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.

Structure development in electrospun fibres of gelatin

Gelatin fibres have been successfully electrospun from water by heating a gelatin solution above the sol-gel transition temperature, and allowing cooling in a controlled environment as the fibres are produced. The development of structure with in these fibres is monitored using wide angle x-ray scattering, in this way the presence of the triple helix structure, which provides the physical cross-linkages in the gel could be probed. There is clear evidence that these structures are obtained in gelatin electrospun from aqueous solutions. In contrast fibres electrospun from a solution of gelatin in glacial acetic acid, showed no evidence of the triple helix structure.

The Upper Valanginian (Early Cretaceous) positive carbon-isotope event recorded in terrestrial plants

Our understanding of the ancient ocean-atmosphere system has focused on oceanic proxies. However, the study of terrestrial proxies is equally necessary to constrain our understanding of ancient climates and linkages between the terrestrial and oceanic carbon reservoirs. We have analyzed carbon-isotope ratios from fossil plant material through the Valanginian and Lower Hauterivian from a shallow-marine, ammonite-constrained succession in the Crimean Peninsula of the southern Ukraine in order to determine if the Upper Valanginian positive carbon-isotope excursion is expressed in the atmosphere. delta(13)C(plant) values fluctuate around -23% to -22% for the Valanginian-Hauterivian, except during the Upper Valanginian where delta(13)C(plant) values record a positive excursion to similar to-18%. Based upon ammonite biostratigraphy from Crimea, and in conjunction with a composite Tethyan marine delta(13)C(carb) curve, several conclusions can be drawn: (1) the delta(13)C(plant) record indicates that the atmospheric carbon reservoir was affected; (2) the defined ammonite correlations between Europe and Crimea are synchronous; and (3) a change in photosynthetic carbon-isotope fractionation, caused by a decrease in atmospheric PCO2, occurred during the Upper Valanginian Positive delta(13)C excursion. Our new data, combined with other paleoenvironmental and paleoclimatic information, indicate that the Upper Valanginian was a cool period (icehouse) and highlights that the Cretaceous period was interrupted by periods of cooling and was not an equable climate as previously thought. (C) 2005 Elsevier B.V. All rights reserved.

Can genetically-modified cotton contribute to sustainable development in Africa?

Genetically modified (GM) crops and sustainable development remain the foci of much media attention, especially given current concerns about a global food crisis. However, whilst the latter is embraced with enthusiasm by almost all groups, GM crops generate very mixed views. Some countries have welcomed GM, but others, notably those in Europe, adopt a cautious stance. This article aims to review the contribution that GM crops can make to agricultural sustainability in the developing world. Following brief reviews of both issues and their linkages, notably the pros and cons of GM cotton as a contributory factor in sustainability, a number of case studies from resourcepoor cotton farmers in Makhathini Flats, South Africa, is presented for a six-year period. Data on expenditure, productivity and income indicate that Bacillus thuringiensis (Bt) cotton is advantageous because it reduces costs, for example, of pesticides, and increases income, and the indications are that those benefits continued over at least the six years covered by the studies. There are repercussions of the additional income in the households; debts are reduced and money is invested in children's education and in the farms. However, in the general GM debate, the results show that GM crops are not miracle products which alleviate poverty at a stroke, but nor is there evidence that they will cause the scale of environmental damage associated with indiscriminate pesticide use. Indeed, for some GM antagonists, perhaps even the majority, such debates are irrelevant – the transfer of genes between species is unnatural and unethical. For them, GM crops will never be acceptable despite the evidence and pressure to increase world food production.

Soil fertility management in the mid-hills of Nepal: Practices and perceptions

Sustaining soil fertility is essential to the prosperity of many households in the mid-hills of Nepal, but there are concerns that the breakdown of the traditional linkages between forest, livestock, and cropping systems is adversely affecting fertility. This study used triangulated data from surveys of households, discussion groups, and key informants in 16 wards in eastern and western Nepal to determine the existing practices for soil fertility management, the extent of such practices, and the perception of the direction of changes in soil fertility. The two principal practices for maintaining soil fertility were the application of farmyard manure (FYM) and of chemical fertilizer (mainly urea and diammonium phosphate). Green manuring, in-situ manuring, slicing terrace risers, and burning plant residues are rarely practiced. FYM usage was variable with more generally applied to khet land (average 6053 kg fresh weight manure ha(-1)) than to bari land (average 4185 kg fresh weight manure ha-1) with manure from goats and poultry preferred above that from cows and buffaloes. Almost all households (98%) apply urea to khet land and 87% to bari land, with 45% applying diammonium phosphate to both types of land. Application rates and timings of applications varied considerably both within and between wards suggesting poor knowledge transfer between the research and farming communities. The benefits of chemical fertilizers in terms of ease of application and transportation in comparison with FYM, were perceived to outweigh the widely reported detrimental hardening of soil associated with their continued usage. Among key informants, FYM applied in conjunction with chemical fertilizer was the most popular amendment, with FYM alone preferred more than chemical fertilizer alone - probably because of the latter's long-term detrimental effects. Key informant and householder surveys differed in their perception of fertility changes in the last decade probably because of differences in age and site-specific knowledge. All key informants felt that fertility had declined but among households, only about 40% perceived a decline with the remainder about evenly divided between no change and an increase. Householders with small landholdings (< 0.5 ha) were more likely to perceive increasing soil fertility while those with larger landholdings (> 2 ha) were more likely to perceive declining fertility. Perceived changes in soil fertility were not related to food self-sufficiency. The reasons for the slow spread of new technologies within wards and the poor understanding of optimal use of chemical fertilizers in conjunction with improved quality FYM may repay further investigation in terms of sustaining soil fertility in this region.

