Conservation strategy maps: a tool to facilitate biodiversity action planning illustrated using the heath fritillary butterfly

1. The UK Biodiversity Action Plan (UKBAP) identifies invertebrate species in danger of national extinction. For many of these species, targets for recovery specify the number of populations that should exist by a specific future date but offer no procedure to plan strategically to achieve the target for any species. 2. Here we describe techniques based upon geographic information systems (GIS) that produce conservation strategy maps (CSM) to assist with achieving recovery targets based on all available and relevant information. 3. The heath fritillary Mellicta athalia is a UKBAP species used here to illustrate the use of CSM. A phase 1 habitat survey was used to identify habitat polygons across the county of Kent, UK. These were systematically filtered using relevant habitat, botanical and autecological data to identify seven types of polygon, including those with extant colonies or in the vicinity of extant colonies, areas managed for conservation but without colonies, and polygons that had the appropriate habitat structure and may therefore be suitable for reintroduction. 4. Five clusters of polygons of interest were found across the study area. The CSM of two of them are illustrated here: the Blean Wood complex, which contains the existing colonies of heath fritillary in Kent, and the Orlestone Forest complex, which offers opportunities for reintroduction. 5. Synthesis and applications. Although the CSM concept is illustrated here for the UK, we suggest that CSM could be part of species conservation programmes throughout the world. CSM are dynamic and should be stored in electronic format, preferably on the world-wide web, so that they can be easily viewed and updated. CSM can be used to illustrate opportunities and to develop strategies with scientists and non-scientists, enabling the engagement of all communities in a conservation programme. CSM for different years can be presented to illustrate the progress of a plan or to provide continuous feedback on how a field scenario develops.

Integrating methods for developing sustainability indicators that can facilitate learning and action

Bossel's (2001) systems-based approach for deriving comprehensive indicator sets provides one of the most holistic frameworks for developing sustainability indicators. It ensures that indicators cover all important aspects of system viability, performance, and sustainability, and recognizes that a system cannot be assessed in isolation from the systems upon which it depends and which in turn depend upon it. In this reply, we show how Bossel's approach is part of a wider convergence toward integrating participatory and reductionist approaches to measure progress toward sustainable development. However, we also show that further integration of these approaches may be able to improve the accuracy and reliability of indicators to better stimulate community learning and action. Only through active community involvement can indicators facilitate progress toward sustainable development goals. To engage communities effectively in the application of indicators, these communities must be actively involved in developing, and even in proposing, indicators. The accuracy, reliability, and sensitivity of the indicators derived from local communities can be ensured through an iterative process of empirical and community evaluation. Communities are unlikely to invest in measuring sustainability indicators unless monitoring provides immediate and clear benefits. However, in the context of goals, targets, and/or baselines, sustainability indicators can more effectively contribute to a process of development that matches local priorities and engages the interests of local people.

CAFS in action

For those few readers who do not know, CAFS is a system developed by ICL to search through data at speeds of several million characters per second. Its full name is Content Addressable File Store Information Search Processor, CAFS-ISP or CAFS for short. It is an intelligent hardware-based searching engine, currently available with both ICL's 2966 family of computers and the recently announced Series 39, operating within the VME environment. It uses content addressing techniques to perform fast searches of data or text stored on discs: almost all fields are equally accessible as search keys. Software in the mainframe generates a search task; the CAFS hardware performs the search, and returns the hit records to the mainframe. Because special hardware is used, the searching process is very much more efficient than searching performed by any software method. Various software interfaces are available which allow CAFS to be used in many different situations. CAFS can be used with existing systems without significant change. It can be used to make online enquiries of mainframe files or databases or directly from user written high level language programs. These interfaces are outlined in the body of the report.

