An assessment of the business value of traceability practices in the italian fishery processing industry

Traceability is often perceived by food industry executives as an additional cost of doing business, one to be avoided if possible. However, a traceability system can in fact comply the regulatory requirements, increase food safety and recall performance, improving marketing performances and, as well as, improving supply chain management. Thus, traceability affects business performances of firms in terms of costs and benefits determined by traceability practices. Costs and benefits affect factors such as, firms’ characteristics, level of traceability and ,lastly, costs and benefits perceived prior to traceability implementation. This thesis was undertaken to understand how these factors are linked to affect the outcome of costs and benefits. Analysis of the results of a plant level survey of the Italian ichthyic processing industry revealed that processors generally adopt various level of traceability while government support appears to increase the level of traceability and the expectations and actual costs and benefits. None of the firms’ characteristics, with the exception of government support, influences costs and level of traceability. Only size of firms and level of QMS certifications are linked with benefits while precision of traceability increases benefits without affecting costs. Finally, traceability practices appear due to the request from “external“ stakeholders such as government, authority and customers rather than “internal” factors (e.g. improving the firm management) while the traceability system does not provide any added value from the market in terms of price premium or market share increase.

Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

Different approaches to identify markers for meat quality and production traits in pigs: analysis of the transcriptome in post mortem skeletal muscle and investigation of candidate genes

Due to the growing attention of consumers towards their food, improvement of quality of animal products has become one of the main focus of research. To this aim, the application of modern molecular genetics approaches has been proved extremely useful and effective. This innovative drive includes all livestock species productions, including pork. The Italian pig breeding industry is unique because needs heavy pigs slaughtered at about 160 kg for the production of high quality processed products. For this reason, it requires precise meat quality and carcass characteristics. Two aspects have been considered in this thesis: the application of the transcriptome analysis in post mortem pig muscles as a possible method to evaluate meat quality parameters related to the pre mortem status of the animals, including health, nutrition, welfare, and with potential applications for product traceability (chapters 3 and 4); the study of candidate genes for obesity related traits in order to identify markers associated with fatness in pigs that could be applied to improve carcass quality (chapters 5, 6, and 7). Chapter three addresses the first issue from a methodological point of view. When we considered this issue, it was not obvious that post mortem skeletal muscle could be useful for transcriptomic analysis. Therefore we demonstrated that the quality of RNA extracted from skeletal muscle of pigs sampled at different post mortem intervals (20 minutes, 2 hours, 6 hours, and 24 hours) is good for downstream applications. Degradation occurred starting from 48 h post mortem even if at this time it is still possible to use some RNA products. In the fourth chapter, in order to demonstrate the potential use of RNA obtained up to 24 hours post mortem, we present the results of RNA analysis with the Affymetrix microarray platform that made it possible to assess the level of expression of more of 24000 mRNAs. We did not identify any significant differences between the different post mortem times suggesting that this technique could be applied to retrieve information coming from the transcriptome of skeletal muscle samples not collected just after slaughtering. This study represents the first contribution of this kind applied to pork. In the fifth chapter, we investigated as candidate for fat deposition the TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) gene. This gene is involved in mechanisms regulating energy homeostasis in skeletal muscle and is associated with predisposition to obesity in humans. By resequencing a fragment of the TBC1D1 gene we identified three synonymous mutations localized in exon 2 (g.40A>G, g.151C>T, and g.172T>C) and 2 polymorphisms localized in intron 2 (g.219G>A and g.252G>A). One of these polymorphisms (g.219G>A) was genotyped by high resolution melting (HRM) analysis and PCR-RFLP. Moreover, this gene sequence was mapped by radiation hybrid analysis on porcine chromosome 8. The association study was conducted in 756 performance tested pigs of Italian Large White and Italian Duroc breeds. Significant results were obtained for lean meat content, back fat thickness, visible intermuscular fat and ham weight. In chapter six, a second candidate gene (tribbles homolog 3, TRIB3) is analyzed in a study of association with carcass and meat quality traits. The TRIB3 gene is involved in energy metabolism of skeletal muscle and plays a role as suppressor of adipocyte differentiation. We identified two polymorphisms in the first coding exon of the porcine TRIB3 gene, one is a synonymous SNP (c.132T> C), a second is a missense mutation (c.146C> T, p.P49L). The two polymorphisms appear to be in complete linkage disequilibrium between and within breeds. The in silico analysis of the p.P49L substitution suggests that it might have a functional effect. The association study in about 650 pigs indicates that this marker is associated with back fat thickness in Italian Large White and Italian Duroc breeds in two different experimental designs. This polymorphisms is also associated with lactate content of muscle semimembranosus in Italian Large White pigs. Expression analysis indicated that this gene is transcribed in skeletal muscle and adipose tissue as well as in other tissues. In the seventh chapter, we reported the genotyping results for of 677 SNPs in extreme divergent groups of pigs chosen according to the extreme estimated breeding values for back fat thickness. SNPs were identified by resequencing, literature mining and in silico database mining. analysis, data reported in the literature of 60 candidates genes for obesity. Genotyping was carried out using the GoldenGate (Illumina) platform. Of the analyzed SNPs more that 300 were polymorphic in the genotyped population and had minor allele frequency (MAF) >0.05. Of these SNPs, 65 were associated (P<0.10) with back fat thickness. One of the most significant gene marker was the same TBC1D1 SNPs reported in chapter 5, confirming the role of this gene in fat deposition in pig. These results could be important to better define the pig as a model for human obesity other than for marker assisted selection to improve carcass characteristics.

