The human genome encodes information that instructs human development, physiology, medicine, and evolution. Massive amount of genomic data has generated an ever-growing pool of hypothesis. Genome editing, broadly defined as targeted changes to the genome, posits to deliver the promise of genomic revolution to transform basic science and personalized medicine. This thesis aims to contribute to this scientific endeavor with a particular focus on the development of effective human genome engineering tools.

Η Πακλιταξέλη αποτελεί ένα από τα πιο ευρέως διαδεδομένα χημειοθεραπευτικά φάρμακα και ενδείκνυται κυρίως σε καρκίνο του πνεύμονα, του μαστού, των ωοθηκών, καθώς και σε σάρκωμα Kaposi ασθενών με AIDS. Ωστόσο, η χρήση της συνδέεται με αρκετές παρενέργειες, γεγονός που επέβαλε την τροποποίησή της σε Συστήματα Ελεγχόμενης Χορήγησης (DDS). Τα συγκεκριμένα συστήματα επιτρέπουν την εκλεκτική μεταφορά του φαρμάκου στον καρκινικό ιστό με μηχανισμούς παθητικής ή ενεργητικής στόχευσης, καθώς και τον έλεγχο του φαρμακοκινητικού προφίλ. Ιδιαίτερα ελπιδοφόρα φαίνεται να είναι η ενσωμάτωση της PTX σε πολυμερικές νανοκάψουλες. Η δομή πυρήνα - κελύφους των νανοκαψακίων καλύπτει τη χορήγηση μίας μεγάλης ποικιλίας ενεργών συστατικών, με το ενδιαφέρον να εστιάζεται σε αντινεοπλασματικά, αντιφλεγμονώδη, αντιικά και ανοσοκατασταλτικά. Η εισαγωγή των φαρμάκων στα νανοκαψάκια μπορεί να οδηγεί σε αύξηση της αποτελεσματικότητας και σταθερότητας των δραστικών ουσιών, καλύτερη in vivo συμπεριφορά και υψηλότερη ενδοκυτταρική πρόσληψη. Ορισμένες μελέτες προτείνουν την εγκαψακίωση νανοσωματιδίων οξειδίου του σιδήρου (SPIONs) σε συστήματα χορήγησης φαρμάκων, τα οποία έχουν αποδειχθεί πολύτιμα εργαλεία τόσο στον τομέα της διάγνωσης (μαγνητική τομογραφία πυρηνικού συντονισμού), όσο και της θεραπείας. Με εφαρμογή εξωτερικού εναλλασσόμενου μαγνητικού πεδίου καθίσταται εφικτή η συσσώρευση των μαγνητικών νανοφορέων στον ιστό - στόχο (μαγνητική στόχευση), ενώ η θεραπεία επέρχεται μέσω επαγωγής μαγνητικής υπερθερμίας. Η εν λόγω μεταπτυχιακή διατριβή πραγματεύεται την εγκαψακίωση της ΡΤΧ και των SPIONs σε πολυμερικές νανοκάψουλες, παρασκευασμένες από το συμπολυμερές πολυ(γαλακτικού οξέος) – πολυ(αιθυλενογλυκόλης) (PLA-PEG). Το PLA αποτελεί ένα βιοαποικοδομήσιμο πολυμερές, το οποίο δημιουργεί έναν πυρήνα, ικανό να εγκαψακιώσει και να προστατέψει υδρόφοβες ουσίες. Από την άλλη μεριά, το PEG είναι ένα υδρόφιλο, βιοσυμβατό πολυμερές, το οποίο προσδίδει στερεοχημική σταθεροποίηση στα συστήματα και παρατείνει το χρόνο κυκλοφορίας τους. Πιο συγκεκριμένα, παρασκευάστηκαν μαγνητικά νανοκαψάκια με συμπολυμερή PLA-PEG, διαφορετικού μοριακού βάρους, με τη μέθοδο της καθίζησης (nanoprecipitation). Οι μαγνητικοί νανοκρυσταλλίτες συντέθηκαν με την τεχνική της θερμικής αποικοδόμησης, ενώ ως πρόδρομη ένωση χρησιμοποιήθηκε ελαϊκός σίδηρος [Fe(Olate)3]. Διερευνήθηκαν διάφορες παράμετροι σχετικά με την σύνθεση (ποσότητα SPIONs, αναλογία πολυμερούς/ελαίου, ποσότητα φαρμάκου), έτσι ώστε να δημιουργηθούν βέλτιστοι νανοφορείς. Επιπλέον, εξετάστηκε η σταθερότητα των διασπορών τόσο στο χρόνο, όσο και στην παρουσία ηλεκτρολυτών (NaCl) με μέτρηση της υδροδυναμικής διαμέτρου και του επιφανειακού φορτίου, χρησιμοποιώντας την τεχνική της δυναμικής σκέδασης φωτός (DLS). Ακολούθησε μορφολογική εκτίμηση των νανοκαψακίων με τη βοήθεια ηλεκτρονικής μικροσκοπίας διάδοσης (ΤΕΜ) και δομικός χαρακτηρισμός τους μέσω φασματοσκοπίας FTIR. Σε επόμενο στάδιο, μετρήθηκε το ποσοστό φόρτωσης της ΡΤΧ με χρήση υγρής χρωματογραφίας (HPLC) και πραγματοποιήθηκαν μελέτες αποδέσμευσης, παρουσία και μη εξωτερικού εναλλασσόμενου μαγνητικού πεδίου, σε διάλυμα φωσφορικών (pH =7.4) στους 37 oC για 24 h. Τέλος, εξετάστηκε η κυτταροτοξικότητα των «φορτωμένων» (με ΡΤΧ) μαγνητικών νανοκαψακίων και συγκρίθηκε με εκείνη των «κενών» νανοφορέων, αλλά και του φαρμάκου. Ο έλεγχος αυτός πραγματοποιήθηκε με χρώση καρκινικών κυττάρων (σειρά Α549) από ιωδιούχο προπίδιο (ΡΙ) και μέτρηση του φθορισμού των νεκρών κυττάρων από κυτταρομετρία ροής. Τα αποτελέσματα ήταν ιδιαιτέρως ικανοποιητικά, καθώς οι νανοφορείς παρουσιάζουν σταθερότητα στο χρόνο (έλεγχος περιόδου ενός μηνός), αλλά και παρουσία ηλεκτρολυτών. Το ποσοστό φόρτωσης της ΡΤΧ υπολογίστηκε ~1.2 %, ενώ η απόδοση εγκαψακίωσης κυμαινόταν από 15 - 25 %. Επίσης, παρουσίασαν υψηλή απόδοση εγκαψακίωσης SPIONs (~65 %), εξαρτώμενη από την πολυμερική σύνθεση των νανοφορέων. Οι μελέτες απελευθέρωσης παρουσίασαν παρατεταμένη αποδέσμευση της πακλιταξέλης, η οποία αποκρίνεται σε παρουσία εξωτερικού μαγνητικού πεδίου. Τέλος, τα «κενά» (χωρίς φάρμακο) μαγνητικά νανοκαψάκια δεν παρουσίασαν κυτταροτοξικότητα, σε αντίθεση με τα «φορτωμένα» με φάρμακο, τα οποία προκάλεσαν μεγαλύτερη τοξικότητα σε καρκινικά κύτταρα και από το ελεύθερο φάρμακο. Τα παραπάνω αποτελέσματα δικαιολογούν την περαιτέρω διερεύνηση της πιθανής χρησιμοποίησης των PLA-PEG μαγνητικών νανοκαψακίων ως φορείς στοχευμένης χορήγησης της Πακλιταξέλης. / Paclitaxel is one of the most widely used chemotherapeutic drugs and is particularly suitable to lung, breast, ovarian cancer and AIDS - related Kaposi sarcoma. However, its use is associated with several side effects, certain of them attributable to the formulation used clinically today, which imposed its formulation in Targetable Drug Delivery Systems (TDDS). These systems allow selective delivery of drug in the tumor tissue by passive or active targeting mechanisms and control of the pharmacokinetic profile. Particularly promising appears to be the encapsulation of PTX in polymeric nanocapsules. The core - shell structure of the nanocapsules covers the delivery of a wide variety of active ingredients, with interest focused on anti-neoplastic, anti-inflammatory, antiviral and immunosuppressive. The nanoencapsulation of drugs can increase the efficiency and the stability of active substances, while allowing better in vivo behavior and higher intracellular uptake. Some studies suggest the encapsulation of iron oxide nanoparticles (SPIONs) in such systems, which have been proven valuable tools in both diagnosis (through nuclear magnetic resonance imaging) and therapy. The application of an external alternating magnetic field permits the accumulation of magnetic nanocarrier in target-tissue (magnetic targeting), while the treatment occurs by inducing magnetic hyperthermia. This thesis discusses the encapsulation of PTX and SPIONs in polymeric nanocapsules, prepared from biocompatible poly (lactic acid) - poly (ethylene glycol) (PLA-PEG) copolymers. The PLA is a biodegradable polymer, which generates a core capable to encapsulate and protect hydrophobic substances. On the other hand, the PEG is a hydrophilic, biocompatible polymer, which gives steric stabilization systems and prolong their circulation time after intravenous administration. Specifically, magnetic nanocapsules were synthesized with varying molecular weight of copolymers PLA-PEG through the nanoprecipitation method, while the magnetic nanoparticles were composed through thermal decomposition and oleate iron [Fe (Olate) 3] was used as a precursor. The optimum parameters were determined, conferring to the nanocapsules high stability. In addition, they were characterized with regard to their size and zeta potential at different salt concentrations (up to 2M NaCl) using dynamic light scattering (DLS). Then, the morphological characteristics of nanocapsules were evaluated by transmission electron microscopy (TEM) and their structural characterization by spectroscopy FTIR. In the next step, the Paclitaxel loading was determined with liquid chromatography (HPLC) and release studies were conducted in phosphate buffer (pH = 7.4) at 37 oC for 24 h, including triggered drug-release by application of AC magnetic field. Finally, the cytotoxicity of drug-loaded (with PTX) magnetic nanocapsules was tested and compared to that of blank (without drug) nanocarriers and free drug. For these studies the cancer cell line A549 was used and after their incubation with the nanocapsules or the free drug, the dead cells were stained by propidium iodide (PI) and measured by flow cytometry. The obtained results were particularly satisfactory, as nanocarriers show stability over time (up to one month) and at high salt concentrations, much higher than the physiologic one. The loading of PTX was measured to be 1.2%, for a theoretical loading of 1.9 %, and the yield of encapsulation ranged from 15-25%. The nanocapsules also showed high encapsulation efficiency for SPIONs (~ 65%), depending on the polymeric composition of nanocarriers. Drug release studies showed that the nanocapsules exhibited controlled release properties. Furthermore, the release appeared to respond to the presence of external magnetic field. Finally, the «blank» magnetic nanocapsules did not exhibit cytotoxicity, whereas the «loaded» nanocarriers caused higher toxicity than the free drug. These results justify further investigation of the PLA-PEG magnetic nanocapsules as drug delivery systems of Paclitaxel.

Molecular biology has become an integral part of the diagnosis of infectious diseases. Recently, quantitative real-time PCR (QPCR) methods (often in the form of so-called TaqMan® systems) have been developed for the diagnosis of a wide range of infectious diseases; these techniques found valuable clinical application in the diagnosis and evaluation of progress and therapeutic success of viral diseases. The use of QPCR as a tool for diagnostic virological and viral research laboratories has greatly increased in recent years. It often replaces conventional PCR and amplicon detection systems which are more complex and laborious, with a higher risk of amplicon carry-over contamination. The new QPCR methods presented here utilize broadly targeted primers and probes for rational and sensitive detection and quantification of variable RNA viruses. They take advantage of the dual properties, both RNA and DNA dependent DNA polymerase activities, of the rTth thermostable polymerase, and thermolabile UNG with dUTP to protect against inadvertent contamination of samples with amplimers. In paper one, a novel QPCR approach to detect and quantify human enteroviral (EV) RNA in patients with neurological disorders such as aseptic meningitis is presented. In the second paper, the development of a novel serological technique, quantitative PCR enhanced immunoassay (QPIA), for serodiagnosis of EV infection, is described. In paper three the subject is the development of a touch-down QPCR (TD-QPCR) for detection and preliminary genogrouping of norovirus (NV), a group of Caliciviruses. In paper four a rational, broadly targeted, system for detection of diverse influenza viruses, yet being able to discriminate between influenza A, B and C, is designed and evaluated. In the last paper, another rational broadly targeted system, for detection of corona viruses in humans and animals, is described. The technologies described in this collection of papers have common features. They are a platform for further development of diagnostic tools for screening and detection of viruses in known viral diseases, maybe also for discovering new viruses.

