Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake

© 2015 John Wiley & Sons Ltd. RNA viruses exist as complex mixtures of genotypes, known as quasispecies, where the evolution potential resides in the whole community of related genotypes. Quasispecies structure and dynamics have been studied in detail for virus infecting animals and plants but remain unexplored for those infecting micro-organisms in environmental samples. We report the first metagenomic study of RNA viruses in an Antarctic lake (Lake Limnopolar, Livingston Island). Similar to low-latitude aquatic environments, this lake harbours an RNA virome dominated by positive single-strand RNA viruses from the order Picornavirales probably infecting micro-organisms. Antarctic picorna-like virus 1 (APLV1), one of the most abundant viruses in the lake, does not incorporate any mutation in the consensus sequence from 2006 to 2010 and shows stable quasispecies with low-complexity indexes. By contrast, APLV2-APLV3 are detected in the lake water exclusively in summer samples and are major constituents of surrounding cyanobacterial mats. Their quasispecies exhibit low complexity in cyanobacterial mat, but their run-off-mediated transfer to the lake results in a remarkable increase of complexity that may reflect the convergence of different viral quasispecies from the catchment area or replication in a more diverse host community. This is the first example of viral quasispecies from natural aquatic ecosystems and points to ecological connectivity as a modulating factor of quasispecies complexity.Spanish Polar Programme and the Spanish Ministry of Economy and Competitiveness (CTM2008-05134-E/ANT and CTM2009-08644-E).Peer Reviewe

Comparative Pathogenesis, Genomics and Phylogeography of Mousepox

Ectromelia virus (ECTV), the causative agent of mousepox, has threatened laboratory mouse colonies worldwide for almost a century. Mousepox has been valuable for the understanding of poxvirus pathogenesis and immune evasion. Here, we have monitored in parallel the pathogenesis of nine ECTVs in BALB/cJ mice and report the full-length genome sequence of eight novel ECTV isolates or strains, including the first ECTV isolated from a field mouse, ECTV-MouKre. This approach allowed us to identify several genes, absent in strains attenuated through serial passages in culture, that may play a role in virulence and a set of putative genes that may be involved in enhancing viral growth in vitro. We identified a putative strong inhibitor of the host inflammatory response in ECTV-MouKre, an isolate that did not cause local foot swelling and developed a moderate virulence. Most of the ECTVs, except ECTV-Hampstead, encode a truncated version of the P4c protein that impairs the recruitment of virions into the A-type inclusion bodies, and our data suggest that P4c may play a role in viral dissemination and transmission. This is the first comprehensive report that sheds light into the phylogenetic and geographic relationship of the worldwide outbreak dynamics for the ECTV species.Peer Reviewe

The genome sequence of the emerging common midwife toad virus identifies an evolutionary intermediate within ranaviruses

Worldwide amphibian population declines have been ascribed to global warming, increasing pollution levels, and other factors directly related to human activities. These factors may additionally be favoring the emergence of novel pathogens. In this report, we have determined the complete genome sequence of the emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in several amphibian species across Europe. Phylogenetic and gene content analyses of the first complete genomic sequence from a ranavirus isolated in Europe show that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome structure is novel and represents an intermediate evolutionary stage between the two previously described ALRV groups. We find that CMTV clusters with several other ranaviruses isolated from different hosts and locations which might also be included in this novel ranavirus group. This work sheds light on the phylogenetic relationships within this complex group of emerging, disease-causing viruses. © 2012, American Society for Microbiology.Peer Reviewe

The genome sequence of the emerging common midwife toad virus identifies an evolutionary intermediate within ranaviruses

Worldwide amphibian population declines have been ascribed to global warming, increasing pollution levels, and other factors directly related to human activities. These factors may additionally be favoring the emergence of novel pathogens. In this report, we have determined the complete genome sequence of the emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in several amphibian species across Europe. Phylogenetic and gene content analyses of the first complete genomic sequence from a ranavirus isolated in Europe show that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome structure is novel and represents an intermediate evolutionary stage between the two previously described ALRV groups. We find that CMTV clusters with several other ranaviruses isolated from different hosts and locations which might also be included in this novel ranavirus group. This work sheds light on the phylogenetic relationships within this complex group of emerging, disease-causing viruses.This work was supported by grant AGL 2009-08711 from the Spanish Ministerio de Ciencia e Innovación. Alberto López-Bueno and Carla Mavián are recipients of the Ramón y Cajal and Formación del Personal Investigador fellowships, respectively, from the same institutio

