Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity

BACKGROUND The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation. In this work a broad phylogenetic study has been undertaken which, considered in the context of the functional characteristics of some fully characterised CDF transporters, has aimed at identifying molecular determinants of substrate selectivity and at suggesting metal specificity for newly identified CDF transporters. RESULTS Representative CDF members from all three kingdoms of life (Archaea, Eubacteria, Eukaryotes) were retrieved from genomic databases. Protein sequence alignment has allowed detection of a modified signature that can be used to identify new hypothetical CDF members. Phylogenetic reconstruction has classified the majority of CDF family members into three groups, each containing characterised members that share the same specificity towards the principally-transported metal, i.e. Zn, Fe/Zn or Mn. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The function of some conserved amino acids was assessed by site-directed mutagenesis in the poplar Zn2+ transporter PtdMTP1 and compared with similar experiments performed in prokaryotic members. An essential structural role can be assigned to a widely conserved glycine residue, while aspartate and histidine residues, highly conserved in putative transmembrane domains, might be involved in metal transport. The potential role of group-conserved amino acid residues in metal specificity is discussed. CONCLUSION In the present study phylogenetic and functional analyses have allowed the identification of three major substrate-specific CDF groups. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The modified signature sequence proposed in this work can be used to identify new hypothetical CDF members

A match coefficient approach for damage imaging in structural components by ultrasonic synthetic aperture focus

Ultrasonic Synthetic Aperture Focus (SAF) techniques are commonly used to image structural defects. In this paper, a variation of SAF based on ideas borrowed from Matched Field Processing (MFP) is evaluated to reduce artifacts and sidelobes of the resulting images. In particular, instead of considering the full RF ultrasonic waveforms for the SAF time backpropagation, only selected features from the waveforms are utilized to form a “data vector” and a “replica” (expected) vector of MFP. These vectors are adaptive for the pair of transmitter-receiver and the focus point. The image is created as a matched filter between these two vectors. Experimental results are shown for an isotropic and homogenous metallic plate with simulated defects, probed by six piezoelectric patches used as receivers or transmitters

Feeding habits of European hake, Merluccius merluccius (Actinopterygii: Gadiformes: Merlucciidae), from the northeastern Mediterranean Sea

European hake, Merluccius merluccius (Linnaeus, 1758), is an important predator of deep Mediterranean upper shelf slope communities, being a nektobenthic species inhabiting a wide depth range (20–1000 m) throughout the Mediterranean Sea and the northeastern Atlantic region (Carpentieri et al. 2005). It is one of the chief commercial and most heavily exploited species of demersal fishery in all northern Mediterranean countries. Recent time-series studies referring to the western part of the Adriatic Sea have shown catches to be made up mainly of specimens shorter than 20 cm TL, with survey catch rates apparently increasing between 1985 and 1995 and decreasing in the following years both in the northern(Piccinetti and Piccinetti Manfrin 1971, Manfrin et al. 1998) and southern Adriatic Sea (Marano et al. 1998). In 2006, annual hake landings were estimated to be around 76 000 t in the Mediterranean (Anonymous 2008) and around 18 000 t in the Adriatic Sea (Anonymous 2007), with the species being the most abundant in the demersal group of the Adriatic Sea (Ungaro et al. 2001). As a rule, hake feeds predominantly on fish and crustaceans, and the proportion of piscivory increases with hake length; crustaceans appearing mostly in the stomach of <16 cm hakes in the northern-central Adriatic Sea (Karlovac 1959, Županovic 1968, Piccinetti and Piccinetti Manfrin 1971, Jukic 1972, Froglia 1973, Jardas 1976). The presently reported study analysed the diet of the hake in the northeast Mediterranean, which, given its abundance, plays an important role in comprehending the food chain dynamics. Despite hake's environmental and economic importance (Oliver and Massuti 1995) in the Mediterranean, much of its ACTA ICHTHYOLOGICA ET PISCATORIA (2011) 41 (4): 277–284 DOI: 10.3750/AIP2011.41.4.0

Feeding strategy and ontogenetic changes in diet of gurnards (Teleostea: Scorpaeniformes: Triglidae) from the Adriatic Sea