As the area of nucleic acid based technologies develops, so will our understanding of how structural variations in DNA and RNA pathogens are associated with disease. The overall goal of this thesis is the development of broadly targeted measurement techniques for variable viral RNA by Real-Time PCR (here referred to as quantitative reverse transcriptase PCR, QRT-PCR). In papers I & II, broadly targeted and specific QRT-PCRs were used to study expression of endogenous and exogenous betaretrovirus sequences in human tissues. Results from human tissues demonstrated endogenous betaretrovirus expression in a tissue-specific manner, highest in reproductive tissues. Despite the high sensitivity, no exogenous betaretrovirus was found in human breast cancer samples. The limits of primer and probe degeneracy for detection of a diverse set of retroviral sequences was evaluated. These methods are useful for further investigations on the pathophysiological contribution(s) of endogenous betaretrovirus and to investigate whether an exogenous betaretrovirus is involved in human breast cancer. In papers III & IV, we developed and applied broadly targeted one-step QRT-PCRs for influenza viruses and coronaviruses. In addition to the generic primers, two novel probe design strategies were used in order to be able to broadly amplify these diverse sets of viruses: A triplex system for simultaneous detection and quantification of influenza A, B and C (3QRT-PCR and further developed 3QRT-PCR-MegB; where MegB stands for MegaBeacon) based on TaqMan® and MegB probes, and a pan-CoV QRT-PCR, based on three TaqMan® probes i.e., degeneracy was distributed on three probes. Probe fault tolerance was thus increased in two ways, either with short probes with/without locked nucleic acid (LNA) nucleotides concentrated to conserved stretches, or with long probes (MegB), compensating mismatching positions with many matching ones. Clinical samples, negative by antigen detection with immunofluorescence (IFA), were influenza A positive with 3QPCR-MegB. Avian pooled samples, negative with an earlier pan-CoV QPCR, came out positive with the triple-probe system. Assay evaluation with clinical samples and reference strains revealed good clinical diagnostic potential. Thus, the thesis describes several strategies to counteract sequence variation of RNA viruses and describes a set of broadly targeted QRT-PCRs useful for scientific screening or diagnostics of betaretroviruses and respiratory viruses.

A new class of polymer coated lanthanide fluoride nanoparticle aggregates (NPAs) was developed as potential MRI contrast agents. The NPA synthesis has been perfected to control the size distribution and optimize relaxivities. Polyacrylic acid was used as a stabilizing polymer, and was conjugated to folic acid to improve targeting to SK-BR-3 breast cancer cells. Terbium was incorporated in the synthesis to study the passive and active targeting properties of NPAs. Through a series of microscopy experiments, a significant difference in uptake between NPAs with and without targeting moieties occurs after 48 hours of incubation. The relaxivity of the optimized nanoparticles was measured to be 56 s-1(mg/ml)-1 using a 1.5 T scanner, which may be compared to that of the commercially available Gd3+-DTPA [R1 = 7 s-1(mg/ml)-1]. Abdominal perfusion studies in rats also demonstrated that the NPAs provide better contrast of the vasculature than Gd3+-DTPA does at the same mass concentration.

