Delineation of hydrocarbon contaminants with multi-frequency complex conductivity imaging

The characterization of contaminated sites is a serious issue that requires a number of techniques to be deployed in the field to reconstruct the geometry, hydraulic properties and state of contamination of the shallow subsurface, often at the hundreds of meter scale with metric resolution. Among the techniques that have been proposed to complement direct investigations (composed of drilling, sampling, and laboratory characterization) are geophysical methods, which can provide extensive spatial coverage both laterally and at depth with the required resolution. However, geophysical methods only measure physical properties that are indirectly related to contamination, and their correlation may be difficult to ascertain without direct ground truth. In this study, we present a successful example where the results of complex conductivity measurements conducted in an imaging framework are compared with direct evidence of subsoil contamination at a jet fuel impacted site. Thus, proving that a combination of direct and indirect investigations can be successfully used to image a site in its complex (potentially 3D) structure in order to build a reliable conceptual model of the site

Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

ABSTRACT The ability to adhere and adapt to the human respiratory tract mucosa plays a pivotal role in the pathogenic lifestyle of nontypeable Haemophilus influenzae (NTHi). However, the temporal events associated with a successful colonization have not been fully characterized. In this study, by reconstituting the ciliated human bronchial epithelium in vitro, we monitored the global transcriptional changes in NTHi and infected mucosal epithelium simultaneously for up to 72 h by dual RNA sequencing. The initial stage of colonization was characterized by the binding of NTHi to ciliated cells. Temporal profiling of host mRNA signatures revealed significant dysregulation of the target cell cytoskeleton elicited by bacterial infection, with a profound effect on the intermediate filament network and junctional complexes. In response to environmental stimuli of the host epithelium, NTHi downregulated its central metabolism and increased the expression of transporters, indicating a change in the metabolic regime due to the availability of host substrates. Concurrently, the oxidative environment generated by infected cells instigated bacterial expression of stress-induced defense mechanisms, including the transport of exogenous glutathione and activation of the toxin-antitoxin system. The results of this analysis were validated by those of confocal microscopy, Western blotting, Bio-plex, and real-time quantitative reverse transcription-PCR (qRT-PCR). Notably, as part of our screening for novel signatures of infection, we identified a global profile of noncoding transcripts that are candidate small RNAs (sRNAs) regulated during human host infection in Haemophilus species. Our data, by providing a robust and comprehensive representation of the cross talk between the host and invading pathogen, provides important insights into NTHi pathogenesis and the development of efficacious preventive strategies. IMPORTANCE Simultaneous monitoring of infection-linked transcriptome alterations in an invading pathogen and its target host cells represents a key strategy for identifying regulatory responses that drive pathogenesis. In this study, we report the progressive events of NTHi colonization in a highly differentiated model of ciliated bronchial epithelium. Genome-wide transcriptome maps of NTHi during infection provided mechanistic insights into bacterial adaptive responses to the host niche, with modulation of the central metabolism as an important signature of the evolving milieu. Our data indicate that infected epithelia respond by substantial alteration of the cytoskeletal network and cytokine repertoire, revealing a dynamic cross talk that is responsible for the onset of inflammation. This work significantly enhances our understanding of the means by which NTHi promotes infection on human mucosae and reveals novel strategies exploited by this important pathogen to cause invasive disease

WATZON: the Italian network of ecohydrology and critical zone observatories

The Italian initiative WATZON (WATer mixing in the critical ZONe) is a network of instrumented sites, bringing together six pre-existing long-term research observatories monitoring different compartments of the Critical Zone - the Earth's permeable near-surface layer from the tops of the trees to the bottom of the groundwater. These observatories cover different climatic and physiographic characteristics over the country, providing information over a climate and eco-hydrologic transect connecting the Mediterranean to the Alps. With specific initial scientific questions, monitoring strategies, databases, and modeling activities, the WATZON observatories and sites is well representative of the heterogeneity of the critical zone and of the scientific communities studying it. Despite this diversity, all WATZON sites share a common eco-hydrologic monitoring and modelling program with three main objectives: 1) assessing the description of water mixing process across the critical zone by using integrated high-resolution isotopic, geophysical and hydrometeorological measurements from point to catchment scale, under different physiographic conditions and climate forcing; 2) testing water exchange mechanisms between subsurface reservoirs and vegetation, and assessing ecohydrological dynamics in different environments by coupling the high-resolution data set from different critical zone study sites of the initiative with advanced ecohydrological models at multiple spatial scales; 3) developing a process-based conceptual framework of ecohydrological processes in the critical zone to translate scientific knowledge into evidence to support policy and management decisions concerning water and land use in forested and agricultural ecosystems. This work provides an overview of the WATZON network, its objectives, scientific questions, and data management, with a specific focus on existing initiatives for linking data and models based on WATZON data

