Habitat Constraints in Epikarstic Waters of an Iberian Peninsula Cave System

14 páginas, 6 figuras, 11 tables et al..The epikarstic waters of a restricted sector of the Ojo Guareña cave (north Iberian Peninsula) were investigated to characterize the physico-chemical variation in an annual cycle, to improve the scarce knowledge of the aquatic cave fauna on the Iberian Peninsula, to look for distribution patterns of species per habitat along the annual cycle, and to search for the environmental basis (either physico- or hydro-geochemical) that could explain species distribution in the epikarst. The habitats studied included all puddles and gours present in the sector selected making a total of 51 chemical and 42 biological samples for the entire cycle. The waters show no appreciable contaminationand exhibit small chemical variations throughout the year which are patently affected by external weather conditions. The 53 taxa found belong to ten higher taxonomic groups (Oligochaeta, Turbellaria, Mollusca, Copepoda, Ostracoda, Isopoda, Bathynellacea, Tardigrada, Acarina and Cnidaria), and consist mainly of crustacea with a total of 27 species. Fourteen species were stygobionts (belonging to ten genera), nine of which are new to science and ten of which are endemic. Cave pools that appeared to be more stable in terms of water volume and mineralization, had a lower pCO2 and were carbonate oversaturated, harboured the greatest number of taxa. It is these pools that can maintain strictly cave dwelling species. Pools with lower levels of mineralization and greater water volume fluctuations had a lower diversity of fauna and in general lacked stygobiotic species.Projects PASCALIS EVK2-CT-2001-00121; Convenio Junta de Castilla y León-CSIC (2002-2004) and BTE2002-04492-C02-02.Peer reviewe

Data on individual PCR efficiency values as quality control for circulating miRNAs

AbstractThis data article contains data related to the research article entitled “Variability in microRNA recovery from plasma: Comparison of five commercial kits, doi:10.1016/j.ab.2015.07.018” Brunet-Vega (2015) [1]. PCR efficiency, along with RNA and cDNA quality, are the most important factors affecting the quality of qPCR results. Constant amplification efficiency in all compared samples is indispensable when relative quantification is used to measure changes in gene expression. An easy way to measure PCR efficiency, without the need of a standard curve, is LinRegPCR software. Individual PCR efficiency can be determined as a part of qPCR quality control. This is especially important when the initial RNA quantity is so low that cannot be accurately quantified, such as in circulating RNA extractions. This data article reports the Cqs and PCR efficiencies of 5 miRNAs quantified in RNA isolated from 4 patients with colorectal cancer (CRC) and 4 healthy donors using five commercially available kits

Interpretation of flat energy spectra upstream of fast interplanetary shocks

Interplanetary shocks are large-scale heliospheric structures often caused by eruptive phenomena at the Sun, and represent one of the main sources of energetic particles. Several interplanetary shock crossings by spacecraft at $1$ AU have revealed enhanced energetic-ion fluxes that extend far upstream of the shock. Surprisingly, in some shock events, ion fluxes with energies between $100$ keV and about $2$ MeV acquire similar values (which we refer to as ``overlapped'' fluxes), corresponding to flat energy spectra in that range. In contrast, closer to the shock, the fluxes are observed to depend on energy. In this work, we analyze three interplanetary shock-related energetic particle events observed by the Advanced Composition Explorer spacecraft where flat ion energy spectra were observed upstream of the shock. We interpret these observations via a velocity filter mechanism for particles in a given energy range. This reveals that low energy particles tend to be confined to the shock front and cannot easily propagate upstream, while high energy particles can. The velocity filter mechanism has been corroborated from observations of particle flux anisotropy by the Solid-State Telescope of Wind/3DP

Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma

Helicobacter pylori is a common pathogen associated with several severe digestive diseases. Although multiple virulence factors have been described, it is still unclear the role of virulence factors on H. pylori pathogenesis and disease progression. Whole genome sequencing could help to find genetic markers of virulence strains. In this work, we analyzed three complete genomes from isolates obtained at the same point in time from a stomach of a patient with adenocarcinoma, using multiple available bioinformatics tools. The genome analysis of the strains B508A-S1, B508A-T2A and B508A-T4 revealed that they were cagA, babA and sabB/hopO negative. The differences among the three genomes were mainly related to outer membrane proteins, methylases, restriction modification systems and flagellar biosynthesis proteins. The strain B508A-T2A was the only one presenting the genotype vacA s1, and had the most distinct genome as it exhibited fewer shared genes, higher number of unique genes, and more polymorphisms were found in this genome. With all the accumulated information, no significant differences were found among the isolates regarding virulence and origin of the isolates. Nevertheless, some B508A-T2A genome characteristics could be linked to the pathogenicity of H. pylori. Keywords: Helicobacter pylori; genomic comparison; virulence factors; gastric adenocarcinom

Micromorphological Study of Site Formation Processes at El Sidrón Cave (Asturias, Northern Spain): Encrustations over Neanderthal Bones

