Subcellular localisation of proteins in fluorescent microscope images using a random forest

This paper presents a system that employs random forests to formulate a method for subcellular localisation of proteins. A random forest is an ensemble learner that grows classification trees. Each tree produces a classification decision, and an integrated output is calculated. The system classifies the protein-localisation patterns within fluorescent microscope images. 2D images of HeLa cells that include all major classes of subcellular structures, and the associated feature set are used. The performance of the developed system is compared against that of the support vector machine and decision tree approaches. Three experiments are performed to study the influence of the training and test set size on the performance of the examined methods. The calculated classification errors and execution times are presented and discussed. The lowest classification error (2.9%) has been produced by the developed system.<br /

Functional Analysis of the Dictyostelium discoideum Rho GTPases RacH and RacA

In this study, we investigated the functions of the two Rho GTPases RacA and RacH in Dictyostelium discoideum. Both genes are constitutively expressed and mRNA and protein are present throughout the complete developmental cycle of Dictyostelium. RacA belongs to the subfamily of Rho BTB proteins that are characterised by a modular organisation, consisting of a GTPase domain, a praline-rich region, a tandem of two BTB domains and a C-terminal region of unknown function. Thus RacA promises to be both, a highly specific adaptor molecule thanks to its BTB domains, and a regulator of signal transduction due to its GTPase domain. The particularity about RacH is that, in contrast to the other characterised Rho GTPases residing at the plasma membrane, RacH was targeted to the nuclear envelope, ER and Golgi apparatus. The pivotal process regulated by Rho GTPases is the rearrangement of the actin cytoskeleton. Therefore we investigated the role of RacA and RacH in cytoskeleton-dependent processes by analysing the performance of the respective knock out mutants in processes depending on the re-organisation of the cortical actin cytoskeleton. RacA-KO cells show conditional defects when cultured in supension: they are severly impaired in growth, cytokinesis and cell shape probably due to lowered cortical tension and F-actin distribution and reveal a slight chemotactical defect as well as reduced rates of pino- and phagocytosis. Considering the correspondence in phenotypes of cells lacking either RacA, PAKa or myosin II and the PAKa-binding by RacA, a model in which RacA acts in concert with Rac1 GTPases as a regulator of PAKa activity working in parallel to the PI3-kinase/PKB pathway that elicits PAKa activity upon chemoattractant stimulation, is proposed. Moreover putative RacA binding partners have been identified. Cells deficient in RacH have a decreased rate of fluid phase endocytosis and exocytosis and a divergent performance in the endocytosis process in comparison to the WT, but no other apparent defects. In a cell-free system RacH stimulated actin polymerisation, suggesting that it might be involved in actin-based trafficking of vesicular compartments, more specifically in the delivery of cargo to early endosomes. The lack of RacH causes defective early endocytosis leading to defects also observed at later stages of this process. By means of chimeric constructs and alanine exchange mutants it was also shown that several regions of the molecule, not only the hypervariable region, determine targeting of RacH and that targeting to the correct membrane compartment probably makes interactions with appropriate regulators and effectors possible, and is therefore essential for function

An investigation into the replication biology of Helicoverpa armigera stunt virus

Tetraviruses are a family of small non-enveloped positive sense RNA viruses that exclusively infect members of the order Lepidoptera. Their replication biology is poorly studied because, with the exception of Providence virus (PrV), tetraviruses are unable to replicate in tissue culture cells. The overall aim of the research described in this thesis was to develop a fundamental understanding of the replication of tetraviruses, focussing on the site of replication within host cells and in particular, the subcellular localisation of the viral replicase. Helicoverpa armigera stunt virus (HaSV, Genus: Omegatetravirus) was chosen for this study because it is the only tetravirus for which the cDNAs have been shown to be infectious. In the absence of tissue culture cell lines susceptible to HaSV infection, the approach was to use confocal fluorescence microscopy to examine the subcellular localisation of the HaSV replicase fused to enhanced green fluorescent protein (EGFP) in mammalian and insect tissue culture cells. The replicase (with EGFP fused at its C-terminus) localised to punctate structures throughout the cytoplasm of transfected HeLa and Sf9 cells. These structures were then shown – using live cell imaging and time lapse photography – to behave similarly to cellular endocytic organelles and fluorescence partially overlapped with membranes containing the late endosomal marker protein CD63. Biochemical fractionation of Sf9 cells expressing the replicase via a recombinant baculovirus (as well as transfected HeLa and Sf9 cells expressing EGFP-replicase fusion proteins) demonstrated that the replicase was strongly associated with detergentresistant membranes (DRMs) in these cells. Deletion analysis of the replicase coding sequence revealed two regions involved in the generation of the punctuate structures. Firstly, the C-terminal half of the replicase RNAdependant RNA polymerase domain was found to be essential for targeting and the tight association with DRMs while the second region, within the Nterminal 44 amino acids, enhanced localisation through a combination of secondary structural elements and sequence-specific functions. A comparative immunofluorescence study on PrV, which replicates as a persistent infection in an insect midgut cell line, showed that the PrV replicase also localised to punctate structures in the cytoplasm. Biochemical fractionation showed that the replicase was also strongly associated with DRMs. This thesis describes the development of new experimental systems for the study of tetravirus replication biology and the data lead to the conclusion that the HaSV replicase associates with DRMs derived from alternate endocytic pathway organelles

