Control of DNA conformation using 3'-S-phosphorothiolate-modified linkages

An in-depth study into the incorporation of multiple 3'-S-phosphorothiolate modifications into oligodeoxynucleotides (ODNs) and their subsequent effect on ODN/DNA and ODN/RNA duplex stability. 3'-S-Phosphorothiolate linkages increase the stability of ODN/RNA duplexes and decrease the stability of ODN/DNA duplexes.

Duplex stability of DNA.DNA and DNA.RNA duplexes containing 3 '-S-phosphorothiolate linkages

3′-S-Phosphorothiolate (3′-SP) linkages have been incorporated into the DNA strand of both a DNA·RNA duplex and a DNA·DNA duplex. Thermal melting (Tm) studies established that this modification significantly stabilises the DNA·RNA duplex with an average increase in Tm of about 1.4 °C per modification. For two or three modifications, the increase in Tm was larger for an alternating, as compared to the contiguous, arrangement. For more than three modifications their arrangement had no effect on Tm. In contrast to the DNA·RNA duplex, the 3′-S-phosphorothiolate linkage destabilised the DNA·DNA duplex, irrespective of the arrangement of the 3′-SP linkages. The effect of ionic strength on duplex stability was similar for both the phosphorothiolate-substituted and the unmodified RNA·DNA duplexes. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and comparisons are also drawn between the current study and those previously conducted with other modifications that have a similar conformational effect.

Stabilization of multi-stranded nucleic acid structures using 3'-S-phosphorothiolate linkages

3 '-S-Phosphorothiolate linkages incorporated into an oligodeoxynucleotide have been shown to stabilise duplex formation with a complementary RNA strand, but destabilise a duplex formed with a complementary DNA strand. The four-stranded i-motif structure is also stabilised this modification.

Recent climatic trends and linkages to river discharge in Central Vietnam

In this study, change in rainfall, temperature and river discharge are analysed over the last three decades in Central Vietnam. Trends and rainfall indices are evaluated using non-parametric tests at different temporal levels. To overcome the sparse locally available network, the high resolution APHRODITE gridded dataset is used in addition to the existing rain gauges. Finally, existing linkages between discharge changes and trends in rainfall and temperature are explored. Results are indicative of an intensification of rainfall (+15%/decade), with more extreme and longer events. A significant increase in winter rainfall and a decrease in consecutive dry days provides strong evidence for a lengthening wet season in Central Vietnam. In addition, trends based on APHRODITE suggest a strong orographic signal in winter and annual trends. These results underline the local variability in the impacts of climatic change at the global scale. Consequently, it is important that change detection investigations are conducted at the local scale. A very weak signal is detected in the trend of minimum temperature (+0.2°C/decade). River discharge trends show an increase in mean discharge (31 to 35%/decade) over the last decades. Between 54 and 74% of this increase is explained by the increase in precipitation. The maximum discharge also responds significantly to precipitation changes leading to a lengthened wet season and an increase in extreme rainfall events. Such trends can be linked with a likely increase in floods in Central Vietnam, which is important for future adaptation planning and management and flood preparedness in the region. Copyright © 2012 John Wiley & Sons, Ltd.

Linkages between property asset returns and interest rates: evidence for the UK

This paper considers the effect of short- and long-term interest rates, and interest rate spreads upon real estate index returns in the UK. Using Johansen's vector autoregressive framework, it is found that the real estate index cointegrates with the term spread, but not with the short or long rates themselves. Granger causality tests indicate that movements in short term interest rates and the spread cause movements in the returns series. However, decomposition of the forecast error variances from VAR models indicate that changes in these variables can only explain a small proportion of the overall variability of the returns, and that the effect has fully worked through after two months. The results suggest that these financial variables could potentially be used as leading indicators for real estate markets, with corresponding implications for return predictability.

Nicked-site substrates for a serine recombinase reveal enzyme–DNA communications and an essential tethering role of covalent enzyme–DNA linkages

To analyse the mechanism and kinetics of DNA strand cleavages catalysed by the serine recombinase Tn3 resolvase, we made modified recombination sites with a single-strand nick in one of the two DNA strands. Resolvase acting on these sites cleaves the intact strand very rapidly, giving an abnormal half-site product which accumulates. We propose that these reactions mimic second-strand cleavage of an unmodified site. Cleavage occurs in a synapse of two sites, held together by a resolvase tetramer; cleavage at one site stimulates cleavage at the partner site. After cleavage of a nicked-site substrate, the half-site that is not covalently linked to a resolvase subunit dissociates rapidly from the synapse, destabilizing the entire complex. The covalent resolvase–DNA linkages in the natural reaction intermediate thus perform an essential DNA-tethering function. Chemical modifications of a nicked-site substrate at the positions of the scissile phosphodiesters result in abolition or inhibition of resolvase-mediated cleavage and effects on resolvase binding and synapsis, providing insight into the serine recombinase catalytic mechanism and how resolvase interacts with the substrate DNA.

