Optimizing the Design of Oligonucleotides for Homology Directed Gene Targeting

BACKGROUND: Gene targeting depends on the ability of cells to use homologous recombination to integrate exogenous DNA into their own genome. A robust mechanistic model of homologous recombination is necessary to fully exploit gene targeting for therapeutic benefit. METHODOLOGY/PRINCIPAL FINDINGS: In this work, our recently developed numerical simulation model for homology search is employed to develop rules for the design of oligonucleotides used in gene targeting. A Metropolis Monte-Carlo algorithm is used to predict the pairing dynamics of an oligonucleotide with the target double-stranded DNA. The model calculates the base-alignment between a long, target double-stranded DNA and a probe nucleoprotein filament comprised of homologous recombination proteins (Rad51 or RecA) polymerized on a single strand DNA. In this study, we considered different sizes of oligonucleotides containing 1 or 3 base heterologies with the target; different positions on the probe were tested to investigate the effect of the mismatch position on the pairing dynamics and stability. We show that the optimal design is a compromise between the mean time to reach a perfect alignment between the two molecules and the stability of the complex. CONCLUSION AND SIGNIFICANCE: A single heterology can be placed anywhere without significantly affecting the stability of the triplex. In the case of three consecutive heterologies, our modeling recommends using long oligonucleotides (at least 35 bases) in which the heterologous sequences are positioned at an intermediate position. Oligonucleotides should not contain more than 10% consecutive heterologies to guarantee a stable pairing with the target dsDNA. Theoretical modeling cannot replace experiments, but we believe that our model can considerably accelerate optimization of oligonucleotides for gene therapy by predicting their pairing dynamics with the target dsDNA

Public-private partnerships and the politics of alcohol policy in England : the Coalition Government's Public Health 'Responsibility Deal'

BACKGROUND: The 2010-2015 Conservative-led Coalition Government launched their flagship Public Health Responsibility Deal (PHRD) for England in 2011; a year before their alcohol strategy. This co-regulatory regime placed alcohol industry actors at the heart of policy-making, but was viewed with scepticism by public health actors. This article examines the ways in which the PHRD structured the alcohol policy environment throughout this period, which included the rejection of evidence-based policies such as minimum unit pricing. METHODS: This article draws on 26 semi-structured interviews with policy actors (parliamentarians, civil servants, civil society actors and academics) in 2018. Respondents were identified and recruited using purposive sampling. Interviews were recorded, transcribed and analysed using thematic coding. RESULTS: The PHRD shaped the context of alcohol policy development at Westminster throughout this period. It circumscribed the policy space by taking evidence-based measures not amenable to industry partnership off the agenda. While the PHRD created important opportunities for industry engagement with policy-makers, it undermined public health actors' access to government, particularly following their withdrawal from the process. Moreover, the PHRD demonstrates the enduring appeal of partnership as a policy idea for governments, despite a lack of evidence of their effectiveness. CONCLUSIONS: This study of the PHRD demonstrates the ways in which industry actors are able to influence policy through long-term relationship building and partnership working on policy decision-making. Whilst such partnership approaches may appear to have the potential to mitigate some of alcohol harms, they create fundamental conflicts of interest, and may undermine the very causes they seek to further

Sexotic: The interplay between sexualization and exoticization

The introduction reflects on the methodological value and implications of the concept „sexotic“, situates it in the research on processes of sexualization and exoticization and demonstrates how the individual contributions to the special issue relate to three central topics that can be approached via the sexotic: mobilities and migrations, arts and media, science and moralities

Dynamic Computable General Equilibrium Model and Sensitivity Analysis for Shadow Price of Water Resource in China

A novel dynamic computable general equilibrium model based on National Water Resource Input Holding Output Table is proposed to calculate the Shadow Price of water resource in China. Unlike previous approaches, the dynamic Shadow Price of water resource is largely based on the scarcity extent and can reflect the marginal long-term value in the balanced growth path of China. Firstly, the basic concepts of dynamic Input Output analysis and Turnpike Theory are reviewed. Then, Dynamic Computable General Equilibrium (DCGE) is elaborated to calculate the Shadow Price, including the definition and computer-based algorithm. Furthermore, Shadow Price of water resource in China from 1949 to 2050 is calculated based on the DCGE. Also the sensitivity analysis of the DCGE for Shadow Price of water resource in China is presented. Dynamic Shadow Price of water resource has two meanings for China government: (1) Project evaluation. Every large-scale project in China must have national economic evaluation and the dynamic Shadow Price is prerequisite for national economic evaluation. (2) Market price of water resource. A lesson from this paper is that Shadow Price of water resource in domestic market of China should be rewritten according to the dynamic Shadow Price. In addition, the parallel computations approach could also be used to solve these problems in different countries or for different natural resources

Efficient Group Testing Algorithms with a Constrained Number of Positive Responses

Group testing is a well known search problem that consists in detecting the defective members of a set of objects O by performing tests on properly chosen subsets (pools) of the given set O. In classical group testing the goal is to find all defectives by using as few tests as possible. We consider a variant of classical group testing in which one is concerned not only with minimizing the total number of tests but aims also at reducing the number of tests involving defective elements. The rationale behind this search model is that in many practical applications the devices used for the tests are subject to deterioration due to exposure to or interaction with the defective elements. As an example, consider the leak testing procedures aimed at guaranteeing safety of sealed radioactive sources. Personnel involved in these procedures are at risk of being exposed to radiation whenever a leak in the tested sources is present. The number of positive tests admitted by a leak testing procedure should depend on the dose of radiation which is judged to be of no danger for the health. Obviously, the total number of tests should also be taken into account in order to reduce the costs and the work load of the safety personnel. In this paper we consider both adaptive and nonadaptive group testing and for both scenarios we provide almost matching upper and lower bounds on the number of “yes” responses that must be admitted by any strategy performing at most a certain number t of tests. The lower bound for the non adaptive case follows from the upper bound on the optimal size of a variant of d-cover free families introduced in this paper, which we believe may be of interest also in other contexts