An investigation into the replication biology of Helicoverpa armigera stunt virus

Tetraviruses are a family of small non-enveloped positive sense RNA viruses that exclusively infect members of the order Lepidoptera. Their replication biology is poorly studied because, with the exception of Providence virus (PrV), tetraviruses are unable to replicate in tissue culture cells. The overall aim of the research described in this thesis was to develop a fundamental understanding of the replication of tetraviruses, focussing on the site of replication within host cells and in particular, the subcellular localisation of the viral replicase. Helicoverpa armigera stunt virus (HaSV, Genus: Omegatetravirus) was chosen for this study because it is the only tetravirus for which the cDNAs have been shown to be infectious. In the absence of tissue culture cell lines susceptible to HaSV infection, the approach was to use confocal fluorescence microscopy to examine the subcellular localisation of the HaSV replicase fused to enhanced green fluorescent protein (EGFP) in mammalian and insect tissue culture cells. The replicase (with EGFP fused at its C-terminus) localised to punctate structures throughout the cytoplasm of transfected HeLa and Sf9 cells. These structures were then shown – using live cell imaging and time lapse photography – to behave similarly to cellular endocytic organelles and fluorescence partially overlapped with membranes containing the late endosomal marker protein CD63. Biochemical fractionation of Sf9 cells expressing the replicase via a recombinant baculovirus (as well as transfected HeLa and Sf9 cells expressing EGFP-replicase fusion proteins) demonstrated that the replicase was strongly associated with detergentresistant membranes (DRMs) in these cells. Deletion analysis of the replicase coding sequence revealed two regions involved in the generation of the punctuate structures. Firstly, the C-terminal half of the replicase RNAdependant RNA polymerase domain was found to be essential for targeting and the tight association with DRMs while the second region, within the Nterminal 44 amino acids, enhanced localisation through a combination of secondary structural elements and sequence-specific functions. A comparative immunofluorescence study on PrV, which replicates as a persistent infection in an insect midgut cell line, showed that the PrV replicase also localised to punctate structures in the cytoplasm. Biochemical fractionation showed that the replicase was also strongly associated with DRMs. This thesis describes the development of new experimental systems for the study of tetravirus replication biology and the data lead to the conclusion that the HaSV replicase associates with DRMs derived from alternate endocytic pathway organelles

Optical imaging methods for the study of disease models from the nano to the mesoscale

The visualisation of disease phenotypes allows scientists to study fundamental mechanisms of disease. Optical imaging methods are useful not only to observe anatomical features of biological samples, but also to infer interactions between molecular species using fluorescence labelling. This thesis presents the development of imaging and analysis tools to study biological questions in three models of disease, with samples ranging from the sub-cellular to the organ scale. First, the role of the alpha-synuclein (a-syn) protein, whose dysfunction is a hallmark of Parkinson’s Disease, was studied with respect to vesicle trafficking at the synapse. Synaptic vesicles are ∼40 nm in diameter; imaging vesicles therefore requires methods with resolution below the diffraction limit. Single-molecule localisation microscopy (SMLM), which circumvents the diffraction limit by separating fluorophore emission in time to localise individual molecules in space with ∼20 nm precision, was thus implemented to study a-syn in purified synaptic boutons. A software package was developed to analyse the colocalisation of a-syn with internalised vesicles, and the clustering of a-syn under differing synaptic calcium levels. The colocalisation of a-syn and internalised vesicles was found to be temperature independent, suggesting that a-syn is involved in non-canonical trafficking mechanisms. Ground truth simulations from a synaptosome model were used to benchmark two cluster analysis methods. Both methods applied on the experimental data showed that a-syn becomes less clustered at low synaptic calcium levels. Second, the spatiotemporal association of ESCRT-II, a protein complex whose role in the budding of the human immunodeficiency virus (HIV) was previously considered dispensable, and the HIV polyprotein Gag was studied during viral egress using novel image analysis tools. A nearest-neighbour analysis showed the ESCRT-II protein EAP45 colocalises with Gag similarly to ALIX, a protein well known to be involved in HIV budding. However, upon deletion of EAP45’s N-terminus, its colocalisation with Gag was significantly impaired, highlighting the importance of this EAP45 domain in linking to Gag. Single particle tracking was used to trace the trajectories of EAP45 and Gag in live cells, and an algorithm was developed to visualise the simultaneous motion of two particles; these analyses revealed three types of potential dynamic interaction between EAP45 and Gag. Finally, an open-source instrument to visualise phenotypes from large organs in 3D was developed for the study of chronic obstructive pulmonary disease (COPD) models. The instrument implements Optical Projection Tomography, a technique which can reconstruct cross-sectional slices of a transparent object from its orthographic projections, using off-the- shelf components and novel ImageJ plugins for artefact correction and volume reconstructions. Excised and cleared mouse lungs were imaged in which high order airways can be discerned with 50 μm resolution. The raw lung data, instructions for building the instrument, the free ImageJ plugins, and a detailed software manual are available in an online repository to encourage the widespread use of OPT for imaging large samples.Gates Cambridg

