Genome analysis and characterisation of the exopolysaccharide produced by Bifidobacterium longum subsp. longum 35624™

The Bifibobacterium longum subsp. longum 35624™ strain (formerly named Bifidobacterium longum subsp. infantis) is a well described probiotic with clinical efficacy in Irritable Bowel Syndrome clinical trials and induces immunoregulatory effects in mice and in humans. This paper presents (a) the genome sequence of the organism allowing the assignment to its correct subspeciation longum; (b) a comparative genome assessment with other B. longum strains and (c) the molecular structure of the 35624 exopolysaccharide (EPS624). Comparative genome analysis of the 35624 strain with other B. longum strains determined that the sub-speciation of the strain is longum and revealed the presence of a 35624-specific gene cluster, predicted to encode the biosynthetic machinery for EPS624. Following isolation and acid treatment of the EPS, its chemical structure was determined using gas and liquid chromatography for sugar constituent and linkage analysis, electrospray and matrix assisted laser desorption ionization mass spectrometry for sequencing and NMR. The EPS consists of a branched hexasaccharide repeating unit containing two galactose and two glucose moieties, galacturonic acid and the unusual sugar 6-deoxy-L-talose. These data demonstrate that the B. longum 35624 strain has specific genetic features, one of which leads to the generation of a characteristic exopolysaccharide.

Preparation and characterization of Pr0.6Sr0.4FeO3-δ-Ce0.9Pr0.1O2-δ nanofiber structured composite cathode for IT-SOFCs

In this work, Pr_0.6Sr_0.4FeO_3-δ -Ce_0.9Pr_0.1O_2-δ (PSFO-CPO) nanofibers were synthesized by a one-step electrospin technique for use in intermediate-temperature solid oxide fuel cell (IT-SOFC) applications. PSFO-CPO nanofibers were produced with a diameter of about 100nm and lengths exceeding tens of microns. The thermal expansion coefficient (TEC) matches with standard GDC electrolytes and the resulting conductivity also satisfies the needs of IT-SOFCs cathodes. EIS analysis of the nanofiber structured electrode gives a polarization resistance of 0.072Ωcm² at 800°C, smaller than that from the powdered cathode with the same composition. The excellent electrochemical performance can be attributed to the well-constructed microstructure of the nanofiber structured cathode, which promotes surface oxygen diffusion and charge transfer processes. All the results imply that the one-step electrospin method is a facile and practical way of improving the cathode properties and that PSFO-CPO is a promising cathode material for IT-SOFCs.

Generation and Characterisation of a Canine EGFP-HMGA2 Prostate Cancer In Vitro Model

The architectural transcription factor HMGA2 is abundantly expressed during embryonic development. In several malignant neoplasias including prostate cancer, high re-expression of HMGA2 is correlated with malignancy and poor prognosis. The let-7 miRNA family is described to regulate HMGA2 negatively. The balance of let-7 and HMGA2 is discussed to play a major role in tumour aetiology. To further analyse the role of HMGA2 in prostate cancer a stable and highly reproducible in vitro model system is precondition. Herein we established a canine CT1258-EGFP-HMGA2 prostate cancer cell line stably overexpressing HMGA2 linked to EGFP and in addition the reference cell line CT1258-EGFP expressing solely EGFP to exclude EGFP-induced effects. Both recombinant cell lines were characterised by fluorescence microscopy, flow cytometry and immunocytochemistry. The proliferative effect of ectopically overexpressed HMGA2 was determined via BrdU assays. Comparative karyotyping of the derived and the initial CT1258 cell lines was performed to analyse chromosome consistency. The impact of the ectopic HMGA2 expression on its regulator let-7a was analysed by quantitative real-time PCR. Fluorescence microscopy and immunocytochemistry detected successful expression of the EGFP-HMGA2 fusion protein exclusively accumulating in the nucleus. Gene expression analyses confirmed HMGA2 overexpression in CT1258-EGFP-HMGA2 in comparison to CT1258-EGFP and native cells. Significantly higher let-7a expression levels were found in CT1258-EGFP-HMGA2 and CT1258-EGFP. The BrdU assays detected an increased proliferation of CT1258-HMGA2-EGFP cells compared to CT1258-EGFP and native CT1258. The cytogenetic analyses of CT1258-EGFP and CT1258-EGFP-HMGA2 resulted in a comparable hyperdiploid karyotype as described for native CT1258 cells. To further investigate the impact of recombinant overexpressed HMGA2 on CT1258 cells, other selected targets described to underlie HMGA2 regulation were screened in addition. The new fluorescent CT1258-EGFP-HMGA2 cell line is a stable tool enabling in vitro and in vivo analyses of the HMGA2-mediated effects on cells and the development and pathogenesis of prostate cancer.

