Semantically selective augmentation for deep compact person re-identification

We present a deep person re-identification approach that combines semantically selective, deep data augmentation with clustering-based network compression to generate high performance, light and fast inference networks. In particular, we propose to augment limited training data via sampling from a deep convolutional generative adversarial network (DCGAN), whose discriminator is constrained by a semantic classifier to explicitly control the domain specificity of the generation process. Thereby, we encode information in the classifier network which can be utilized to steer adversarial synthesis, and which fuels our CondenseNet ID-network training. We provide a quantitative and qualitative analysis of the approach and its variants on a number of datasets, obtaining results that outperform the state-of-the-art on the LIMA dataset for long-term monitoring in indoor living spaces

Procedures for high quality RNA extraction from Paracentrotus lividus (LAMARCK, 1816) embryos and gonadal tissue

The extraction protocol described below is part of the CISAS project, aimed at the realization, within CNR, of an “International Centre of advanced study in environment, ecosystem and human health”. In this report we describe a RNA extraction protocol from Paracentrotus lividus embryos and gonadal tissue

Development of a biosensor for copper detection in aqueous solutions using an Anemonia sulcata recombinant GFP

Fluorescent proteins from marine organisms represent potential candidates for biosensor development. In this paper, we described the isolation of a native green fluorescent protein from Anemonia sulcata and the cloning and purification of its equivalent as a recombinant protein in Escherichia coli. Furthermore, the spectroscopic behaviours of the native and recombinant GFPs were investigated as a function of Cu2+, Cd2+, Pb 2+ and Ni2+ concentration. Our results suggest the high selectivity of both proteins at copper than the other metals and, for the recombinant protein, a great sensitivity at a very low concentration (0.1-1 μM). Moreover, starting from these data, using the combination of molecular biology techniques and optical setup, we developed a device for the detection of Cu2+ in water solutions. The quenching effect detected with the device showed that the relative attenuation of the signal (0.46±0.02 AU) was slightly larger than the data measured by fluorescence spectra (0.65±0.03 AU). The good sensitivity in the span of two orders of the magnitude of Cu2+ concentration, the fact that the instrument is made up of low-cost and sturdy parts and the selective quenching of rAsGFP to copper ions make this setup suited as a low cost, on-the-field, copper ion-specific biosensor. © 2013 Springer Science+Business Media

Esperimento pilota mirato all’analisi dell’effetto della stimolazione immunitaria su A. viridis, finalizzato alla produzione di composti biologicamente attivi

L’esperimento mira a valutare l’eventuale attività antibatterica di peptidi prodotti da individui di Anemonia viridis in seguito a stimolazione immunitaria e quindi alla realizzazione di un protocollo riproducibile e ottimizzato per la produzione di tali composti

Applicazione di un protocollo di immuno-stimolazione su individui di Pracambarus clarkii mirato alla produzione di peptidi con attività biologica

Uno dei principali problemi inerenti l’identificazione e l’analisi di nuovi peptidi naturali di origine marina è la disponibilità in termini quantitativi del materiale bioattivo (Cragg et al., 1997). Infatti, le concentrazioni di tali peptidi negli invertebrati marini sono spesso meno del 10-6 % del peso umido, ed il loro rendimento a seguito delle procedure di estrazione tradizionali risulta ancora più basso. Tuttavia, sono molteplici i fattori che possono influenzare l'esito della identificazione degli Anti Microbial Peptides (AMP), come le variazioni geografiche e stagionali (sito di campionamento), le diverse fasi della vita (specie pelagiche o bentoniche), l'età, il sesso e lo stato fisiologico (malattia, allevamento, muta). A causa della difficoltà nell’ottenere quantità sufficienti di composti bioattivi, potrebbe essere più produttivo dissezionare in diversi tessuti/organi gli invertebrati selezionati per poi estrarre il materiale da saggiare (Haug et al., 2002a, 2002b, 2004) ciò al fine di separare i peptidi di interesse da migliaia di sostanze inattive. Dividere gli organismi in parti differenti selezionando ciascun tessuto potrebbe anche fornire l'indicazione se l'animale produce da sé il principio attivo o se esso proviene dalla dieta o ancora è associato a parassiti o microrganismi. La maggior parte degli AMP marini sono stati di fatto isolati dal compartimento sangue, sia dall’emolinfa/fluido celomatico (sangue intero) o dagli emociti/celomociti (cellule del sangue). Alcuni peptidi tuttavia sono stati scoperti e isolati da altri tessuti, ma essendo questi circondati (negli invertebrati marini) dagli emociti/celomociti, è possibile che provengano da questi ultimi. Inoltre tutte le variabili analitiche hanno una potenziale influenza sul risultato sia in termini quantitativi che qualitativi oltre che per la stabilità del campione anche per la riproducibilità del protocollo. Tra queste variabili ricadono le condizioni di conservazione del campione (tempo trascorso dall’estrazione, la temperatura prima dell’estrazione ed alla separazione, il congelamento e la liofilizzazione), la tipologia del campione ed il metodo di prelievo, la separazione delle cellule dal sangue (velocità di centrifugazione, durata e temperatura), l’uso del tampone (tipo, pH, forza ionica e temperatura), l'uso e il tipo di anticoagulanti e cocktail inibitori della proteasi. Inoltre, dati bibliografici riportano come la stimolazione immunitaria determini un aumento sia quantitativamente che qualitativamente della produzione di peptidi antimicrobici. Per tale motivo si è proceduto ad effettuare un esperimento pilota per valutare se in tali condizioni fosse superiore la quantità di piccoli peptidi sintetizzati rispetto ad individui non stimolati e se nei differenti tempi di stimolazione selezionati, emergesse una differenziazione a carico dei peptidi prodotti in relazione ad una possibile attività di natura antibatterica

