Raul Arias Carrasco
@utem.cl
Assistant Professor
Universidad Tecnológica Metropolitana
RESEARCH, TEACHING, or OTHER INTERESTS
Biotechnology, Biomedical Engineering
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Marcos Godoy, Yoandy Coca, Rudy Suárez, Marco Montes de Oca, Jacob W. Bledsoe, Ian Burbulis, Diego Caro, Juan Pablo Pontigo, Vinicius Maracaja-Coutinho, Raúl Arias-Carrasco,et al.
MDPI AG
Maintaining the high overall health of farmed animals is a central tenant of their well-being and care. Intense animal crowding in aquaculture promotes animal morbidity especially in the absence of straightforward methods for monitoring their health. Here, we used bacterial 16S ribosomal RNA gene sequencing to measure bacterial population dynamics during P. salmonis infection. We observed a complex bacterial community consisting of a previously undescribed core pathobiome. Notably, we detected Aliivibrio wodanis and Tenacibaculum dicentrarchi on the skin ulcers of salmon infected with P. salmonis, while Vibrio spp. were enriched on infected gills. The prevalence of these co-occurring networks indicated that coinfection with other pathogens may enhance P. salmonis pathogenicity.
Yoandy Coca, Marcos Godoy, Juan Pablo Pontigo, Diego Caro, Vinicius Maracaja-Coutinho, Raúl Arias-Carrasco, Leonardo Rodríguez-Córdova, Marco Montes de Oca, César Sáez-Navarrete, and Ian Burbulis
Springer Science and Business Media LLC
AbstractAn unbalanced composition of gut microbiota in fish is hypothesized to play a role in promoting bacterial infections, but the synergistic or antagonistic interactions between bacterial groups in relation to fish health are not well understood. We report that pathogenic species in the Piscirickettsia, Aeromonas, Renibacterium and Tenacibaculum genera were all detected in the digesta and gut mucosa of healthy Atlantic salmon without clinical signs of disease. Although Piscirickettsia salmonis (and other pathogens) occurred in greater frequencies of fish with clinical Salmonid Rickettsial Septicemia (SRS), the relative abundance was about the same as that observed in healthy fish. Remarkably, the SRS-positive fish presented with a generalized mid-gut dysbiosis and positive growth associations between Piscirickettsiaceae and members of other taxonomic families containing known pathogens. The reconstruction of metabolic phenotypes based on the bacterial networks detected in the gut and mucosa indicated the synthesis of Gram-negative virulence factors such as colanic acid and O-antigen were over-represented in SRS positive fish. This evidence indicates that cooperative interactions between organisms of different taxonomic families within localized bacterial networks might promote an opportunity for P. salmonis to cause clinical SRS in the farm environment.
Cristian Morales, Raul Arias-Carrasco, Vinicius Maracaja-Coutinho, Pamela Seron, Fernando Lanas, Luis A. Salazar, and Nicolás Saavedra
MDPI AG
Cholesterol metabolism is important at the physiological level as well as in several diseases, with small RNA being an element to consider in terms of its epigenetic control. Thus, the aim of this study was to identify differences between bacterial small RNAs present at the gut level in hypercholesterolemic and normocholesterolemic individuals. Twenty stool samples were collected from hypercholesterolemic and normocholesterolemic subjects. RNA extraction and small RNA sequencing were performed, followed by bioinformatics analyses with BrumiR, Bowtie 2, BLASTn, DESeq2, and IntaRNA, after the filtering of the reads with fastp. In addition, the prediction of secondary structures was obtained with RNAfold WebServer. Most of the small RNAs were of bacterial origin and presented a greater number of readings in normocholesterolemic participants. The upregulation of small RNA ID 2909606 associated with Coprococcus eutactus (family Lachnospiraceae) was presented in hypercholesterolemic subjects. In addition, a positive correlation was established between small RNA ID 2149569 from the species Blautia wexlerae and hypercholesterolemic subjects. Other bacterial and archaeal small RNAs that interacted with the LDL receptor (LDLR) were identified. For these sequences, the prediction of secondary structures was also obtained. There were significant differences in bacterial small RNAs associated with cholesterol metabolism in hypercholesterolemic and normocholesterolemic participants.
Cristian Morales, Gabriel Rojas, Camilo Rebolledo, Marcelo Rojas-Herrera, Raúl Arias-Carrasco, Sara Cuadros-Orellana, Vinicius Maracaja-Coutinho, Kathleen Saavedra, Pamela Leal, Fernando Lanas,et al.