Iron Uptake and Homeostasis in Microorganisms

Preface. Iron is considered to be a minor element employed, in a variety of forms, by nearly all living organisms. In some cases, it is utilised in large quantities, for instance for the formation of magnetosomes within magnetotactic bacteria or during use of iron as a respiratory donor or acceptor by iron oxidising or reducing bacteria. However, in most cases the role of iron is restricted to its use as a cofactor or prosthetic group assisting the biological activity of many different types of protein. The key metabolic processes that are dependent on iron as a cofactor are numerous; they include respiration, light harvesting, nitrogen fixation, the Krebs cycle, redox stress resistance, amino acid synthesis and oxygen transport. Indeed, it is clear that Life in its current form would be impossible in the absence of iron. One of the main reasons for the reliance of Life upon this metal is the ability of iron to exist in multiple redox states, in particular the relatively stable ferrous (Fe2+) and ferric (Fe3+) forms. The availability of these stable oxidation states allows iron to engage in redox reactions over a wide range of midpoint potentials, depending on the coordination environment, making it an extremely adaptable mediator of electron exchange processes. Iron is also one of the most common elements within the Earth’s crust (5% abundance) and thus is considered to have been readily available when Life evolved on our early, anaerobic planet. However, as oxygen accumulated (the ‘Great oxidation event’) within the atmosphere some 2.4 billion years ago, and as the oceans became less acidic, the iron within primordial oceans was converted from its soluble reduced form to its weakly-soluble oxidised ferric form, which precipitated (~1.8 billion years ago) to form the ‘banded iron formations’ (BIFs) observed today in Precambrian sedimentary rocks around the world. These BIFs provide a geological record marking a transition point away from the ancient anaerobic world towards modern aerobic Earth. They also indicate a period over which the bio-availability of iron shifted from abundance to limitation, a condition that extends to the modern day. Thus, it is considered likely that the vast majority of extant organisms face the common problem of securing sufficient iron from their environment – a problem that Life on Earth has had to cope with for some 2 billion years. This struggle for iron is exemplified by the competition for this metal amongst co-habiting microorganisms who resort to stealing (pirating) each others iron supplies! The reliance of micro-organisms upon iron can be disadvantageous to them, and to our innate immune system it represents a chink in the microbial armour, offering an opportunity that can be exploited to ward off pathogenic invaders. In order to infect body tissues and cause disease, pathogens must secure all their iron from the host. To fight such infections, the host specifically withdraws available iron through the action of various iron depleting processes (e.g. the release of lactoferrin and lipocalin-2) – this represents an important strategy in our defence against disease. However, pathogens are frequently able to deploy iron acquisition systems that target host iron sources such as transferrin, lactoferrin and hemoproteins, and thus counteract the iron-withdrawal approaches of the host. Inactivation of such host-targeting iron-uptake systems often attenuates the pathogenicity of the invading microbe, illustrating the importance of ‘the battle for iron’ in the infection process. The role of iron sequestration systems in facilitating microbial infections has been a major driving force in research aimed at unravelling the complexities of microbial iron transport processes. But also, the intricacy of such systems offers a challenge that stimulates the curiosity. One such challenge is to understand how balanced levels of free iron within the cytosol are achieved in a way that avoids toxicity whilst providing sufficient levels for metabolic purposes – this is a requirement that all organisms have to meet. Although the systems involved in achieving this balance can be highly variable amongst different microorganisms, the overall strategy is common. On a coarse level, the homeostatic control of cellular iron is maintained through strict control of the uptake, storage and utilisation of available iron, and is co-ordinated by integrated iron-regulatory networks. However, much yet remains to be discovered concerning the fine details of these different iron regulatory processes. As already indicated, perhaps the most difficult task in maintaining iron homeostasis is simply the procurement of sufficient iron from external sources. The importance of this problem is demonstrated by the plethora of distinct iron transporters often found within a single bacterium, each targeting different forms (complex or redox state) of iron or a different environmental condition. Thus, microbes devote considerable cellular resource to securing iron from their surroundings, reflecting how successful acquisition of iron can be crucial in the competition for survival. The aim of this book is provide the reader with an overview of iron transport processes within a range of microorganisms and to provide an indication of how microbial iron levels are controlled. This aim is promoted through the inclusion of expert reviews on several well studied examples that illustrate the current state of play concerning our comprehension of how iron is translocated into the bacterial (or fungal) cell and how iron homeostasis is controlled within microbes. The first two chapters (1-2) consider the general properties of microbial iron-chelating compounds (known as ‘siderophores’), and the mechanisms used by bacteria to acquire haem and utilise it as an iron source. The following twelve chapters (3-14) focus on specific types of microorganism that are of key interest, covering both an array of pathogens for humans, animals and plants (e.g. species of Bordetella, Shigella, , Erwinia, Vibrio, Aeromonas, Francisella, Campylobacter and Staphylococci, and EHEC) as well as a number of prominent non-pathogens (e.g. the rhizobia, E. coli K-12, Bacteroides spp., cyanobacteria, Bacillus spp. and yeasts). The chapters relay the common themes in microbial iron uptake approaches (e.g. the use of siderophores, TonB-dependent transporters, and ABC transport systems), but also highlight many distinctions (such as use of different types iron regulator and the impact of the presence/absence of a cell wall) in the strategies employed. We hope that those both within and outside the field will find this book useful, stimulating and interesting. We intend that it will provide a source for reference that will assist relevant researchers and provide an entry point for those initiating their studies within this subject. Finally, it is important that we acknowledge and thank wholeheartedly the many contributors who have provided the 14 excellent chapters from which this book is composed. Without their considerable efforts, this book, and the understanding that it relays, would not have been possible. Simon C Andrews and Pierre Cornelis

