Insights into RNA design from novel molecular tools

RNA, previously recognized merely as a messenger of genetic information, has been recently rediscovered as a versatile molecule with a central role in cellular regulation. These regulatory functions are enabled by its specific chemical makeup that allows it to fold into intricate and flexible structures. In stark contrast with DNA, RNA forms a variety of structural motifs that serve as efficient points of contact in molecular recognition. It is therefore clear, that dynamic RNA structures dictate the binding availability of interfaces that play important roles in molecular regulation inside living cells. As such, the need for tools that can accurately capture and predict RNA structure in vivo continues to be essential to understand RNA function. To this end, my dissertation focuses on the development of molecular tools to predict and characterize accessible RNA interfaces in their native environment. First, I established the usefulness of a fluorescence-based in vivo oligonucleotide hybridization approach to identify accessible interfaces by characterizing numerous RNA regions in several biologically relevant molecules in E. coli. I then described these RNA interactions using a biophysical model based on thermodynamic principles and incorporating large sets of data collected using this fluorescence-based system. This approach displayed improved prediction capabilities of RNA accessibility compared to un-optimized versions without incorporation of in vivo data. Finally, I detailed the development and application of a high throughput tool for the large-scale characterization of accessible interfaces within native RNAs in a single experiment. In this approach, in vivo oligonucleotide hybridization was coupled to transcriptional elongation control to allow analysis via next generation sequencing. This tool was used to obtain complete landscapes of functional structure for 72 regulatory molecules in a single experiment (>1000 regions). Altogether the results of this high throughput approach revealed a pattern indicating that RNA-RNA interaction sites are either highly accessible or highly protected, suggesting their binding status (e.g. actively bound or unbound). In addition, within bacterial small RNAs, our approached revealed the role of the global regulator Hfq as universal structural relaxer. The compendium of these tools provides a unique and fundamental perspective in the study of functional RNA structure, namely, the identification of dynamic structures. Furthermore, the information provided by these approaches significantly aids in the design of synthetic RNAs for a variety of purposes, including gene expression control.Chemical Engineerin

Softswitch Design and Performance Analysis

The increasing number of subscribers’ demands in telecommunication sector has motivated the operators to provide high quality of service in cost effective way. Moreover, operators need to have an open structure system so that they can move their systems to the next generation network architecture. For this purpose, Softswitch is an appropriate technology because it is a safe and cost efficient solution and though it can migrate from traditional circuit-switching based telephone system to internet protocol packet-switching based networking. Softswitch network divides the logical switch into several parts with different functions such as signaling gateway, media gateway, media server, etc. Standard communication protocols are implemented between those parts. Softswitch is software-based system to make connection between devices, and moreover to control voice calls, data and routes calls through different entities of the networks. Softswitch supports management functions such as provisioning, fault handling and reporting, billing, operational support, etc. Softswitch suitable for all types of traffic and services so it is very demanding in the competitive world of mobile operators. In this thesis, Softswitch has been studied and analyzed in details. Softswitch network consisted of different integrated modules such as transportation, calling and signaling, service application and management. Each module provides different services such as call control, routing, billing and network management. Each module is discussed from functional and service point of views. Softswitch based wireless network architecture as well as variety of service solutions is presented. Different protocol interfaces in softswitch network such as signaling system number 7 are explained. Moreover, bearer calls, independent call control protocol, gateway control protocol, IP bearer control protocol are explained as well. Variety of softswitch network architectures analysis has been done based on their performance and the applicability. Three Softswitch network architectures are proposed which are validated through simulations.fi=Opinnäytetyö kokotekstinä PDF-muodossa.|en=Thesis fulltext in PDF format.|sv=Lärdomsprov tillgängligt som fulltext i PDF-format

To Waive and Waive Not: Property and Flexibility in the Digital Era: 23rd Annual Horace S. Manges Lecture, April 6, 2010

Even in an era when creative works can sometimes be made collectively, and where copying and modifying existing works is often easy, individual ownership of discrete creative works still makes sense. Individual creative effort is still the crucial ingredient for many high quality works, and the control conferred by ownership is often the most efficient, and even more frequently the most fair, social arrangement. Even so, a common argument against property rights in the digital era is that they come with a heavy transactional burden. The need to clear permission to use digital works is said to impede the potential of high velocity distribution models and participatory creative efforts. Too many property rights, too many clearance and licensing deals, too much friction in the great digital creativity machine—all stand in the way of progress. There are, broadly speaking, three solutions to the problem. First, society can cut back on the number of property rights, or rework the structure of rights with an eye toward transactional efficiencies. Second, right holders or society in general can invest in rights clearance mechanisms that make it easier for users and consumers of rights-protected works to transact more efficiently. Third, legal rules can be tailored to make it easier for right holders to commit to a binding non-enforcement of their rights. The purpose of this brief Article is to explore in some depth this third option. I begin by describing how waiver contributes to the supple texture of property rights, making it easy for individuals to exercise choices after rights have been granted. This is, in my view, a cornerstone feature of property rights, and one of their chief advantages over other entitlements and incentive regimes. Next, I show how waiver fits with other basic features of property rights. I argue that waiver can be thought of as an aspect of the structure of rights, as well as a (particularly simple) rights clearance mechanism. Finally, I describe some simple ideas that could clarify knotty issues surrounding legal requirements for waiver of intellectual property rights. The most important are: 1) binding, easily verified waiver mechanisms that are "good against the world"; and 2) scope of waiver rules that make it simple for right holders to selectively waive rights, for example, permitting some uses and not others. I conclude with a call for more attention to the waiver strategy as a way of retaining our traditional commitment to property while easing the transactional burden that property rights entail