Frontiers Media SA
IntroductionIn recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition.MethodsStool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe).ResultsSignificant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (α=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups.ConclusionOur results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.
Raúl Arias-Carrasco, Jeevan Giddaluru, Lucas E. Cardozo, Felipe Martins, Vinicius Maracaja-Coutinho, and Helder I. Nakaya
Biological Research Springer Science and Business Media LLC
AbstractThe current COVID-19 pandemic has already claimed more than 3.7 million victims and it will cause more deaths in the coming months. Tools that track the number and locations of cases are critical for surveillance and help in making policy decisions for controlling the outbreak. However, the current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We developed a user-friendly web tool, named OUTBREAK, that facilitates epidemic surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. We applied our tool to visualize the SARS 2003, MERS, and COVID19 epidemics, and provided them as examples on the website. Through the zoom feature, it is also possible to visualize cases at city and even neighborhood levels. We made the tool freely available at https://outbreak.sysbio.tools/. OUTBREAK has the potential to guide and help health authorities to intervene and minimize the effects of outbreaks.
Camila Lopez-Crisosto, Raul Arias-Carrasco, Pablo Sepulveda, Luis Garrido-Olivares, Vinicius Maracaja-Coutinho, Hugo E. Verdejo, Pablo F. Castro, and Sergio Lavandero
Elsevier BV
Thaís A.R. Ramos, Nilbson R.O. Galindo, Raúl Arias-Carrasco, Cecília F. da Silva, Vinicius Maracaja-Coutinho, and Thaís G. do Rêgo
F1000 Research Ltd
Non-coding RNAs (ncRNAs) are important players in the cellular regulation of organisms from different kingdoms. One of the key steps in ncRNAs research is the ability to distinguish coding/non-coding sequences. We applied seven machine learning algorithms (Naive Bayes, Support Vector Machine, K-Nearest Neighbors, Random Forest, Extreme Gradient Boosting, Neural Networks and Deep Learning) through model organisms from different evolutionary branches to create a stand-alone and web server tool (RNAmining) to distinguish coding and non-coding sequences. Firstly, we used coding/non-coding sequences downloaded from Ensembl (April 14th, 2020). Then, coding/non-coding sequences were balanced, had their trinucleotides count analysed (64 features) and we performed a normalization by the sequence length, resulting in total of 180 models. The machine learning algorithms validations were performed using 10-fold cross-validation and we selected the algorithm with the best results (eXtreme Gradient Boosting) to implement at RNAmining. Best F1-scores ranged from 97.56% to 99.57% depending on the organism. Moreover, we produced a benchmarking with other tools already in literature (CPAT, CPC2, RNAcon and TransDecoder) and our results outperformed them. Both stand-alone and web server versions of RNAmining are freely available at https://rnamining.integrativebioinformatics.me/.
Vinicius Maracaja-Coutinho, Raúl Arias-Carrasco, Helder I. Nakaya, and Victor Aliaga-Tobar
Springer New York
Cristopher Segovia, Raul Arias-Carrasco, Alejandro J. Yañez, Vinicius Maracaja-Coutinho, and Javier Santander
Public Library of Science (PLoS)
Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting). The repertoire of ncRNAs present in the genome of P. salmonis and its possible role in bacterial physiology and pathogenesis are unknown. Here, we predicted and analyzed the core ncRNAs of P. salmonis base on structure and correlate this prediction to RNA sequencing data. We identified a total of 69 ncRNA classes related to tRNAs, rRNA, thermoregulators, antitoxins, ribozymes, riboswitches, miRNAs and antisense-RNAs. Among these ncRNAs, 29 classes of ncRNAs are shared between all P. salmonis genomes, constituting the core ncRNAs of P. salmonis. The ncRNA core of P. salmonis could serve to develop diagnostic tools and explore the role of ncRNA in fish pathogenesis.
José Manuel Matamala, Raul Arias-Carrasco, Carolina Sanchez, Markus Uhrig, Leslie Bargsted, Soledad Matus, Vinicius Maracaja-Coutinho, Sebastian Abarzua, Brigitte van Zundert, Renato Verdugo,et al.