Mapping and controlling molecular processes: The application of control theory and system identification algorithms to ASOPS and other fast pulse spectroscopies

Asynchronous Optical Sampling (ASOPS) [1,2] and frequency comb spectrometry [3] based on dual Ti:saphire resonators operated in a master/slave mode have the potential to improve signal to noise ratio in THz transient and IR sperctrometry. The multimode Brownian oscillator time-domain response function described by state-space models is a mathematically robust framework that can be used to describe the dispersive phenomena governed by Lorentzian, Debye and Drude responses. In addition, the optical properties of an arbitrary medium can be expressed as a linear combination of simple multimode Brownian oscillator functions. The suitability of a range of signal processing schemes adopted from the Systems Identification and Control Theory community for further processing the recorded THz transients in the time or frequency domain will be outlined [4,5]. Since a femtosecond duration pulse is capable of persistent excitation of the medium within which it propagates, such approach is perfectly justifiable. Several de-noising routines based on system identification will be shown. Furthermore, specifically developed apodization structures will be discussed. These are necessary because due to dispersion issues, the time-domain background and sample interferograms are non-symmetrical [6-8]. These procedures can lead to a more precise estimation of the complex insertion loss function. The algorithms are applicable to femtosecond spectroscopies across the EM spectrum. Finally, a methodology for femtosecond pulse shaping using genetic algorithms aiming to map and control molecular relaxation processes will be mentioned.

Nature protection in Greece: an appraisal of the factors shaping integrative conservation and policy effectiveness

The proliferation of designated areas following the implementation of Natura 2000 in Greece has initiated changes in the protected area design and conservation policy making aiming at delivering action for biodiversity and integrative planning on a wider landscape. Following the sustainability concept, an integrative approach cannot realistically take place simply by extending the protected area and designations. The paper addresses public involvement and inter-sectoral coordination as major procedural elements of integrative management and evaluates the nature and strength of their negative or positive influences on the fulfillment of an integrative vision of nature conservation. A review of the history of protected areas and administration developments in Greece provide useful input in the research. The analysis has shown that the selected network of Natura 2000 sites has been superimposed upon the existing system and resulted in duplication of administrative effort and related legislation. As a result the overall picture of protected areas in the country appears complex, confusing and fragmented. Major failures to integrated conservation perspective can be traced to structural causes rooted in politico-economic power structures of mainstream policy and in a rather limited political commitment to conservation. It is concluded that greater realisation. of integrated conservation in Greece necessitates policy reforms related mainly to sectoral legal frameworks to promote environmentalism as well as an increased effort by the managing authorities to facilitate a broader framework of public dialogue and give local communities incentives to sustainably benefit from protected areas. (C) 2006 Elsevier Ltd. All rights reserved.