A review of palaeoclimates and palaeoenvironments in the Levant and Eastern Mediterranean from 25,000 to 5000 years BP: setting the environmental background for the evolution of human civilisation

The southern Levant has a long history of human habitation and it has been previously suggested that climatic changes during the Late Pleistocene-Holocene stimulated changes in human behaviour and society. In order to evaluate such linkages, it is necessary to have a detailed understanding of the climate record. We have conducted an extensive and up-to-date review of terrestrial and marine climatic conditions in the Levant and Eastern Mediterranean during the last 25,000 years. We firstly present data from general circulation models (GCMs) simulating the climate for the last glacial maximum (LGM), and evaluate the output of the model by reference to geological climate proxy data. We consider the types of climate data available from different environments and proxies and then present the spatial climatic "picture" for key climatic events. This exercise suggests that the major Northern Hemisphere climatic fluctuations of the last 25,000 years are recorded in the Eastern Mediterranean and Levantine region. However, this review also highlights problems and inadequacies with the existing data. (c) 2006 Elsevier Ltd. All rights reserved.

The heliospheric magnetic field over the Hale cycle

The concept that open magnetic flux of the Sun (rooted with one and only one footpoint at the Sun) is a conserved quantity is taking root in the heliospheric community. Observations show that the Sun's open magnetic flux returns to the baseline from one solar minimum to the next. The temporary enhancement in the 1 AU heliospheric magnetic flux near solar maximum can be accounted for by the temporary creation of closed magnetic flux (with two footpoints at the Sun) during the ejection of coronal mass ejections (CMEs), which are more frequent near solar maximum. As a part of the International Heliophysical Year activities, this paper reviews two recently discussed consequences of open flux conservation: the reversal of open magnetic flux over the solar cycle driven by Coronal Mass Ejections and the impacts of open flux conservation on the global structure of the heliospheric magnetic field. These studies demonstrate the inherent linkages between coronal mass ejections, footpoint motions back at the Sun, and the global structure and evolution of the heliospheric magnetic field.

Towards an assessment of multiple ecosystem processes and services via functional traits

Managing ecosystems to ensure the provision of multiple ecosystem services is a key challenge for applied ecology. Functional traits are receiving increasing attention as the main ecological attributes by which different organisms and biological communities influence ecosystem services through their effects on underlying ecosystem processes. Here we synthesize concepts and empirical evidence on linkages between functional traits and ecosystem services across different trophic levels. Most of the 247 studies reviewed considered plants and soil invertebrates, but quantitative trait–service associations have been documented for a range of organisms and ecosystems, illustrating the wide applicability of the trait approach. Within each trophic level, specific processes are affected by a combination of traits while particular key traits are simultaneously involved in the control of multiple processes. These multiple associations between traits and ecosystem processes can help to identify predictable trait–service clusters that depend on several trophic levels, such as clusters of traits of plants and soil organisms that underlie nutrient cycling, herbivory, and fodder and fibre production. We propose that the assessment of trait–service clusters will represent a crucial step in ecosystem service monitoring and in balancing the delivery of multiple, and sometimes conflicting, services in ecosystem management.

Stages of organizational transformation in transition economies: A dynamic capabilities approach

How do organizations previously dominated by the state develop dynamic capabilities that would support their growth in a competitive market economy? We develop a theoretical framework of organizational transformation that explains the processes by which organizations learn and develop dynamic capabilities in transition economies. Specifically, the framework theorizes about the importance of, and inter-relationships between, leadership, organizational learning, dynamic capabilities, and performance over three stages of transformation. Propositions derived from this framework explain the pre-conditions enabling organizational learning, the linkages between types of learning and functions of dynamic capabilities, and the feedback from dynamic capabilities to organizational learning that allows firms in transition economies to regain their footing and build long-term competitive advantage. We focus on transition contexts, where these processes have been magnified and thus offer new insights into strategizing in radically altered environments.

Shock persistence in a dual economy model of India

This article examines shock persistence in agricultural and industrial output in India. Drawing on the dual economy literature, the linkages between the sectors through the terms of trade are emphasised. However different dual economy models make differing assumptions regarding the categorisation of variables as being either endogenous or exogenous and this distinction is crucial in explaining the pattern of shock persistence. Using annual data for 1955-95, our results show that shocks to both output series are permanent while those to the terms of trade are transient.

The Fox genes of Branchiostoma floridae

The Fox genes are united by encoding a fork head domain, a deoxyribonucleic acid (DNA)-binding domain of the winged-helix type that marks these genes as encoding transcription factors. Vertebrate Fox genes are classified into 23 subclasses named from FoxA to FoxS. We have surveyed the genome of the amphioxus Branchiostoma floridae, identifying 32 distinct Fox genes representing 21 of these 23 subclasses. The missing subclasses, FoxR and FoxS, are specific to vertebrates, and in addition, B. floridae has one further group, FoxAB, that is not found in vertebrates. Hence, we conclude B. floridae has maintained a high level of Fox gene diversity. Expressed sequence tag and complementary DNA sequence data support the expression of 23 genes. Several linkages between B. floridae Fox genes were noted, including some that have evolved relatively recently via tandem duplication in the amphioxus lineage and others that are more ancient.