Targeted Energy Transfer is a resonance phenomenon in coupled anharmonic oscillators. In this thesis we investigate if the concept of Targeted Energy Transfer is applicable to Bose-Einsteain condensates in optical lattices. The model used to describe Bose-Einstein condensates in optical lattices is based on the Gross-Pitaevskii equation. Targeted Energy Transfer in these systems would correspond to energy being transferred from one lattice site to another. We also try to expand the concept of Targeted Energy Transfer to a system consisting of three sites, where one of the sites are considered a perturbation to the system. We have concluded that it is possible to achieve Targeted Energy Transfer in a three-site system. The set-up of the system will in some of the cases studied lead to interesting properties, such as more energy being transferred to the acceptor site than what was initially localized on the donor site.

Alpha-helical coiled-coils are common protein structural motifs with varied mechanical roles, such as, tropomyosin in muscle contraction or neck-stalks of kinesins and myosins, in motor proteins. Using computer simulations, we characterized elastic properties of coiled-coils both, globally and locally. Normal mode analysis for global elastic properties revealed a buckling instability due to inherently present weak non-bonded forces. We characterized this using a critical buckling length (lc). For coiled-coils, lc was significantly less than their persistence length thereby governing the filament conformation. We also found that mutations to the hydrophobic residues at the knob-into-hole interface affect elasticity of coiled-coils significantly. We built a flexibility map of tropomyosin using a local fluctuation analysis and found regional variations in flexibilities due to such breaks in the knob-into-hole packing. Overall, flexibility varies by more than twofold and increases towards the C-terminal region of the molecule. Actin binding sites in zones and broken core regions due to acidic residues at the hydrophobic face such as, the Asp137 and the Glu218, are found to be the most labile with moduli for splay and broad face bending as 70 nm and 116 nm, respectively. Such variations in flexibility could be relevant to the tropomyosin function, especially for moving across the non-uniform surface of F-actin to regulate myosin binding. Non-claret disjunction (Ncd), is a Kinesin-14 family protein that walks to the microtubule's minus end. Although available structures show its alpha-helical coiled-coil neck in either pre- or post-stroke orientations, little is known about the transition between these two states. Using a combination of molecular dynamics simulations and structural analyses, we find that the neck travel is a guided diffusion involving sequential intermediate contacts with the motor head. The post-stroke is at a higher free-energy minimum than the pre-stroke. The importance of intermediate contacts correlates with the existing motility data including those of mutant Ncds and other members of the kinesin-14 family. While the forward motion has a ~4.5 kBT (kB: Boltzmann constant, T = 300 K) free energy barrier, recovery stroke goes nearly downhill in free energy. The hysteresis in forward and reverse neck motion energetics arises from the mechanical compliance of the protein, and together with guided diffusion, it may be key for the directed motility of Ncd. Although it is known that neighboring Ncds on a microtubule (MT) have an attractive interaction and a group of Ncds act cooperatively, the physical basis of neither this attraction nor the cooperativity is known. From structural analysis of Ncd neighbors on an MT lattice we find that steric hindrances between the coiled-coil neck-stalks of longitudinal neighbors drive synchrony among a group of Ncds on a single protofilament. Across lateral dimers, surface loop L2 of the motor-head (MH) that is not bound to the MT (unbound-MH) in a pre-stroke dimer, is seen to have strong attraction to the nucleotide pocket in the MH that is bound to MT (bound-MH) of its off-axis neighbor. Such an attraction will however impede the motility in both the dimers. We hence propose rules that drive motor binding to an MT site in the presence of immediate neighbors such that motility of the group is not compromised. The unbound-MH, whose role in the walking step of an Ncd was unclear, is thus seen to regulate MT decoration.