Complete genome sequence of the European sheatfish virus

Viral diseases are an increasing threat to the thriving aquaculture industry worldwide. An emerging group of fish pathogens is formed by several ranaviruses, which have been isolated at different locations from freshwater and seawater fish species since 1985.We report the complete genome sequence of European sheatfish ranavirus (ESV), the first ranavirus isolated in Europe, which causes high mortality rates in infected sheatfish (Silurus glanis) and in other species. Analysis of the genome sequence shows that ESV belongs to the amphibian- like ranaviruses and is closely related to the epizootic hematopoietic necrosis virus (EHNV), a disease agent geographically confined to the Australian continent and notifiable to the World Organization for Animal HealthThis work was supported by grant AGL 2009-08711 from the Spanish Ministerio de Ciencia e Innovación. Alberto López-Bueno and Carla Mavian are recipients of Ramón y Cajal and Formación de Personal Investigador fellowships, respectively, from the same institutio

Novel polyomavirus and papillomavirus detected in gilthead seabream infected by lymphocystis disease virus

Lymphocystis disease virus (LCDV), a member of the genus Lymphocystivirus, family Iridoviridae, is the etiological agent of the lymphocystis disease (LCD), a common pathology that has been described in more than 150 different fish species worldwide. Direct sequencing of the virome of lymphocystis lesions from affected gilthead seabream (Sparus aurata) was used to obtain the complete genome sequence of a new LCDV species, named LCDV-Sa, that is the largest vertebrate iridovirus sequenced to date. This approach allowed us to assemble the full-length circular genomes of two previously unknown viruses, tentatively identified as members of the Polyomaviridae and Papillomaviridae families, and named Sparus aurata polyomavirus 1 (SaPyV1) and Sparus aurata papillomavirus 1 (SaPV1), respectively. SaPyV1 genome is a circular 7,299-bp-long DNA with a 52.1% GC content, and contains five nonoverlapping ORFs carried on opposite DNA strands in an organization reminiscent to that found in polyomaviruses. Phylogenetic analyses based on the amino acid sequence of the large T antigen and the VP1 proteins revealed that SaPyV1 clustered with the other currently available polyomavirus-like full-length genomes obtained from fish. SaPV1 genome corresponds to a circular 5,748-bp-long DNA and has a GC content of 39.5%. Although this genome is smaller than that of previously described papillomaviruses (about 8 kbp), it presents a typical papillomavirus organization, with seven ORFs carried on the same strand. Similarity searches identified distant orthologues of the early E1 and E2 proteins involved in replication and transcription, and late structural proteins L1 and L2. Furthermore, one of the others ORFs encodes a small protein (52 amino acids) that contains both a pRB binding domain (LXCXE) and a C-terminal PDZ class 2 binding motif, with are elements typically present in the longer E7 and E6 proteins found in most known papillomaviruses. The conserved genomic organization, the similarity of the main proteins, and the phylogenetical analysis, based on the amino acid sequence of the L1 protein, support that SaPV1 is the first member of the Papillomaviridae family described in fish. Epizootic surveys carried out in gilthead seabream farms in the Mediterranean area showed that LCD is frequently associated with the concurrent appearance of one or both of the new viruses, 98.3% of diseased fish being positive for SaPyV1 and/or SaPV1. In LCDV-infected asymptomatic fish, SaPyV1 and/or SaPV1 were detected in 32.1% of the animals analysed.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Ecosystem function decays by fungal outbreaks in Antarctic microbial mats

Antarctica harbours a remarkably diverse range of freshwater bodies and terrestrial ecosystems, where microbial mats are considered the most important systems in terms of biomass and metabolic capabilities. We describe the presence of lysis plaque-like macroscopic blighted patches within the predominant microbial mats on Livingston Island (Antarctic Peninsula). Those blighting circles are associated with decay in physiological traits as well as nitrogen depletion and changes in the spatial microstructure; these alterations were likely related to disruption of the biogeochemical gradients within the microbial ecosystem caused by an unusually high fungal abundance and consequent physical alterations. This phenomenon has been evidenced at a time of unprecedented rates of local warming in the Antarctic Peninsula area, and decay of these ecosystems is potentially stimulated by warmer temperaturesWe thank the LIMNOPOLAR team members for their assistance in collecting samples and the UTM and Las Palmas Navy crew for logistical support. We are grateful to Warwick F. Vincent for comments that improved the final manuscript. This study was supported by grants CGL2005–06549-CO2-1, POL2006–06635 and CTM2011– 28736 to A.Q. CTM2008–05134-E/ANT and CTM2009–08644-E to A.A., and CTM2012–38222-C02–02 to A.dR. D.V. was supported by the Spanish Ministry of Science and Innovation grant BES-2006–14027, A.LB. by the Ramón y Cajal contract RYC-2010–06300, and D.AdC. by the Marie Curie IIF grant PIIF-GA-2012-328287. In memoriam: We are grateful to Fernando Pinto for technical assistance with LTSE

