Drip and Mate Operations Acting in Test Tube Systems and Tissue-like P systems

The operations drip and mate considered in (mem)brane computing resemble the operations cut and recombination well known from DNA computing. We here consider sets of vesicles with multisets of objects on their outside membrane interacting by drip and mate in two different setups: in test tube systems, the vesicles may pass from one tube to another one provided they fulfill specific constraints; in tissue-like P systems, the vesicles are immediately passed to specified cells after having undergone a drip or mate operation. In both variants, computational completeness can be obtained, yet with different constraints for the drip and mate operations

Activity-regulated RNA editing in select neuronal subfields in hippocampus

RNA editing by adensosine deaminases is a widespread mechanism to alter genetic information in metazoa. In addition to modifications in non-coding regions, editing contributes to diversification of protein function, in analogy to alternative splicing. However, although splicing programs respond to external signals, facilitating fine tuning and homeostasis of cellular functions, a similar regulation has not been described for RNA editing. Here, we show that the AMPA receptor R/G editing site is dynamically regulated in the hippocampus in response to activity. These changes are bi-directional, reversible and correlate with levels of the editase Adar2. This regulation is observed in the CA1 hippocampal subfield but not in CA3 and is thus subfield/celltype-specific. Moreover, alternative splicing of the flip/flop cassette downstream of the R/G site is closely linked to the editing state, which is regulated by Ca(2+). Our data show that A-to-I RNA editing has the capacity to tune protein function in response to external stimuli

Finite Models of Splicing and Their Complexity

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 comparadosOver 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

Chemical genetic dissection of efferent IRE1α signalling

The Endoplasmic Reticulum is the cellular organelle primarily responsible for producing proteins on the secretory pathway, a pathway important in the production of biopharmaceuticals. One of the requirements for the successful production of a functional protein is correct folding of the polypeptide sequence. During conditions such as viral infection, mutant protein expression and cell differentiation the endoplasmic reticulum is placed under conditions of stress. IRE1 is a protein kinase and endoribonuclease, which along with PERK and ATF6, forms part of the Unfolded Protein Response, the system by which the cell deals with the stress caused by a high protein load. IRE1 is capable of increasing the protein folding capacity of the ER, by upregulating chaperone proteins and reducing the load by attenuating translation, (protective response). This action is mediated by splicing of the mRNA coding for the bZIP transcription factor XBP-1. IRE1 is also capable of causing apoptotic responses via TRAF2 (cell injuring response) resulting in the activation of JNK and NFκB. In this study, using site directed mutagenesis a panel of IRE1 mutants was produced and screened for alterations to the protective and cell injuring responses. Of these the D711A mutant was shown in mouse embryonic fibroblasts to retain endoribonuclease activity, and to display an attenuated cell injuring response. When this mutant was applied to an industrial CHO cell line it appeared to exhibit an increase in biopharmaceutical productivity over the wild type IRE1, indicating its potential for use in the biopharmaceutical cell lines

The Interaction Between Prpf8 and Dzip1 and its Role in Mitral Valve Prolapse

Mitral Valve Prolapse (MVP) is one of the most common cardiac diseases affecting 1 in 40 individuals worldwide. Functionally, MVP is the abnormal billowing of one or both of the mitral valve leaflets into the left atrium during ventricular systole. Structurally, the valves experience an accumulation of proteoglycans, an increase of collagen and hyperplasia. An echocardiogram can be used to diagnose the disease as well as determine the severity of it. MVP can cause several underlying effects such as regurgitation, arrhythmias and even sudden cardiac death in severe cases. Although there is very little known about the cause of the disease, recent discoveries have identified various genetic associations with MVP. This is the basis by which we structure this proposal. A linkage analysis was conducted on a large family with non-syndromic MVP to find a common cause for the disease. Through this linkage analysis a specific region of genes was identified, in particular, a cilia gene, DZIP1 was found along with the point mutation in the gene. Through expression, knockout studies and biochemical approaches we have gained a better understanding of what DZIP1 and the mutation of DZIP1S14R/+ are doing during cardiac development. Currently, little is known about how mutations in the cilia gene can influence the development of MVP. To address this question, a two-hybrid screening was completed, in which DZIP1 wild type plasmid and mutant DZIP1 plasmid were used to determine DZIP1\u27s binding partners. A pre-mRNA processing factor protein named Prpf8, which is a fundamental component of the spliceosome, was found to interact with the wild type DZIP1 plasmid but was the only protein found to not interact with the mutant DZIP1 plasmid. Additionally, the previous GWAS completed on patients with MVP identified a single nucleotide polymorphism (SNP) in close proximity to the PRPF8 locus, which led us to hypothesize that this SNP could function as an enhancer to regulate Prpf8 expression. Here we present data that shows that Prpf8 is expressed in the mitral valves at various embryonic and postnatal stages, and that it co-localizes with DZIP1. Verification of the two-hybrid screening result was tested through co-immunoprecipitation from protein collected from wild type (Dzip1+/+) and mutant (Dzip1S14R/+) adult mouse tail fibroblasts. Furthermore, through collaborators at INSERM, chromatin conformation capture experiments on chromosome 17 (where PRPF8 is located) determined four potential regulatory sequences that are in close proximity to PRPF8\u27s transcription start site. With the given data, luciferase assays indicated sequences with enhancer function. The studies presented will establish a broad mechanism by which DZIP1 mutations regulate RNA splicing, resulting in myxomatous valves and MVP in patients