Assessing root water uptake transit time by simulating isotope transport in Hydrus-1D

Stable isotopes (2H and 18O) are common natural tracers for the investigation of water transport in the soil-plant-atmosphere continuum. Isotopic data can be coupled with soil water content data to inversely estimate soil hydraulic and transport parameters. The calibration of a hydrological model by inverse modelling is a prerequisite to determine the temporal origin of xylem water taken by roots. In this study, we used isotopic data to calibrate Hydrus-1D via inverse modelling to simulate one-dimensional water flow and isotope transport in a controlled soil-plant-atmosphere system. We propose the following protocol i) to estimate root water uptake transit time of irrigation water, and ii) to assess the sensitivity of the transit time distribution to the variation in the water available for root uptake. The dataset was obtained from an isotope-tracing experiment carried out between May and July 2018 on an olive tree placed in a pot inside a glasshouse. Meteorological variables and sap flow were monitored at 5-minute intervals, whereas shallow soil moisture (0-6 cm depth) was measured manually with an impedance probe at the daily timescale. The olive tree was irrigated with water of known isotopic composition. The pot surface was covered by a plastic sheet to avoid evaporation. Soil at different depths, twigs, wood cores and root samples were collected weekly for isotopic analyses. Water from soil and the xylem tissues was extracted by cryogenic vacuum distillation. Based on the results of a previous study carried out on the same dataset, we considered that no isotopic fractionation occurred during the water uptake and the transport within the olive tree. We used soil water content and δ18O data at different soil depths to optimize flow (soil hydraulic and root water uptake parameters) and transport (longitudinal dispersivity) parameters. Numerical simulations of isotope transport were validated with sap flow data (compared to actual transpiration) and δ18O in xylem water. Given that the timing of irrigation water for plant transpiration is fundamental for assessing the vulnerability of olive trees to drought, we will be proposing various scenarios based on different irrigation events to mimic drought periods. Based on these scenarios, we will be evaluating the sensitivity of the root water uptake transit time to the different water availability in the soil profile. Afterwards, the same protocol will be exploited to determine the root water uptake transit time for different tree species under various environmental conditions

Association of LEC and tnpA Helicobacter pylori genes with gastric cancer in a Brazilian population

<p>Abstract</p> <p>Background</p> <p><it>H. pylori </it>seroprevalence in Brazilians varies and is dependent on socioeconomic status, sanitation conditions and ethnicity; furthermore, <it>H. pylori </it>is not always associated with the incidence of gastric cancer, suggesting the role of more virulent strains. The purpose of this study was to analyze the association of more virulent <it>H. pylori </it>strains with gastric cancer.</p> <p>Methods</p> <p>DNA was extracted from gastric biopsies of thirty-four cases of gastric cancer (11 intestinal-type, 23 diffuse-type), and thirty-four of patients with endoscopic gastritis. The presence of <it>cag</it>PAI genes (<it>cagA</it>, <it>cagA </it>promoter, <it>cagE</it>, <it>cagM</it>, <it>tnpB</it>, <it>tnpA</it>, <it>cagT </it>and the left end of the <it>cag</it>II (LEC)) and <it>babA </it>were analyzed by PCR.</p> <p>Results</p> <p>Comparison of <it>H. pylori </it>isolates from gastric cancer and gastritis patients showed significant associations of <it>tnpA </it>and LEC with gastric cancer (73.5% [OR, 6.66; 95% CI, 2.30-19.25] and 58.8% [OR, 10.71; 95% CI, 3.07-37.28] of cases, respectively). Other <it>cag</it>PAI genes were detected in both groups at similar frequencies.</p> <p>Conclusions</p> <p><it>tnpA </it>and LEC of <it>H. pylori cag</it>PAI were associated with gastric cancer; nonetheless, these results were restricted within this group of patients and further studies are needed to confirm these results in a larger sample and determine their role in gastric carcinogenesis.</p

Application of PCR amplicon sequencing using a single primer pair in PCR amplification to assess variations in Helicobacter pylori CagA EPIYA tyrosine phosphorylation motifs