El Sidrón Cave is an archaeological and anthropological reference site of the Neanderthal world. It shows singular activity related to cannibalisation, and all existing processes are relevant to explain the specific behaviour of the concerned individuals. This paper presents geoarchaeological data, primarily based on mineralogical and petrographic techniques, from an investigation of the nature of the encrustations or hard coatings that affect a large part of the Neanderthal bone remains and their relationship with the depositional and post-depositional processes at the archaeological site. Crusts and patina were found to be numerous and diverse, mainly composed of calcite and siliciclastic grains, with different proportions and textures. The analysis indicated different origins and scenarios from their initial post-mortem accumulation to the final deposit recovered during the archaeological work. The presence of micromorphological features, such as clotted-peloidal micrite, needle-fibre calcite (NFC) aggregates, clay coatings, iron–manganese impregnation, and/or adhered aeolian dust may indicate that a significant proportion of the remains were affected by subaerial conditions in a relatively short period of time in a shelter, cave entrance, or shallower level of the karstic system, prior to their accumulation in the Ossuary Gallery.This work has been supported since 1999 through different research contracts between the Government of the Principality of Asturias, the University of Oviedo, the University of Alicante, the National Museum of Natural Sciences (CSIC, Madrid), and the University of Salamanca

Usefulness of Housekeeping Genes for the Diagnosis of Helicobacter pylori Infection, Strain Discrimination and Detection of Multiple Infection

Background: Helicobacter pylori infects human stomachs of over half the world's population, evades the immune response and establishes a chronic infection. Although most people remains asymptomatic, duodenal and gastric ulcers, MALT lymphoma and progression to gastric cancer could be developed. Several virulence factors such as flagella, lipopolysaccharide, adhesins and especially the vacuolating cytotoxin VacA and the oncoprotein CagA have been described for H. pylori. Despite the extensive published data on H. pylori, more research is needed to determine new virulence markers, the exact mode of transmission or the role of multiple infection. Materials and Methods: Amplification and sequencing of six housekeeping genes (amiA, cgt, cpn60, cpn70, dnaJ, and luxS) related to H. pylori pathogenesis have been performed in order to evaluate their usefulness for the specific detection of H. pylori, the genetic discrimination at strain level and the detection of multiple infection. A total of 52 H. pylori clones, isolated from 14 gastric biopsies from 11 patients, were analyzed for this purpose. Results: All genes were specifically amplified for H. pylori and all clones isolated from different patients were discriminated, with gene distances ranged from 0.9 to 7.8%. Although most clones isolated from the same patient showed identical gene sequences, an event of multiple infection was detected in all the genes and microevolution events were showed for amiA and cpn60 genes. Conclusions: These results suggested that housekeeping genes could be useful for H. pylori detection and to elucidate the mode of transmission and the relevance of the multiple infection

Detection of Helicobacter pylori Microevolution and Multiple Infection from Gastric Biopsies by Housekeeping Gene Amplicon Sequencing

Despite the great efforts devoted to research on Helicobacter pylori, the prevalence of single-strain infection or H. pylori mixed infection and its implications in the mode of transmission of this bacterium are still controversial. In this study, we explored the usefulness of housekeeping gene amplicon sequencing in the detection of H. pylori microevolution and multiple infections. DNA was extracted from five gastric biopsies from four patients infected with distinct histopathological diagnoses. PCR amplification of six H. pylori-specific housekeeping genes was then assessed on each sample. Optimal results were obtained for the cgt and luxS genes, which were selected for amplicon sequencing. A total of 11,833 cgt and 403 luxS amplicon sequences were obtained, 2042 and 112 of which were unique sequences, respectively. All cgt and luxS sequences were clustered at 97% to 9 and 13 operational taxonomic units (OTUs), respectively. For each sample from a different patient, a single OTU comprised the majority of sequences in both genes, but more than one OTU was detected in all samples. These results suggest that multiple infections with a predominant strain together with other minority strains are the main way by which H. pylori colonizes the human stomach

Droplet Digital PCR Detects Low-Density Infection in a Significant Proportion of Helicobacter Pylori -Negative Gastric Biopsies of Dyspeptic Patients

Dyspeptic patients (n = 236) were tested for H. pylori by histology, urea breath test, and rapid urease test. Patients were classified as having 3 positive (n = 25, control group), 2 positive (n = 12), one positive (n = 41), or zero positive (n = 158) diagnostic tests. DNA was extracted from gastric biopsies. Triplicate ddPCR testing for each of the 16S rDNA, ureA, and vacA(s) genes was performed using a QX200 ddPCR system (Bio-Rad). A gene was considered positive when detected by at least 2 of 3 repeated ddPCRs. H. pylori positivity was defined as having 2 or more positive genes. All the biopsies of the control patients were positive for all 3 16S rDNA, ureA, and vacA(s) genes. H. pylori infection was detected in 57 (36%), 22 (54%), and 9 (75%) patients with zero, 1, and 2 positive diagnostic tests, respectively. The density of infection was 5, 121, 599, and 3,133 copies of H. pylori genome equivalents for patients with zero, 1, and 2 of 3 positive test results and for the control group, respectively. ddPCR detected low-density "occult" H. pylori infection in a significant proportion (36%) of patients diagnosed as negative by conventional methods. The number of conventional positive tests was related to the density of infection

