Pharmaceutical biotechnology has been emerging as a defined, increasingly important area of science dedicated to the discovery and delivery of drugs and therapies for the treatment of various human diseases. In contrast to the advancement in pharmaceutical biotechnology, current drug discovery efforts are facing unprecedented challenges. Difficulties in identifying novel drug targets and developing effective and safe drugs are closely related to the complexity of the network of interacting human proteins. Protein-protein interactions mediate virtually all cellular processes. Therefore both identification and understanding of protein-protein interactions are essential to the process of deciphering disease mechanisms and developing treatments. Unfortunately, our current knowledge and understanding of the human interactome is largely incomplete. Most of the unknown protein-protein interactions are expected to be weak and/or transient, hence are not easily identified. These unknown or uncharacterized interactions could affect the efficacy and toxicity of drug candidates, contributing to the high rate of failure. In an attempt to facilitate the ongoing efforts in drug discovery, we describe herein a series of novel methods and their applications addressing the broad topic of protein-protein interactions. We have developed a highly efficient site-specific protein cross-linking technology mediated by the genetically incorporated non-canonical amino acid L-DOPA to facilitate the identification and characterization of weak protein-protein interactions. We also established a protocol to incorporate L-DOPA into proteins in mammalian cells to enable in vivo site-specific protein cross-kinking. We then applied the DOPA-mediated cross-linking methodology to design a protein probe which can potentially serve as a diagnostic tool or a modulator of protein-protein interactions in vivo. To deliver such engineered proteins or other bioanalytical reagents into single live cells, we established a laser-assisted cellular nano-surgery protocol which would enable detailed observations of cell-to-cell variability and communication. Finally we investigated a possible experimental scheme to genetically evolve a fluorescent peptide, which has tremendous potential as a tool in cellular imaging and dynamic observation of protein-protein interactions in vivo. We aim to contribute to the discovery and development of new drugs and eventually to the overall health of our society by adding the technology above to the array of currently available bioanalytical tools. / text

Cells utilize various signal transduction networks to regulate metabolism. Nevertheless, a quantitative understanding of the relationship between growth factor signaling and metabolic state at the single cell level has been lacking. The signal transduction and metabolic states could vary widely among individual cells. However, such cell-to-cell variation might be masked by the bulk measurements obtained from conventional biochemical methods. To assess the spatiotemporal dynamics of metabolism in individual intact cells, we developed genetically encoded biosensors based on fluorescent proteins. As a key redox cofactor in metabolism, NADH has been implicated in the Warburg effect, the abnormal metabolism of glucose that is a hallmark of cancer cells. To date, however, sensitive and specific detection of NADH in the cytosol of individual live cells has been difficult. We engineered a fluorescent biosensor of NADH by combining a circularly permuted green fluorescent protein variant with a bacterial NADH-binding protein Rex. The optimized biosensor Peredox reports cytosolic \(NADH:NAD^+\) ratios in individual live cells and can be calibrated with exogenous lactate and pyruvate. Notably pH resistant, this biosensor can be used in several cultured and primary cell types and in a high-content imaging format. We then examined the single cell dynamics of glycolysis and energy-sensing signaling pathways using Peredox and other fluorescent biosensors: AMPKAR, a sensor of the AMPK activity; and FOXO3-FP, a fluorescently-tagged protein domain from Forkhead transcription factor FOXO3 to report on the PI3K/Akt pathway activity. With perturbation to growth factor signaling, we observed a transient response in the cytosolic \(NADH:NAD^+\) redox state. In contrast, with partial inhibition of glycolysis by iodoacetate, individual cells varied substantially in their responses, and cytosolic \(NADH:NAD^+\) ratios oscillated between high and low states with a regular, approximately half-hour period, persisting for hours. These glycolytic NADH oscillations appeared to be cell-autonomous and coincided with the activation of the PI3K/Akt pathway but not the AMPK pathway. These results suggest a dynamic coupling between growth factor signaling and metabolic parameters. Overall, this thesis presents novel optical tools to assess metabolic dynamics – and to unravel the elaborate and complex integration of glucose metabolism and signaling pathways at the single cell level.

Single molecules and single cells are the fundamental building blocks in biology. Facilitated by the advancement of technology, quantitative single-molecule and single-cell measurements provide a unique perspective toward many biological systems by revealing individual stochasticity and population heterogeneity. Taking advantage of these approaches, we studied chromosome organization and gene expression in bacteria and discovered new biophysical mechanisms: chromosome organization by a nucleoid-associated protein in live bacteria, and transcriptional bursting by the regulation of DNA supercoiling in bacteria.