Regulation of hydraulic function and consequences for drought-related mortality in mature woody plants

Precipitation and temperature patterns are expected to shift over at least the next century due to anthropogenic climate change. Effects of these shifts may be felt most acutely in arid and semi-arid regions where water is already the most limiting resource. Vegetation mortality due to drought is a likely outcome of predicted future climate, with consequences for ecosystem structure and function and feedbacks on regional and global climate. Yet, mechanisms and interactions of key plant drought responses and the end-point of mortality remain poorly understood. In this dissertation I examine the roles of xylem cavitation resistance and stomatal control of water loss in enhancing the susceptibility of species to drought-related mortality. I focused first on Pinus edulis (piñon) and Juniperus monosperma (juniper) woodlands in Southwestern United States. In Chapter 2, I used a hydraulic model to show that piñon mortality under experimental drought occurred in the absence of complete hydraulic failure, but under conditions of chronically low hydraulic conductance and transpiration. Hydraulic limitations, carbon starvation, and pathogen activity were likely all involved in this mortality. In Chapter 3, utilizing the same rainfall manipulation experiment, I showed that prolonged drought reduced both species ability to respond to the pulsed precipitation characteristic of semi-arid ecosystems. Transpiration was lower in the drought treatment than in the controls even after differences in pulse size and soil moisture were taken into account, suggesting physiological changes within the trees over the timescale of the experiment. In Chapter 4, I examined the relationship between leaf water potential regulation strategy and xylem cavitation vulnerability as a driver of drought-related mortality, using a global dataset drawn from the literature. Rather than simple classification as either isohydric or anisohydric, I found species to be evenly distributed along a continuum of leaf water potential regulation. Conifers maintained a lower loss of hydraulic conductance in their branches but a greater proportion had experienced drought-related mortality, relative to angiosperms. Together, this research shows that hydraulic constraints may have an important role in carbon starvation leading to drought-related mortality, while highlighting the need for further research on carbon reserves, mobility, and allocation during drought

Market Principles for Pesticides

Overall, pesticide use is growing in developing countries. United States\u27 pesticide use changed in content, but remains substantial in volume. Critics of pesticide policy, including many of the speakers at this symposium, are concerned that pesticide problems are worsening. Surprisingly, thirty years after the Federal Insecticide, Fungicide, and Rodenticide Act ( FIFRA ) reforms and the victory over DDT, the critics are not yet prepared to declare victory. Even worse from the perspective of environmental pressure groups is the change in attitude toward DDT, a substance whose name invokes extraordinary invective, where the current picture is not quite what the advocacy groups predicted. The New York Times recently joined public health advocates in favoring the continued use of DDT to combat malaria in developing countries.\u27 As a result, environmental pressure groups have been forced to retreat from their goal of a global ban on DDT. Is command and control regulation of pesticides a success story? We contend that it is not. Instead we argue that the regulatory structure created by FIFRA is inferior to the outcomes obtainable under a market approach to pesticides. To make our argument, we first outline current pesticide use and reasons farmers continue to use them in Part I. We then describe the principles that inform a market approach to environmental problems in Part II, followed by a discussion on how decisions about pesticide use are made, something that the current regulatory structure largely ignores. Next, in Part III, we briefly outline four examples that illustrate the problems with centralized regulatory solutions and the superiority of decentralized approaches to environmental problems. We conclude in Part IV by offering some policy principles for pesticides. The reader should note that this Article is not a comprehensive statement of the case against central planning in pesticides, something that space considerations prevent here and which we hope to provide in the future. Rather, because of the power of the pesticide fables that currently dominate the current debate, our goal is simply to suggest that there are alternatives to FIFRA and other one-size-fits-all rules, such as the ban on DDT production, that need to be considered

Market Principles for Pesticides

Overall, pesticide use is growing in developing countries. United States\u27 pesticide use changed in content, but remains substantial in volume. Critics of pesticide policy, including many of the speakers at this symposium, are concerned that pesticide problems are worsening. Surprisingly, thirty years after the Federal Insecticide, Fungicide, and Rodenticide Act ( FIFRA ) reforms and the victory over DDT, the critics are not yet prepared to declare victory. Even worse from the perspective of environmental pressure groups is the change in attitude toward DDT, a substance whose name invokes extraordinary invective, where the current picture is not quite what the advocacy groups predicted. The New York Times recently joined public health advocates in favoring the continued use of DDT to combat malaria in developing countries.\u27 As a result, environmental pressure groups have been forced to retreat from their goal of a global ban on DDT. Is command and control regulation of pesticides a success story? We contend that it is not. Instead we argue that the regulatory structure created by FIFRA is inferior to the outcomes obtainable under a market approach to pesticides. To make our argument, we first outline current pesticide use and reasons farmers continue to use them in Part I. We then describe the principles that inform a market approach to environmental problems in Part II, followed by a discussion on how decisions about pesticide use are made, something that the current regulatory structure largely ignores. Next, in Part III, we briefly outline four examples that illustrate the problems with centralized regulatory solutions and the superiority of decentralized approaches to environmental problems. We conclude in Part IV by offering some policy principles for pesticides. The reader should note that this Article is not a comprehensive statement of the case against central planning in pesticides, something that space considerations prevent here and which we hope to provide in the future. Rather, because of the power of the pesticide fables that currently dominate the current debate, our goal is simply to suggest that there are alternatives to FIFRA and other one-size-fits-all rules, such as the ban on DDT production, that need to be considered

Non-parametric Sequential and Adaptive Designs for Survival Trials

This thesis deals with fixed samples size, sequential and adaptive survival trials and consists of two major parts. In the first part fixed sample size, sequential and adaptive testing methods are derived that utilize data from a survival as well as a categorical surrogate endpoint in a fully non-parametric way without the need to assume any type of proportional hazards. In the second part extensions to quality-adjusted survival endpoints are discussed. In existing adaptive methods for confirmatory survival trials with flexible adaptation rules strict type-I-error control is only ensured if the interim decisions are based solely on the primary endpoint. In trials with long-term follow-up it is often desirable to base interim decisions also on correlated short-term endpoints, such as a surrogate marker. Surrogate information available at the interim analysis may be used to predict future event times. If interim decisions, such as selection of a subgroup or changes to the recruitment process, depend on this information, control of the type-I-error is no longer formally guaranteed for methods assuming an independent increments structure. In this thesis the weighted Kaplan-Meier estimator, a modification of the classical Kaplan-Meier estimator incorporating discrete surrogate information, is used to construct a non-parametric test statistic for the comparison of survival distributions, a generalization of the average hazard ratio. It is shown in this thesis how this test statistic can be used in fixed design, group-sequential and adaptive trials, such that the type-I-error is controlled. Asymptotic normality of the multivariate average hazard ratio is first verified in the fixed sample size context and then applied to noninferiority testing in a three-arm trial with non-proportional hazards survival data. In the next step the independent increments property is shown to hold asymptotically for the weighted Kaplan-Meier estimator. Consequently, for all test statistics based on it. Standard methods for the calculation of group-sequential rejection boundaries are applicable. For adaptive designs the weighted Kaplan-Meier estimator is modified to support stage-wise left-truncated and right-censored data to ensure independence of the stage-wise test statistics, even when interim decisions are based on surrogate information. Standard combination test methodology can then be used to ensure strict type-I-error control. Quality-adjusted survival is an integrated measure of quality-of-life data, which has gained interest in recent years. In this thesis a novel non-parametric two-sample test for quality-adjusted survival distributions is developed, that allows adjustment for covariate-dependent censoring, whereby the censoring is assumed to follow a proportional hazards model. It is shown how this result can be used to design adaptive trials with a quality-adjusted survival endpoint

Stabilization of Linear Systems with Structured Perturbations

The problem of stabilization of linear systems with bounded structured uncertainties are considered in this paper. Two notions of stability, denoted quadratic stability (Q-stability) and μ-stability, are considered, and corresponding notions of stabilizability and detectability are defined. In both cases, the output feedback stabilization problem is reduced via a separation argument to two simpler problems: full information (FI) and full control (FC). The set of all stabilizing controllers can be parametrized as a linear fractional transformation (LFT) on a free stable parameter. For Q-stability, stabilizability and detectability can in turn be characterized by Linear Matrix Inequalities (LMIs), and the FI and FC Q-stabilization problems can be solved using the corresponding LMIs. In the standard one-dimensional case the results in this paper reduce to well-known results on controller parametrization using state-space methods, although the development here relies more heavily on elegant LFT machinery and avoids the need for coprime factorizations