Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

In December 2019, rising pneumonia cases caused by a novel β-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide, causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern, since then several scientists are dedicated to its study. It has been observed that many human viruses have codon usage biases that match highly expressed proteins in the tissues they infect and depend on the host cell machinery for the replication and co-evolution. In this work, we analysed 91 molecular features and codon usage patterns for 339 viral genes and 463 human genes that consisted of 677,873 codon positions. Hereby, we selected the highly expressed genes from human lung tissue to perform computational studies that permit to compare their molecular features with those of SARS, SARS-CoV-2 and MERS genes. The integrated analysis of all the features revealed that certain viral genes and overexpressed human genes have similar codon usage patterns. The main pattern was the A/T bias that together with other features could propitiate the viral infection, enhanced by a host dependant specialization of the translation machinery of only some of the overexpressed genes. The envelope protein E, the membrane glycoprotein M and ORF7 could be further benefited. This could be the key for a facilitated translation and viral replication conducting to different comorbidities depending on the genetic variability of population due to the host translation machinery. This is the first codon usage approach that reveals which human genes could be potentially deregulated due to the codon usage similarities between the host and the viral genes when the virus is already inside the human cells of the lung tissues. Our work leaded to the identification of additional highly expressed human genes which are not the usual suspects but might play a role in the viral infection and settle the basis for further research in the field of human genetics associated with new viral infections. To identify the genes that could be deregulated under a viral infection is important to predict the collateral effects and determine which individuals would be more susceptible based on their genetic features and comorbidities associated.Fil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Mendoza Bertelli, Andrea Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biociencias, Biotecnología y Biología Traslacional; Argentin

Revisiting the phylogenetic history of helminths through genomics, the case of the new echinococcus oligarthrus genome

The first parasitic helminth genome sequence was published in 2007; since then, only ~200 genomes have become available, most of them being draft assemblies. Nevertheless, despite the medical and economical global impact of helminthic infections, parasite genomes in public databases are underrepresented. Recently, through an integrative approach involving morphological, genetic, and ecological aspects, we have demonstrated that the complete life cycle of Echinococcus oligarthrus (Cestoda: Taeniidae) is present in South America. The neotropical E. oligarthrus parasite is capable of developing in any felid species and producing human infections. Neotropical echinococcosis is poorly understood yet and requires a complex medical examination to provide the appropriate intervention. Only a few cases of echinococcosis have been unequivocally identified and reported as a consequence of E. oligarthrus infections. Regarding phylogenetics, the analyses of mitogenomes and nuclear datasets have resulted in discordant topologies, and there is no unequivocal taxonomic classification of Echinococcus species so far. In this work, we sequenced and assembled the genome of E. oligarthrus that was isolated from agoutis (Dasyprocta azarae) naturally infected and performed the first comparative genomic study of a neotropical Echinococcus species. The E. oligarthrus genome assembly consisted of 86.22 Mb which showed ~90% identity and 76.3% coverage with Echinococcus multilocularis and contained the 85.0% of the total expected genes. Genetic variants analysis of whole genome revealed a higher rate of intraspecific genetic variability (23,301 SNPs; 0.22 SNPs/kb) rather than for the genomes of E. multilocularis and Echinococcus canadensis G7 but lower with respect to Echinococcus granulosus G1. Comparative genomics against E. multilocularis, E. granulosus G1, and E. canadensis G7 revealed 38,762, 125,147, and 170,049 homozygous polymorphic sites, respectively, indicating a higher genetic distance between E. oligarthrus and E. granulosus sensu lato species. The SNP distribution in chromosomes revealed a higher SNP density in the longest chromosomes. Phylogenetic analysis using whole-genome SNPs demonstrated that E. oligarthrus is one of the basal species of the genus Echinococcus and is phylogenetically closer to E. multilocularis. This work sheds light on the Echinococcus phylogeny and settles the basis to study sylvatic Echinococcus species and their developmental evolutionary features.Fil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Arrabal, Juan Pablo. Ministerio de Salud. Instituto Nacional de Medicina Tropical; ArgentinaFil: Rosenzvit, Mara Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: De Oliveira, Guilherme Corrêa. Instituto Tecnológico Vale.; BrasilFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

Dioctophyme renale in a domestic cat (Felis catus): Renal location and nephrectomy

