Stratigraphy and sedimentology of distal-alluvial and lacustrine deposits of the western-central Ebro Basin (NE Iberia) reflecting the onset of the middle Miocene Climatic Optimum

The stratigraphic and sedimentologic study of Miocene deposits in the Plana Negra-Sancho Abarca area fills a gap in the Ebro Basin knowledge. Five main lithofacies were characterized and mapped. The boundary between regional tectosedimentary units T5 and T6 is recognized as a conformity at a major facies change. Unit T5, up to 130m thick, consists of mudstones with interbedded sandstones and limestones. Unit T6, with 30 to 62m of preserved thickness, is made of limestones, marls and minor mudstones. Correlation of the studied outcrops with nearby sections that already had detailed magnetoestratigraphic and biostratigraphic data allows dating the studied succession as Burdigalian (early Miocene)-Langhian (middle Miocene), from C5Dr to C5Cn, and the boundary between units T5 and T6 to be located at 16.062-16.099 Ma. Seventeen sedimentary facies associated in seven vertical facies sequences document deposition in fluvial-distal alluvial, palustrine and lacustrine environments. A shallow (2-4m deep) lake body was locus for charophytes, ostracods, bivalves and gastropods to thrive. Occasional bottom currents reworked and transported allochems and fine-siliciclastic sediment offshore, forming laminated limestones. Bioturbation and desiccation features are abundant, indicating wide palustrine areas and episodic exposure. Low-sinuosity channels associated to the Pyrenean-derived Luna fluvial system run across the alluvial-plain. Four evolutionary stages of alluvial progradation-retrogradation and retraction-expansion of the palustrine-lacustrine system, likely related to Pyrenean tectonic activity, are distinguished. Maximum lacustrine expansion took place at the beginning of unit T6 deposition. This is consistent with initial conditions of increasing humidity of the Middle Miocene Climatic Optimum (MMCO)

Increased in vivo inhibition of gene expression by combining RNA interference and U1 inhibition

Inhibition of gene expression can be achieved with RNA interference (RNAi) or U1 small nuclear RNA—snRNA—interference (U1i). U1i is based on U1 inhibitors (U1in), U1 snRNA molecules modified to inhibit polyadenylation of a target pre-mRNA. In culture, we have shown that the combination of RNAi and U1i results in stronger inhibition of reporter or endogenous genes than that obtained using either of the techniques alone. We have now used these techniques to inhibit gene expression in mice. We show that U1ins can induce strong inhibition of the expression of target genes in vivo. Furthermore, combining U1i and RNAi results in synergistic inhibitions also in mice. This is shown for the inhibition of hepatitis B virus (HBV) sequences or endogenous Notch1. Surprisingly, inhibition obtained by combining a U1in and a RNAi mediator is higher than that obtained by combining two U1ins or two RNAi mediators. Our results suggest that RNAi and U1i cooperate by unknown mechanisms to result in synergistic inhibitions. Analysis of toxicity and specificity indicates that expression of U1i inhibitors is safe. Therefore, we believe that the combination of RNAi and U1i will be a good option to block damaging endogenous genes, HBV and other infectious agents in vivo

Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair

Adenovirus virus-associated (VA) RNAs are processed to functional viral miRNAs or mivaRNAs. mivaRNAs are important for virus production, suggesting that they may target cellular or viral genes that affect the virus cell cycle. To look for cellular targets of mivaRNAs, we first identified genes downregulated in the presence of VA RNAs by microarray analysis. These genes were then screened for mivaRNA target sites using several bioinformatic tools. The combination of microarray analysis and bioinformatics allowed us to select the splicing and translation regulator TIA-1 as a putative mivaRNA target. We show that TIA-1 is downregulated at mRNA and protein levels in infected cells expressing functional mivaRNAs and in transfected cells that express mivaRNAI-138, one of the most abundant adenoviral miRNAs. Also, reporter assays show that TIA-1 is downregulated directly by mivaRNAI-138. To determine whether mivaRNAs could target other cellular genes we analyzed 50 additional putative targets. Thirty of them were downregulated in infected or transfected cells expressing mivaRNAs. Some of these genes are important for cell growth, transcription, RNA metabolism and DNA repair. We believe that a mivaRNA-mediated fine tune of the expression of some of these genes could be important in adenovirus cell cycle