Affibody molecules are promising candidates for targeted radionuclide-based imaging and therapy applications. Optimisation of targeting properties would permit the in vivo visualization of cancer-specific surface receptors with high contrast. In therapy, this may increase the ratio of radioactivity uptake between tumour and normal tissues.  This thesis work is based on 5 original research articles (papers I-V) and focuses on optimisation of targeting properties of anti-HER2 affibody molecules by optimising the labelling chemistry. Paper I and II report the comparative evaluation of the anti-HER2 ZHER2:2395 affibody molecule site specifically labelled with 111In (suitable for SPECT imaging) and 68Ga (suitable for PET imaging) using the thiol reactive derivatives of DOTA and NODAGA as chelators. The incorporation of different macrocyclic chelators and labelling with different radionuclides modified the biodistribution properties of affibody molecules. This indicates that the labelling strategy may have a profound effect on the targeting properties of radiotracers and must be carefully optimized. Paper III reports the study of the mechanism of renal reabsorption of anti-HER2 ZHER2:2395 affibody molecule. An unknown receptor (not HER2) is suspected to be responsible for the high reabsorption of ZHER2:2395 molecules in the kidneys. Paper IV reports the optimization and development of in vivo targeting properties of 188Re-labelled anti-HER2 affibody molecules. By using an array of peptide based chelators, it was found that substitution of one amino acid by another or changing its position can have a dramatic effect on the biodistribution properties of 188Re-labelled affibody molecules. This permitted the selection of –GGGC chelator whichdemonstrated the lowest retention of radioactivity in kidneys compared to other variants and showed excellent tumour targeting properties. Paper V reports the preclinical evaluation of 188Re-ZHER2:V2 as a potential candidate for targeted radionuclide therapy of HER2-expressing tumours. In vivo experiments in mice along with dosimetry assessment in both murine and human models revealed that future human radiotherapy studies using 188Re-ZHER2:V2 may be feasible. It would be reasonable to believe that the results of optimisation of anti-HER2 affibody molecules summarized in this thesis can be of importance for the development of other scaffold protein-based targeting agents.

To date, the collection of comprehensive household travel data has been a challenge for most metropolitan planning organizations (MPOs) and state departments of transportation (DOTs) due mainly to high costs. Urban population growth, the expansion of metropolitan regions, and the general unwillingness of the public to complete surveys conflict with limited public funds. The purpose of this research is to leverage targeted marketing data, sometimes referred to as consumer data or just simply marketing data, for travel demand modeling applications. This research reveals a first step in exploring the use of targeted marketing data for representing population characteristics of a region. Four studies were completed: an aggregate validation, a household-level validation for hard-to-reach population groups, an airport passenger model, and a residential location choice model. The two validation studies of this work suggest that targeted marketing data are similar to U.S. Census data at small geographic levels for basic demographic and socioeconomic information. The studies also suggest that the existing coverage errors are at least similar, if not lower than, the levels of those in household travel surveys used today to build travel demand models. The two application studies of this work highlight the benefits of the targeted marketing data over traditional household travel surveys and U.S. Census data particularly well, including the additional behavioral information available at the household-level and the very large sample sizes. These results suggest that the combination of targeted marketing data with other third-party and non-traditional data could be particularly powerful. It offers tremendous opportunities to enhance, or even transform, existing travel demand modeling systems and data collection practices. Inexpensive, up-to-date, and detailed data would allow researchers and decision-makers alike to better understand travel behavior and to be more equipped to make important transportation-related decisions that affect our lives each day.

In this thesis we explore robust statistical syntax analysis for French. Our main concern is to explore methods whereby the linguist can inject linguistic knowledge and/or resources into the robust statistical engine in order to improve results for specific phenomena. We first explore the dependency annotation schema for French, concentrating on certain phenomena. Next, we look into the various algorithms capable of producing this annotation, and in particular on the transition-based parsing algorithm used in the rest of this thesis. After exploring supervised machine learning algorithms for NLP classification problems, we present the Talismane toolkit for syntax analysis, built within the framework of this thesis, including four statistical modules - sentence boundary detection, tokenisation, pos-tagging and parsing - as well as the various linguistic resources used for the baseline model, including corpora, lexicons and feature sets. Our first experiments attempt various machine learning configurations in order to identify the best baseline. We then look into improvements made possible by beam search and beam propagation. Finally, we present a series of experiments aimed at correcting errors related to specific linguistic phenomena, using targeted features. One our innovation is the introduction of rules that can impose or prohibit certain decisions locally, thus bypassing the statistical model. We explore the usage of rules for errors that the features are unable to correct. Finally, we look into the enhancement of targeted features by large scale linguistic resources, and in particular a semi-supervised approach using a distributional semantic resource.