Mosses for monitoring air pollution: towards the standardization of moss-bag technique and the set-up of a new biomaterial

The monitoring of the air quality by mosses provides qualitative and quantitative data using economic, easy-to-manage and eco-friendly methods. Due to peculiar morphological and physiological characteristics, mosses are very suitable adsorbents for a wide variety of pollutants (i.e. metals and metalloids, PAHs, radionuclides) and, when used as transplants in nylon bags, they allow an easy monitoring potentially of any site, with a highly dense sampling network. Nevertheless, the moss-bag technique, although widely applied, is still not based on standardized protocols. It follows that the data collected from biomonitoring surveys are not comparable, thus relegating the active biomonitoring exclusively to academic field or to scientific purposes. Moreover, there are not enough studies comparing bioaccumulation data with those obtained by estimation models or traditional monitoring approaches, neither it is clear how the moss-bag technique can discriminate pollution inputs on a very small scale and within areas relatively close to each other or characterized by different land uses. Another important issue is that the mosses employed as biomonitors are naturally grown species. The collection in nature implies an intrinsic variability of mosses in terms of elemental and chemical composition and, as a consequence, it poses a high degree of uncertainty in the interpretation of the results. Moreover, an uncontrolled harvesting of mosses could lead to a severe environmental impact. In this context, aims of this Doctoral Thesis are: 1) to test the variables affecting the exposure protocol in the view of a standard moss-bag method for the biomonitoring of air pollution; 2) to integrate biomonitoring results with emission data provided by inventories for the evaluation of the atmospheric pollution; 3) to characterize a novel moss biomaterial for biomonitoring purposes. For the standardization assay, more than one thousand moss bags were exposed contemporary in three European territories (Austria, Italy, Spain) belonging to three different climatic areas (Mediterranean, continental and oceanic). For each area, four distinct scenarios (background, urban, agricultural, industrial) were selected for the exposure, on the basis of their level and type of contamination. The moss included in bags was the Pseudoscleropodium purum (Hedw.) M. Fleisch, collected in a pristine area of the Galicia (NE Spain). Shoot apical parts were selected, EDTA-washed and finally devitalized by oven drying at 100 °C. For the first time, all the variables affecting the air pollutant uptake by moss exposed in bags were considered: 1) the moss bags characteristics (round, spherical and flat shapes; nylon net mesh size of 1, 2 and 4 mm; moss amount and moss weight/bag surface area ratio of 15, 30, 45 mg cm-2); 2) the exposure criteria (exposure time of 3, 6, 12 weeks; exposure heights of 4, 7, 10 m above ground); 3) the climatic conditions of the exposure area. The concentrations of metals and metalloids were determined by ICP mass spectrometry and the results were evaluated comparing pre- and post-exposure moss samples. Results showed that the amount of moss included in bags was the most important factor affecting the pollutant accumulation by mosses: the more the moss density inside bags increases, the less metal uptake occurs. The other variables (climate, bag size and shape, exposure time and height) had low or no influence at all. As consequence of the obtained results, the project Mossclone proposed the use of a standard moss bag, spherical-shaped, with a mesh size of 2 mm and filled with a moss amount less than 15 mg per cm2 of bag surface area. In addition, it was suggested to expose the moss-bags for not less than six weeks (to increase the detectability of metal concentrations in moss) and, for practical reasons, at 4 m above the ground. The proposed standardized protocol for moss-bag exposure was then tested in a biomonitoring campaign carried out in the framework of the LIFE-Ecoremed project, in order to assess the air quality of five municipalities belonging to the Italian RIPS “Litorale Domizio-Agro Aversano” (Campania Region, south Italy). In each municipality, two scenarios (urban and agricultural) and two sub-scenarios (a street side and a corresponding green area) were selected, in order to evaluate the anthropogenic pollution, with a particular attention to the vehicular traffic impact on the surrounding areas. The concentrations of twenty PAHs and of thirty-nine elements including rare earths were determined by ICP mass spectrometry in pre- and post-exposure samples of Hypnum cupressiforme Hedw. moss, treated and exposed following the standardized method. After exposure, the concentration of most of the elements and PAHs (in particular the 4- and 5-ringed PAHs) was significantly increased in moss material. The pollutants had a similar spatial distribution pattern over the entire study area, with road traffic and agricultural practices as the major diffuse pollution sources. Hypnum cupressiforme moss bags was able to detect airborne element and PAH inputs and to discriminate different pollution levels in a landscape characterized by a jeopardized structure in which agricultural and urban/residential sites are strictly mixed together. The data obtained in the Italian biomonitoring campaign were combined with those provided by emission inventories, which are a collection of estimations, recorded with spatial disaggregation, on the type, amount and emission sources of pollutants. As a result, it was observed that both approaches (biomonitoring and emission inventory) indicated the same most polluted municipality and a similar spatial pattern, in particular for lead. This suggests that the joint use of emission inventory and moss accumulation could be a valuable resource to reveal contaminants better than the use of a single approach, allowing a more deep investigation on the pollutant emission sources, especially for those contaminants not routinely monitored. To overcome the limits of the use of native mosses, the last part of the PhD thesis is focused on the characterization of a new moss biomaterial, provided by the cloning inside bioreactors. The cloned moss specie in question is the Sphagnum palustre L., whose elemental composition (pre- and post- treatments with EDTA and by devitalization) and molecular profile were given, in comparison with the conspecific field moss, in order to outline a defined fingerprint of the new biomaterial. The morphological and physico-chemical properties of the moss adsorbing surfaces were also examined by electron microscopy, in vitro experiments on metal adsorption and by the chemical analysis of the surface exchange sites. A field exposure test with moss-bags was performed, comparing the clone and the naturally grown P. purum. The clones exhibited a much lower metal concentration (from 10 to 100 times) in their tissues than the native samples, thus making the former better indicators of low metal loading. New DNA markers, also useful for systematic analyses of the Sphagnum genus, were provided in order to characterize and label the clone. The S. palustre clone exhibited acid base properties similar to those of naturally grown Sphagnum samples and showed a significantly higher metal uptake performance. Therefore, the use of this biomaterial, with very homogenous morphological and chemical characteristics and a remarkable metal uptake capability, is strongly recommended in the view of a rigorously standardized moss-bag protocol for the active monitoring of persistent atmospheric pollutants