Middle Eocene Rhodoliths from Tropical and Mid-Latitude Regions

During the greenhouse conditions prevailing in the early–middle Eocene, larger benthic foraminifers (LBF) spread out on carbonate platforms worldwide while rhodolith beds were scarcely represented. This reduction in rhodolith beds coincided with a relative decrease in coralline algal diversity and with a drastic decline of coral reef abundance. Middle Eocene rhodoliths from two tropical (San Jacinto Fold Belt in northern Colombia and Bahoruco Peninsula in the Dominican Republic) and two mid-latitude (Salinas Menores Ravine and Sierra del Zacatín in Southern Spain) localities were studied. Rhodolith rudstones in the tropical areas accumulated on relatively deep (several tens of meters) platform environments and were also redeposited in deeper settings downslope. In Salinas Menores, rhodoliths are dispersed in planktic foraminifer-rich marls. Miliolids are common in the infilling of constructional voids in these rhodoliths, indicating that they originally grew in shallow-water inner-shelf settings and afterwards they were transported to deeper environments. In Sierra del Zacatín, rhodoliths are scarce and coralline algae mainly occur as crusts attached to and intergrowing with corals. Here, LBF dominated shallow-water carbonate platforms. In terms of taxonomic composition, coralline algae of the order Hapalidiales are the most abundant in the study areas, followed by Sporolithales. The order Corallinales is poorly represented except in Salinas Menores, where it is relatively abundant and diverse. The impact of high temperatures due to high levels of atmospheric CO2 during the Eocene and widespread oligotrophic conditions, which favored formation of LBF-rich lithofacies, might account for the low abundance of rhodolith beds at mid and high latitudes. In contrast, the more productive equatorial regions would have favored the formation of rhodolith beds.This research was funded by Research Group RNM-190 of the Junta de Andalucía (JA and JCB), MINECO/FEDER-UE project CGL2015-65404-R and by the Consolidated Research Group IT930-16 of the Basque Government (VP and XOE)

Nitrogen, Iron, and Zinc Acquisition: Key Nutrients to Aspergillus fumigatus Virulence

Aspergillus fumigatus is a ubiquitous soil decomposer and an opportunistic pathogen that is characterized by its large metabolic machinery for acquiring nutrients from media. Lately, an ever-increasing number of genes involved in fungal nutrition has been associated with its virulence. Of these, nitrogen, iron, and zinc metabolism-related genes are particularly noteworthy, since 78% of them have a direct implication in virulence. In this review, we describe the sensing, uptake and regulation process of the acquisition of these nutrients, the connections between pathways and the virulence-implicated genes. Nevertheless, only 40% of the genes mentioned in this review have been assayed for roles in virulence, leaving a wide field of knowledge that remains uncertain and might offer new therapeutic and diagnostic targets.This research was funded by the Basque Government: grant number IT1362-19. U.P.-C. and S.C.-S. received a predoctoral fellowship from the University of the Basque Country and Basque Government, respectively

Flexible multiplex PCR to detect SARS-CoV-2, coronavirus OC43 and influenza A virus in nasopharyngeal swab samples

Introduction Quantitative reverse transcription PCR (RT-qPCR) is the leading tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Given that it will almost certainly continue to coexist with other respiratory viruses in the coming years, our study aimed to design a multiplex PCR system not affected by supplier outages and with reduced cost compared to the existing commercially available kits. Methods and results In this study, combinations of four primers/probe sets were used to construct a flexible RT-qPCR assay which is capable of discriminating between SARS-CoV-2 and the seasonal human coronavirus HCoV-OC43, or even influenza A virus. Additionally, the human RPP30 gene was used as an internal control. To demonstrate the robustness of the assay, it was applied to a collection of 150 clinical samples. The results showed 100% sensitivity and specificity compared to the automatized system used at the hospital and were better when indeterminate samples were analysed. Conclusions This study provides an efficient method for the simultaneous detection of SARS-CoV-2, HCoV-OC43 and influenza A virus, and its efficacy has been tested on clinical samples showing outstanding results. Significance and impact of the study The multiplex RT-qPCR design offers an accessible and economical alternative to commercial detection kits for hospitals and laboratories with limited economic resources or facing situations of supply shortage.This research was funded by Basque Government, grants numbers 2020333042 and IT1362‐19. LM‐S have received a predoctoral Grant from Basque Government

Response of Horticultural Soil Microbiota to Different Fertilization Practices

Environmentally friendly agricultural production necessitates manipulation of microbe–plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.This work was supported by the Earth Microbiome Project; the METAMAHA project funded by the Basque Government’s Department of Industry, Trade, and Tourism (SAIOTEK program; S-PE13UN130); and IT1014-16 and IT1213-19 Consolidated Research Group Projects

Procedimiento de identificación de compuestos inhibidores del proceso de polimerización de filamentos tau tipo PHFs y sus aplicaciones.