A healthy immune system's core challenge is to mount appropriate responses to an immense and unknown variety of antigenic stimuli. By unraveling the regulatory networks that drive and control immune-cell behaviors, we can begin to identify the means by which proper balance can be achieved and aberrant behaviors clinically corrected. Traditionally, major advances in our understanding of cellular immunological processes depended critically on both improved perturbation and enhanced observation methods. In my doctoral research, I have pursued both strategies to elucidate the differentiation and effector functions of adaptive immune Th17 cells. These cells exemplify the need for balance: while Th17 cells are needed to induce clearance of fungal infections and extracellular bacteria, irregular responses have been strongly implicated in autoimmunity. / Chemistry and Chemical Biology

Acute myeloid leukemia (AML) is a clonal neoplastic disorder organized as a cellular hierarchy, with the self-renewing leukemia stem cell (LSC) at the apex. Recurrent mutations in transcription factors (TF) and epigenetic regulators suggest that AML is driven by aberrant transcriptional circuits, but these circuits have not been fully defined in an LSC model. To study transcriptional mechanisms relevant to leukemogenesis in vivo, we generated a murine serial transplantation model of MLL-AF9-driven, myelomonocytic leukemia with genetically- and phenotypically-defined LSCs. Using this model, we pursued two related lines of investigation. First, we performed an in vivo RNA interference (RNAi) screen to identify transcription factors required for LSC function. This screen highlighted the circadian rhythm TFs, Clock and Bmal1, as genes essential for the survival of murine leukemia cells, and we validated this finding with CRISPR/Cas-based genome editing and knockdown studies in AML cell lines. Utilizing luciferase reporter mice to track expression of the circadian target gene Per2, we demonstrated that both leukemic and normal hematopoietic cells have the capacity for oscillating, circadian-dependent gene expression. Importantly, using murine knockout models, we found that normal hematopoietic stem and progenitor cells (HSPC), in contrast to leukemia cells, do not depend on Bmal1. We further demonstrated that selective depletion of LSCs following circadian perturbation is mediated through enhanced myeloid differentiation. ChIP-Seq studies revealed that the circadian rhythm network is integrally connected to the LSC self-renewal circuitry and highlighted putative Clock/Bmal1 targets in leukemia, providing a mechanistic basis for our findings. Second, we performed a functional and genomic characterization of our MLL-AF9 serial transplantation model to explore mechanisms of disease evolution and clonal selection in AML. Limiting dilution studies demonstrated that serial transplantation results in a reduction in disease latency, dramatic enrichment of leukemia-initiating cells (LIC), and reconfiguration of the LSC hierarchy. While mutations in known AML-associated genes were not linked to disease progression, RNA-sequencing (RNA-Seq) demonstrated that the increase in LIC frequency in serially transplanted leukemias is driven by changes in cell cycle and differentiation. In aggregate, these studies offer insights into the biological mechanisms regulating LSC self-renewal and disease evolution in AML.

