Interrogation of telomerase structure and function with telomeric DNA

The studies described in this dissertation are directed toward understanding one of the components of a mechanism that cancer cells use to escape apoptosis and maintain genetic stability, resulting in cellular immortalization. Telomeres are nucleoprotein structures at the ends of eukaryotic chromosomes that are essential for safeguarding genomic stability and in regulating the lifespan of cellular replication. Telomerase is a specialized ribonucleoprotein complex that functions as a reverse transcriptase to extend the 3' end of the telomere, resulting in telomere conservation, and thus chromosomal stabilization. In greater than 85% of all cancer cells, telomerase is upregulated to rescue eroded telomeres and stabilize chromosomes, resulting in cellular immortalization. Because most somatic cells do not express detectable levels of telomerase, telomere-telomerase interactions are important in understanding cellular immortalization and aging, and developing specific anti-cancer therapeutics. Despite the great interest in telomerase, the mechanism of telomerase-catalyzed reverse transcription is not fully understood, and little is known about the structure of this intriguing enzyme. Each chapter, herein, describes novel research that investigates telomerase oligomerization and interactions between telomerase and model telomeric structures. More specifically, Chapter II focuses on the characterization and visualization of cooperative Euplotes aedicualtus telomerase dimers by gel filtration chromatography and electron microscopy. Chapter III details the formation, isolation, and characterization of G-quadruplex DNA structures by native gel electrophoresis, while Chapter IV documents novel interactions between a subset of G-quadruplex DNA structures and Euplotes aediculatus telomerase. Chapter V concludes the dissertation with a retrospective analysis of the research herein

Impurity in a Luttinger liquid away from half-filling: a numerical study

Conformal field theory gives quite detailed predictions for the low energy spectrum and scaling exponents of a massless Luttinger liquid at generic filling in the presence of an impurity. While these predictions were verified for half-filled systems, there was till now no analysis away from this particular filling. Here, we fill in this gap by numerically investigating a quarter-filled system using the density matrix renormalization group technique. Our results confirm conformal field theory predictions, and suggest that they are indeed valid for arbitrary fillings.Comment: 9 pages (include figures), one reference added in this new versio

Spontaneous Inter-layer Coherence in Double-Layer Quantum-Hall Systems I: Charged Vortices and Kosterlitz-Thouless Phase Transitions

At strong magnetic fields double-layer two-dimensional-electron-gas systems can form an unusual broken symmetry state with spontaneous inter-layer phase coherence. In this paper we explore the rich variety of quantum and finite-temperature phase transitions associated with this broken symmetry. We describe the system using a pseudospin language in which the layer degree-of-freedom is mapped to a fictional spin 1/2 degree-of-freedom. With this mapping the spontaneous symmetry breaking is equivalent to that of a spin 1/2 easy-plane ferromagnet. In this language spin-textures can carry a charge. In particular, vortices carry e/2 electrical charge and vortex-antivortex pairs can be neutral or carry charge e. We derive an effective low-energy action and use it to discuss the charged and collective neutral excitations of the system. We have obtained the parameters of the Landau-Ginzburg functional from first-principles estimates and from finite-size exact diagonalization studies. We use these results to estimate the dependence of the critical temperature for the Kosterlitz-Thouless phase transition on layer separation.Comment: 56 pages, 19 figures available upon request at [email protected]. RevTex 3.0. IUCM94-00

Atomic layer deposited electron transport layers in efficient organometallic halide perovskite devices

Amorphous TiO2 and SnO2 electron transport layers (ETLs) were deposited by low-temperature atomic layer deposition (ALD). Surface morphology and x-ray photoelectron spectroscopy (XPS) indicate uniform and pinhole free coverage of these ALD hole blocking layers. Both mesoporous and planar perovskite solar cells were fabricated based on these thin films with aperture areas of 1.04 cm2 for TiO2 and 0.09 cm2 and 0.70 cm2 for SnO2. The resulting cell performance of 18.3 % power conversion efficiency (PCE) using planar SnO2 on 0.09 cm2 and 15.3 % PCE using mesoporous TiO2 on 1.04 cm2 active areas are discussed in conjunction with the significance of growth parameters and ETL composition

The IMPROVE guidelines (Ischaemia Models: Procedural Refinements Of in Vivo Experiments)

Most in vivo models of ischaemic stroke target the middle cerebral artery and a spectrum of stroke severities, from mild to substantial, can be achieved. This review describes opportunities to improve the in vivo modelling of ischaemic stroke and animal welfare. It provides a number of recommendations to minimise the level of severity in the most common rodent models of middle cerebral artery occlusion, while sustaining or improving the scientific outcomes. The recommendations cover basic requirements pre-surgery, selecting the most appropriate anaesthetic and analgesic regimen, as well as intraoperative and post-operative care. The aim is to provide support for researchers and animal care staff to refine their procedures and practices, and implement small incremental changes to improve the welfare of the animals used and to answer the scientific question under investigation. All recommendations are recapitulated in a summary poster (see supplementary information)

Multi-ancestry genome-wide study in >2.5 million individuals reveals heterogeneity in mechanistic pathways of type 2 diabetes and complications

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes. To characterise the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study (GWAS) data from 2,535,601 individuals (39.7% non-European ancestry), including 428,452 T2D cases. We identify 1,289 independent association signals at genome-wide significance (P&lt;5×10 - 8 ) that map to 611 loci, of which 145 loci are previously unreported. We define eight non-overlapping clusters of T2D signals characterised by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial, and enteroendocrine cells. We build cluster-specific partitioned genetic risk scores (GRS) in an additional 137,559 individuals of diverse ancestry, including 10,159 T2D cases, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned GRS are more strongly associated with coronary artery disease and end-stage diabetic nephropathy than an overall T2D GRS across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings demonstrate the value of integrating multi-ancestry GWAS with single-cell epigenomics to disentangle the aetiological heterogeneity driving the development and progression of T2D, which may offer a route to optimise global access to genetically-informed diabetes care. </p

Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P &lt; 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.</p

Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments

Rowena F. Stern is with University of British Columbia, Ales Horak is with University of British Columbia, Rose L. Andrew is with University of British Columbia, Mary-Alice Coffroth is with State University of New York at Buffalo, Robert A. Andersen is with the Bigelow Laboratory for Ocean Sciences, Frithjof C. Küpper is with the Scottish Marine Institute, Ian Jameson is with CSIRO Marine and Atmospheric Research, Mona Hoppenrath is with the German Center for Marine Biodiversity Research, Benoît Véron is with University of Caen Lower Normandy and the National Institute for Environmental Studies, Fumai Kasai is with the National Institute for Environmental Studies, Jerry Brand is with UT Austin, Erick R. James is with University of British Columbia, Patrick J. Keeling is with University of British Columbia.Background -- Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known “species”, as a reference to measure the natural diversity in three marine environments. Methodology/Principal Findings -- In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. Conclusions/Significance -- COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.This project was funded by Genome Canada and the Canadian Barcode of Life Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

PEG−peptide conjugates

The remarkable diversity of the self-assembly behavior of PEG−peptides is reviewed, including self-assemblies formed by PEG−peptides with β-sheet and α-helical (coiled-coil) peptide sequences. The modes of self-assembly in solution and in the solid state are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized