Binding of small molecules to DNA junctions

Previous results in our laboratory suggest that the (CG) 4 segments whether present in a right-handed or a left-handed conformation form distinctive junctions with adjacent random sequences. These junctions and their associated sequences have unique structural and thermodynamic properties that may be recognized by DNA-binding molecules. This study probes these sequences by using the following small ligands: actinomycin D, 1,4-bis(((di(aminoethyl)amino)ethyl)amino)anthracene-9,10-dione, ametantrone, and tris(phenanthroline)ruthenium (II). These ligands may recognize the distinctive features associated to the (CG)4 segment and its junctions and thus interact preferentially near these sequences. Restriction enzyme inhibition assays were used to determine whether or not binding interactions took place, and to approximate locations of these interactions. These binding studies are first carried out using two small synthetic oligomers BZ-III and BZ-IV. The (5meCG)4 segment present in BZ-III adopts the Z-conformation in the presence of 50 m M Co(NH3)63+. In BZ-IV, the unmethylated (CG)4 segment changes to a non-B conformation in the presence of 50 m M Co(NH3)63+. BZ-IV, containing the (CG)4 segment, was inserted into a clone plasmid then digested with the restriction enzyme Hinf I to produce a larger fragment that contains the (CG)4 segment. The results obtained on the small oligomers and on the larger fragment for restriction enzyme Mbo I indicate that 1,4-bis(((di(aminoethyl)amino)ethyl)amino)anthracene-9,10-dione binds more efficiently at or near the (CG)4 segment. Restriction enzymes EcoRV, Sac I and Not I with cleavage sites upstream and downstream of the (CG)4 insert were used to further localize binding interactions in the vicinity of the (CG)4 insert. RNA polymerase activity was studied in a plasmid which contained the (CG)4 insert downstream from the promoter sites of SP6 and T7 RNA polymerases. Activities of these two polymerases were studied in the presence of each one of the ligands used throughout the study. Only actinomycin D and spider, which bind at or near the (CG)4 segment, alter the activities of SP6 and T7 RNA polymerases. Surprisingly, enhancement of polymerase activity was observed in the presence of very low concentrations of actinomycin D. These results suggest that the conformational features of (CG) segments may serve in regulatory functions of DNA. ^

Morphology of soleus and EDL neuromuscular junctions in the transected rat model following fetal tissue transplant

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Influence of fetal tissue transplant on the morphology of the neuromuscular junctions of tibialis anterior and medial gastrocnemius following spinal transection in the rat

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Role of Vinculin in Regulating Force-Sensitive Dynamics of Adherens Junctions During Collective Cell Migration

Dynamic processes such as morphogenesis and tissue patterning require the precise control of many cellular processes, especially cell migration. Historically, these processes are thought to be mediated by genetic and biochemical signaling pathways. However, recent advances have unraveled a previously unappreciated role of mechanical forces in regulating these homeostatic processes in of multicellular systems. In multicellular systems cells adhere to both deformable extracellular matrix (ECM) and other cells, which are sources of applied forces and means of mechanical support. Cells detect and respond to these mechanical signals through a poorly understood process called mechanotransduction, which can have profound effects on processes such as cell migration. These effects are largely mediated by the sub cellular structures that link cells to the ECM, called focal adhesions (FAs), or cells to other cells, termed adherens junctions (AJs).

Overall this thesis is comprised of my work on identifying a novel force dependent function of vinculin, a protein which resides in both FAs and AJs - in dynamic process of collective migration. Using a collective migration assay as a model for collective cell behavior and a fluorescence resonance energy transfer (FRET) based molecular tension sensor for vinculin I demonstrated a spatial gradient of tension across vinculin in the direction of migration. To define this novel force-dependent role of vinculin in collective migration I took advantage of previously established shRNA based vinculin knock down Marin-Darby Canine Kidney (MDCK) epithelial cells.

The first part of my thesis comprises of my work demonstrating the mechanosensitive role of vinculin at AJ’s in collectively migrating cells. Using vinculin knockdown cells and vinculin mutants, which specifically disrupt vinculin’s ability to bind actin (VinI997A) or disrupt its ability to localize to AJs without affecting its localization at FAs (VinY822F), I establish a role of force across vinculin in E-cadherin internalization and clipping. Furthermore by measuring E-cadherin dynamics using fluorescence recovery after bleaching (FRAP) analysis I show that vinculin inhibition affects the turnover of E-cadherin at AJs. Together these data reveal a novel mechanosensitive role of vinculin in E-cadherin internalization and turnover in a migrating cell layer, which is contrary to the previously identified role of vinculin in potentiating E-cadherin junctions in a static monolayer.

For the last part of my thesis I designed a novel tension sensor to probe tension across N-cadherin (NTS). N-cadherin plays a critical role in cardiomyocytes, vascular smooth muscle cells, neurons and neural crest cells. Similar to E-cadherin, N-cadherin is also believed to bear tension and play a role in mechanotransduction pathways. To identify the role of tension across N-cadherin I designed a novel FRET-based molecular tension sensor for N-cadherin. I tested the ability of NTS to sense molecular tension in vascular smooth muscle cells, cardiomyocytes and cancer cells. Finally in collaboration with the Horwitz lab we have been able to show a role of tension across N-cadherin in synaptogenesis of neurons.

Morphology of soleus and EDL neuromuscular junctions in the transected rat model following fetal tissue transplant

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Influence of fetal tissue transplant on the morphology of the neuromuscular junctions of tibialis anterior and medial gastrocnemius following spinal transection in the rat

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Neuronal networks with gap junctions: A study of piece-wise linear planar neuron models

The presence of gap junction coupling among neurons of the central nervous systems has been appreciated for some time now. In recent years there has been an upsurge of interest from the mathematical community in understanding the contribution of these direct electrical connections between cells to large-scale brain rhythms. Here we analyze a class of exactly soluble single neuron models, capable of producing realistic action potential shapes, that can be used as the basis for understanding dynamics at the network level. This work focuses on planar piece-wise linear models that can mimic the firing response of several different cell types. Under constant current injection the periodic response and phase response curve (PRC) is calculated in closed form. A simple formula for the stability of a periodic orbit is found using Floquet theory. From the calculated PRC and the periodic orbit a phase interaction function is constructed that allows the investigation of phase-locked network states using the theory of weakly coupled oscillators. For large networks with global gap junction connectivity we develop a theory of strong coupling instabilities of the homogeneous, synchronous and splay state. For a piece-wise linear caricature of the Morris-Lecar model, with oscillations arising from a homoclinic bifurcation, we show that large amplitude oscillations in the mean membrane potential are organized around such unstable orbits.

Gap junctions and emergent rhythms

Gap junction coupling is ubiquitous in the brain, particularly between the dendritic trees of inhibitory interneurons. Such direct non-synaptic interaction allows for direct electrical communication between cells. Unlike spike-time driven synaptic neural network models, which are event based, any model with gap junctions must necessarily involve a single neuron model that can represent the shape of an action potential. Indeed, not only do neurons communicating via gaps feel super-threshold spikes, but they also experience, and respond to, sub-threshold voltage signals. In this chapter we show that the so-called absolute integrate-and-fire model is ideally suited to such studies. At the single neuron level voltage traces for the model may be obtained in closed form, and are shown to mimic those of fast-spiking inhibitory neurons. Interestingly in the presence of a slow spike adaptation current the model is shown to support periodic bursting oscillations. For both tonic and bursting modes the phase response curve can be calculated in closed form. At the network level we focus on global gap junction coupling and show how to analyze the asynchronous firing state in large networks. Importantly, we are able to determine the emergence of non-trivial network rhythms due to strong coupling instabilities. To illustrate the use of our theoretical techniques (particularly the phase-density formalism used to determine stability) we focus on a spike adaptation induced transition from asynchronous tonic activity to synchronous bursting in a gap-junction coupled network.

Electrical characterization of CVD diamond-n(+) silicon junctions

The electrical characteristics of CVD-diamond/n(+)-Si heterojunction devices are reported. Below 250 K the diodes show an unusual inversion of their rectification properties. This behavior is attributed to an enhanced tunneling component due to interface states, which change their occupation with the applied bias. The temperature dependence of the loss tangent shows two relaxation processes with different activation energies. These processes are likely related with two parallel charge transport mechanisms, one through the diamond grain, and the other through the grain boundary. (C) 2001 Elsevier Science B.V. Ah rights reserved.

Electrical characterization of pn-junctions of PPV and silicon

Poly(phenylene vinylene) (PPV) grown via the precursor route, deposited on top of heavily doped n-type silicon, was studied using electrical measurement techniques. The results are compared to PPV grown via deposition of soluble derivative (MEH-PPV). The two types are very similar. They have comparable free carrier densities and both show minority-carrier effects. The activation energy found via the loss tangent is 0.13 eV. The effect of exposure to oxygen is visible in the capacitance and the current.

Processing of polycaprolactone and polycaprolactone-based copolymers into 3D scaffolds and their cellular responses

Synthetic polymers have attracted much attention in tissue engineering due to their ability to modulate biomechanical properties. This study investigated the feasibility of processing poly(varepsilon-caprolactone) (PCL) homopolymer, PCL-poly(ethylene glycol) (PEG) diblock, and PCL-PEG-PCL triblock copolymers into three-dimensional porous scaffolds. Properties of the various polymers were investigated by dynamic thermal analysis. The scaffolds were manufactured using the desktop robot-based rapid prototyping technique. Gross morphology and internal three-dimensional structure of scaffolds were identified by scanning electron microscopy and micro-computed tomography, which showed excellent fusion at the filament junctions, high uniformity, and complete interconnectivity of pore networks. The influences of process parameters on scaffolds' morphological and mechanical characteristics were studied. Data confirmed that the process parameters directly influenced the pore size, porosity, and, consequently, the mechanical properties of the scaffolds. The in vitro cell culture study was performed to investigate the influence of polymer nature and scaffold architecture on the adhesion of the cells onto the scaffolds using rabbit smooth muscle cells. Light, scanning electron, and confocal laser microscopy showed cell adhesion, proliferation, and extracellular matrix formation on the surface as well as inside the structure of both scaffold groups. The completely interconnected and highly regular honeycomb-like pore morphology supported bridging of the pores via cell-to-cell contact as well as production of extracellular matrix at later time points. The results indicated that the incorporation of hydrophilic PEG into hydrophobic PCL enhanced the overall hydrophilicity and cell culture performance of PCL-PEG copolymer. However, the scaffold architecture did not significantly influence the cell culture performance in this study.

‘Live your liberation, don’t lobby for it’ : Australian queer student activists’ perspectives of same-sex marriage

One topic covered in Australian queer university student print media is the legalisation of same-sex marriage. The legalisation of same-sex marriage is currently generating much debate in Western queer communities. Same-sex marriage is legalised in some countries such as, Canada, Spain, the Netherlands and Belgium. It has been outlawed in Australia and most states in the US. Campaigns continue to reverse these restrictions. Other countries, such as the UK and New Zealand allow same-sex civil unions, providing couples with the rights afforded to married couples. There is a range of research documenting queer communities’ attitudes towards this issue (for example Lannutti 2005; Clarke, Burgoyne and Burns 2006; Yep, Lovaas and Elia 2003; Wolfson 1993; Egan and Sherrill 2005). These studies document broad community views as well as those of community sub-sections. For example, Yip (2004) looks at the views of gay and lesbian Christians on same-sex marriage and Lahey and Alderson (2004) document the experiences of same-sex couples who have gotten married or who are waiting to get married. Philosophical analyses consider the legalisation of same-sex marriage in relation to, for example, liberalism, equal rights, liberation, queer theory, citizenship, history, activism, religious discourse and feminism (Ferguson 2007; Jordan 2005; Josephson 2005; Lipton 2006; Sullivan and Chauncey 2005; Riggs 2007). This paper explores Australian queer university student activist media’s representation of same-sex marriage, and the debates surrounding its legalisation. It examines a selection of queer student media from four metropolitan Australian universities, and the 2003 and 2004 editions of national queer student publication, Querelle. This paper uses discourse analysis of queer student activists’ media representations of marriage to investigate this issue in one specific context – metropolitan Australian universities. This paper thus contributes to the history of queer activism, documenting what one group of young people say about the legalisation of same-sex marriage, and furthers research on queer perspectives of marriage and same-sex relationships.

Up the junction? Exploiting knowledge-based development through supply chain and SME cluster interactions

Maximisation of Knowledge-Based Development (KBD) benefits requires effective dissemination and utilisation mechanisms to accompany the initial knowledge creation process. This work highlights the potential for interactions between Supply Chains (SCs) and Small and Medium sized Enterprise Clusters (SMECs), (including via ‘junction’ firms which are members of both networks), to facilitate such effective dissemination and utilisation of knowledge. In both these network types there are firms that readily utilise their relationships and ties for ongoing business success through innovation. The following chapter highlights the potential for such beneficial interactions between SCs and SMECs in key elements of KBD, particularly knowledge management, innovation and technology transfer. Because there has been little focus on the interactions between SCs and SMECs, particularly when firms simultaneously belong to both, this chapter examines the conduits through which information and knowledge can be transferred and utilised. It shows that each network type has its own distinct advantages in the types of information searched for and transferred amongst network member firms. Comparing and contrasting these advantages shows opportunities for both networks to leverage the knowledge sharing strengths of each other, through these ‘junctions’ to address their own weaknesses, allowing implications to be drawn concerning new ways of utilising relationships for mutual network gains.

Combined optic-flow and stereo-based navigation of urban canyons for a UAV

We present a novel vision-based technique for navigating an Unmanned Aerial Vehicle (UAV) through urban canyons. Our technique relies on both optic flow and stereo vision information. We show that the combination of stereo and optic-flow (stereo-flow) is more effective at navigating urban canyons than either technique alone. Optic flow from a pair of sideways-looking cameras is used to stay centered in a canyon and initiate turns at junctions, while stereo vision from a forward-facing stereo head is used to avoid obstacles to the front. The technique was tested in full on an autonomous tractor at CSIRO and in part on the USC autonomous helicopter. Experimental results are presented from these two robotic platforms operating in outdoor environments. We show that the autonomous tractor can navigate urban canyons using stereoflow, and that the autonomous helicopter can turn away from obstacles to the side using optic flow. In addition, preliminary results show that a single pair of forward-facing fisheye cameras can be used for both stereo and optic flow. The center portions of the fisheye images are used for stereo, while flow is measured in the periphery of the images.

Web-based and traditional public participation in comprehensive planning : a comparative study

The present paper examines whether the potential advantages of the expanding practice of web-based public participation only complement the benefits of the traditional techniques, or are empowering enough to replace them. The question is examined in a real-world case of neighbourhood revitalization, in which both techniques were practiced simultaneously. Comparisons are made at four major planning junctions, in order to study the contributions of each technique to the qualities of involvement, trust, and empowerment. The results show that web-based participants not only differ from the participants of traditional practices, but they also differ from each other on the basis of their type of web participation. The results indicate that web-based participation is an effective and affective complementary means of public participation, but it cannot replace the traditional unmediated techniques.