The fascinating capability of cellular self-organization during tissue development and repair is a central question in developmental biology and regenerative medicine. Understanding the dynamic morphogenic and regenerative processes of biological tissues will have important implications in biology and medicine. Nevertheless, the elucidation of the cellular self-organization processes is hindered by a lack of effective tools for monitoring the spatiotemporal gene expression distribution and a lack of ability to perturb the self-organization processes in living cells and tissues. Multimodal modularities that allow both single cell perturbation and gene detection are required to enable a new paradigm in the investigation of complex tissue morphogenic processes. To address this critical challenge in the field of developmental and regenerative medicine, we are developing a multimodal gold nanorod-locked nucleic acid (GNR-LNA) composite for single cell gene expression analysis in living cells and tissues at the transcriptional level. Using antisense RNA sequences, we design LNA probes for detecting specific molecular targets in living cells. The LNA probes bind to the GNR spontaneously due to the intrinsic affinity between the GNR and LNA. In close proximity, the fluorescent probes are effectively quenched by the GNR. Therefore, a fluorescent signal is only observed when the specific target thermodynamically displaces the LNA probe from the GNR. Furthermore, the GNR also serves as a transducer for photothermal ablation. Thus, we established a novel modularity for imaging the spatiotemporal gene expression distribution in living cells and tissues. The single cell analysis capability of our techniques enables us to adopt a unique approach to study the tissue regenerative processes during normal development and diseases, and this will have a profound impact on regenerative medicine and disease treatment in future. Moreover, we applied this GNR-LNA probe to explore the endothelial cell mRNA dynamics during capillary morphogenesis. Three different types of cells were identified due to their different roles during endothelial cell capillary-like formation process. Our findings indicated that the endothelial cell behavior is directly related to the Dll4 mRNA expression, and Dll4 expression in ECs determine the cell fate. Our GNR-LNA probe enable us to investigate the correlations between Dll4 mRNA expression and cell behavior during capillary morphogenesis. Experimental results indicated that: (1) When the endothelial cells aggregate, the cells migrate with certain displacement, the Dll4 mRNA expression decreases. (2) When the endothelial cells sprout, the cells migrate with small displacement but the cell shape changes to an ellipse shape, the Dll4 mRNA expression begin to increase. (3) When the endothelial cells elongate and form cell-cell contract with adjacent cells, the Dll4 expression decreased to a certain level and keep stable until the cell activity change to another stage. Furthermore, it has been demonstrated endothelial cells compete for the leader cell position during wound healing, collective cell migration, and tip cell formation during angiogenic process. It has been demonstrated that endothelial cells compete for the tip cell formation through Notch signaling pathway. However, how the mechanical force regulates tip cell formation is still unclear, and if mechanoregulation of tip cell formation through Notch pathway still unknown. Mechanical and chemical regulations of tissue morphogenesis and angiogenesis are being investigated in both in vitro capillary-like network formation assay and in vivo mice retina angiogenesis assay. Here, we investigated the mechanoregulation of mechanotransduction of tissue morphogenesis and angiogenesis using both in vitro endothelial cell tube formation model and in vivo mice retina blood vessel development model. Our results demonstrated that (1) Notch pathway negatively regulates tip cell formation: inhibition of Notch pathway (DAPT) enhances tip cell formation, induces Dll4 and Notch1 activity, activation of Notch pathway (Jag1 peptide) inhibits tip cell formation, suppresses Dll4 and Notch1 activity. (2) Mechanical force negatively regulate tip cell formation: (a) Decrease mechanical force via Rho kinase inhibitor Y-27632, myosin II inhibitor Blebbistatin, or laser ablation, enhances tip cell formation and induces Dll4 activity through mediation of Dll4-Notch1 lateral inhibition, (b) increase mechanical force via traction force inducer Nocodazole and Calyculin A, suppresses tip cell formation and inhibits Dll4 activity through activation of Notch pathway. (3) Mechanical force negatively regulates tip cell formation partially via mediation of Notch pathway. Mechanical force is necessary for tip cell formation and negatively regulate tip/stalk selection via Dll4-Notch1 lateral inhibition. Interruption of mechanical force enhance tip cell formation via suppression of Dll4-Notch1 lateral inhibition, thus resulting the increase of Dll4 expression. Enhance of mechanical force inhibits tip cell formation via activation of Dll4-Notch1 lateral inhibition, thus resulting the decreases of Dll4 expression. All these finding wills have great significance for various biomedical applications, such as tissue engineering, cancer, and drug screening.

Infectious diseases resulting from bacterial pathogens are the most common causes of patient morbidity and mortality worldwide. The rapid identification of the pathogens and their antibiotic resistances is crucial for proper clinical management. However, the standard culture-based diagnostic approach requires a minimum of two days from the initial specimen collection to result reporting. As a consequence, broad-spectrum antibiotics are often prescribed under the worst-case assumption without knowledge of the pathogens or their resistances. The current clinical practice results in improper treatment of the patient and causes the rapid emergence of multi-drug resistant pathogens. A rapid diagnostics system has therefore been developed which performs hybrid electrokinetic sample preparation and volume reduction, for single-cell antimicrobial susceptibility testing (AST). The system combines multiple electrokinetic forces for sample preparation, which reduces the sample volume for over 3 orders of magnitude and minimizes the matrix effects of physiological samples for enhanced sensitivity. The device is integrated with a single-cell AST system with microfluidic confinement and electrokinetic loading to phenotypically determine the bacterial antibiotic resistance at the single-cell level. The applicability of the system has been demonstrated for performing direct AST with urine and blood samples within one hour, enabling rapid infectious disease diagnostics in non-traditional healthcare settings.

