Novel DNA probes with low background and high hybridization-triggered fluorescence

Novel fluorogenic DNA probes are described. The probes (called Pleiades) have a minor groove binder (MGB) and a fluorophore at the 5′-end and a non-fluorescent quencher at the 3′-end of the DNA sequence. This configuration provides surprisingly low background and high hybridization-triggered fluorescence. Here, we comparatively study the performance of such probes, MGB-Eclipse probes, and molecular beacons. Unlike the other two probe formats, the Pleiades probes have low, temperature-independent background fluorescence and excellent signal-to-background ratios. The probes possess good mismatch discrimination ability and high rates of hybridization. Based on the analysis of fluorescence and absorption spectra we propose a mechanism of action for the Pleiades probes. First, hydrophobic interactions between the quencher and the MGB bring the ends of the probe and, therefore, the fluorophore and the quencher in close proximity. Second, the MGB interacts with the fluorophore and independent of the quencher is able to provide a modest (2–4-fold) quenching effect. Joint action of the MGB and the quencher is the basis for the unique quenching mechanism. The fluorescence is efficiently restored upon binding of the probe to target sequence due to a disruption in the MGB–quencher interaction and concealment of the MGB moiety inside the minor groove

Small Earth Imaging Spectrometer

Advances in several key sensor technologies make it possible now to build a high performance, very compact and low cost imaging spectrometer for spacebourne terrestrial remote sensing. We describe an instrument based on a highly innovative optical design that incorporates state of the art focal plane arrays, electronics, focal plane cooling and dimensionally stable ceramics for the optical elements and structure. The instrument is optimized for viewing the earth\u27s solid surface and adjacent coastal oceans. It has very high signal-to-noise performance over the full spectral range covered, from 400 to 2450 nanometers (nm). Spectral sampling is in 200 10-nm wide, contiguous bands. The instrument combines a high spatial resolution panchromatic imaging system with a modest spatial resolution imaging spectrometer. It weighs 25 kg, requires less than 100 watts of power, and is approximately 30 by 20 by 10 cm in dimension, fitting well within the capacity of Pegasus-class small spacecraft missions. The instrument is well suited to support studies in earth system science as well as commercial remote sensing. Several applications in these areas will be highlighted to set in context the performance requirements that were used to define the sensor design and choice of sensor technologies

A novel endonuclease IV post-PCR genotyping system

Here we describe a novel endonuclease IV (Endo IV) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded DNA. The three component substrate is characterized by single-stranded DNA target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base gap. The oligonucleotide probe contains a non-fluorescent quencher at the 5′ end and fluorophore attached to the 3′ end through a special rigid linker. Fluorescence of the oligonucleotide probe is efficiently quenched by the interaction of terminal dye and quencher when not hybridized. Upon hybridization of the oligonucleotide probe and helper probe to their complementary target, the phosphodiester linkage between the rigid linker and the 3′ end of the probe is efficiently cleaved, generating a fluorescent signal. In this study, the use of the Endo IV assay as a post-PCR amplification detection system is demonstrated. High sensitivity and specificity are illustrated using single nucleotide polymorphism detection

States Of Discontent

Latin America’s recent inclusionary turn centers on changing relationships between the popular sectors and the state. Yet the new inclusion unfolds in a region in which most states are weak and prone to severe pathologies, such as corruption, inefficiency, and particularism. The first part of the chapter outlines an argument, developed at more length elsewhere, regarding how “state crises” helped drive the consolidation of three distinct party system trajectories among the eight South American countries where the Left would eventually win power. The second part of the chapter argues that these trajectories differed in three ways that likely conditioned how the concomitant inclusionary Left turn unfolded in each case: the institutionalization of left-wing parties, the occurrence of state transformation via constitutional reform, and the level of state capacity. The discussion helps highlight the central role of the state and its pathologies in both driving alternative paths of political development and in conditioning the politics of inclusion. By putting the emphasis on the state and its pathologies, we can better consider not just the sources of sociopolitical exclusion but also the limits of sociopolitical inclusion

Advancing the application of systems thinking in health:analysing the contextual and social network factors influencing the use of sustainability indicators in a health system - a comparative study in Nepal and Somaliland

BACKGROUND: Health systems strengthening is becoming a key component of development agendas for low-income countries worldwide. Systems thinking emphasizes the role of diverse stakeholders in designing solutions to system problems, including sustainability. The objective of this paper is to compare the definition and use of sustainability indicators developed through the Sustainability Analysis Process in two rehabilitation sectors, one in Nepal and one in Somaliland, and analyse the contextual factors (including the characteristics of system stakeholder networks) influencing the use of sustainability data. METHODS: Using the Sustainability Analysis Process, participants collectively clarified the boundaries of their respective systems, defined sustainability, and identified sustainability indicators. Baseline indicator data was gathered, where possible, and then researched again 2 years later. As part of the exercise, system stakeholder networks were mapped at baseline and at the 2-year follow-up. We compared stakeholder networks and interrelationships with baseline and 2-year progress toward self-defined sustainability goals. Using in-depth interviews and observations, additional contextual factors affecting the use of sustainability data were identified. RESULTS: Differences in the selection of sustainability indicators selected by local stakeholders from Nepal and Somaliland reflected differences in the governance and structure of the present rehabilitation system. At 2 years, differences in the structure of social networks were more marked. In Nepal, the system stakeholder network had become more dense and decentralized. Financial support by an international organization facilitated advancement toward self-identified sustainability goals. In Somaliland, the small, centralised stakeholder network suffered a critical rupture between the system's two main information brokers due to competing priorities and withdrawal of international support to one of these. Progress toward self-defined sustainability was nil. CONCLUSIONS: The structure of the rehabilitation system stakeholder network characteristics in Nepal and Somaliland evolved over time and helped understand the changing nature of relationships between actors and their capacity to work as a system rather than a sum of actors. Creating consensus on a common vision of sustainability requires additional system-level interventions such as identification of and support to stakeholders who promote systems thinking above individual interests