196,058 research outputs found
Environmental proteomics: A long march in the pedosphere
No full textEnvironmental proteomics, the study of the expression profile of proteins extracted directly from living organisms and some stabilized extracellular proteins present in environmental samples, is a developing branch of soil science since the seminal papers appeared twenty years ago. Soil microbial communities hold the key to understanding terrestrial biodiversity; they are extremely complex and their physiological responses to dynamic environmental parameters are under-characterized. Therefore, the slow development of environment-related proteomic databases, and the high chemical reactivity of environmental matrices hamper the extraction, quantification, and characterization of proteins; and soil proteomics remains still in its infancy. We underscore the main achievements of environmental proteomics focusing on soil ecosystems, and we identify technical gaps that need to be bridged in the context of relevant ecological concepts that have received little attention in the development of proteomics methods. This analysis offers a new framework of research of soil proteomics toward improved understanding of the causal linkages between the structure and function of the soil microbiome, and a broader grasp of the sensitivity of terrestrial ecosystems to environmental change
Proteomic analysis of Cupriavidus metallidurans CH34 as a model for soil bacteria under viable but non culturable status
No full textOffgel proteomics of Cupriavidus metallidurans CH34 in artificial soil under viable but not culturable state
No full textOffgel proteomics of Cupriavidus metallidurans CH34 in artificial soil under viable but not culturable state
Bacterial culturability and the viable but non-culturable (VBNC) state studied by a proteomic approach using an artificial soil
No full textGram-negative bacteria in soil rapidly adapt to various stresses, including nutrient limitation and desiccation, by
adopting the viable but non-culturable (VBNC) state as a survival strategy. Due to the physico-chemical and
microbiological complexity of soils, little is understood on the effects of nutrient availability and moisture level
on the transition from the VBNC state to culturability in soil. We evaluated the effects of gluconate or water on
the transition of the soil borne bacterium C. metallidurans strain CH34 from the VBNC state to culturability by
experiments of inoculation into artificial soils and bacterial metaproteomic analysis. Incubation without water or
nutrients reduced the bacterial culturability to zero in 12 d, and addition of both water or gluconate restored the
bacterial culturability to high levels within 24 h. The proteomic analysis showed that under water and nutrient
limitation, proteins related to the cell shape and protein synthesis were rapidly down-regulated and stressrelated
proteins were quickly up-regulated during the transition from culturability to VBNC state. Reversion
from the VBNC state to a culturable state with water or gluconate led to highly different bacterial proteomic
profiles of C. metallidurans. Gluconate availability restored main protein biosynthesis and energy metabolic
pathways, whereas water addition led to up-regulation of only six proteins, one of which degrade sigma factors
involved in expression of genes controlling bacterial resistance under nutrient limitation. Proteins regulated
during the transition between culturable and VBNC states could also be involved in the phenotypic VBNC for
other soil bacteria, and can highlight some of the microbial genetic mechanisms allowing the entering and
exiting from the VBNC state. Implications of the VBNC in microbial diversity and soil functionality are discussed
Gaming as a Key Approach for the Recovery Process of a Public Space: The Case Study of the Old Chemical Plant ‘Chimica Arenella’ in Palermo
No full textThis poster describes the FORGE (FactOry of uRban GamEs) project, a proposal that our research group launched in partnership with the Municipality of Palermo (Italy) and other local stakeholders in 2019.
