Genomic characterization of the italian wolf (Canis lupus): the genes involved in black coat colour determination and application of microarray technique for snps detection.

This study provides a comprehensive genetic overview on the endangered Italian wolf population. In particular, it focuses on two research lines. On one hand, we focalised on melanism in wolf in order to isolate a mutation related with black coat colour in canids. With several reported black individuals (an exception at European level), the Italian wolf population constituted a challenging research field posing many unanswered questions. As found in North American wolf, we reported that melanism in the Italian population is caused by a different melanocortin pathway component, the K locus, in which a beta-defensin protein acts as an alternative ligand for the Mc1r. This research project was conducted in collaboration with Prof. Gregory Barsh, Department of Genetics and Paediatrics, Stanford University. On the other hand, we performed analysis on a high number of SNPs thanks to a customized Canine microarray useful to integrate or substitute the STR markers for genotyping individuals and detecting wolf-dog hybrids. Thanks to DNA microchip technology, we obtained an impressive amount of genetic data which provides a solid base for future functional genomic studies. This study was undertaken in collaboration with Prof. Robert K. Wayne, Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA).

Detection and localization of GLUTs in spermatozoa from different domestic species

Sperm cells need hexoses as a substrate for their function, for both the maintenance of membrane homeostasis and the movement of the tail. These cells have a peculiar metabolism that has not yet been fully understood, but it is clear that they obtain energy from hexoses through glycolisis and/or oxidative phosphorylation. Spermatozoa are in contact with different external environments, beginning from the testicular and epididymal fluid, passing to the seminal plasma and finally to the female genital tract fluids; in addition, with the spread of reproductive biotechnologies, sperm cells are diluted and stored in various media, containing different energetic substrates. To utilize these energetic sources, sperm cells, as other eukaryotic cells, have a well-constructed protein system, that is mainly represented by the GLUT family proteins. These transporters have a membrane-spanning α-helix structure and work as an enzymatic pump that permit a fast gradient dependent passage of sugar molecules through the lipidic bilayer of sperm membrane. Many GLUTs have been studied in man, bull and rat spermatozoa; the presence of some GLUTs has been also demonstrated in boar and dog spermatozoa. The aims of the present study were - to determine the presence of GLUTs 1, 2, 3, 4 and 5 in boar, horse, dog and donkey spermatozoa and to describe their localization; - to study eventual changes in GLUTs location after capacitation and acrosome reaction in boar, stallion and dog spermatozoa; - to determine possible changes in GLUTs localization after capacitation induced by insulin and IGF stimulation in boar spermatozoa; - to evaluate changes in GLUTs localization after flow-cytometric sex sorting in boar sperm cells. GLUTs 1, 2, 3 and 5 presence and localization have been demonstrated in boar, stallion, dog and donkey spermatozoa by western blotting and immunofluorescence analysis; a relocation in GLUTs after capacitation has been observed only in dog sperm cells, while no changes have been observed in the other species examined. As for boar, the stimulation of the capacitation with insulin and IGF didn’t cause any change in GLUTs localization, as well as for the flow cytometric sorting procedure. In conclusion, this study confirms the presence of GLUTs 1, 2 ,3 and 5 in boar, dog, stallion and donkey spermatozoa, while GLUT 4 seems to be absent, as a confirmation of other studies. Only in dog sperm cells capacitating conditions induce a change in GLUTs distribution, even if the physiological role of these changes should be deepened.

Development and applications of hollow fiber flow field-flow fractionation in the bioanalytical field. Studies of aggregation phenomena in complex protein samples

Recent advances in the fast growing area of therapeutic/diagnostic proteins and antibodies - novel and highly specific drugs - as well as the progress in the field of functional proteomics regarding the correlation between the aggregation of damaged proteins and (immuno) senescence or aging-related pathologies, underline the need for adequate analytical methods for the detection, separation, characterization and quantification of protein aggregates, regardless of the their origin or formation mechanism. Hollow fiber flow field-flow fractionation (HF5), the miniaturized version of FlowFFF and integral part of the Eclipse DUALTEC FFF separation system, was the focus of this research; this flow-based separation technique proved to be uniquely suited for the hydrodynamic size-based separation of proteins and protein aggregates in a very broad size and molecular weight (MW) range, often present at trace levels. HF5 has shown to be (a) highly selective in terms of protein diffusion coefficients, (b) versatile in terms of bio-compatible carrier solution choice, (c) able to preserve the biophysical properties/molecular conformation of the proteins/protein aggregates and (d) able to discriminate between different types of protein aggregates. Thanks to the miniaturization advantages and the online coupling with highly sensitive detection techniques (UV/Vis, intrinsic fluorescence and multi-angle light scattering), HF5 had very low detection/quantification limits for protein aggregates. Compared to size-exclusion chromatography (SEC), HF5 demonstrated superior selectivity and potential as orthogonal analytical method in the extended characterization assays, often required by therapeutic protein formulations. In addition, the developed HF5 methods have proven to be rapid, highly selective, sensitive and repeatable. HF5 was ideally suitable as first dimension of separation of aging-related protein aggregates from whole cell lysates (proteome pre-fractionation method) and, by HF5-(UV)-MALS online coupling, important biophysical information on the fractionated proteins and protein aggregates was gathered: size (rms radius and hydrodynamic radius), absolute MW and conformation.

