Bioaccumulation modelling and sensitivity analysis for discovering key players in contaminated food webs: the case study of PCBs in the Adriatic Sea

Modelling bioaccumulation processes at the food web level is the main step to analyse the effects of pollutants at the global ecosystem level. A crucial question is understanding which species play a key role in the trophic transfer of contaminants to disclose the contribution of feeding linkages and the importance of trophic dependencies in bioaccumulation dynamics. In this work we present a computational framework to model the bioaccumulation of organic chemicals in aquatic food webs, and to discover key species in polluted ecosystems. As a result, we reconstruct the first PCBs bioaccumulation model of the Adriatic food web, estimated after an extensive review of published concentration data. We define a novel index aimed to identify the key species in contaminated networks, Sensitivity Centrality, and based on sensitivity analysis. The index is computed from a dynamic ODE model parametrised from the estimated PCBs bioaccumulation model and compared with a set of established trophic indices of centrality. Results evidence the occurrence of PCBs biomagnification in the Adriatic food web, and highlight the dependence of bioaccumulation on trophic dynamics and external factors like fishing activity. We demonstrate the effectiveness of the introduced Sensitivity Centrality in identifying the set of species with the highest impact on the total contaminant flows and on the efficiency of contaminant transport within the food web

Circulating tumour cells: insights into tumour heterogeneity

Tumour heterogeneity is a major barrier to cure breast cancer. It can exist between patients with different intrinsic subtypes of breast cancer or within an individual patient with breast cancer. In the latter case, heterogeneity has been observed between different metastatic sites, between metastatic sites and the original primary tumour, and even within a single tumour at either a metastatic or a primary site. Tumour heterogeneity is a function of two separate, although linked, processes. First, genetic instability is a hallmark of malignancy, and results in ‘fixed’ genetic changes that are almost certainly carried forward through progression of the cancer over time, with increasingly complex additional genetic changes in new metastases as they arise. The second type of heterogeneity is due to differential but ‘plastic’ expression of various genes important in the biology and response to various therapies. Together, these processes result in highly variable cancers with differential response, and resistance, to both targeted (e.g. endocrine or anti‐human epithelial growth receptor type 2 ( HER 2) agents) and nontargeted therapies (e.g. chemotherapy). Ideally, tumour heterogeneity would be monitored over time, especially in relation to therapeutic strategies. However, biopsies of metastases require invasive and costly procedures, and biopsies of multiple metastases, or serially over time, are impractical. Circulating tumour cells ( CTC s) represent a potential surrogate for tissue‐based cancer and therefore might provide the opportunity to monitor serial changes in tumour biology. Recent advances have enabled accurate and reliable quantification and molecular characterization of CTC s with regard to a number of important biomarkers including oestrogen receptor alpha and HER 2. Preliminary data have demonstrated that expression of these markers between CTC s in individual patients with metastatic breast cancer reflects the heterogeneity of the underlying tumours. Future studies are designed to determine the clinical utility of these novel technologies in either research or routine clinical settings.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/99056/1/joim12047.pd

No more time to stay ‘single’ in the detection of Anisakis pegreffii, A. simplex (s. s.) and hybridization events between them: a multi-marker nuclear genotyping approach

A multi-marker nuclear genotyping approach was performed on larval and adult specimens of Anisakis spp. (N = 689) collected from fish and cetaceans in allopatric and sympatric areas of the two species Anisakis pegreffii and Anisakis simplex (s. s.), in order to: (1) identify specimens belonging to the parental taxa by using nuclear markers (allozymes loci) and sequence analysis of a new diagnostic nuclear DNA locus (i.e. partial sequence of the EF1 α−1 nDNA region) and (2) recognize hybrid categories. According to the Bayesian clustering algorithms, based on those markers, most of the individuals (N = 678) were identified as the parental species [i.e. A. pegreffii or A. simplex (s. s.)], whereas a smaller portion (N = 11) were recognized as F1 hybrids. Discordant results were obtained when using the polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLPs) of the internal transcribed spacer (ITS) ribosomal DNA (rDNA) on the same specimens, which indicated the occurrence of a large number of ‘hybrids’ both in sympatry and allopatry. These findings raise the question of possible misidentification of specimens belonging to the two parental Anisakis and their hybrid categories derived from the application of that single marker (i.e. PCR–RFLPs analysis of the ITS of rDNA). Finally, Bayesian clustering, using allozymes and EF1 α−1 nDNA markers, has demonstrated that hybridization between A. pegreffii and A. simplex (s. s.) is a contemporary phenomenon in sympatric areas, while no introgressive hybridization takes place between the two species

