Biology subjects

Galindo-Villegas, J.

Publications and source records attributed to Galindo-Villegas, J..

4 recordsLinked to original sources

bioRxiv2022

CircPrime: a web-based platform for design of specific circular RNA primers

BackgroundCircular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. The tenth of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication. ResultsHere, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods. ConclusionsUser-friendly CircPrime web platform (http://circprime.elgene.net/) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database (NCBI).

bioinformatics↗

bioRxiv2021

An insight into neurotoxic and toxicity of spike fragments SARS-CoV-2 by exposure environment: A threat to aquatic health?

The Spike protein (S protein) is a critical component in the infection of the new coronavirus (SARS-CoV-2). The objective of this work was to evaluate whether peptides from S protein could cause negative impact in the aquatic animals. The aquatic toxicity of SARS-CoV-2 spike protein peptides derivatives has been evaluated in tadpoles (n = 50 tadpoles / 5 replicates of 10 animals) from species Physalaemus cuvieri (Leptodactylidae). After synthesis, purification, and characterization of peptides (PSDP2001, PSDP2002, PSDP2003) an aquatic contamination has been simulatedwith these peptides during 24 hours of exposure in two concentrations (100 and 500 ng/mL). The control group ("C") was composed of tadpoles kept in polyethylene containers containing de-chlorinated water. Oxidative stress, antioxidant biomarkers and neurotoxicity activity were assessed. In both concentrations, PSPD2002 and PSPD2003 increased catalase and superoxide dismutase antioxidants enzymes activities, as well as oxidative stress (nitrite levels, hydrogen peroxide and reactive oxygen species). All three peptides also increased acetylcholinesterase activity in the highest concentration. These peptides showed molecular interactions in silico with acetylcholinesterase and antioxidant enzymes. Aquatic particle contamination of SARS-CoV-2 has neurotoxics effects in P. cuvieri tadpoles. These findings indicate that the COVID-19 can constitute environmental impact or biological damage potential. HIGHLIGHTSO_LISARS-CoV-2 spike protein peptides (PSDP) were synthesized, purified, and characterized by solid phase peptide synthesis. C_LIO_LIPSDP peptides promoted REDOX imbalance and acute neurotoxicity in tadpoles (Physalaemus cuvieri) C_LIO_LIIn silico studies have shown interactionsbetween peptides and acetylcholinesterase and antioxidant enzymes C_LIO_LIAquatic particle contamination of SARS-CoV-2 can constitute additional environmental damage C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/425914v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1b86f96org.highwire.dtl.DTLVardef@1a6225corg.highwire.dtl.DTLVardef@19d953org.highwire.dtl.DTLVardef@10af7ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin

Interspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples of G. aculeatus and P. pungitius and subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.

genomics↗

bioRxiv2018

Olfactory sensory neurons mediate ultra-rapid antiviral immune responses in teleosts in a TrkA-dependent manner

The nervous system is known to regulate host immune responses. However, the ability of neurons to detect danger and initiate immune responses at barrier tissues is unclear. Vertebrate olfactory sensory neurons (OSNs) are located in direct contact with the external environment and therefore directly exposed to pathogens. Here, we report that nasal delivery of rhadboviruses induced apoptosis in crypt OSNs in rainbow trout olfactory organ (OO) via the interaction of the OSN TrkA receptor with viral glycoprotein. This signal resulted in pro-inflammatory responses in the OO and dampened inflammation in the olfactory bulb (OB). CD8+ cells infiltrated the OO within minutes of nasal viral delivery and this response was abrogated when TrkA was blocked. Infiltrating CD8+ cells originated from the microvasculature surrounding the OB and not the periphery. Ablation of crypt neurons in zebrafish resulted in increased susceptibility to rhabdoviral challenge. Our results, therefore, indicate a novel function for OSNs as a first layer of pathogen detection in vertebrates.

immunology↗