Machine learning tools for protein annotation: the cases of transmembrane β-barrel and myristoylated proteins

Biology is now a “Big Data Science” thanks to technological advancements allowing the characterization of the whole macromolecular content of a cell or a collection of cells. This opens interesting perspectives, but only a small portion of this data may be experimentally characterized. From this derives the demand of accurate and efficient computational tools for automatic annotation of biological molecules. This is even more true when dealing with membrane proteins, on which my research project is focused leading to the development of two machine learning-based methods: BetAware-Deep and SVMyr. BetAware-Deep is a tool for the detection and topology prediction of transmembrane beta-barrel proteins found in Gram-negative bacteria. These proteins are involved in many biological processes and primary candidates as drug targets. BetAware-Deep exploits the combination of a deep learning framework (bidirectional long short-term memory) and a probabilistic graphical model (grammatical-restrained hidden conditional random field). Moreover, it introduced a modified formulation of the hydrophobic moment, designed to include the evolutionary information. BetAware-Deep outperformed all the available methods in topology prediction and reported high scores in the detection task. Glycine myristoylation in Eukaryotes is the binding of a myristic acid on an N-terminal glycine. SVMyr is a fast method based on support vector machines designed to predict this modification in dataset of proteomic scale. It uses as input octapeptides and exploits computational scores derived from experimental examples and mean physicochemical features. SVMyr outperformed all the available methods for co-translational myristoylation prediction. In addition, it allows (as a unique feature) the prediction of post-translational myristoylation. Both the tools here described are designed having in mind best practices for the development of machine learning-based tools outlined by the bioinformatics community. Moreover, they are made available via user-friendly web servers. All this make them valuable tools for filling the gap between sequential and annotated data.

Solid state micro and nanopore sensors for single entity detection

A general description of the work presented in this thesis can be divided into three areas of interest: micropore fabrication, nanopore modification, and their applications. The first part of the thesis is related to the novel, reliable, cost-effective, potable, mass-productive, robust, and ease of use micropore flowcell that works based on the RPS technique. Based on our first goal, which was finding an alternate materials and processes that would shorten production times while lowering costs and improving signal quality, the polyimide film was used as a substrate to create precise pores by femtosecond laser, and the resulting current blockades of different sizes of the nanoparticles were recorded. Based on the results, the device can detecting nano-sized particles by changing the current level. The experimental and theoretical investigation, scanning electron microscopy, and focus ion beam were performed to explain the micropore's performance. The second goal was design and fabrication of a leak-free, easy-to-assemble, and portable polymethyl methacrylate flowcell for nanopore experiments. Here, ion current rectification was studied in our nanodevice. We showed a self-assembly-based, controllable, and monitorable in situ Poly(l-lysine)- g-poly(ethylene glycol) coating method under voltage-driven electrolyte flow and electrostatic interaction between nanopore walls and PLL backbones. Using designed nanopore flowcell and in situ monolayer PLL-g-PEG functionalized 20±4 nm SiN nanopores, we observed non-sticky α-1 anti-trypsin protein translocation. additionally, we could show the enhancement of translocation events through this non-sticky nanopore, and also, estimate the volume of the translocated protein. In this study, by comparing the AAT protein translocation results from functionalized and non-functionalized nanopore we demonstrated the 105 times dwell time reduction (31-0.59ms), 25% amplitude enhancement (0.24-0.3 nA), and 15 times event’s number increase (1-15events/s) after functionalization in 1×PBS at physiological pH. Also, the AAT protein volume was measured, close to the calculated AAT protein hydrodynamic volume and previous reports.

Skin as a promising biomatrix for the early detection of misfolded proteins by RT-QuIC in neurodegenerative diseases

Real-Time Quaking-Induced Conversion (RT-QuIC) is an ultrasensitive assay capable of detecting pathological aggregates of misfolded proteins in biospecimens. In recent years, efforts have been made to find a more feasible and convenient biomatrix as an alternative to CSF, and skin biopsy may be a suitable candidate. This project aimed to evaluate the diagnostic performance of skin RT-QuIC in 3 different cohorts of patients: 1. Creutzfeldt-Jakob disease (CJD), 2. Lewy body disease (LBD), and 3. Isolated REM sleep behavior disorder (iRBD). We studied 71 punch skin samples of 35 patients with CJD, including five assessed in vitam, using 2 two different substrates: Bank vole 23-230 (Bv23-230) and Syrian hamster 23-231 (Ha23-231) recombinant prion protein. Skin prion RT-QuIC showed a 100% specificity with both substrates and a higher sensitivity with the Bv23-230 than Ha23-231 (87.5% vs. 65.6%, respectively). Forty-one patients underwent both lumbar puncture (LB) and skin biopsy; CSF and skin RT-QuIC showed a high level of concordance (38/41, 92.7%). Then, we analyzed samples taken in vitam (n=69) or postmortem (n=49) from patients with Parkinson’s disease (PD), dementia with Lewy bodies (DLB), incidental Lewy body pathology, and neurological controls. Skin α-syn RT-QuIC distinguished LBD patients with an overall accuracy of 94.1% in the two cohorts (sensitivity, 89.2%; specificity, 96.3%). Seventy-nine patients underwent both CSF and skin α-syn RT-QuIC, and the two assays yielded similar diagnostic accuracy (skin, 97.5%; CSF, 98.7%). Finally, we studied 91 iRBD patients and 41 control. In the skin, RT-QuIC showed a sensitivity of 76.9%, specificity of 97.6%, and 82.0% accuracy. 128 participants (88 patients plus 40 controls) underwent both CSF and skin RT-QuIC. The two protocols showed 99.2% of concordance. These works confirmed that skin punch biopsies might represent a valid and convenient alternative to CSF analysis for an early diagnosis of prion diseases and LB-related pathologies.