Identification and characterisation of telomere regulatory and signalling pathways after induction of telomere dysfunction

Telomeres are DNA-protein complexes which cap the ends of eukaryotic linear chromosomes. In normal somatic cells telomeres shorten and become dysfunctional during ageing due to the DNA end replication problem. This leads to activation of signalling pathways that lead to cellular senescence and apoptosis. However, cancer cells typically bypass this barrier to immortalisation in order to proliferate indefinitely. Therefore enhancing our understanding of telomere dysfunction and pathways involved in regulation of the process is essential. However, the pathways involved are highly complex and involve interaction between a wide range of biological processes. Therefore understanding how telomerase dysfunction is regulated is a challenging task and requires a systems biology approach. In this study I have developed a novel methodology for visualisation and analysis of gene lists focusing on the network level rather than individual or small lists of genes. Application of this methodology to an expression data set and a gene methylation data set allowed me to enhance my understanding of the biology underlying a senescence inducing drug and the process of immortalisation respectively. I then used the methodology to compare the effect of genetic background on induction of telomere uncapping. Telomere uncapping was induced in HCT116 WT, p21-/- and p53-/- cells using a viral vector expressing a mutant variant of hTR, the telomerase RNA template. p21-/- cells showed enhanced sensitivity to telomere uncapping. Analysis of a candidate pathway, Mismatch Repair, revealed a role for the process in response to telomere uncapping and that induction of the pathway was p21 dependent. The methodology was then applied to analysis of the telomerase inhibitor GRN163L and synergistic effects of hypoglycaemia with this drug. HCT116 cells were resistant to GRN163L treatment. However, under hypoglycaemic conditions the dose required for ablation of telomerase activity was reduced significantly and telomere shortening was enhanced. Overall this new methodology has allowed our group and collaborators to identify new biology and improve our understanding of processes regulating telomere dysfunction.

Preparation and characterization of grafted nonwoven membranes for bioseparations

Protein purification plays a crucial role in biotechnology and biomanufacturing, where downstream unit operations account for 40%-80% of the overall costs. To overcome this issue, companies strive to simplify the separation process by reducing the number of steps and replacing expensive separation devices. In this context, commercially available polybutylene terephthalate (PBT) melt-blown nonwoven membranes have been developed as a novel disposable membrane chromatography support. The PBT nonwoven membrane is able to capture products and reduce contaminants by ion exchange chromatography. The PBT nonwoven membrane was modified by grafting a poly(glycidyl methacrylate) (GMA) layer by either photo-induced graft polymerization or heat induced graft polymerization. The epoxy groups of GMA monomer were subsequently converted into cation and anion exchangers by reaction with either sulfonic acid groups or diethylamine (DEA), respectively. Several parameters of the procedure were studied, especially the effect of (i) % weight gain and (ii) ligand density on the static protein binding capacity. Bovine Serum Albumin (BSA) and human Immunoglobulin G (hIgG) were utilized as model proteins in the anion and cation exchange studies. The performance of ion exchange PBT nonwovens by HIG was evaluated under flow conditions. The anion- and cation- exchange HIG PBT nonwovens were evaluated for their ability to selectively adsorb and elute BSA or hIgG from a mixture of proteins. Cation exchange nonwovens were not able to reach a good protein separation, whereas anion exchange HIG nonwovens were able to absorb and elute BSA with very high value of purity and yield, in only one step of purification.

Development and characterisation of solution processed vanadium oxide and transparent metal oxide thin films

Metal oxide thin films are important for modern electronic devices ranging from thin film transistors to photovoltaics and functional optical coatings. Solution processed techniques allow for thin films to be rapidly deposited over a range of surfaces without the extensive processing of comparative vapour or physical deposition methods. The production of thin films of vanadium oxide prepared through dip-coating was developed enabling a greater understanding of the thin film formation. Mechanisms of depositing improved large area uniform coverage on a number of technologically relevant substrates were examined. The fundamental mechanism for polymer-assisted deposition in improving thin film surface smoothness and long range order has been delivered. Different methods were employed for adapting the alkoxide based dip-coating technique to produce a variety of amorphous and crystalline vanadium oxide based thin films. Using a wide range of material, spectroscopic and optical measurement techniques the morphology, structure and optoelectronic properties of the thin films were studied. The formation of pinholes on the surface of the thin films, due to dewetting and spinodal effects, was inhibited using the polymer assisted deposition technique. Uniform thin films with sub 50 nm thicknesses were deposited on a variety of substrates controlled through alterations to the solvent-alkoxide dilution ratios and employing polymer assisted deposition techniques. The effects of polymer assisted deposition altered the crystallized VO thin films from a granular surface structure to a polycrystalline structure composed of high density small in-plane grains. The formation of transparent VO based thin film through Si and Na substrate mediated diffusion highlighted new methods for material formation and doping.