Joint Biplots for CoDa

Compositional data (CoDa) consist of vectors of positive values summing to a unit, or in general, to some fixed constant for all vectors. They appear as proportions, percentages, concentrations, absolute and relative frequencies. Sometimes, compositions arise from non-negative data (such as counts, area, weights, volume) that have been scaled by the total of the components because the analyst is not interested in the total sum of the vector. The multidimensional analysis of this kind of data requires a careful consideration because the sample space for CoDa is the simplex. The first consistent methodological proposal to deal with CoDa was proposed by Aitchison (1986) when he introduced the log-ratio approach. Basically, the idea that this approach conveys is to move from the simplex space to the real space by using log.ratio transformations, applying standard statistical methods, and finally, by means of an inverse log-ratio transformation, to interpret the results in the simplex space. Starting from this paper, pairwise, centered, additive and isometric log-ratio transformations, in short plr, clr, alr (Aitchison, 1986) and ilr respectively, are proposed in literature (Egozucue et al., 2003). In the context of dimension-reducing techniques, Aitchison (1983) proposed applying principal component analysis (PCA) after having applied a centered log-ratio (clr) transformation to CoDa. Aitchison and Greenacre (2002) suggested an adaptation of the biplot to CoDa. The biplot is a well established graphical aid in other branches of statistical analysis and can prove to be a useful exploratory and expository tool for compositions. In literature many papers on dimensional-reduction techniques for CoDa are proposed. Based on log-ratio strategy, Gallo (2012a, 2012b, 2013) recently proposed to use three-mode analysis of compositional data.\ud Starting from Gallo (2012b), we propose using of plr and clr joint biplots. Where in some cases the plr joint biplot is the only ones that show clearly the correlations