A multi-specific approach in fish diet studies provides insight into the complexity of trophic interactions in marine communities. The feeding habits of three gurnard species, Aspitrigla cuculus, Chelidonichthys lucerna and Eutrigla gurnardus (Scorpaeniformes: Triglidae), from the north-middle Adriatic Sea were studied to evaluate prey-resource partitioning amongst species and within species, comparing juveniles' and adults' diet for each gurnard species. A total of 1818 specimens (390 A. cuculus, 973 C. lucerna, 455 E. gurnardus) were collected by bottom trawling and they were assigned to size classes (juveniles or adults) on the basis of macroscopic evaluation of the gonads. Stomach contents were analysed. A common dietary preference for Crustacea was found in all species and size classes considered. Nevertheless, gurnards showed distinct feeding behaviour: C. lucerna and E. gurnardus were generalist-opportunistic predators, showing a varied diet based on epi-benthic, bentho-pelagic and necto-benthic preys belonging to different taxa such as Teleostei and Mollusca, while A. cuculus may be considered a specialist feeder, feeding almost exclusively on necto-benthic invertebrates. Morisita's index calculated for critical size classes (juveniles and adults) pointed out differences. At the inter-specific level, possible dietary competition between A. cuculus and E. gurnardus (C > 0.65) was found for all size classes combined, due to the prey abundance of Lophogaster typicus (Crustacea: Mysida). At the intra-specific level, high diet overlap was found between juveniles and adults of C. cuculus (C = 0.98) and between juveniles and adults of E. gurnardus (C > 0.84). In contrast, C. lucerna did not compete with increasing body size (C < 0.20), showing a clear change from crustaceans to fish in its diet preferences. The possibility that A. cuculus and E. gurnardus may compete for the same prey resources while C. lucerna shows food resource partitioning is discussed. Better understanding of the ecology of these coexisting predators should lead to improved conservation and improved fisheries management

Development, Validation and Preliminary Experiments of a Measuring Technique for Eggs Aging Estimation Based on Pulse Phase Thermography

Assessment of the freshness of hen eggs destinated to human consumption is an extremely important goal for the modern food industry and sale chains, as eggs show a rapid natural aging which also depends on the storage conditions. Traditional techniques, such as candling and visual observation, have some practical limitations related to the subjective and qualitative nature of the analysis. The main objective of this paper is to propose a robust and automated approach, based on the use of pulsed phase thermography (PPT) and image processing, that can be used as an effective quality control tool to evaluate the freshness of eggs. As many studies show that the air chamber size is proportional to the egg freshness, the technique relies on the monitoring of the air chamber parameters to infer egg aging over time. The raw and phase infrared images are acquired and then post-processed by a dedicated algorithm which has been designed to automatically measure the size of the air chamber, in terms of normalized area and volume. The robustness of the method is firstly assessed through repeatability and reproducibility tests, which demonstrate that the uncertainty in the measure of the air chamber size never exceeds 5%. Then, an experimental campaign on a larger sample of 30 eggs, equally divided into three size categories (M, L, XL), is conducted. For each egg, the main sizes of the air chamber are measured with the proposed method and their evolution over time is investigated. Results have revealed, for all the egg categories, the existence of an analytic relationship and a high degree of correlation (R-2 &gt; 0.95) between the geometric data of the air chamber and the weight loss, which is a well-known marker of egg aging

Messa a punto di tecniche termografiche per il rilievo di difetti di fusione in getti di titanio commercialmente puro

Nel presente lavoro vengono riportati i risultati di uno studio sperimentale sull’applicazione di tecniche dimisura basate su termografia attiva per il rilievo di difettosità in provini di Ti commercialmente puro di grado2, realizzati mediante il metodo della fusione a cera persa. Le tecniche di termografia attiva ad infrarossimesse a punto hanno consentito di evidenziare la presenza di difetti sub-superficiali, non individuabiliattraverso i metodi convenzionali che utilizzano liquidi penetranti. In particolare sono state sperimentate siatecniche di termografia pulsata (“pulse phase”), basate sull’acquisizione delle mappe di temperaturasuperficiale dopo riscaldamento impulsivo dei provini, sia tecniche di termografia modulata (“lock-in”), basatesul rilievo delle mappe di temperatura durante l’applicazione di una sollecitazione termica sinusoidale. Laverifica dei risultati ottenuti con il metodo termografico è stata effettuata attraverso il confronto conosservazioni radiografiche a raggi ? e con indagini di tomografia rX computerizzata in 3D

An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping

Transcription factors (TFs) bind DNA in a sequence-specific manner and are generally cell type-specific factors and/or developmental master regulators. In contrast, general TFs (GTFs) are part of very large protein complexes and serve for RNA polymerases’ recruitment to promoter sequences, generally in a cell type-independent manner. Whereas, several TFs have been proven to serve as anchors for the 3D genome organization, the role of GTFs in genome architecture have not been carefully explored. Here, we used ChIP-seq and Hi-C data to depict the role of TFIIIC, one of the RNA polymerase III GTFs, in 3D genome organization. We find that TFIIIC genome occupancy mainly occurs at specific regions, which largely correspond to Alu elements; other characteristic classes of repetitive elements (REs) such as MIR, FLAM-C and ALR/alpha are also found depending on the cell’s developmental origin. The analysis also shows that TFIIIC-enriched regions are involved in cell type-specific DNA looping, which does not depend on colocalization with the master architectural protein CTCF. This work extends previous knowledge on the role of TFIIIC as a bona fide genome organizer whose action participates in cell type-dependent 3D genome looping via binding to REs