Preparation and characterization of multifunctional bio-based polymers exhibiting enhanced properties

Driven by environmental reasons and the expected depletion of crude oil, bio-based polymers are currently undergoing a renaissance in the attempt to replace fossil-based ones. The present work aims at contributing in the development of the steps that start from biomass and move to new polymeric multifunctional materials. The study focuses on two bio-based building blocks (itaconic and vanillic acids) characterized by exploitable functionalities, i.e. a lateral double bond and a substituted aromatic ring respectively, able to confer interesting properties to the final polymers. The lateral double bond of dimethyl itaconate was functionalized via thia-Michael addition reaction obtaining a thermo-stable building block that can undergo polycondensation under classical conditions of reaction. The addition of a long lateral chain allows the polymer to express antimicrobial activity against Staphylococcus aureus making it attractive for packaging and targeting antimicrobial applications. Moreover, the architecture of the homopolymer was modified by means of copolymerization with dimethyl 2,5-furandicarboxylate thus improving the rigidity and obtaining a thermo-processable material. Potential applications as thermoset or thermoplastic material have been discussed. As concerns vanillic acid, the presence of aromatic rings on the polymer backbone imparts high thermal stability, but brittle behaviour in the homopolymer. Therefore, the architecture of the polyester was successfully tuned by means of copolymerization with a flexible bio-based comonomer, i.e. ω-pentadecalactone, providing processable random copolymers. An in depth investigation of water transport mechanism has been undertaken on the synthesized polyesters. Since the copolymers present a succession of aromatic and aliphatic units, as a consequence of the chemical structure water vapor permeability interposes between polyethylene and poly(ethylene terephthalate) proving that the copolyesters are suitable for packaging applications. Moving towards a sustainable model of development, novel sustainable synthetic pathways for the eco-design of new bio-based polymeric structures with high value functionalities and different potential applications have been successfully developed.

Development and characterisation of a neurogenic model of brain cancer

Primary glioblastoma (GB), the most common and aggressive adult brain tumour, is refractory to conventional therapies and characterised by poor prognosis. GB displays striking cellular heterogeneity, with a sub-population, called Glioblastoma Stem Cells (GSCs), intrinsically resistant to therapy, hence the high rate of recurrence. Alterations of the tumour suppressor gene PTEN are prevalent in primary GBM, resulting in the inhibition of the polarity protein Lgl1 due to aPKC hyperactivation. Dysregulation of this molecular axis is one of the mechanisms involved in GSC maintenance. After demonstrating that the PTEN/aPKC/Lgl axis is conserved in Drosophila, I deregulated it in different cells populations of the nervous system in order to individuate the cells at the root of neurogenic brain cancers. This analysis identified the type II neuroblasts (NBs) as the most sensitive to alterations of this molecular axis. Type II NBs are a sub-population of Drosophila stem cells displaying a lineage similar to that of the mammalian neural stem cells. Following aPKC activation in these stem cells, I obtained an adult brain cancer model in Drosophila that summarises many phenotypic traits of human brain tumours. Fly tumours are indeed characterised by accumulation of highly proliferative immature cells and keep growing in the adult leading the affected animals to premature death. With the aim to understand the role of cell polarity disruption in this tumorigenic process I carried out a molecular characterisation and transcriptome analysis of brain cancers from our fly model. In summary, the model I built and partially characterised in this thesis work may help deepen our knowledge on human brain cancers by investigating many different aspects of this complicate disease.

Preparation and assessment of immobilized laccase-based micro- and nanocatalysts for the degradation of anthropogenic compounds

Since the dawn of its presence on earth, the human being has been able to exploit the enzymes for its subsistence. More recent is the meeting between the enzymatic processes and the urgent need for technologies that aim to preserve our planet. In this field nowadays enzymatic catalysis is tested either to depollution/remediation as well as waste disposal. The work presented in this thesis, regarding both these two topics, is tailored on two European projects (EU 2020), MADFORWATER and TERMINUS respectively. Firstly, production of micro- and nanocatalysts via immobilization of laccases (a lignin-degrader enzyme) is performed. In the second part of the thesis laccase is applied to a tertiary treatment of wastewater with the aim to degrade 9 pharmaceutical active compounds in batch reactors. Despite several optimizations, poor degradation is reached and we did not proceed with the study of different bioreactor setups. Therefore, the focus is moved to a project concerning the production of smart multi-layer plastic packaging containing enzymes to improve the possibilities of recycling. In this field shielded nanocatalysts produced via coating techniques able to interact with redox mediators are investigated. The target substrate in this second project is produced in laboratory (i.e. polyurethane like compounds), starting from monomers whose degradation had already been tested, as a proof of concept. The first enzyme studied is still the laccase.