Experiencias en la impartición a distancia de varias asignaturas del grado de Ingeniería Informática

[SPA] El presente trabajo reporta las experiencias obtenidas en la impartición de varias asignaturas del Grado de Ingeniería Informática en la Universidad Católica San Antonio de Murcia, durante el curso 2010-2011. La principal contribución del trabajo está dada por la recomendación de un conjunto de actividades metodológicas utilizadas para la enseñanza a distancia, destacando las principales fortalezas. Se analiza de manera crítica algunas evidencias relacionadas con la evaluación del proceso de enseñanza aprendizaje desde el punto de vista de los resultados obtenidos por los estudiantes, la labor del profesor, el uso de las herramientas, la efectividad de las metodologías utilizadas, entre otros.[ENG] This paper shows the most relevant experiencies collected form the teaching of sevelar subjects of the Computer Engineering Degree, at Universidad Católica San Antonio de Murcia, during the curse 2010-2011. The main contribution of this work is related with the recomendation of a set of teaching learning activities using in on line teaching. The most importat strengths are reported. Some evidences related to the evaluaciotn of the teaching/learning process are given. They are based on the analysis of the results obtained by students, the teacher's work, the use of tools, the effectiveness of the methodologies used, etc.Campus Mare Nostrum, Universidad Politécnica de Cartagena, Universidad de Murcia, Región de Murci

Cancer-associated fibroblast-derived gene signatures determine prognosis in colon cancer patients

© The Author(s)Paracrine communication between tumor and surrounding stroma arbitrates the malignant behavior of cancer progression [1]. Fibroblasts, which are the main cell type within the stroma and are called cancer-associated fibroblasts (CAFs), orchestrate the crosstalk with cancer cells [2, 3] and express several markers associated with prognosis [4]. There is increasing evidence that a stroma-specific signature could be used for risk assessment in colon cancer (CC). According to the Consensus Molecular Subtype classification (CMS) in CC, the mesenchymal or CMS4 group is characterized by stromal invasion, extracellular matrix remodeling and TGF-β signaling activation. It is associated with the worst prognosis rates [5, 6]. Genes correlating with the mesenchymal subtype are mostly expressed by CAFs and other stromal cells, rather than by tumor cells [7]. Accordingly, our group defined a gene expression profile associated with CAFs with high pro-migratory effects on colon tumor cells, which was associated with patients’ poor prognosis. These were mostly advanced-stage patients [8].This research is supported by PI17/01847, PI18/01020 and PI20/00602 from the Instituto de Salud Carlos III and co-financed by the European Development Regional Fund (FEDER) “A way to achieve Europe” (ERDF); by “CIBER de Cáncer”, CB16/12/00273, CB16/12/00301 and CB16/12/00446, from the Instituto de Salud Carlos III-FEDER; and by the Fundación Científica AECC (a multifaceted approach to targeting pancreatic cancer). The JDLR group also acknowledges the funding provided by the Instituto de Salud Carlos III (ISCiii, AES) in grants PI18/00591 and PT17/0009/0008, co-financed by the European Development Regional Fund (FEDER)

Article Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6, Two Bacteriocinogenic Isolated Strains from Andalusian Spontaneous Fermented Sausages

Traditional spontaneously fermented foods are well known for their sensory and safety properties, which is mainly due to their indigenous microflora. Within this group of food, Mediterranean dry-cured sausages stand out as a significant source of lactic-acid bacterial strains (LAB) with biotechnological properties, such as their antimicrobial activity. The aim of this study was to investigate the biodiversity of antagonistic LAB strains from different Andalusian traditional sausages, such as salchichón and chorizo. First, a screening was carried out focusing on the antimicrobial activity against foodborne pathogens, such as Listeria monocytogenes, Escherichia coli, Clostridium perfringens, and Staphylococcus aureus, selecting two strains due to their higher antibiosis properties, both in agar and liquid media. These bacteria were identified as Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6. In addition, genomic studies confirmed the presence of certain structural genes related to the production of bacteriocins. Finally, the culture supernatants of both strains were purified and analyzed by LC-MS/MS, obtaining the relative molecular mass and the amino acid sequence and identifying the peptides as the bacteriocins Pediocin-PA and Leucocin K. In conclusion, genomes and antimicrobial substances of P. acidilactici ST6, a Pediocin-PA producer, and Lpb. paraplantarum BPF2, a Leucocin K producer, isolated from Andalusian salchichón and chorizo, respectively, are presented in this work. Although further studies are required, these strains could be used alone or in combination as starters or protective cultures for the food industryPRIMA program, under BioProMedFood project (Reference Number: 2019-SECTION2-4; CUP: J34I19004820005)PRIMA program is supported by the European Union H2020 program and innovation progra