Λόγω της αύξησης των τιμών του αργού πετρελαίου, τα τελευταία χρόνια η παραγωγή βιοντίζελ (biodiesel) έχει αποκτήσει μεγάλο ενδιαφέρον. Η χρήση των φυτικών ελαίων ως πρώτη ύλη στη βιομηχανία παραγωγής βιοντίζελ έχει πολλά μειονεκτήματα. Επομένως, το ενδιαφέρον των ερευνητών έχει στραφεί στη χρήση των SCO (ελαίων μονοκύτταρων οργανισμών), ως μία εναλλακτική πρώτη ύλη. Στην παρούσα διπλωματική εργασία, η βιομηχανική γλυκερόλη μετατράπηκε σε SCO από διάφορα στελέχη ελαιογόνων Ζυγομυκήτων, οι οποίοι καλλιεργήθηκαν υπό μη-ασηπτικές συνθήκες, χρησιμοποιώντας εκλεκτικά, περιοριστικά ως προς την πηγή αζώτου θρεπτικά μέσα καλλιέργειας, τα οποία ανέστειλαν τη βακτηριακή αύξηση. Όταν οι μύκητες Thamnidium elegans, Mortierella ramanniana, Mortierella isabellina, Zygorhynchus moelleri, Mucor sp. και Cunninghamella echinulatα καλλιεργήθηκαν σε pH6 υπό μη-ασηπτικές συνθήκες, ήταν ικανοί να παράγουν 1,2- 4,1 g/l βιομάζα και να συνθέτουν 17,5- 49,3% wt/wt λιπίδια επί της ξηρής τους βιομάζας. Τα επίπεδα σύνθεσης της βιομάζας ήταν ~50% χαμηλότερα από εκείνα που επιτεύχθηκαν όταν οι Ζυγομύκητες καλλιεργήθηκαν υπό ασηπτικές συνθήκες. Διάφορες αντι-βακτηριακές ουσίες (αιθέρια έλαια, αντιβιοτικά) χρησιμοποιήθηκαν ώστε να επιτευχθεί υψηλότερη συσσώρευση βιομάζας και λιπιδίων από τους Ζυγομύκητες. Σε pH5, ο μύκητας M. ramanniana παρήγαγε 4,4 g/l βιομάζα που περιείχε 22% wt/wt λιπίδια, ενώ ο μύκητας T. elegans παρήγαγε 3,4 g/l βιομάζα που περιείχε 45% wt/wt λιπίδια επί της ξηρής τους βιομάζας. Όταν προστέθηκε στο μέσο καλλιέργειας αιθέριο έλαιο θυμαριού, 4,8 g/l βιομάζα συντέθηκαν από το μύκητα Τ. elegans που περιείχαν 42,6% wt/wt λιπίδια. Επιπλέον, όταν προστέθηκαν στο μέσο καλλιέργειας αντιβιοτικά και αιθέριο έλαιο, ο μύκητας T. elegans ήταν ικανός να παράγει 7,9 g/l βιομάζα που περιείχε 31,5 % wt/wt λιπίδια. Τα αποτελέσματα έδειξαν ότι αν και ο πληθυσμός των βακτηρίων ανέστειλε την αύξηση των μυκήτων, η συσσώρευση των λιπιδίων δεν επηρεάστηκε από την παρουσία των βακτηρίων στο μέσο καλλιέργειας, συγκρινόμενα με αποτελέσματα πειραμάτων που πραγματοποιήθηκαν υπό ασηπτικές συνθήκες (control). Ως εκ τούτου, αναπτύχθηκε μια διεργασία δύο σταδίων στις κωνικές φιάλες και στο βιοαντιδραστήρα, κατά την οποία η αύξηση του μύκητα πραγματοποιήθηκε υπό ασηπτικές συνθήκες (1ο στάδιο) και ακολούθησε η συσσώρευση των λιπιδίων που πραγματοποιήθηκε υπό μη-ασηπτικές συνθήκες (2ο στάδιο). Στο 2ο στάδιο, προστέθηκε στο θρεπτικό μέσο καλλιέργειας αιθέριο έλαιο θυμαριού ως αντι- βακτηριακή ουσία. Από αυτή τη διεργασία, υψηλές ποσότητες λιπιδίων συσσωρεύτηκαν μέσα στο μυκήλιο του μύκητα, με απόδοση που έφτασε περίπου 13% wt/wt μικροβιακού ελαίου ανά καταναλωθείσα γλυκερόλη. / Biodiesel production has gained much interest during last years as an alternative fuel source, which arises from the escalating prices of petroleum fuels. The use of plant oils as feedstock for the biodiesel manufacture has many drawbacks, thus the interest has turned to single cell oil (SCO) as an alternative. In this thesis, raw glycerol was converted into SCO by oleaginous Zygomycetes, cultivated under non-aseptic conditions, using selective nitrogen limited media that inhibit the bacterial growth. Thamnidium elegans, Mortierella ramanniana, Mortierella isabellina, Zygorhynchus moelleri, Mucor sp. and Cunninghamella echinulata, cultivated at pH6 under non-aseptic conditions, were able to produce 1.2- 4.1 g/l of biomass and synthesized 17.5- 49.3 % wt/wt of lipids in their biomass. These accumulation levels in biomass were ~50% lower compared to those achieved when Zygomycetes grown under aseptic conditions. Various anti-bacterial compounds, including essential oils and antibiotics were used in order to achieve a higher biomass and lipid accumulation. At pH5, M. ramanniana produced 4.4 g/l biomass containing 22% wt/wt lipids in their biomass, while T. elegans produced 3.4 g/l biomass containing 45% wt/wt of lipids. When thyme essential oil was added into the growth medium, T. elegans produced 4.8 g/l biomass containing 42.6% wt/wt lipids. Furthermore, with the addition of antibiotics together with essential oil into the medium, the production of SCO was further improved with T. elegans being able to produce 7.9 g/l of biomass containing 31.5% wt/wt lipids. The obtained data showed that although bacterial populations inhibited the fungal growth, lipid accumulation remained unaffected by the presence of bacteria in the growth medium compared to control experiments (conducted under aseptic conditions). Therefore, a two-stage process was developed in both flasks and bioreactor, in which growth was performed under aseptic conditions (1st stage) followed by lipid accumulation performed under non-aseptic conditions (2nd stage) in the presence of thyme essential oil as an antibacterial agent. Large amounts of lipids were accumulated inside the mycelia, yielding around 13% wt/wt of oil per glycerol consumed.