<p>Abstract</p> <p>Background</p> <p>The presence of various EPIYA tyrosine phosphorylation motifs in the CagA protein of <it>Helicobacter pylori </it>has been suggested to contribute to pathogenesis in adults. In this study, a unique PCR assay and sequencing strategy was developed to establish the number and variation of <it>cagA </it>EPIYA motifs.</p> <p>Findings</p> <p>MDA-DNA derived from gastric biopsy specimens from eleven subjects with gastritis was used with M13- and T7-sequence-tagged primers for amplification of the <it>cagA </it>EPIYA motif region. Automated capillary electrophoresis using a high resolution kit and amplicon sequencing confirmed variations in the <it>cagA </it>EPIYA motif region. In nine cases, sequencing revealed the presence of AB, ABC, or ABCC (Western type) <it>cagA </it>EPIYA motif, respectively. In two cases, double <it>cagA </it>EPIYA motifs were detected (ABC/ABCC or ABC/AB), indicating the presence of two <it>H. pylori </it>strains in the same biopsy.</p> <p>Conclusion</p> <p>Automated capillary electrophoresis and Amplicon sequencing using a single, M13- and T7-sequence-tagged primer pair in PCR amplification enabled a rapid molecular typing of <it>cagA </it>EPIYA motifs. Moreover, the techniques described allowed for a rapid detection of mixed <it>H. pylori </it>strains present in the same biopsy specimen.</p

Helicobacter pylori (H pylori) infection in Greece: the changing prevalence during a ten-year period and its antigenic profile

BACKGROUND: To evaluate changes in H pylori infection prevalence in Greece during a ten-year period, and to examine its antigenic profile. METHODS: Three groups of patients were studied. Group O-87: Banked serum samples of 200 consecutive adult outpatients, from the Hepato-Gastroenterology clinic of a teaching hospital at Athens, collected in 1987. Group O-97: Serum samples of 201 similarly selected outpatients from the same Unit, collected in 1997. Group BD-97: Serum samples of 120 consecutive blood donors from the same hospital, collected in 1997. H pylori IgG antibody seroprevalence was studied by a quantitative ELISA. Antigenic profile was studied by western-blot IgG assay, in 62 IgG positive patients of O-97 and BD-97. Results were analyzed by conventional statistics and multivariate regression analysis. RESULTS: The H pylori seroprevalence increased with age in the three tested groups. In O-97, seroprevalence did not differ from that, in BD-97. On the contrary, there was a significant decrease in seropositivity between O-87 and O-97 (59.5% vs 49.2%, p = 0.039). Multiple regression analysis showed that age over 35 years (OR:3.45, 95% CI:1.59–7.49, p = 0.002) and year of patients' selection – that is 1987 or 1997 – (OR:1.73, 95% CI:1.14–2.65 for 1987, p = 0.010), were independent risk factors of H pylori infection. The seroprevalence of CagA+ and VacA+ strains was 77.4% and 58.5%, respectively, and type I(CagA+/VacA+) strains were significantly more common than type II(CagA-/VacA-) strains (59.7% vs 22.6%, p < 0.001). CONCLUSIONS: During a ten-year period, we found a significant decrease of H pylori infection in Greece and our data support the birth cohort phenomenon as an explanation for the age-dependent increase of H pylori infection. The prevalence of CagA and/or VacA positive strains is relatively high, in a country with low incidence of gastric cancer

Phylogenetic analysis, based on EPIYA repeats in the cagA gene of Indian Helicobacter pylori, and the implications of sequence variation in tyrosine phosphorylation motifs on determining the clinical outcome

The population of India harbors one of the world’s most highly diverse gene pools, owing to the influx of successive waves of immigrants over regular periods in time. Several phylogenetic studies involving mitochondrial DNA and Y chromosomal variation have demonstrated Europeans to have been the first settlers in India. Nevertheless, certain controversy exists, due to the support given to the thesis that colonization was by the Austro-Asiatic group, prior to the Europeans. Thus, the aim was to investigate pre-historic colonization of India by anatomically modern humans, using conserved stretches of five amino acid (EPIYA) sequences in the cagA gene of Helicobacter pylori. Simultaneously, the existence of a pathogenic relationship of tyrosine phosphorylation motifs (TPMs), in 32 H. pylori strains isolated from subjects with several forms of gastric diseases, was also explored. High resolution sequence analysis of the above described genes was performed. The nucleotide sequences obtained were translated into amino acids using MEGA (version 4.0) software for EPIYA. An MJ-Network was constructed for obtaining TPM haplotypes by using NETWORK (version 4.5) software. The findings of the study suggest that Indian H. pylori strains share a common ancestry with Europeans. No specific association of haplotypes with the outcome of disease was revealed through additional network analysis of TPMs