Dioctophymosis is caused by Dioctophyme renale, nematode with indirect life cycle. Its intermediate host is a freshwater oligochaete and its definitive host is a wild or household carnivore. The adult nematode develops in the definite host, generally locating itself in the kidney. This article was meant to describe the first nephrectomy performed in a domestic cat due to renal dioctophymosis in Argentina. The subject showed a non-specific appearance of generally feeling ill, hematuria and mild diarrhea. It was diagnosed through abdominal ultrasound, followed by exploratory celiotomy and nephrectomy. After verifying absence of free specimens, the right kidney was removed. This organ was found to be enlarged in a spheroidal manner in contrast to the left kidney, with significant thickening of the renal capsule, excessive congestion of vessels and adhesions involving the caudal vena cava. An adult nematode was removed from the right kidney and identified as Dioctophyme renale. Reports of feline dioctophymosis are scarce being most of them necropsy findings. In this we are presenting a confirmed case of D. renale removed by surgery from a live cat. The results presented here reinforces the fact that cats are also appropriate definitive hosts for this parasite.Fil: Butti, M.J.. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Laboratorio de Parasitosis Humanas y Zoonosis Parasitarias; ArgentinaFil: Gamboa, María Inés. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Laboratorio de Parasitosis Humanas y Zoonosis Parasitarias; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; ArgentinaFil: Terminiello, J.D.. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: Franchini, Gisela Raquel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; ArgentinaFil: Giorello, Alejandra Nahili. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; ArgentinaFil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Luna, M.F.. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: López Merlo, Mariana Lucía. Universidad Nacional de la Plata. Facultad de Cs.veterinarias. Centro de Fisiologia Reproductiva y Metodos Complementarios de Diagnostico.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Radman, Nilda Ester. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Laboratorio de Parasitosis Humanas y Zoonosis Parasitarias; Argentin

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe

Generation, analysis and integration of molecular data for the application in the control of parasitic diseases: construction of new bioinformatics platforms

El parásito Echinococcus canadensis G7 (filo Platelmintos, clase Cestoda) es uno de los agentes causantes de la echinococcosis, zoonosis crónica que afecta tanto a los seres humanos como a mamíferos domésticos y salvajes, y considerada una enfermedad prioritaria por la Organización Mundial de la Salud. A pesar de su gravedad e incidencia en el mundo aún no se dispone de datos genómicos o herramientas terapéuticas y de diagnóstico eficaces para el tratamiento de la infección. La información presentada en esta tesis permite comprender características biológicas de esta especie y provee información que puede ser utilizada para el diseño de nuevas herramientas de control. En este trabajo se secuenció, ensambló y anotó el genoma de 115 Mb de E. canadensis G7. Se identificaron 11435 genes y mediante análisis de ortología se determinaron 881 grupos de genes específicos de cestodos y 581 grupos específicos del género Echinococcus. Estos análisis permitieron identificar genes que podrían ser nuevos blancos terapéuticos. Este es el primer trabajo de genómica comparativa entre las especies de Echinococcus, y mediante el cual se determinó un alto grado de variabilidad genética entre E. canadensis G7 y E. granulosus G1, a pesar de que ambas especies pertenecen al complejo E. granulosus sensu lato y presentan un fenotipo similar del estadío de metacestodo. Los análisis filogenéticos basados en el análisis de SNPs de genomas completos confirmaron a E. canadensis G7 como una especie diferente respecto a E. granulosus G1. Asimismo, se identificaron SNPs en genes del metabolismo de Echinococcus que podrían tener un impacto en su función. La validación de SNPs permitió desarrollar nuevos marcadores moleculares nucleares para diferenciar las especies de Echinococcus que infectan a animales y al hombre en Argentina, y complementan a los marcadores mitocondriales y ribosomales utilizados. Además, se analizaron tres características epigenéticas particulares: la distribución de islas CpG, el sistema de metilación del ADN y componentes de la vía de pequeños ARN basados en el análisis estructural proteína-ARN. Los resultados sugieren que Echinococcus posee mecanismos de regulación génica aún desconocidos y diferenciales entre las especies. Por otra parte, el estudio del uso de codones de Echinococcus reveló que la principal fuerza evolutiva que moldea su uso es la selección. Si bien se identificaron codones que son utilizados más frecuentemente no se encontraron diferencias entre las tres especies de Echinococcus. Los datos generados en esta tesis contribuyeron a la construcción de la base de datos WormBase ParaSite (https://parasite.wormbase.org/), especializada en parásitos platelmintos y nematodos y del Nodo Bioinformático IMPaM (http://impam2.fmed.uba.ar/) en el que se implementaron herramientas especializadas para el análisis de cestodos. La disponibilidad de un nuevo genoma es fundamental para entender la biología de un organismo patógeno, y más aún en aquellos con limitaciones para su mantenimiento y manipulación en el laboratorio.The parasite Echinococcus canadensis G7 (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis, a chronic zoonosis that affects humans and domestic and wild mammals and is considered a priority disease by the World Health Organization. Despite its severity and incidence worldwide, neither genomic data, nor diagnostic and therapeutic tools for the treatment of infection are yet available. The information presented in this thesis provides the understanding of biological features of these species and valuable information that can be used for the design of novel control tools of these parasites. In this work, the E. canadensis G7 genome of 115 Mb in size was sequenced, assembled and annotated. A total of 11435 genes were identified which were classified into 881 cestode-specific groups of genes and 581 Echinococcus genus-specific groups of genes using orthology analysis. These analyses allowed the identification of genes that could be new drug targets. This is the first work performing comparative genomics analysis among the different Echinococcus species. The study of genetic variability among the Echinococcus species revealed a high degree of variability between E. canadensis G7 and E. granulosus G1, even though both species have similarities in the phenotype of the metacestode stage and belong to the E. granulosus sensu lato complex. Phylogenetic analyses based on whole genome SNPs analysis confirmed E. canadensis G7 as a different species from E. granulosus G1. SNPs were also identified in Echinococcus metabolic pathways genes suggesting that they could have an impact on their function. The SNPs validation allowed the identification of regions that work as new molecular markers to distinguish among the Echinococcus species that infect animals and humans in Argentina; and complement the mitochondrial and ribosomal markers that are currently used. Furthermore; three particular epigenetic features were analysed: the distribution of CpG islands, the DNA methylation system and the small RNA pathway components based on structural proteinRNA analysis. The results suggested that Echinococcus species have unknown gene regulation mechanisms with some differences among the species. In addition, the study of codons usage bias of Echinococcus revealed that the main evolutionary force shaping the codon usage is selection. Although there are codons that are more frequently used than others, no differences among the three Echinococcus species were found. The data reported in this thesis contributed to the construction of the WormBase ParaSite database (https://parasite.wormbase.org/), specialized in Platyhelminthes and nematodes parasites and the IMPaM bioinformatics node (http://impam2.fmed.uba.ar/) in which specialized tools were implemented for the analysis of cestodes genomes. The availability of a new genome is essential to understand the biology of any pathogenic organism, mainly in those having limitations for the mantainance and manipulation in the laboratoryFil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