Characterization of translationally controlled tumour protein from the sea anemone Anemonia viridis and transcriptome wide identification of cnidarian homologues

Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure. The pattern of mRNA expression profile was also defined in A. viridis. These analyses revealed a constitutive mRNA expression especially in tissues with active proliferation. Additionally, the transcriptional profile of A. viridis TCTP (AvTCTP) after challenges with different abiotic/biotic stresses showed induction by extreme temperatures, heavy metals exposure and immune stimulation. These results suggest the involvement of AvTCTP in the sea anemone defensome taking part in environmental stress and immune responses

Gene expression changes after parental exposure to metals in the sea urchin affect timing of genetic programme of embryo development

It is widely accepted that phenotypic traits can be modulated at the epigenetic level so that some conditions can affect the progeny of exposed individuals. To assess if the exposure of adult animals could result in effects on the offspring, the Mediterranean sea urchin and its wellcharacterized gene regulatory networks (GRNs) was chosen as a model. Adult animals were exposed to known concentrations of zinc and cadmium (both individually and in combination) for 10 days, and the resulting embryos were followed during the development. The oxidative stress occurring in parental gonads, embryo phenotypes and mortality, and the expression level of a set of selected genes, including members of the skeletogenic and endodermal GRNs, were evaluated. Increased oxidative stress at F0, high rates of developmental aberration with impaired gastrulation, in association to deregulation of genes involved in skeletogenesis (dri, hex, sm50, p16, p19, msp130), endodermal specification (foxa, hox11/13b, wnt8) and epigenetic regulation (kat2A, hdac1, ehmt2, phf8 and UBE2a) occurred either at 24 or 48 hpf. Results strongly indicate that exposure to environmental pollutants can affect not only directly challenged animals but also their progeny (at least F1), influencing optimal timing of genetic programme of embryo development, resulting in an overall impairment of developmental success

The nucleic acid-binding protein PcCNBP is transcriptionally regulated during the immune response in red swamp crayfish Procambarus clarkii

Gene family encoding cellular nucleic acid binding proteins (CNBP) is well conserved among vertebrates; however, there is limited knowledge in lower organisms. In this study, a CNBP homolog from the red swamp crayfish Procambarus clarkii was characterised. The full-length cDNA of PcCNBP was of 1257 bp with a 5′-untranslated region (UTR) of 63 bp and a 3′-UTR of 331 bp with a poly (A) tail, and an open-reading frame (ORF) of 864 bp encoding a polypeptide of 287 amino acids with the predicted molecular weight of about 33 kDa. The predicted protein possesses 7 tandem repeats of 14 amino acids containing the CCHC zinc finger consensus sequence, two RGG-rich single-stranded RNA-binding domain and a nuclear localization signal, strongly suggesting that PcCNBP was a homolog of vertebrate CNBP. The PcCNBP transcript was constitutively expressed in all tested tissues of unchallenged crayfish, including hepatopancreas, gill, eyestalk, haemocytes, intestine, stomach and cuticle with highest expression in haemocytes, intestine, gills and hepatopancreas. The mRNA expression of PcCNBP in haemocytes was modulated at transcriptional level by different immune challenges, suggesting its involvement in the immune response of P. clarkii during both bacteria and viruses infection

Identification of RNA-binding proteins that partner with Lin28a to regulate Dnmt3a expression

Lin28 is an evolutionary conserved RNA-binding protein that plays important roles during embryonic development and tumorigenesis. It regulates gene expression through two different post-transcriptional mechanisms. The first one is based on the regulation of miRNA biogenesis, in particular that of the let-7 family, whose expression is suppressed by Lin28. Thus, loss of Lin28 leads to the upregulation of mRNAs that are targets of let-7 species. The second mechanism is based on the direct interaction of Lin28 with a large number of mRNAs, which results in the regulation of their translation. This second mechanism remains poorly understood. To address this issue, we purified high molecular weight complexes containing Lin28a in mouse embryonic stem cells (ESCs). Numerous proteins, co-purified with Lin28a, were identified by proteomic procedures and tested for their possible role in Lin28a-dependent regulation of the mRNA encoding DNA methyltransferase 3a (Dnmt3a). The results show that Lin28a activity is dependent on many proteins, including three helicases and four RNA-binding proteins. The suppression of four of these proteins, namely Ddx3x, Hnrnph1, Hnrnpu or Syncrip, interferes with the binding of Lin28a to the Dnmt3a mRNA, thus suggesting that they are part of an oligomeric ribonucleoprotein complex that is necessary for Lin28a activity