New polymeric materials for vascular surgery

The dramatic impact that vascular diseases have on human life quality and expectancy nowadays is the reason why both medical and scientific communities put great effort in discovering new and effective ways to fight vascular pathologies. Among the many different treatments, endovascular surgery is a minimally-invasive technique that makes use of X-ray fluoroscopy to obtain real-time images of the patient during interventions. In this context radiopaque biomaterials, i.e. materials able to absorb X-ray radiation, play a fundamental role as they are employed both to enhance visibility of devices during interventions and to protect medical staff and patients from X-ray radiations. Organic-inorganic hybrids are materials that combine characteristics of organic polymers with those of inorganic metal oxides. These materials can be synthesized via the sol-gel process and can be easily applied as thin coatings on different kinds of substrates. Good radiopacity of organic-inorganic hybrids has been recently reported suggesting that these materials might find applications in medical fields where X-ray absorption and visibility is required. The present PhD thesis aimed at developing and characterizing new radiopaque organic-inorganic hybrid materials that can find application in the vascular surgery field as coatings for the improvement of medical devices traceability as well as for the production of X-ray shielding objects and garments. Novel organic-inorganic hybrids based on different polyesters (poly-lactic acid and poly-ε-caprolactone) and polycarbonate (poly-trimethylene carbonate) as the polymeric phase and on titanium oxide as the inorganic phase were synthesized. Study of the phase interactions in these materials allowed to demonstrate that Class II hybrids (where covalent bonds exists between the two phases) can be obtained starting from any kind of polyester or polycarbonate, without the need of polymer pre-functionalization, thanks to the occurrence of transesterification reactions operated by inorganic molecules on ester and carbonate moieties. Polyester based hybrids were successfully coated via dip coating on different kinds of textiles. Coated textiles showed improved radiopacity with respect to the plain fabric while remaining soft to the touch. The hybrid was able to coat single fibers of the yarn rather than coating the yarn as a whole. Openings between yarns were maintained and therefore fabric breathability was preserved. Such coatings are promising for the production of light-weight garments for X-ray protection of medical staff during interventional fluoroscopy, which will help preventing pathologies that stem from chronic X-ray exposure. A means to increase the protection capacity of hybrid-coated fabrics was also investigated and implemented in this thesis. By synthesizing the hybrid in the presence of a suspension of radiopaque tantalum nanoparticles, PDMS-titania hybrid materials with tunable radiopacity were developed and were successfully applied as coatings. A solution for enhancing medical device radiopacity was also successfully investigated. High metal radiopacity was associated with good mechanical and protective properties of organic-inorganic hybrids in the form of a double-layer coating. Tantalum was employed as the constituent of the first layer deposited on sample substrates by means of a sputtering technique. The second layer was composed of a hybrid whose constituents are well-known biocompatible organic and inorganic components, such as the two polymers PCL and PDMS, and titanium oxide, respectively. The metallic layer conferred to the substrate good X-ray visibility. A correlation between radiopacity and coating thickness derived during this study allows to tailor radiopacity simply by controlling the metal layer sputtering deposition time. The applied metal deposition technique also permits easy shaping of the radiopaque layer, allowing production of radiopaque markers for medical devices that can be unambiguously identified by surgeons during implantation and in subsequent radiological investigations. Synthesized PCL-titania and PDMS-titania hybrids strongly adhered to substrates and show good biocompatibility as highlighted by cytotoxicity tests. The PDMS-titania hybrid coating was also characterized by high flexibility that allows it to stand large substrate deformations without detaching nor cracking, thus being suitable for application on flexible medical devices.

Mesenchymal stromal cell: new applications for regenerative medicine

In the last decades mesenchymal stromal cells (MSC), intriguing for their multilineage plasticity and their proliferation activity in vitro, have been intensively studied for innovative therapeutic applications. In the first project, a new method to expand in vitro adipose derived-MSC (ASC) while maintaining their progenitor properties have been investigated. ASC are cultured in the same flask for 28 days in order to allow cell-extracellular matrix and cell-cell interactions and to mimic in vivo niche. ASC cultured with this method (Unpass cells) were compared with ASC cultured under classic condition (Pass cells). Unpass and Pass cells were characterized in terms of clonogenicity, proliferation, stemness gene expression, differentiation in vitro and in vivo and results obtained showed that Unpass cells preserve their stemness and phenotypic properties suggesting a fundamental role of the niche in the maintenance of ASC progenitor features. Our data suggests alternative culture conditions for the expansion of ASC ex vivo which could increase the performance of ASC in regenerative applications. In vivo MSC tracking is essential in order to assess their homing and migration. Super-paramagnetic iron oxide nanoparticles (SPION) have been used to track MSC in vivo due to their biocompatibility and traceability by MRI. In the second project a new generation of magnetic nanoparticles (MNP) used to label MSC were tested. These MNP have been functionalized with hyperbranched poly(epsilon-lysine)dendrons (G3CB) in order to interact with membrane glycocalix of the cells avoiding their internalization and preventing any cytotoxic effects. In literature it is reported that labeling of MSC with SPION takes long time of incubation. In our experiments after 15min of incubation with G3CB-MNP more then 80% of MSC were labeled. The data obtained from cytotoxic, proliferation and differentiation assay showed that labeling does not affect MSC properties suggesting a potential application of G3CB nano-particles in regenerative medicine.