Cestodes in the genomic era

The first cestode genomes were obtained by an international consortium led by the Wellcome Sanger Institute that included representative institutions from countries where the sequenced parasites have been studied for decades, in part because they are etiological agents of endemic diseases (Argentina, Uruguay, Mexico, Canada, UK, Germany, Switzerland, Ireland, USA, Japan, and China). After this, several complete genomes were obtained reaching 16 species to date. Cestode genomes have smaller relative size compared to other animals including free-living flatworms. Moreover, the features genome size and repeat content seem to differ in the two analyzed orders. Cyclophyllidean species have smaller genomes and with fewer repetitive content than Diphyllobothriidean species. On average, cestode genomes have 13,753 genes with 6 exons per gene and 41% GC content. More than 5,000 shared cestode proteins were accurately annotated by the integration of gene predictions and transcriptome evidence being more than 40% of these proteins of unknown function. Several gene losses and reduction of gene families were found and could be related to the extreme parasitic lifestyle of these species. The application of cutting-edge sequencing technology allowed the characterization of the terminal sequences of chromosomes that possess unique characteristics. Here, we review the current status of knowledge of complete cestode genomes and place it within a comparative genomics perspective. Multidisciplinary work together with the implementation of new technologies will provide valuable information that can certainly improve our chances to finally eradicate or at least control diseases caused by cestodes.Fil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biociencias, Biotecnología y Biología Traslacional; ArgentinaFil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Cucher, Marcela Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

MicroRNA discovery in the human parasite Echinococcus multilocularis from genome-wide data

