Дисертації з теми "Maintenance of genetic information"

Godkänd; 2016; 20160509 (yamald); Nedanstående person kommer att hålla licentiatseminarium för avläggande av teknologie licentiatexamen. Namn: Yamur K. Al-Douri Ämne: Drift och underhållsteknik /Operation and Maintenance Engineering Uppsats: Information Assurance for Maintenance of Railway Track Examinator: Professor Uday Kumar, Institutionen för samhällsbyggnad och naturresurser, Avdelning: Drift, underhåll och akustik, Luleå tekniska universitet. Diskutant: Dr Rikard Granström, Trafikverket, Luleå. Tid: Fredag 10 juni, 2016 kl 10.00 Plats: F1031, Luleå tekniska universitet

Organizations that depend on the use of IT in their business models must maintain their systems and keep their systems current to survive (Filipek, 2008; Kulkarni, Kumar, Mookerjee, & Sethi, 2009; Unterkalmsteiner et al., 2012). As most IT departments allocate as much as 80% of their budget to maintain stability while leaving only the other 20% to allow improvements (Telea et al., 2010), high cost of stability may be a reason many IT organizations cannot afford efficient staffing and even jeopardize the existence of the organization (Filipek, 2008; Talib, Abdullah, Atan, & Murad, 2010). The purpose of this exploratory mixed methods study was to discover the IT programming standards used in IT departments that predict a decrease in project maintenance costs. This study employed an exploratory mixed methods data collection and analysis to develop and test a collection of universal programming standards. The qualitative portion of the study resulted in a list of IT programming standards from the Fortune 20 companies of 2011. Surveyed from IT departments in the Fortune 500 companies of 2011, the quantitative portion of this study correlate the degree of enforcement of each IT programming standard to a decrease in average project maintenance costs using a backward stepwise regression. Using a 95% confidence interval and a 5% margin of error (α = .05), the backward stepwise regression discarded 18 of the 22 IT programming standards. The remaining correlations give evidence that a) the more the department enforces waiting for feedback the higher the maintenance costs, b) the more the department enforces having the architectural team develop coding guidelines the lower the maintenance costs, and c) the more the IT department enforces the following of change management procedures, the higher the maintenance costs.

The genetic code is highly conserved across all domains of life, enabling horizontal gene transfer (HGT) between organisms and across ecosystems via horizontally-transferred genetic elements such as viruses and plasmids. While HGT increases genetic diversity, it poses a risk to engineered biological systems by introducing new genes that destabilize engineered functions or allowing the expression of engineered genes in wild organisms with unknown effects. A model organism engineered with an alternative genetic code may provide new insight into the origins of the genetic code while also providing a stable chassis for engineered biological systems.

The Isaacs Lab recently developed an Escherichia coli strain lacking both UAG stop codons and Release Factor 1, resulting in the first genomically recoded organism (GRO) with an unassigned codon in its genetic code. Here, we demonstrate that this alternative genetic code lacking UAG codon assignment confers resistance to multiple viruses (λ, M13, PI, MS2) at titers up to 10¹¹ PFU/mL and impairs conjugative plasmid function (F and RK2) up to 10⁵-fold. Propagating viruses on a mixed microbial community containing standard and alternative genetic codes also reduced viral population fitness and prompted viral adaptation to the alternative genetic code. In investigating the molecular mechanism underlying the resistance to viruses and conjugative plasmids, we found that UAG-ending genes elicit ribosomal stalling and the tmRNAmediated ribosomal rescue response, resulting in degradation of UAG-ending proteins and suggesting that genomic recoding may be a broadly applicable strategy to impair horizontal gene transfer into other organisms.

To prevent the expression of engineered genes in wild organisms, we reassigned the UAG codon in the GRO to a sense codon incorporating the non-standard amino acid 4-acetylphenylalanine (pAcF) through the introduction of an orthogonal translation system (OTS). We then created a library of UAG-containing variants and assessed escape of UAG-containing genes from the GRO into wild-type organisms for both a non-selective green fluorescent protein (GFP) and selective chloramphenicol acetyltransferase (CAT) gene. While 1 UAG codon impaired the expression of GFP in wild-type organisms, at least 2 UAG codons were required in CAT to consistently prevent escaped expression in wild-type organisms with a standard genetic code. Additionally, sequencing revealed that wild-type organisms enabled expression of CAT by mutating UAG codons to UGG coding for tryptophan or CAG coding for glutamine. By placing UAG at sites in proteins that cannot tolerate a tryptophan or glutamine substitution, we can create UAG-containing genes further isolated from expression in wild organisms.