Geoarchaeological study of the Sidrón cave (Piloña, Asturias)

El relleno sedimentario que alberga el registro arqueológico y antropológico de la Galería del Osario (cueva de El Sidrón) presenta una alta complejidad, tanto en los tipos de sedimentos como en su distribución espacial en la cavidad. Los principales factores que rigen esta complejidad son la naturaleza episódica y altamente energética de gran parte de las unidades litoestratigráficas reconocidas y la irregular geometría del propio conducto, que compartimenta significativamente las áreas de deposición. A modo de resumen puede indicarse que en la Galería del Osario quedan representados todos los tipos de materiales detríticos típicos de depósitos alóctonos en ambiente kárstico; desde materiales bien seleccionados de granulometría fina representativos de facies de encharcamiento (arcillas de la unidad O) o de desbordamiento (Unidad IV), a depósitos groseros mal seleccionados correspondientes a coladas de barro y detritos en masa (Unidad II y base de unidad III), pasando por típicas facies fluvio-kársticas o de canal compuestas por materiales arenosos con laminaciones y estructuras de flujo (unidades I y II). Los restos óseos se concentran en la unidad III. El área fuente se sitúa en cotas superiores a la Galería del Osario, es decir, en los niveles intermedio o superior del sistema kárstico, y el depósito o entrada de material óseo a la Galería del Osario se activaría en episodios de alta energía relacionado con eventos de inundación y/o tormenta.The sedimentary infill bearing the archaeological and anthropological record of the Ossuary Gallery (the Sidrón cave) shows high complexity in both sediment types and their spatial distribution in the cavity. The main factors that govern this complexity are the episodic and highly energetic nature of the recorded sedimentary infill units and the irregular geometry of the gallery itself, which significantly compartmentalized areas of deposition. Briefly, all types of typical allochthonous detrital material deposits in karst environments are represented in the Ossuary Gallery; from well-sorted fine-grained sediment facies representative of backswamp (clays of the unit O) or slackwater (Unit IV), to poorly-sorted coarse-grained deposits corresponding to mudflows and debris flows (Unit II and Unit III base), and typical channel facies composed of laminated sands and silts (units I and II). The bone and lithic remains are concentrated in unit III. The source area is above the Ossuary Gallery, at the intermediate or higher karst levels. The input of archeological material to the Ossuary Gallery was triggered in high energy episodes in association to flood events and / or storms.Este trabajo se ha financiado desde 1999 mediante diferentes contratos de investigación realizados entre el Gobierno del Principado de Asturias, la Universidad de Oviedo, la Universidad de Alicante, el Museo Nacional de Ciencias Naturales (CSIC, Madrid) y la Universidad de Salamanca

Economic impact of inflammatory bowel disease in Catalonia: a population-based analysis

Background: Inflammatory bowel disease (IBD) has a major economic impact on healthcare costs.Objectives: The aim of this study was to evaluate the current healthcare expenditure associated with IBD in a population-wide study in Catalonia.Design: Retrospective observational study.Methods: All patients with IBD included in the Catalan Health Surveillance System (CHSS) were considered eligible. The CHSS compiles data on more than 7 million individuals in 2020 (34,823 with IBD). Data on the use of healthcare resources and its economic impact were extracted applying the International Classification of Diseases, 10th revision, Clinical Modification codes (ICD-10-CM codes). Health expenditure, comorbidities, and hospitalization were calculated according to the standard costs of each service provided by the Department of Health of the Catalan government. The data on the IBD population were compared with non-IBD population adjusted for age, sex, and income level. IBD costs were recorded separately for Crohn's disease (CD) and ulcerative colitis (UC).Results: Prevalence of comorbidities was higher in patients with IBD than in those without. The risk of hospitalization was twice as high in the IBD population. The overall healthcare expenditure on IBD patients amounted to 164Meuro. The pharmacy cost represents the 60%. The average annual per capita expenditure on IBD patients was more than 3.4-fold higher (IBD 4200euro, non-IBD 1200euro). Average costs of UC were 3400euro and 5700euro for CD.Conclusion: The risk of comorbidities was twice as high in patients with IBD and their use of healthcare resources was also higher than that of their non-IBD counterparts. Per capita healthcare expenditure was approximately 3.4 times higher in the population with IBD.Trial registration: The study was not previously registered. Economic impact of inflammatory bowel disease in CataloniaThe manuscript includes data of the most recent epidemiologic data about the high economic impact of IBD in Catalonia