Mining in Ghana’s forests: cross-sectoral linkages and the prospects for REDD

Strategies to Reduce Emissions from Deforestation and Degradation (REDD) are being pursued in numerous developing countries. Proponents contest that REDD mechanisms could deliver sustainable development by contributing to both environmental protection and economic development, particularly in poor forest communities. However, among the challenges to REDD, and natural resource management more generally, is the need to develop a comprehensive understanding of cross-sectoral linkages and addressing how they impact the pursuit of sustainable development. Drawing on an exploratory case-study of Ghana, this paper aims to outline the linkages between the forestry and minerals sectors. It is argued that contemporary debates give incommensurate attention to the reclamation of large-scale mine sites located in forest reserves, and neglect to consider more nuanced links which characterise the forestry-mining nexus in Ghana. A review of key stakeholders further elucidates the complex networks which characterise these linkages and highlights the important role of traditional authorities in governing across sectors. If the multiple roles of local resource users and traditional authorities continue to be neglected in policy mechanisms, schemes such as REDD will continue to fall short of achieving sustainable development.

Fire, climate and vegetation linkages in the Bolivian Chiquitano Seasonally Dry Tropical Forest

South American seasonally-dry tropical forests (SDTF) are critically endangered, with only a small proportion of their original distribution remaining. This paper presents a 12,000 year reconstruction of climate change, fire and vegetation dynamics in the Bolivian Chiquitano SDTF, based upon pollen and charcoal analysis, to examine the resilience of this ecosystem to drought and fire. Our analysis demonstrates a complex relationship between climate, fire and floristic composition over multi-millennial time scales, and reveals that moisture variability is the dominant control upon community turnover in this ecosystem. Maximum drought during the early Holocene, consistent with regional drought reconstructions, correlates with a period of significant fire activity between 8,000 and 7,000 cal yr BP which resulted in a decrease in SDTF diversity. As fire activity declined, but severe regional droughts persisted through the mid-Holocene, SDTF, including Anadenanthera and Astronium, became firmly established in the Bolivian lowlands. The trend of decreasing fire activity during the last two millennia promotes the idea among forest ecologists that SDTF are threatened by fire. Our analysis shows that the Chiquitano seasonally dry biome has been more resilient to Holocene changes in climate and fire regime than previously assumed, but raises questions over whether this resilience will continue in the future under increased temperatures and drought coupled with a higher frequency anthropogenic fire regime.

Influence of interlayer tunneling on the quantized Hall phases in intentionally disordered multilayer structures

Stability of the quantized Hall phases is studied in weakly coupled multilayers as a function of the interlayer correlations controlled by the interlayer tunneling and by the random variation of the well thicknesses. A strong enough interlayer disorder destroys the symmetry responsible for the quantization of the Hall conductivity, resulting in the breakdown of the quantum Hall effect. A clear difference between the dimensionalities of the metallic and insulating quantum Hall phases is demonstrated. The sharpness of the quantized Hall steps obtained in the coupled multilayers with different degrees of randomization was found consistent with the calculated interlayer tunneling energies. The observed width of the transition between the quantized Hall states in random multilayers is explained in terms of the local fluctuations of the electron density.

Linkages between growth, poverty and the labour market

From a methodological point of view, this paper makes two contributions to the literature. One contribution is the proposal of a new measure of pro-poor growth. This new measure provides the linkage between growth rates in mean income and in income inequality. In this context, growth is defined as pro-poor (or anti-poor) if there is a gain (or loss) in the growth rate due to a decrease (or increase) in inequality. The other contribution is a decomposition methodology that explores linkages growth patterns, and labour market performances. Through the decomposition analysis, growth in per capita income is explained in terms of four labour market components: the employment rate, hours of work, the labour force participation rate, and productivity. The proposed methodology are then applied to the Brazilian National Household Survey (PNAD) covering the period 1995-2004. The paper analyzes the evolution of Brazilian social indicators based on per capita income exploring links with adverse labour market performance.