No description available.

Major changes in expression occur in Arabidopsis in response to cold. It is now clear that genome-wide changes in alternative splicing (AS) also occur in Arabidopsis during the cold-response and many of the genes which undergo cold-induced AS have been linked to roles in either the regulation of the cold-response or regulation of AS. Mutations in splicing factors in Arabidopsis, such as STA1 and SRL1 have been shown to lead to both changes in AS and changes in cold-sensitivity/tolerance, suggesting an important the role for AS in regulating the cold-response. Less is known about the effect of cold on AS in barley or how AS impacts the barley cold-response. There are only a few studied examples of cold-induced AS changes in barley genes, although this is rapidly changing due to both the publication of the barley genome and next generation sequencing of the transcriptome. To investigate AS in the barley cold response, 11 barley genes with cold-induced AS changes were identified and the AS change was analyzed in detail. The barley genes FRY2 and SUA change AS after 30 minutes exposure to cold and are both genes have been linked to roles in regulating AS, indicating a complex role for AS in the earliest stages in the cold-response. The Serine Arginine (SR)-Rich protein genes have been shown to change AS and affect AS under stress conditions in Arabidopsis, rice and other plant species but little is known about the SR protein genes in barley or how the genes change splicing/expression in response to cold. The 16 members of the barley SR protein gene family were identified and analyzed for cold-induced expression changes using available microarray and RNA-Seq data. The HvRS41 gene showed a >2 fold increase in expression after 3h exposure to 6°C in a cold-based microarray experiment. A cold-based microarray experiment in Arabidopsis showed a similar cold-induced expression of the AtRS40 gene, a RS-type SR protein gene with high homology to HvRS41. The cold-induced expression of HvRS41 and AtRS40 indicate a role for the RS-type SR protein genes in the cold response. The RS-type SR proteins form a splicing complex with FRY2 which could potentially be regulated through both AS and expression change during the cold-response. The Barley SR Proteins were dived into six sub-groups previously established for plant SR protein genes. Five out of the six sub-groups of the barley SR protein genes contained AS which could be validated through RT-PCR based methods. The SR-type SR protein genes contained was shown to contain three genes (HvSR34, HvSR30a and HvSR34) within barley. All 3 barley SR-type protein genes showed AS change in response to low temperatures, indicating a role for the barley SR-type SR protein genes in regulating AS during the cold-response. The role for SR-type SR protein genes in regulating AS was tested through a creation of a barley transgenic line over-expressing gene the HvSR34. The HvSR34 overexpression lines are in the process of being tested for changes in AS and cold tolerance.

Thesis (Ph.D.)--McMaster University, 2006. / Supervisor: Turlough M. Finan.

Understanding normal and cancer cell biology requires the development and application of systems biology approaches capable of probing the functional human proteome, and the protein-protein interactions (PPIs) within it. Such technologies will facilitate our understanding of how molecular events drive phenotypic outcomes, and how these processes are perturbed in disease conditions. In this thesis, I first describe the development of a mammalian, Gateway compatible, lentivirus-based protein-fragment complementation assay (magical-PCA), for the in vivo high-throughput identification of PPIs in mammalian cells. This technology provides a vast improvement over current PCA methodologies by allowing for pooled, proteome-scale mapping of PPIs in any mammalian cell line of interest, using any bait protein of interest. A proof-of-concept pooled genome-scale screen using the magical-PCA approach was performed using the human mitochondrial protein TOMM22 as a bait, providing evidence that this technology is amenable to proteome-wide screens. Moreover, the TOMM22 screens offered novel insight into links between TOMM22 and proteins involved in mitochondrial organization, apoptosis, and cell cycle dynamics. Second, I performed a pooled genome-scale magical-PCA screen with the oncoprotein BMI1, a component of the E3 ubiquitin ligase complex involved in histone H2A mono-ubiquitination and gene silencing, to identify novel BMI1 protein interactors. Consequently, I have uncovered a novel physical and functional association between BMI1 and components of the mammalian splicing machinery. I further discovered that BMI1 knockdown influenced the alternative splicing of a number of cellular pre-mRNAs in colon cancer cell lines, suggesting that the association between BMI1 and cellular splicing factors impinges on pre-mRNA processing. Importantly, BMI1 expression was shown to influence the alternative splicing of the SS18 oncoprotein towards an exon 8-excluded isoform, which was shown in this study to promote cell proliferation when assessed in an anchorage-independent growth assay. Together, these studies highlight the development of a new methodology for the detection and proteome-scale screening of mammalian PPIs. A proof-of-concept screen with human TOMM22 highlighted the utility of the approach, as I was able to detect both strong and weak or transient PPIs. Application of my screening methodology to BMI1 provided crucial insight into the function of this oncoprotein, and BMI1-driven tumorigenesis.

Members of the Mef2 transcription factor family are extensively studied within the muscle field for their ability to cooperate with the myogenic regulatory factors MyoD and myogenin during muscle differentiation. Although it is known that Mef2 pre-mRNAs undergo alternative splicing, the different splice forms have not been functionally annotated. In this thesis, my studies aimed to characterize three Mef2D splice forms: MEF2Dα'β, MEF2Dαβ, MEF2Dαø. Our results show that MEF2D splice forms can be differentially phosphorylated by p38 MAPK and PKA in vitro. Gene expression analysis using cell lines over-expressing each Mef2D splice form suggests that they can differentially activate desmin, myosin heavy chain and myogenin expression. Mass spectrometry analyses from our pull-down assays reveal known and novel MEF2D binding partners. Our work suggests that Mef2D splice forms have overlapping but distinct roles and provides new insight into the importance of Mef2D alternative splicing during skeletal myogenesis.

Durante las dos últimas décadas ha surgido una colaboración estrecha entre informáticos, bioquímicos y biólogos moleculares, que ha dado lugar a la investigación en un área conocida como la computación biomolecular. El trabajo en esta tesis pertenece a este área, y estudia un modelo de cómputo llamado sistema de empalme (splicing system). El empalme es el modelo formal del corte y de la recombinación de las moléculas de ADN bajo la influencia de las enzimas de la restricción.Esta tesis presenta el trabajo original en el campo de los sistemas de empalme, que, como ya indica el título, se puede dividir en dos partes. La primera parte introduce y estudia nuevos modelos finitos de empalme. La segunda investiga aspectos de complejidad (tanto computacional como descripcional) de los sistema de empalme. La principal contribución de la primera parte es que pone en duda la asunción general que una definición finita, más realista de sistemas de empalme es necesariamente débil desde un punto de vista computacional. Estudiamos varios modelos alternativos y demostramos que en muchos casos tienen más poder computacional. La segunda parte de la tesis explora otro territorio. El modelo de empalme se ha estudiado mucho respecto a su poder computacional, pero las consideraciones de complejidad no se han tratado apenas. Introducimos una noción de la complejidad temporal y espacial para los sistemas de empalme. Estas definiciones son utilizadas para definir y para caracterizar las clases de complejidad para los sistemas de empalme. Entre otros resultados, presentamos unas caracterizaciones exactas de las clases de empalme en términos de clases de máquina de Turing conocidas. Después, usando una nueva variante de sistemas de empalme, que acepta lenguajes en lugar de generarlos, demostramos que los sistemas de empalme se pueden usar para resolver problemas. Por último, definimos medidas de complejidad descriptional para los sistemas de empalme. Demostramos que en este respecto los sistemas de empalme finitos tienen buenas propiedades comparados / Over the last two decades, a tight collaboration has emerged between computer scientists, biochemists and molecular biologists, which has spurred research into an area known as DNAComputing (also biomolecular computing). The work in this thesis belongs to this field, and studies a computational model called splicing system. Splicing is the formal model of the cutting and recombination of DNA molecules under the influence of restriction enzymes.This thesis presents original work in the field of splicing systems, which, as the title already indicates, can be roughly divided into two parts: 'Finite models of splicing' on the onehand and 'their complexity' on the other. The main contribution of the first part is that it challenges the general assumption that a finite, more realistic definition of splicing is necessarily weal from a computational point of view. We propose and study various alternative models and show that in most cases they have more computational power, often reaching computational completeness. The second part explores other territory. Splicing research has been mainly focused on computational power, but complexity considerations have hardly been addressed. Here we introduce notions of time and space complexity for splicing systems. These definitions are used to characterize splicing complexity classes in terms of well known Turing machine classes. Then, using a new accepting variant of splicing systems, we show that they can also be used as problem solvers. Finally, we study descriptional complexity. We define measures of descriptional complexity for splicing systems and show that for representing regular languages they have good properties with respect to finite automata, especially in the accepting variant.

The maximum capacity of an optical fiber transmission system more than doubled every year to match the fast-growing communication need. The technology break through in dry fiber fabrication opens the possibility for fiber bandwidth all the way from 1.3 mm to 1.6 mm. The fast increasing demand of communication capacity results in the emergence of wavelength division multiplexing (WDM) technology, which results in the need for wideband optical amplifier. Cr4+:YAG has a strong spontaneous emission that covers 1.3 mm to 1.6 mm. Besides, its absorption spectrum is between 0.9 mm to 1.2 mm, which matches with the pumping source in current erbium doped optical amplifier. Such a fiber is, therefore, eminently suitable for optical amplifier applications. We have successfully fused the double cladding Cr4+:YAG crystal fiber with single mode fiber by fusion splicer. The crystal fibers are grown by the laser-heated pedestal growth technique. The splicing parameters are optimized to achieve an insertion loss of below 1 dB. Since, the core diameter tapering will increase the propagation loss and reduce the gross gain. Adiabatically tapered fiber is discussed. Simulations are performed to predict the loss, and compare with the experimental results, then find out the way to improve the gross gain. Numerical simulation indicates that the gross gain could reach 37.2 dB at 0.5 W pump, if the core diameter of the double cladding Cr4+:YAG crystal fiber is reduced to 5 mm. In the future, in order to increase gross gain we will improve the mode matching between the cores of single mode fiber and the double cladding Cr4+:YAG crystal fiber. Gradual change of the refractive index at the splicing region as well as high Cr4+ doping concentration can also improve the gross gain.

DNA-basierte Systeme beschreiben formal ein alternatives Berechnungskonzept, beruhend auf der Anwendung molekularbiologischer Operationen. Der Grundgedanke ist dabei die Entwicklung alternativer und universeller Rechnerarchitekturen. Infolge der zugrunde liegenden maximalen Parallelität sowie der hohen Komplexität entsprechender Systeme ist die Korrektheit jedoch schwer zu beweisen. Um dies zu ermöglichen werden in der Arbeit zunächst für drei verschiedene Systemklassen mit unterschiedlichen Berechnungsparadigmen strukturelle operationelle Semantiken definiert und bekannte Formalismen der Prozesstheorie adaptiert. Nachfolgend werden Tableaubeweissysteme beschrieben, mithilfe derer einerseits Invarianten und andererseits die jeweilige Korrektheit von DNA-basierten Systemen mit universeller Berechnungsstärke bewiesen werden können. Durch Anwendung dieser Konzepte konnte für drei universelle Systeme die Korrektheit gezeigt und für ein System widerlegt werden.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2009. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Oregon, 2000. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 56-59). Also available for download via the World Wide Web; free to University of Oregon users.