FORGE will be hosted in what was previously a chemical plant (the former ‘Chimica Arenella’) and is an open factory designed to collect needs and to generate interventions for urban Innovation. The four key terms we have used for the project are urban, game, factory and participation. In fact, FORGE employs a participatory methodological model based on the concept of game, aimed at supporting social and economic development through a platform for participatory codesign. FORGE also plays a key role in fostering social inclusion, becoming a ‘participation hub’ and an urban center for the whole city
Celiac disease in pediatric patients according to HLA genetic risk classes: a retrospective observational study
No full textBackground: Celiac disease (CD) is an autoimmune enteropathy in which HLA-DQ haplotypes define susceptibility. Our aim was to evaluate if belonging to a certain HLA-DQ class risk could be associated to the clinical, serological and histological presentation of CD. Methods: We performed a retrospective observational monocentric study including all 300 patients diagnosed with CD, who underwent HLA typing. Clinical, serological and histological data was collected from clinical records and their association with HLA-DQ class risk was verified through statistical tests. Results: In our sample mean age at onset was 6.7 ± 4.2 years, with a prevalence of females (n = 183; 61%), typical symptoms (n = 242; 80.6%) and anti-tTG IgA ≥ 100 U/mL (n = 194; 64.7%). Family history was present only in 19% (n = 57) of patients, and it was not significantly associated with any of the clinical and demographical data analyzed or the belonging to a certain HLA-DQ class risk. We found in the male population more frequently a coexistence of CD and atopic syndrome (males: n = 47; 40.2%; females: n = 50; 27.3%; p = 0.020). Early age of onset, instead, was associated with typical symptoms (m = 6.4 ± 4; p = 0.045) and elevated liver enzymes (m = 5 ± 3.8; p < 0.001), while later age of onset was associated with presence of other autoimmune diseases (m = 8.2 ± 4; p = 0.01). We observed statistically significant influences of HLA class risk on antibodies and liver enzymes levels: G1, G4 and G2 classes showed more frequently anti-tTG IgA ≥ 100 U/mL (n = 44; 80%, n = 16; 69.6%, n = 48; 67.6% respectively; p-value = 0.037), and in patients from G2 class we found enhanced liver enzymes (n = 28; 39.4%; p-value = 0.005). HLA class risk was still significantly associated with anti-tTG ≥ 100 (p = 0.044) and with hypertransaminasemia (p = 0.010) after a multiple logistic regression adjusted for the effect of gender, age at onset and family history. Conclusions: We failed to prove an association between HLA-DQ genotypes and the clinical features in our CD pediatric patients. Although, our results suggest an effect of the DQB1–02 allele not only on the level of antibodies to tTG, but possibly also on liver involvement
Utilisation of chemically stabilized arsenic-contaminated soil in a landfill cover
No full textThe aim of the study was to determine if an As-contaminated soil, stabilized using zerovalent iron (Fe0) and its combination with gypsum waste, coal fly ash, peat, or sewage sludge, could be used as a construction material at the top layer of the landfill cover. A reproduction of 2 m thick protection/vegetation layer of a landfill cover using a column setup was used to determine the ability of the amendments to reduce As solubility and stimulate soil functionality along the soil profile. Soil amendment with Fe0 was highly efficient in reducing As in soil porewater reaching 99 % reduction, but only at the soil surface. In the deeper soil layers (below 0.5 m), the Fe treatment had a reverse effect, As solubility increased dramatically exceeding that of the untreated soil or any other treatment by one to two orders of magnitude. A slight bioluminescence inhibition of Vibrio fischeri was detected in the Fe0 treatment. Soil amendment with iron and peat showed no toxicity to bacteria and was the most efficient in reducing dissolved As in soil porewater throughout the 2 m soil profile followed by iron and gypsum treatment, most likely resulting from a low soil density and a good air diffusion to the soil. The least suitable combination of soil amendments for As immobilization was a mixture of iron with coal fly ash. An increase in all measured enzyme activities was observed in all treatments, particularly those receiving organic matter. For As to be stable in soil, a combination of amendments that can keep the soil porous and ensure the air diffusion through the entire soil layer of the landfill cover is required
Microbial community structure and proteolytic activity in the rhizosphere of maize plants differing in nitrogen use efficiency
No full textThe rhizosphere, the thin soil layer influenced by the presence of plant roots has different physico-chemical properties from the bulk soil because of the active or passive rhizodepositions, which sustain larger and more active microbial populations in the rhizosphere than in bulk soil, and this plays a key role in soil organic matter decomposition and nutrient solubilization. The rhizosphere is chemically complex and dynamic microenvironment and this makes it difficult to study. Progresses in the study of the rhizosphere can be achieved by using rhizoboxes allowing the plant growth and precise sampling of rhizosphere. Plants select microbial bacterial and fungal populations in the rhizosphere during the plant growth, and while plant mechanisms involved in increased N uptake efficiency have been clarified, the importance of the rhizosphere microbial communities in nutrient availability to plants are still poorly understood.
Nitrogen is the main nutrient limiting the plant growth and the crop yields and today, the nitrogen use efficiency (NUE) of crops at field scale is still relatively low, with detrimental effects on groundwater quality and atmosphere due to NO3- leaching and NH3 and nitrous oxide emissions caused be excessive fertilization, and large efforts have been carried out to increase the NUE to enhance the crop production and reduce the environmental impact of agriculture, especially through plant breeding and preparation of fertilizers with slow N release.
We evaluated the changes in the biochemical activity and microbial community structure induced by the inbred maize (Zea mais L.) lines Lo5 and T250 characterized by high and low NUE using rhizobox experiments. The adopted experimental approach allowed to describe the relative plant induced changes on the different rhizosphere chemical and microbiological components and provide information to improve the crop NUE. In this work we studied the changes in the biochemical activity and microbial community structure in the rhizosphere of the inbred maize (Zea mais L.) lines Lo5 and T250 characterized by high and low NUE, repectively, using rhizobox experiments. Because of the importance of the proteolytic activity in soil N mineralization, the proteolytic activity in the rhizosphere of the two maize lines was also studied by the assessment of the diversity and abundance of the apr and npr genes coding for coding for alkaline protease and neutral metalloprotease, respectively, and determination of the protease activity.
The results showed that the Lo5 plant, having the higher NUE, induced the greater modification in the rhizosphere chemical properties, induced significantly faster depletion of inorganic N, higher bacteria diversity, proteolytic populations and protease activity. The importance of the plant activity in modifying microbial community structure, protease functions and rhizosphere biochemical activity will be presented
Availability of different nitrogen forms changes the microbial communities and enzyme activities in the rhizosphere of maize lines with different nitrogen use efficiency
No full textWe studied how the Lo5 and T250 maize lines, characterized by high and low nitrogen use efficiency (NUE), respectively, modified the microbial biomass, enzymatic activities and microbial community structure in the rhizosphere after exposure to different N forms. The two maize lines were grown for 4 weeks in rhizoboxes allowing precise sampling of rhizosphere and bulk soil with no nutrient additions, and then exposed to with nitric-, ammonium- and urea-N. After N exposure, the plants were inserted back into their original rhizoboxes to allow the root exudates diffusion into the rhizosphere. After 24 h rhizosphere soil were sampled and analyzed. Microbial biomass and soil enzymatic activities were increased after the exposure to different N forms of both maize lines. The plant exposure to different N forms also induced changes in the rhizosphere bacterial and fungal communities composition. Plant responses to the availability of different N forms was a dominant factor regulating activity and composition of the rhizosphere microbial communities, likely due to changes in the rhizodepositions. Therefore different N forms used for fertilization of agriculturally relevant plants such as maize can result in different plant mediated effects on the microbial activity and community structure in the rhizosphere
Contact with soil-borne humic substances interfere with the prion identification by mass spectrometry
No full textWe studied the effects of humic substances (HS) extracted from soil on the identification of the recombinant ovine prion protein (RecPrP) by denaturing (sodium dodecyl sulfate polyacrylamide gel electrophoresis [SDS-PAGE]) and native PAGE (N-PAGE), and mass spectrometry (MS), at various HS to RecPrP contact ratios. The results showed that the contact with HS did not alter RecPrP electrophoretic mobility but affected protein identification by MS. Contact between RecPrP and HS resulted in a lower coverage percentage of specific RecPrP domains that led to a prion misidentification, more evident after N-PAGE than SDS-PAGE. The analysis of the nonidentified protein domains suggests that lower quality of RecPrP identification could be due to hydrophobic interactions between the prion protein and HS, but the mechanism by which HS hamper the correct identification of RecPrP remains to be established. Our results may have implications in the prion environmental risk assessment
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