Identification of the het-r vegetative incompatibility gene of Podospora anserina as a member of the fast evolving HNWD gene family

In fungi, vegetative incompatibility is a conspecific non-self recognition mechanism that restricts formation of viable heterokaryons when incompatible alleles of specific het loci interact. In Podospora anserina, three non-allelic incompatibility systems have been genetically defined involving interactions between het-c and het-d, het-c and het-e, het-r and het-v. het-d and het-e are paralogues belonging to the HNWD gene family that encode proteins of the STAND class. HET-D and HET-E proteins comprise an N-terminal HET effector domain, a central GTP binding site and a C-terminal WD repeat domain constituted of tandem repeats of highly conserved WD40 repeat units that define the specificity of alleles during incompatibility. The WD40 repeat units of the members of this HNWD family are undergoing concerted evolution. By combining genetic analysis and gain of function experiments, we demonstrate that an additional member of this family, HNWD2, corresponds to the het-r non-allelic incompatibility gene. As for het-d and het-e, allele specificity at the het-r locus is determined by the WD repeat domain. Natural isolates show allelic variation for het-

Infection levels and species diversity of ascaridoid nematodes in Atlantic cod, Gadus morhua, are correlated with geographic area and fish size

Atlantic cod (Gadus morhua) is among the most important commercial fish species on the world market. Its infection by ascaridoid nematodes has long been known, Pseudoterranova even being named cod worm. In the present study, 755 individuals were sampled in the Barents, Baltic and North Seas during 2012–2014. Prevalences for Anisakis in whole fish and in fillets in the different fishing areas varied from 16 to 100% and from 12 to 90% respectively. Abundance was also greatly influenced by the sampling area. Generalized additive model results indicate higher numbers of Anisakis in the North Sea, even after the larger body size was accounted for. Numbers and prevalence of Anisakis were positively related to fish length or weight. The prevalence of parasites in whole fish and in fillets was also influenced by the season, with the spring displaying a peak for the prevalence in whole fish and, at the same time, a drop for the prevalence in fillets. Whereas 46% of cod had Anisakis larvae in their fillets, the majority (39%) had parasites mainly in the ventral part of the fillet and only 12% had parasites in their dorsal part. This observation is of importance for the processing of the fish. Indeed, the trimming of the ventral part of the cod fillet would allow the almost total elimination of ascaridoids except for cod from the Baltic Sea where there was no difference between the dorsal and the ventral part. The presence of other ascaridoid genera was also noticeable in some areas. For Pseudoterranova, the highest prevalence (45%) in whole fish was observed in the Northern North Sea, whereas the other areas had prevalences between 3 and 16%. Contracaecum was present in every commercial size cod sampled in the Baltic Sea with an intensity of up to 96 worms but no Contracaecum was isolated from the Central North Sea. Non-zoonotic Hysterothylacium was absent from the Baltic Sea but with a prevalence of 83% in the Barents and the Northern North Sea. A subsample of worms was identified with genetic-molecular tools and assigned to the species A. simplex (s.s.), A. pegreffii, P. decipiens (s.s.), P. krabbei, C. osculatum and H. aduncum. In addition to high prevalence and abundance values, the cod sampled in this study presented a diversity of ascaridoid nematodes with a majority of fish displaying a co-infection. Out of 295 whole infected fish, 269 were co-infected by at least 2 genera