A Robust Tucker3 Model for Compositional Data

Double counting is inherent to the output concept, therefore it is preferable to use manufacturing value added (MVA) instead to measure the manufacturing production. While the issue of double counting in production statistics is successfully addressed by using MVA, commodity exchange in trade data is still measured as output. The relevance of value added has increased in the recent years due to the unbundling of the production process, where different stages of value chain take place in different countries. We want to represent the export statistics through value added to output ratio using data from international statistical databases. The data sets considered are organized by country, commodity or activity and year (activities are classified according to the International Standard Industrial Classification of all economic activities (ISIC)) and thus they are three-way compositional data.\ud Different methods exist for analysis of multi-way data and we choose Tucker3 because it provides a compromise between parsimonious and flexible models. The Tucker3 method as most of the N-way methods is based on alternating least squares (ALS) which makes it vulnerable to the presence of outliers in the data. Even a single outliying data point can\ud strongly influence the resulting model and the conclusions based on it. A robust version of Tucker3 was presented by Pravdova et al. (2001) but it suffers from two main deficiencies. First of all the robust initialization of the algorithm is based on MCD which will not work in high dimensions. And secondly, the method is not suitable for applying on compositional data. We propose to select the initial subset using robust PCA and to transform the compositional data applying ilr transformation (Egozcue et al., 2003). Furthermore, since to our knowledge there is no readily available software for computing robust Tucker3 models, we provide\ud implementation of the proposed algorithm in R. The method is compared to its competitors both in terms of its efficiency and the computational effort needed

The Paired Domain-containing Factor Pax8 and the Homeodomain-containing Factor TTF-1 Directly Interact and Synergistically Activate Transcription

Pax genes encode for transcription factors essential for tissue development in many species. Pax8, the only member of the family expressed in the thyroid tissue, is involved in the morphogenesis of the gland and in the transcriptional regulation of thyroid-specific genes. TTF-1, a homeodomain-containing factor, is also expressed in the thyroid tissue and has been demonstrated to play a role in thyroid-specific gene expression. Despite the presence of Pax8 and TTF-1 also in a few other tissues, the simultaneous expression of the two transcription factors occurs only in the thyroid, supporting the idea that Pax8 and TTF-1 might cooperate to influence thyroid-specific gene expression. In this report, we describe a physical and functional interaction between these two factors. The fusion protein GST-Pax8 is able to bind TTF-1 present in thyroid or in non-thyroid cell extracts, and by using bacterial purified TTF-1 we demonstrate that the interaction is direct. By co-immunoprecipitation, we also show that the interaction between the two proteins occurs in vivo in thyroid cells. Moreover, Pax8 and TTF-1 when co-expressed in HeLa cells synergistically activate Tg gene transcription. The synergism requires the N-terminal activation domain of TTF-1, and deletions of Pax8 indicate that the C-terminal domain of the protein is involved. Our results demonstrate a functional cooperation and a physical interaction between transcription factors of the homeodomain-containing and of the paired domain-containing gene families in the regulation of tissue-specific gene expression

A Factorized Version Space Algorithm for "Human-In-the-Loop" Data Exploration

International audienceWhile active learning (AL) has been recently applied to help the user explore a large database to retrieve data instances of interest, existing methods often require a large number of instances to be labeled in order to achieve good accuracy. To address this slow convergence problem, our work augments version space-based AL algorithms, which have strong theoretical results on convergence but are very costly to run, with additional insights obtained in the user labeling process. These insights lead to a novel algorithm that factorizes the version space to perform active learning in a set of subspaces. Our work offers theoretical results on optimality and approximation for this algorithm, as well as optimizations for better performance. Evaluation results show that our factorized version space algorithm significantly outperforms other version space algorithms, as well as a recent factorization-aware algorithm, for large database exploration

Very early onset and greater vulnerability in schizophrenia: A clinical and neuroimaging study