As biotechnology increasingly targets open-environment applications such as bioremediation or disease treatment in humans, we require methods to stabilize and control the genetic information that we encode in engineered biological systems. Because alternative genetic codes can both confer resistance to horizontal gene transfer into an engineered system and restrict expression of engineered genes in wild-type organisms, genomic recoding of organisms to contain alternative genetic codes is a promising path towards increasing the stability and safety of engineered biological systems. However, open-environment applications will expose engineered biological systems to new stresses not represented in the laboratory environment, and further work is required to validate these methods will be robust in conditions of limiting nutrients or other cellular stresses. Additionally, while we have demonstrated genetic isolation of the GRO with respect to genes both entering and leaving the cell, we cannot currently have both properties simultaneously because UAG is the sole open codon. We envision that current research into further codon reassignments, including the reassignment of sense codons, will pave the way for alternate genetic codes with multiple codon reassignments. By expanding recoding efforts to multiple species, we envision the development of synthetic microbial communities with alternate genetic codes that are genetically isolated and robust to perturbation by HGT.

This dissertation addresses the problems of program comprehension to support the evolution of large-scale software systems. The research concerns how software engineers locate features and concepts along with categorizing changes within very large bodies of source code along with their versioned histories. More specifically, advanced Information Retrieval (IR) and Natural Language Processing (NLP) are utilized and enhanced to support various software engineering tasks. This research is not aimed at directly improving IR or NLP approaches; rather it is aimed at understanding how additional information can be leveraged to improve the final results. The work advances the field by investigating approaches to augment and re-document source code with different types of abstract behavior information. The hypothesis is that enriching the source code corpus with meaningful descriptive information, and integrating this orthogonal information (semantic and structural) that is extracted from source code, will improve the results of the IR methods for indexing and querying information. Moreover, adding this new information to a corpus is a form of supervision. That is, apriori knowledge is often used to direct and supervise machine-learning and IR approaches.

The main contributions of this dissertation involve improving on the results of previous work in feature location and source code querying. The dissertation demonstrates that the addition of statically derived information from source code (e.g., method stereotypes) can improve the results of IR methods applied to the problem of feature location. Further contributions include showing the effects of eliminating certain textual information (comments and function calls) from being included when performing source code indexing for feature/concept location. Moreover, the dissertation demonstrates an IR-based method of natural language topic extraction that assists developers in gaining an overview of past maintenance activities based on software repository commits.

The ultimate goal of this work is to reduce the costs, effort, and time of software maintenance by improving the results of previous work in feature location and source code querying, and by supporting a new platform for enhancing program comprehension and facilitating software engineering research.

Recent methods to infer genetic networks are based on identifying gene interactions by similarities in expression profiles. These methods are founded on the assumption that interacting genes share higher similarities in their expression profiles than non-interacting genes. In this dissertation this assumption is validated when using mutual information as a similarity measure. Three algorithms that calculate mutual information between expression data are developed: 1) a basic approach implemented with the histogram technique; 2) an extension of the basic approach that takes into consideration time delay between expression profiles; 3) an extension of the basic approach that takes into consideration that genes are regulated in a complex manner by multiple genes. In our experiments we compare the mutual information distributions for profiles of interacting and non-interacting genes. The results show that interacting genes do not share higher mutual information in their expression profiles than non-interacting genes, thus contradicting the basic assumption that similarity measures need to fulfil. This indicates that mutual information is not appropriate as similarity measure, which contradicts earlier proposals.

Understanding forces creating or maintaining the vast amount of biodiversity has been a major task of biologists. Genetic variation plays a major role in the creation of biodiversity because in contrast to environmental influence, genetic variants can be inherited. For a species in natural environments, genetic variation is generated by mutation, eliminated by genetic drift or selective sweep, and maintained by balancing selection that favors different alleles in different environments or time. In my dissertation, I will address how spatially heterogeneous environmental selection maintains genetic variation in two aspects.

Genes in the genome vary vastly in their level of polymorphism. Previous studies have used features within the genome, such as recombination rate or expression level, to explain the variation in gene polymorphism. One factor, however, that has often been overlooked is the effect of environmental adaptation on gene polymorphism. Specifically, if different alleles of a gene are responsible for local adaptation to distinct environments, the polymorphism of this gene will be actively maintained by spatially heterogeneous environmental selection. In the first part (Chapter 2) of my dissertation, I used publicly available genomic data from Arabidopsis thaliana to address this question. I found that environmental relevance of a gene has a significantly positive relationship with the variation in polymorphism level among genes in the Arabidopsis genome, consistent with the hypothesis that environmental selection actively maintains the polymorphism of environmentally responsive genes.

A biological species is formed by a mating pool of individuals, and for two populations of the same species, differentiation is often homogenized by gene flow. Reproductive isolation between populations allows genetic differentiation, and therefore speciation, the process in which full reproductive isolation is achieved between populations, plays important role in generating biodiversity. In the second part of my dissertation I used Boechera stricta to address how environmental selection contributes to speciation. In Chapter 3, I used niche modeling to show that environmental factors have more important roles than geographical distance in the genetic differentiation of EAST and WEST subspecies, and local water availability is the most important factor. In Chapter 4, I performed large-scale greenhouse experiments to identify key traits responsible for the EAST-WEST local adaptation, and that those traits have significantly larger differentiation between subspecies than neutral expectation. In Chapter 5, I performed quantitative trait loci mapping for those important traits and fitness in both parental environments and greenhouse. In summary, the second part of my dissertation provides an example to study ecological speciation from the environment, trait, to the genetic level.