SiPM and front-end electronics development for Cherenkov light detection

The Italian Institute of Nuclear Physics (INFN) is involved in the development of a demonstrator for a SiPM-based camera for the Cherenkov Telescope Array (CTA) experiment, with a pixel size of 6$\times$6 mm$^2$. The camera houses about two thousands electronics channels and is both light and compact. In this framework, a R&D program for the development of SiPMs suitable for Cherenkov light detection (so called NUV SiPMs) is ongoing. Different photosensors have been produced at Fondazione Bruno Kessler (FBK), with different micro-cell dimensions and fill factors, in different geometrical arrangements. At the same time, INFN is developing front-end electronics based on the waveform sampling technique optimized for the new NUV SiPM. Measurements on 1$\times$1 mm$^2$, 3$\times$3 mm$^2$, and 6$\times$6 mm$^2$ NUV SiPMs coupled to the front-end electronics are presentedComment: In Proceedings of the 34th International Cosmic Ray Conference (ICRC2015), The Hague, The Netherlands. All CTA contributions at arXiv:1508.0589

Measurements and tests on FBK silicon sensors with an optimized electronic design for a CTA camera

In October 2013, the Italian Ministry approved the funding of a Research & Development (R&D) study, within the "Progetto Premiale TElescopi CHErenkov made in Italy (TECHE)", devoted to the development of a demonstrator for a camera for the Cherenkov Telescope Array (CTA) consortium. The demonstrator consists of a sensor plane based on the Silicon Photomultiplier (SiPM) technology and on an electronics designed for signal sampling. Preliminary tests on a matrix of sensors produced by the Fondazione Bruno Kessler (FBK-Trento, Italy) and on electronic prototypes produced by SITAEL S.p.A. will be presented. In particular, we used different designs of the electronics in order to optimize the output signals in terms of tail cancellation. This is crucial for applications where a high background is expected, as for the CTA experiment.Comment: 5 pages, 6 figures; Proceedings of the 10th Workshop on Science with the New Generation of High-Energy Gamma-ray experiments (SciNeGHE) - PoS(Scineghe2014)00

An identification procedure for woolly soft-flesh peaches by instrumental assessment

Woolliness in peaches, a negative attribute of sensory texture characterized by the lack of crispness and juiciness, also known as mealiness in other fruits, has been identified fruit-by fruit by instrumental means. The use of a non-supervised clustering data analysis procedure, studying crispness and juiciness, enables four instrumental degrees of texture degradation to be defined, of which woolliness appears to be the last stage. This procedure also provides some information on several experimental factors (ripeness stages, storage time and storage temperature) with regard to the onset of woolliness. It is confirmed through this study that, in Maycrest peaches, woolliness starts to appear after 2 weeks of storage at 5°C. Fruits classified at harvest in 'first' and 'second' ripeness stages are more susceptible to woolliness than those in the third ripeness stage. This clustering procedure may also be effective for studying other species, varieties and quality attributes of fruit

Primordial magnetic fields and the HI signal from the epoch of reionization

The implication of primordial magnetic-field-induced structure formation for the HI signal from the epoch of reionization is studied. Using semi-analytic models, we compute both the density and ionization inhomogeneities in this scenario. We show that: (a) The global HI signal can only be seen in emission, unlike in the standard $\Lambda$CDM models, (b) the density perturbations induced by primordial fields, leave distinctive signatures of the magnetic field Jeans' length on the HI two-point correlation function, (c) the length scale of ionization inhomogeneities is \la 1 \rm Mpc. We find that the peak expected signal (two-point correlation function) is $\simeq 10^{-4} \rm K^2$ in the range of scales $0.5\hbox{-}3 \rm Mpc$ for magnetic field strength in the range $5 \times 10^{-10} \hbox{-}3 \times 10^{-9} \rm G$. We also discuss the detectability of the HI signal. The angular resolution of the on-going and planned radio interferometers allows one to probe only the largest magnetic field strengths that we consider. They have the sensitivity to detect the magnetic field-induced features. We show that thefuture SKA has both the angular resolution and the sensitivity to detect the magnetic field-induced signal in the entire range of magnetic field values we consider, in an integration time of one week.Comment: 19 pages, 5 figures, to appear in JCA