set up a matrix with minimal distances between haplotypes, corroborating the high degree of conservation for the TP53 gene. GENE TP53 seems to be a strong candidate in the construction of Biosensors for breast cancer diagnosis in human populations.

cancer biology↗

bioRxiv2020

Evaluation of diversity levels in HIV-1 virus integrase gene sequences, supporting the lack of target specificity of ivermectin versus the integrase-importin complex in SARS-CoV-2 infection

Therapies with new drugs have been appearing in tests worldwide as potential inhibitors of sars-cov-2 virus replication. Recently, one of these drugs, Ivermectin, was reported as an inhibitor of the nuclear import of HIV-1 proteins in vitro, soon becoming the target of an international prospecting work (not yet published), with patients tested for COVID-19. However, understanding the evolutionary aspects of the biological components involved in the complex drug-nuclear import helps in understanding how these relationships exist in the deactivation of viral infections. Thus, 153 sequences of the HIV-1 integrase gene were analyzed for their genetic structure and molecular diversity and the presence of two distinct groups for the Gene and not only one, was detected; As well as different degrees of structuring for each of these groups. These results support the interpretation of the lack of conservation of the HIV-1 gene and that the number of existing polymorphisms, only for this structure of the complex, implies the non-efficiency of a drug at population levels. Thus, the molecular diversity found in HIV-1 can be extrapolated to other viruses, such as Including, SARS-CoV-2 and the functionality of the drug, interacting with the integrase-importin complex, can be further decreased.

evolutionary biology↗