Analysis of AR/AR-V7signalling pathways in circulating tumour cells of prostate cancer patients

Biomarkers detected in liquid biopsy (such as circulating tumour cells, CTCs) demonstrate high concordance with biomarkers detected in conventional tissue biopsy. Prostate cancer, when metastatic, is treated with androgen deprivation therapy (ADT). However, resistance to ADT evolves into a clinical state referred to as castrate resistant prostate cancer (CRPC), in which increased, abnormal, androgen receptor (AR) signalling through changed AR structures (amplification, point mutations or variant expression) occurs. Although CRPC also facilitates development of other, complex signalling pathways that promote cell survival, our hypothesis is that the abnormal AR signalling is tightly linked to PTEN/AKT and Hippo/YAP pathways that contribute to the oncogenic driver role that confers ADT resistance. This PhD project aims to evaluate the role of AR, PTEN, and Hippo driver pathways in CRPC through analysis of CTCs, which have become important biological correlates and sources to study tumour biology in prostate cancer. The main focus was on the AR splice variant 7 (ARV7), a promising predictive and prognostic CRPC biomarker. The overall outcomes of this PhD project were to (i) investigate the role of AR, PTEN, and Hippo pathways implicated in CRPC, (ii) validate liquid-biopsy-detected AR-V7 as a CRPC biomarker, (iii) define the best antibody to detect AR-V7 CTCs in CRPC patient blood, and (iv) optimise methods that enable multiplex immunocytostaining of prostate cancer cells, including CTCs with a view to conduct ‘proteomic microscopy’ in the future. This work in this PhD puts in place basic procedures and methods that will enable CTC multiplex “proteomic microscopy” a method that could change the current paradigm of CTC analysis by allowing analysis of these rare cells for multiple markers targeting multiple biological pathways at the same time

Investigating bacteroidetes gliding motility

Bacteroidetes gliding motility is a type of surface motility in which rod-shaped bacteria move up to 2 µm s in a corkscrewing motion. Flavobacterium johnsoniae is the primary model organism for the study of Bacteroidetes gliding. SprB is the main adhesin in this organism and moves in a helix along the cell surface. This movement is guided by an underlying track that is anchored to the inner leaflet of the outer membrane. The essential gliding lipoprotein GldJ, which is helically arranged when visualised in fixed cells, is suggested to form this track. However, direct in vivo imaging of GldJ is yet to be achieved. Two currently outstanding questions about Bacteroidetes gliding motility are 1) how adhesion of SprB to the substratum is controlled so that binding only occurs when moving from the leading to the lagging cell pole and 2) how/if the cell discriminate between the poles. In this thesis, a fusion of the HaloTag domain to SprB enabled labelling of SprB with stable and bright dyes. The movement of SprB could then be visualised using single-particle tracking to reveal the underlying track topology. These tracking data suggest that the underlying track is not a single closed loop currently proposed, but rather a complex and potentially dynamic structure that can form multiple loops and cover most of the cell surface. SprB is encoded by the sprB operon that further encodes RemFG, Fjoh_0982, and SprCDF. In this thesis I show that all these components, except fjoh_0982, are required for gliding motility but only sprF are required for SprB helical movement. All the sprB operon components required for gliding are also required for SprB-mediated attachment to glass, indicating that they regulate adhesion of SprB. RemG and SprCD move in a helix reminiscent of the SprB movement pattern. The helical movement does not depend on SprF or SprB, but rather on the SprFhomologous N-terminal domain of SprD. Observations of gliding cells with fluorescently labelled SprC revealed accumulation of SprC near the leading cell pole. This polar accumulation correlated with the direction of movement and was not observed in cells that did not move. Furthermore, a mutant lacking the C-terminal 50 residues of SprD was unable to accumulate SprC at the leading pole. SprB did not show a similar asymmetric distribution in gliding cells. Fluorescence microscopy shows that helically moving sprB operon proteins accumulate at midcell in dividing cells in a GldJ dependent manner. Cross-linking mass spectrometry indicates that GldJ interacts with the sprB operon proteins as well as GldKNO, essential outer membrane components of the type 9 secretion system which is a pre-requisite for Bacteroidetes gliding motility