http://www.dspace.cam.ac.uk:80/handle/1810/221781 Sat, 25 May 2013 21:20:33 GMT 2013-05-25T21:20:33Z http://www.dspace.cam.ac.uk:80/handle/1810/244505 Title: Bleb-driven chemotaxis in Dictyostelium discoideum Authors: Zatulovskiy, Evgeny Abstract: Migrating cells have two basic ways of extending their leading edge: by dendritic actin polymerization beneath the membrane, or by fluid pressure, which produces blebs. Most cells are believed to move using actin-driven projections, but in more physiological conditions, blebbing motility is also apparent. It has been shown that certain cells even can switch between these two modes of motility, although it is not known how this switch is triggered. Besides, it is unclear whether blebbing can be regulated by chemotactic stimuli, and generally, how blebbing is controlled in the cell. In this study I employed a popular model organism – Dictyostelium discoideum – to investigate the role of blebbing in chemotaxis. Here I confirm that in standard conditions Dictyostelium cells move by a combination of F-actin-driven protrusions and blebs. Blebbing is characterized by the rapid projection of hemispherical patches of plasma membrane at 2-4 times the speed of an actin-driven projection, and leaves transient scars of F-actin marking the original cortex in the base of blebs. I demonstrate that Dictyostelium cells can adjust their mode of movement according to the conditions: in a resistive environment they switch almost entirely to “bleb mode”. I show that in chemotaxing cells, blebs are mainly restricted to the leading edge, and they often lead the way when a cell is forced to re-orientate. Bleb location appears to be controlled directly by chemotactic gradients. To investigate how chemoattractant induces blebbing, I have screened signal transduction mutants for altered blebbing. I have found that blebbing is unaffected in many chemotactic mutants, but unexpectedly depends on PI3-kinases and two downstream PIP3-binding proteins of unknown function – PhdA and CRAC. I conclude that Dictyostelium cells move using a hybrid motor in which hydrostatic pressure-driven bleb formation is as important as F-actin-driven membrane extension, and that cells can change the balance between modes as required. I propose that blebbing motility of Dictyostelium cells is a direct response to mechanical resistance of environment. More generally, bleb-driven motility may be a ‘”high-force” mode of movement that is suited to penetrating tissues. Blebs are chemotactic and their induction may involve branches of the chemotactic signal transduction pathway distinct from F-actin regulation. Tue, 12 Mar 2013 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244505 2013-03-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244503 Title: A cylindrical specimen holder for electron cryo-tomography Authors: Palmer, Colin Michael Abstract: The ‘missing wedge’ is a long-standing problem in electron tomography, caused by the use of slab-like flat specimens, which increase in thickness when tilted to high angles. Attempts have been made to reduce the undesirable effects caused by the missing wedge, but the problem remains, particularly for the radiation-sensitive frozen-hydrated specimens used for high resolution imaging. Specimens with cylindrical symmetry offer a way to overcome this problem, since the thickness remains constant at all viewing angles. However, while this has been suggested before, it has never been demonstrated for frozen-hydrated specimens. In this work, I present a way to make cylindrical specimens for electron cryo-tomography, using thin-walled carbon tubes as specimen holders. The tubes are made in a multi-step process, involving carbon deposition on glass micropipette templates and subsequent removal of the glass. Tube diameters are typically a few hundred nanometres, with a wall thickness of 10–20 nm. To make frozen-hydrated specimens, the tubes are filled with an aqueous sample and then plunge-frozen in liquid ethane. Electron images acquired from the tubes have equal quality at all viewing angles, with a tilt range restricted only by the physical limits of the microscope. Tomograms from specimens such as gold particles and liposomes show that the effects of the missing wedge are substantially reduced, with much improved resolution along the electron beam axis. Structural features oriented in all directions are visible in the reconstructions, in marked contrast to tomograms acquired over a more restricted angular range. These results are promising, however some technical challenges remain before this method can be used routinely. Tue, 12 Mar 2013 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244503 2013-03-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/236171 Title: Exploiting network-based approaches for understanding gene regulation and function Authors: Janga, Sarath Chandra Abstract: It is increasingly becoming clear in the post-genomic era that proteins in a cell do not work in isolation but rather work in the context of other proteins and cellular entities during their life time. This has lead to the notion that cellular components can be visualized as wiring diagrams composed of different molecules like proteins, DNA, RNA and metabolites. These systems-approaches for quantitatively and qualitatively studying the dynamic biological systems have provided us unprecedented insights at varying levels of detail into the cellular organization and the interplay between different processes. The work in this thesis attempts to use these systems or network-based approaches to understand the design principles governing different cellular processes and to elucidate the functional and evolutionary consequences of the observed principles. Chapter 1 is an introduction to the concepts of networks and graph theory summarizing the various properties which are frequently studied in biological networks along with an overview of different kinds of cellular networks that are amenable for graph-theoretical analysis, emphasizing in particular on transcriptional, post-transcriptional and functional networks. In Chapter 2, I address the questions, how and why are genes organized on a particular fashion on bacterial genomes and what are the constraints bacterial transcriptional regulatory networks impose on their genomic organization. I then extend this one step further to unravel the constraints imposed on the network of TF-TF interactions and relate it to the numerous phenotypes they can impart to growing bacterial populations. Chapter 3 presents an overview of our current understanding of eukaryotic gene regulation at different levels and then shows evidence for the existence of a higher-order organization of genes across and within chromosomes that is constrained by transcriptional regulation. The results emphasize that specific organization of genes across and within chromosomes that allowed for efficient control of transcription within the nuclear space has been selected during evolution. Chapter 4 first summarizes different computational approaches for inferring the function of uncharacterized genes and then discusses network-based approaches currently employed for predicting function. I then present an overview of a recent high-throughput study performed to provide a ‘systems-wide’ functional blueprint of the bacterial model, Escherichia coli K-12, with insights into the biological and evolutionary significance of previously uncharacterized proteins. In Chapter 5, I focus on post-transcriptional regulatory networks formed by RBPs. I discuss the sequence attributes and functional processes associated with RBPs, methods used for the construction of the networks formed by them and finally examine the structure and dynamics of these networks based on recent publicly available data. The results obtained here show that RBPs exhibit distinct gene expression dynamics compared to other class of proteins in a eukaryotic cell. Chapter 6 provides a summary of the important aspects of the findings presented in this thesis and their practical implications. Overall, this dissertation presents a framework which can be exploited for the investigation of interactions between different cellular entities to understand biological processes at different levels of resolution. Mon, 05 Jul 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/236171 2010-07-05T23:00:00Z