Recent advances in micro technologies have equipped researches with novel tools for interacting with biological molecules and cells. This thesis focuses on the design, fabrication and application of microfluidic platforms for stimuli-responsive drug delivery and the electromechanical characterization of single cells. Stimuli-responsive hydrogels are promising materials for controlled drug delivery due to their ability to respond to changes in local environmental conditions. In particular, nanohydrogel particles have been a topic of considerable interest due to their rapid response times compared to micro and macro-scale counterparts. Owing to their small size and thus low drug-loading capacity, these materials are unsuitable for prolonged drug delivery. To address this issue, stimuli-responsive implantable drug delivery micro devices by integrating microfabricated drug reservoirs with smart nano-hydrogel particles embedded composite membranes have been proposed. In one proposed glucose-responsive micro device, crosslinked glucose oxidase enables the oxidation of glucose into gluconic acid, producing a microenvironment with lower pH values to modulate the pH-responsive nanoparticles. In vitro glucose-responsive drug release profiles were characterized and normoglycemic glucose levels in diabetic rats with device implantation were also recorded. The biophysical properties of single cells have recently been demonstrated as an important indicator of disease diagnosis. Existing technologies are capable of characterizing single parameter either electrical or mechanical rapidly, but not both, which could only collect limited information for cell status evaluation. To address this issue, two microfluidic platforms capable of simultaneously characterizing both the electrical and mechanical properties of single cells based on electrodeformation and integrated impedance spectroscopy with micropipette aspiration have been proposed. In one proposed microfluidic device, a negative pressure was used to suck cells continuously through the aspiration channel with impedance profiles measured. By interpreting impedance profiles, transit time and impedance amplitude ratio can be quantified as cellular mechanical and electrical property indicators. Neural network based cell classification was conducted, demonstrating that two biophysical parameters could provide a higher cell classification success rate than using electrical or mechanical parameter alone.

Little is known regarding the neurophysiological mechanisms by which the neuropeptide prokineticin 2 (PK2) regulates circadian rhythms. Using whole-cell electrophysiology, we have investigated a potential role for regulation of neuronal excitability by PK2 on neurons of the area postrema (AP), a medullary structure known to influence autonomic processes in the central nervous system. In current-clamp recordings, focal application of 1µM PK2 reversibly influenced the excitability of the majority of dissociated AP cells tested, producing both depolarizations (38%) and hyperpolarizations (28%) in a concentration-dependent manner. Slow voltage ramps and ion substitution experiments revealed a PK2-induced Cl- current was responsible for membrane depolarization, while hyperpolarizations were the result of inhibition of an inwardly rectifying non-selective cation current. In contrast to these differential effects on membrane potential, nearly all neurons that displayed spontaneous activity responded to PK2 with a decrease in spike frequency. These observations are in accordance with voltage-clamp experiments showing that PK2 caused a leftward shift in Na+ channel activation and inactivation gating. Lastly, using post hoc single cell RT-PCR technology, we have shown that 7 out of 10 AP neurons depolarized by PK2 were enkephalin-expressing cells. The observed actions on enkephalin neurons indicate PK2 may have specific inhibitory actions on this population of neurons in the AP acting to reduce their sensitivity to incoming signals. These data suggest that PK2 regulates the level of AP neuronal excitability and may impart a circadian influence on AP autonomic control. / Thesis (Master, Physiology) -- Queen's University, 2009-08-18 11:18:05.977