The cestode parasite Echinococcus multilocularis is the aetiological agent of alveolar echinococcosis, responsible for considerable human morbidity and mortality. This disease is a worldwide zoonosis of major public health concern and is considered a neglected disease by the World Health Organization. The complete genome of E. multilocularis has been recently sequenced and assembled in a collaborative effort between the Wellcome Trust Sanger Institute and our group, with the main aim of analyzing protein-coding genes. These analyses suggested that approximately 10% of E. multilocularis genome is composed of protein-coding regions. This shows there is still a vast proportion of the genome that needs to be explored, including non-coding RNAs such as small RNAs (sRNAs). Within this class of small regulatory RNAs, microRNAs (miRNAs) can be found, which have been identified in many different organisms ranging from viruses to higher eukaryotes. MiRNAs are a key regulation mechanism of gene expression at post-transcriptional level and play important roles in biological processes such as development, proliferation, cell differentiation and metabolism in animals and plants. In spite of this, identification of miRNAs directly from genome-wide data only is still a very challenging task. There are many miRNAs that remain unidentified due to the lack of either sequence information of particular phylums or appropriate algorithms to identify novel miRNAs. The motivation for this work is the discovery of new miRNAs in E. multilocularis based on non-target genomic data only, in order to obtain useful information from the currently available unexplored data. In this work, we present the discovery of new pre-miRNAs in the E. multilocularis genome through a novel approach based on machine learning. We have extracted the most commonly used structural features from the folded sequences of the parasite genome: triplets, minimum free energy and sequence length. These features have been used to train a novel deep architecture of self-organizing maps (SOMs). This model can be trained with a high class imbalance and without the artificial definition of a negative class. We discovered 886 pre-miRNA candidates within the E. multilocularis genome-wide data. After that, experimental validation by small RNA-seq analysis clearly showed 23 pre-miRNA candidates with a pattern compatible with miRNA biogenesis, indicating them as high confidence miRNAs. We discovered new pre-miRNA candidates in E. multilocularis using non-target genomic data only. Predictions were meaningful using only sequence data, with no need of RNA-seq data or target analysis for prediction. Furthermore, the methodology employed can be easily adapted and applied on any draft genomes, which are actually the most interesting ones since most non-model organisms have this kind of status and carry real biological and sanitary relevance.Fil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Macchiaroli, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Yones, Cristian Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Milone, Diego Humberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; Argentin

Whole genome analysis of codon usage in Echinococcus

The species of the genus Echinococcus are parasitic platyhelminths that cause echinococcosis and exert a global burden on public and animal health. Here we performed codon usage bias and comparative genomic analyses using whole genome and expression data of three Echinococcus species. The study of 4,710,883 codons, two orders of magnitude more than in previous research works, showed that the codon usage in Echinococcus genes is biased towards the pyrimidines T and C ending codons, with an average effective number of codons equal to 57 revealing a low codon usage bias. The gene annotations and the expression profile of 7613 genes allowed to accurately determine 27 optimal codons for the Echinococcus species, most of them ending in G/C. Approximately the 30% of Echinococcus genes analysed exhibits higher codon usage bias as well as a higher expression profile. Neutrality-plots demonstrated that the selection pressure is the main evolutionary force shaping the codon usage with a contribution of 80%. Comparative genome analyses among several tapeworm species revealed that codon usage patterns are a conserved trait in cestodes parasites. Since cestodes parasites take advantage of the host protein synthesis pathways, this study could provide valuable information associated with the parasite-host relationship that would be useful to determine which host's factors are relevant for shaping the codon usage.Fil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Milone, Diego Humberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Oliveira, Guilherme. Fundación Oswaldo Cruz; BrasilFil: Rosenzvit, Mara Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

High-throughput characterization of Echinococcus spp. metacestode miRNomes

Echinococcosis is a worldwide zoonosis of great public health concern, considered a neglected disease by the World Health Organisation. The cestode parasites Echinococcus granulosus sensu lato (s. l.) and Echinococcus multilocularis are the main aetiological agents. In the intermediate host, these parasites display particular developmental traits that lead to different patterns of disease progression. In an attempt to understand the causes of these differences, we focused on the analysis of microRNAs (miRNAs), small non-coding regulatory RNAs with major roles in development of animals and plants. In this work, we analysed the small RNA expression pattern of the metacestode, the stage of sanitary relevance, and provide a detailed description of Echinococcus miRNAs. Using high-throughput small RNA sequencing, we believe that we have carried out the first experimental identification of miRNAs in E. multilocularis and have expanded the Echinococcus miRNA catalogue to 38 miRNA genes, including one miRNA only present in E. granulosus s. l. Our findings show that although both species share the top five highest expressed miRNAs, 13 are differentially expressed, which could be related to developmental differences. We also provide evidence that uridylation is the main miRNA processing mechanism in Echinococcus spp. These results provide detailed information on Echinococcus miRNAs, which is the first step in understanding their role in parasite biology and disease establishment and/or progression, and their future potential use as drug or diagnostic targets.Fil: Cucher, Marcela Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Macchiaroli, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Maldonado, Lucas Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Brehm, Klaus. Universität Würzburg; AlemaniaFil: Rosenzvit, Mara Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin