Paradigms for computational nucleic acid design

The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape

A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots

Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N^5) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications

Thermodynamic Analysis of Interacting Nucleic Acid Strands

Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality

Effect of mattress deflection on CPR quality assessment for older children and adolescents

Appropriate chest compression (CC) depth is associated with improved CPR outcome. CCs provided in hospital are often conducted on a compliant mattress. The objective was to quantify the effect of mattress compression on the assessment of CPR quality in children. Methods: A force and deflection sensor (FDS) was used during CPR in the Pediatric Intensive Care Unit and Emergency Department of a children's hospital. The sensor was interposed between the chest of the patient and hands of the rescuer and measured CC depth. Following CPR event, each event was reconstructed with a manikin and an identical mattress/backboard/patient configuration. CCs were performed using FDS on the sternum and a reference accelerometer attached to the spine of the manikin, providing a means to Calculate the mattress deflection. Results: Twelve CPR events with 14,487 CC (11 patients, median age 14.9 years) were recorded and reconstructed: 9 on ICU beds (9296 CC), 3 on stretchers (5191 CC). Measured mean CC depth during CPR was 47 +/- 8 mm on ICU beds, and 45 +/- 7 mm on stretcher beds with overestimation of 13 +/- 4 mm and 4 +/- 1 mm, respectively, due to mattress compression. After adjusting for this, the proportion of CC that met the CPR guidelines decreased from 88.4 to 31.8% on ICU beds (p < 0.001), and 86.3 to 64.7% on stretcher (p < 0.001 The proportion of appropriate depth CC was significantly smaller on ICU beds (p < 0.001). Conclusion: CC conducted on a non-rigid surface may not be deep enough. FDS may overestimate CC depth by 28% on ICU beds, and 10% on stretcher beds

Policy options to streamline the carbon market for agricultural nitrous oxide emissions

The majority of emissions of nitrous oxide – a potent greenhouse gas (GHG) – are from agricultural sources, particularly nitrogen fertilizer applications. A growing focus on these emission sources has led to the development in the United States of GHG offset protocols that could enable payment to farmers for reducing fertilizer use or implementing other nitrogen management strategies. Despite the development of several protocols, the current regional scope is narrow, adoption by farmers is low, and policy implementation of protocols has a significant time lag. Here we utilize existing research and policy structures to propose an ‘umbrella’ approach for nitrogen management GHG emissions protocols that has the potential to streamline the policy implementation and acceptance of such protocols. We suggest that the umbrella protocol could set forth standard definitions common across multiple protocol options, and then modules could be further developed as scientific evidence advances. Modules could be developed for specific crops, regions, and practices. We identify a policy process that could facilitate this development in concert with emerging scientific research and conclude by acknowledging potential benefits and limitations of the approach. Key policy insights Agricultural greenhouse gas market options are growing, but are still underutilized Streamlining protocol development through an umbrella process could enable quicker development of protocols across new crops, regions, and practices Effective protocol development must not compromise best available science and should follow a rigorous pathway to ensure appropriate implementation

Search Engine Optimisation in UK news production

This is an Author's Accepted Manuscript of an article published in Journalism Practice, 5(4), 462 - 477, 2011, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/17512786.2010.551020.This paper represents an exploratory study into an emerging culture in UK online newsrooms—the practice of Search Engine Optimisation (SEO), which assesses its impact on news production. Comprising a short-term participant observational case study at a national online news publisher, and a series of semi-structured, in-depth interviews with SEO professionals at three further UK media organisations, the author sets out to establish how SEO is operationalised in the newsroom, and what consequences these practices have for online news production. SEO practice is found to be varied and application is not universal. Not all UK news organisations are making the most of SEO even though some publishers take a highly sophisticated approach. Efforts are constrained by time, resources and management support, as well as off-page technical issues. SEO policy is found, in some cases, to inform editorial policy, but there is resistance to the principal of SEO driving decision-making. Several themes are established which call for further research

Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering

We describe a framework for designing the sequences of multiple nucleic acid strands intended to hybridize in solution via a prescribed reaction pathway. Sequence design is formulated as a multistate optimization problem using a set of target test tubes to represent reactant, intermediate, and product states of the system, as well as to model crosstalk between components. Each target test tube contains a set of desired “on-target” complexes, each with a target secondary structure and target concentration, and a set of undesired “off-target” complexes, each with vanishing target concentration. Optimization of the equilibrium ensemble properties of the target test tubes implements both a positive design paradigm, explicitly designing for on-pathway elementary steps, and a negative design paradigm, explicitly designing against off-pathway crosstalk. Sequence design is performed subject to diverse user-specified sequence constraints including composition constraints, complementarity constraints, pattern prevention constraints, and biological constraints. Constrained multistate sequence design facilitates nucleic acid reaction pathway engineering for diverse applications in molecular programming and synthetic biology. Design jobs can be run online via the NUPACK web application

INTROGRESSION OF COYOTE MITOCHONDRIAL DNA INTO SYMPATRIC NORTH AMERICAN GRAY WOLF POPULATIONS

Mitochondrial DNA (mtDNA) genotypes of gray wolves and coyotes from localities throughout North America were determined using restriction fragment length polymorphisms. Of the 13 genotypes found among the wolves, 7 are clearly of coyote origin, indicating that genetic transfer of coyote mtDNA into wolf populations has occurred through hybridization. The transfer of mtDNA appears unidirectional from coyotes into wolves because no coyotes sampled have a wolf-derived mtDNA genotype. Wolves possessing coyote-derived genotypes are confined to a contiguous geographic region in Minnesota, Ontario, and Quebec, and the frequency of coyote- type mtDNA in these wolf populations is high (\u3e 500%). The ecological history of the hybrid zone suggests that hybridization is taking place in regions where coyotes have only recently become abundant following conversion of forests to farmlands. Dispersing male wolves unable to find conspecific mates may be pairing with female coyotes in deforested areas bordering wolf territories. Our results demonstrate that closely related species of mobile terrestrial vertebrates have the potential for extensive genetic exchange when ecological conditions change suddenly