Although schizophrenia has been diagnosed in children, this group of disorders has received too little attention in the clinical and research literature. Preliminary data suggest that early onset schizophrenia (EOS) and very early onset schizophrenia (VEOS) tend to have a worse outcome than adult onset schizophrenia, and seem to be related to a greater familial vulnerability, due to genetic, psychosocial, and environmental factors. Recently, advanced neuroimaging techniques have revealed structural and functional brain abnormalities in some cerebral areas. This paper reports on a case diagnosed as VEOS, with premorbid year-long psychopathological history. The patient showed atypical proton magnetic resonance spectroscopy findings, and normal brain and spine computer tomography and brain magnetic resonance images

The Italian experience of the national registry of renal biopsies

The Italian experience of the national registry of renal biopsies.BackgroundAlthough several registries collecting data of patients with kidney diseases exist, there are only a few registries which specifically collect data relating to renal biopsy; one such registry is the Italian Registry of Renal Biopsies (IRRB). The aim of this study was to report on the relative frequency of nephropathies according to gender, age at time of biopsy, clinical presentation and renal function, based on the histologic diagnosis during the years 1996 to 2000.MethodsWe evaluated data relating to 14607 renal biopsies, provided by 128 renal units in Italy. Data entry was performed by using the Internet-based database directly (URL http://www.irrb.net). Clinical presentation was defined as urinary abnormalities (UA), nephrotic syndrome (NS), acute nephritic syndrome (ANS). Renal diseases were divided in four major categories: (1) primary glomerulonephritides (GN); (2) secondary GN; (3) tubulointerstitial nephropathies (TIN); and (4) vascular nephropathies (VN).ResultsPrimary GN, TIN, and VN were more frequent in males compared to females while secondary GN was more frequent in females. Diseases whose frequency was higher in males were IgA nephropathy (IgAN), benign nephroangiosclerosis (BNA), and acute tubular necrosis (ATN). A significantly higher frequency of immune-mediated secondary GN, as well as primary GN, including minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and mesangiocapillary GN (MCGN), was shown in females. Primary and secondary GN, TIN, and VN were more frequent in the range 15 to 65 years of age. At the time of biopsy 77% of primary GN and 61% of secondary GN presented with normal renal function. Acute renal failure (ACR) was more present in TIN (52%), while chronic renal failure (CRF) was more frequent in VN (47%).ConclusionWe believe collection of data relating to renal biopsies in a national registry is a useful tool for nephrologists in that it meets one of the current challenges facing the clinical research enterprise. The availability of these data will allow epidemiologic studies in health care to answer the several open questions in both prevention and treatment of renal diseases

The impact of active HIV-1 replication on the physiological age-related decline of immature-transitional B-cells in HIV-1 infected children

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Reversible, High-Affinity Surface Capturing of Proteins Directed by Supramolecular Assembly

The ability to design surfaces with reversible, high-affinity protein binding sites represents a significant step forward in the advancement of analytical methods for diverse biochemical and biomedical applications. Herein, we report a dynamic supramolecular strategy to directly assemble proteins on surfaces based on multivalent host–guest interactions. The host–guest interactions are achieved by one-step nanofabrication of a well-oriented β-cyclodextrin host-derived self-assembled monolayer on gold (β-CD-SAM) that forms specific inclusion complexes with hydrophobic amino acids located on the surface of the protein. Cytochrome c, insulin, α-chymotrypsin, and RNase A are used as model guest proteins. Surface plasmon resonance and static time-of-flight secondary ion mass spectrometry studies demonstrate that all four proteins interact with the β-CD-SAM in a specific manner via the hydrophobic amino acids on the surface of the protein. The β-CD-SAMs bind the proteins with high nanomolar to single-digit micromolar dissociation constants (KD). Importantly, while the proteins can be captured with high affinity, their release from the surface can be achieved under very mild conditions. Our results expose the great advantages of using a supramolecular approach for controlling protein immobilization, in which the strategy described herein provides unprecedented opportunities to create advanced bioanalytic and biosensor technologies