La presente invención presenta un procedimiento de identificación compuestos reguladores, preferentemente inhibidores, del proceso de polimerización de filamentos tau tipo PHFs, basado en un modelo celular eucariota transformado mediante ingeniería genética, que expresa una forma proteica de tau mutante que se comporta como hiperfosforilada, preferentemente la forma tauVLW, que condene mutaciones en las posiciones G272V, de P301L, y de R406W. Otros objetos de la presente invención lo constituyen un modelo celular transformado por un sistema o vector de expresión tauVLW, construcciones genéticas tauVLW y los sistemas de expresión tauVLW necesarios para la expresión de dicha proteína tau hiperfosforilada y para la formación de los filamentos tipo PHFs. Estos compuestos podrán ser utilizados en la elaboración de medicamentos para el tratamiento de la enfermedad de Alzheimer o de otras enfermedades neurodegenerativas denominadas Taupatías.Solicitud: 200303031 (22.12.2003)Nº Pub. de Solicitud: ES2286911A1 (01.12.2007)Nº de Patente: ES2286911B1 (01.11.2008

Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair

Adenovirus virus-associated (VA) RNAs are processed to functional viral miRNAs or mivaRNAs. mivaRNAs are important for virus production, suggesting that they may target cellular or viral genes that affect the virus cell cycle. To look for cellular targets of mivaRNAs, we first identified genes downregulated in the presence of VA RNAs by microarray analysis. These genes were then screened for mivaRNA target sites using several bioinformatic tools. The combination of microarray analysis and bioinformatics allowed us to select the splicing and translation regulator TIA-1 as a putative mivaRNA target. We show that TIA-1 is downregulated at mRNA and protein levels in infected cells expressing functional mivaRNAs and in transfected cells that express mivaRNAI-138, one of the most abundant adenoviral miRNAs. Also, reporter assays show that TIA-1 is downregulated directly by mivaRNAI-138. To determine whether mivaRNAs could target other cellular genes we analyzed 50 additional putative targets. Thirty of them were downregulated in infected or transfected cells expressing mivaRNAs. Some of these genes are important for cell growth, transcription, RNA metabolism and DNA repair. We believe that a mivaRNA-mediated fine tune of the expression of some of these genes could be important in adenovirus cell cycle

Role of age and comorbidities in mortality of patients with infective endocarditis

[Purpose]: The aim of this study was to analyse the characteristics of patients with IE in three groups of age and to assess the ability of age and the Charlson Comorbidity Index (CCI) to predict mortality. [Methods]: Prospective cohort study of all patients with IE included in the GAMES Spanish database between 2008 and 2015.Patients were stratified into three age groups:<65 years,65 to 80 years,and ≥ 80 years.The area under the receiver-operating characteristic (AUROC) curve was calculated to quantify the diagnostic accuracy of the CCI to predict mortality risk. [Results]: A total of 3120 patients with IE (1327 < 65 years;1291 65-80 years;502 ≥ 80 years) were enrolled.Fever and heart failure were the most common presentations of IE, with no differences among age groups.Patients ≥80 years who underwent surgery were significantly lower compared with other age groups (14.3%,65 years; 20.5%,65-79 years; 31.3%,≥80 years). In-hospital mortality was lower in the <65-year group (20.3%,<65 years;30.1%,65-79 years;34.7%,≥80 years;p < 0.001) as well as 1-year mortality (3.2%, <65 years; 5.5%, 65-80 years;7.6%,≥80 years; p = 0.003).Independent predictors of mortality were age ≥ 80 years (hazard ratio [HR]:2.78;95% confidence interval [CI]:2.32–3.34), CCI ≥ 3 (HR:1.62; 95% CI:1.39–1.88),and non-performed surgery (HR:1.64;95% CI:11.16–1.58).When the three age groups were compared,the AUROC curve for CCI was significantly larger for patients aged <65 years(p < 0.001) for both in-hospital and 1-year mortality. [Conclusion]: There were no differences in the clinical presentation of IE between the groups. Age ≥ 80 years, high comorbidity (measured by CCI),and non-performance of surgery were independent predictors of mortality in patients with IE.CCI could help to identify those patients with IE and surgical indication who present a lower risk of in-hospital and 1-year mortality after surgery, especially in the <65-year group