Elsevier BV
Wilson Huanca-Mamani, Raúl Arias-Carrasco, Steffany Cárdenas-Ninasivincha, Marcelo Rojas-Herrera, Gonzalo Sepúlveda-Hermosilla, José Caris-Maldonado, Elizabeth Bastías, and Vinicius Maracaja-Coutinho
MDPI AG
Long non-coding RNAs (lncRNAs) have been defined as transcripts longer than 200 nucleotides, which lack significant protein coding potential and possess critical roles in diverse cellular processes. Long non-coding RNAs have recently been functionally characterized in plant stress–response mechanisms. In the present study, we perform a comprehensive identification of lncRNAs in response to combined stress induced by salinity and excess of boron in the Lluteño maize, a tolerant maize landrace from Atacama Desert, Chile. We use deep RNA sequencing to identify a set of 48,345 different lncRNAs, of which 28,012 (58.1%) are conserved with other maize (B73, Mo17 or Palomero), with the remaining 41.9% belonging to potentially Lluteño exclusive lncRNA transcripts. According to B73 maize reference genome sequence, most Lluteño lncRNAs correspond to intergenic transcripts. Interestingly, Lluteño lncRNAs presents an unusual overall higher expression compared to protein coding genes under exposure to stressed conditions. In total, we identified 1710 putatively responsive to the combined stressed conditions of salt and boron exposure. We also identified a set of 848 stress responsive potential trans natural antisense transcripts (trans-NAT) lncRNAs, which seems to be regulating genes associated with regulation of transcription, response to stress, response to abiotic stimulus and participating of the nicotianamine metabolic process. Reverse transcription-quantitative PCR (RT-qPCR) experiments were performed in a subset of lncRNAs, validating their existence and expression patterns. Our results suggest that a diverse set of maize lncRNAs from leaves and roots is responsive to combined salt and boron stress, being the first effort to identify lncRNAs from a maize landrace adapted to extreme conditions such as the Atacama Desert. The information generated is a starting point to understand the genomic adaptabilities suffered by this maize to surpass this extremely stressed environment.
Paulo P. Amaral, Tommaso Leonardi, Namshik Han, Emmanuelle Viré, Dennis K. Gascoigne, Raúl Arias-Carrasco, Magdalena Büscher, Luca Pandolfini, Anda Zhang, Stefano Pluchino,et al.
Springer Science and Business Media LLC
Pedro S. T. Russo, Gustavo R. Ferreira, Lucas E. Cardozo, Matheus C. Bürger, Raul Arias-Carrasco, Sandra R. Maruyama, Thiago D. C. Hirata, Diógenes S. Lima, Fernando M. Passos, Kiyoshi F. Fukutani,et al.
Springer Science and Business Media LLC
Raúl Arias-Carrasco, Yessenia Vásquez-Morán, Helder I. Nakaya, and Vinicius Maracaja-Coutinho
Springer Science and Business Media LLC
Felipe Torres, Raúl Arias-Carrasco, José C. Caris-Maldonado, Aldina Barral, Vinicius Maracaja-Coutinho, and Artur T. L. De Queiroz
Oxford University Press (OUP)
Abstract Leishmania braziliensis is the etiological agent of cutaneous leishmaniasis, a disease with high public health importance, affecting 12 million people worldwide. Although its genome sequence was originally published in 2007, the two reference public annotations still presents at least 80% of the genes simply classified as hypothetical or putative proteins. Furthermore, it is notable the absence of non-coding RNA (ncRNA) sequences from Leishmania species in public databases. These poorly annotated coding genes and ncRNAs could be important players for the understanding of this protozoan biology, the mechanisms behind host-parasite interactions and disease control. Herein, we performed a new prediction and annotation of L. braziliensis protein-coding genes and non-coding RNAs, using recently developed predictive algorithms and updated databases. In summary, we identified 11 491 ORFs, with 5263 (45.80%) of them associated with proteins available in public databases. Moreover, we identified for the first time the repertoire of 11 243 ncRNAs belonging to different classes distributed along the genome. The accuracy of our predictions was verified by transcriptional evidence using RNA-seq, confirming that they are actually generating real transcripts. These data were organized in a public repository named LeishDB (www.leishdb.com), which represents an improvement on the publicly available data related to genomic annotation for L. braziliensis. This updated information can be useful for future genomics, transcriptomics and metabolomics studies; being an additional tool for genome annotation pipelines and novel studies associated with the understanding of this protozoan genome complexity, organization, biology, and development of innovative methodologies for disease control and diagnostics. Database URL: www.leishdb.com