Plant-pollinator biodiversity and pollination services in a complex Mediterranean landscape

Mediterranean landscapes comprise a complex mosaic of different habitats that vary in the diversity of their floral communities, pollinator communities and pollination services. Using the Greek Island of Lesvos as a model system, we assess the biodiversity value of six common habitats and measure ecosystemic 'health' using pollen grain deposition in three core flowering plants as a measure of pollination services. Three fire-driven habitats were assessed: freshly burnt areas, fully regenerated pine forests and intermediate age scrub; in addition we examined oak woodlands, actively managed olive groves and groves that had been abandoned from agriculture. Oak woodlands, pine forests and managed olive groves had the highest diversity of bees. The habitat characteristics responsible for structuring bee communities were: floral diversity, floral abundance, nectar energy availability and the variety of nectar resources present. Pollination services in two of our plant species, which were pollinated by a limited sub-set of the pollinator community, indicated that pollination levels were highest in the burnt and mature pine habitats. The third species, which was open to all flower visitors, indicated that oak woodlands had the highest levels of pollination from generalist species. Pollination was always more effective in managed olive groves than in abandoned groves. However, the two most common species of bee, the honeybee and a bumblebee, were not the primary pollinators within these habitats. We conclude that the three habitats of greatest overall value for plant-pollinator communities and provision of the healthiest pollination services are pine forests, oak woodland and managed olive groves. We indicate how the highest value habitats may be maintained in a complex landscape to safeguard and enhance pollination function within these habitats and potentially in adjoining agricultural areas. (c) 2005 Elsevier Ltd. All rights reserved.

Identifying and understanding factors influencing the uptake of new technologies on dairy farms in SW England using the theory of reasoned action

Whilst much is known of new technology adopters, little research has addressed the role of their attitudes in adoption decisions; particularly, for technologies with evident economic potential that have not been taken up by farmers. This paper presents recent research that has used a new approach which examines the role that adopters' attitudes play in identifying the drivers of and barriers to adoption. The study was concerned with technologies for livestock farming systems in SW England, specifically oestrus detection, nitrogen supply management, and, inclusion of white clover. The adoption behaviour is analysed using the social-psychology theory of reasoned action to identify factors that affect the adoption of technologies, which are confirmed using principal components analysis. The results presented here relate to the specific adoption behaviour regarding the Milk Development Council's recommended observation times for heat detection. The factors that affect the adoption of this technology are: cost effectiveness, improved detection and conception rates as the main drivers, whilst the threat to demean the personal knowledge and skills of a farmer in 'knowing' their cows is a barrier. This research shows clearly that promotion of a technology and transfer of knowledge for a farming system need to take account of the beliefs and attitudes of potential adopters. (C) 2006 Elsevier Ltd. All rights reserved.

Characterization of a gamma-aminobutyric acid transport system of rhizobium leguminosarum bv. viciae 3841

Spontaneous mutants of Rhizobium leguminosarum bv. viciae 3841 were isolated that grow faster than the wild type on gamma-aminobutyric acid (GABA) as the sole carbon and nitrogen source. These strains (RU1736 and RU1816) have frameshift mutations (gtsR101 and gtsR102, respectively) in a GntR-type regulator (GtsR) that result in a high rate of constitutive GABA transport. Tn5 mutagenesis and quantitative reverse transcription-PCR showed that GstR regulates expression of a large operon (pRL100242 to pRL100252) on the Sym plasmid that is required for GABA uptake. An ABC transport system, GtsABCD (for GABA transport system) (pRL100248-51), of the spermidine/putrescine family is part of this operon. GtsA is a periplasmic binding protein, GtsB and GtsC are integral membrane proteins, and GtsD is an ATP-binding subunit. Expression of gtsABCD from a lacZ promoter confirmed that it alone is responsible for high rates of GABA transport, enabling rapid growth of strain 3841 on GABA. Gts transports open-chain compounds with four or five carbon atoms with carboxyl and amino groups at, or close to, opposite termini. However, aromatic compounds with similar spacing between carboxyl and amino groups are excellent inhibitors of GABA uptake so they may also be transported. In addition to the ABC transporter, the operon contains two putative mono-oxygenases, a putative hydrolase, a putative aldehyde dehydrogenase, and a succinate semialdehyde dehydrogenase. This suggests the operon may be involved in the transport and breakdown of a more complex precursor to GABA. Gts is not expressed in pea bacteroids, and gtsB mutants are unaltered in their symbiotic phenotype, suggesting that Bra is the only GABA transport system available for amino acid cycling.

Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein

Conserved among all coronaviruses are four structural proteins: the matrix (M), small envelope (E), and spike (S) proteins that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in the lumen. The N-terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding, while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C terminus of the N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17 A (monoclinic) and at 1.85 A (cubic), respectively, resolved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core, is oriented similarly to that in the IBV N-NTD, and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggests a common mode of RNA recognition, but they probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs suggests that they use different modes of both RNA recognition and oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

Analysis of protein-protein interactions in the feline calicivirus replication complex

Caliciviruses are a major cause of gastroenteritis in humans and cause a wide variety of other diseases in animals. Here, the characterization of protein-protein interactions between the individual proteins of Feline calicivirus (FCV), a model system for other members of the family Caliciviridae, is reported. Using the yeast two-hybrid system combined with a number of other approaches, it is demonstrated that the p32 protein (the picornavirus 2B analogue) of FCV interacts with p39 (2C), p30 (3A) and p76 (3CD). The FCV protease/RNA polymerase (ProPol) p76 was found to form homo-oligomers, as well as to interact with VPg and ORF2, the region encoding the major capsid protein VP1. A weak interaction was also observed between p76 and the minor capsid protein encoded by ORF3 (VP2). ORF2 protein was found to interact with VPg, p76 and VP2. The potential roles of the interactions in calicivirus replication are discussed.

Mechanisms of inverse agonist action at D-2 dopamine receptors

1 Mechanisms of inverse agonist action at the D-2(short) dopamine receptor have been examined. 2 Discrimination of G-protein-coupled and -uncoupled forms of the receptor by inverse agonists was examined in competition ligand-binding studies versus the agonist [H-3]NPA at a concentration labelling both G-protein-coupled and -uncoupled receptors. 3 Competition of inverse agonists versus [H-3] NPA gave data that were fitted best by a two-binding site model in the absence of GTP but by a one-binding site model in the presence of GTP. K-i values were derived from the competition data for binding of the inverse agonists to G-protein-uncoupled and -coupled receptors. K-coupled and K-uncoupled were statistically different for the set of compounds tested ( ANOVA) but the individual values were different in a post hoc test only for (+)-butaclamol. 4 These observations were supported by simulations of these competition experiments according to the extended ternary complex model. 5 Inverse agonist efficacy of the ligands was assessed from their ability to reduce agonist-independent [S-35]GTPγ S binding to varying degrees in concentration-response curves. Inverse agonism by (+)-butaclamol and spiperone occurred at higher potency when GDP was added to assays, whereas the potency of (-)-sulpiride was unaffected. 6 These data show that some inverse agonists ((+)-butaclamol, spiperone) achieve inverse agonism by stabilising the uncoupled form of the receptor at the expense of the coupled form. For other compounds tested, we were unable to define the mechanism.

Mechanisms of agonist action at D-2 dopamine receptors

In this study, we investigated the biochemical mechanisms of agonist action at the G protein-coupled D-2 dopamine receptor expressed in Chinese hamster ovary cells. Stimulation of guanosine 5'-O-(3-[S-35]thio) triphosphate ([S-35]GTPgammaS) binding by full and partial agonists was determined at different concentrations of [S-35]GTPgammaS (0.1 and 10 nM) and in the presence of different concentrations of GDP. At both concentrations of [S-35]GTPgammaS, increasing GDP decreased the [S-35]GTPgammaS binding observed with maximally stimulating concentrations of agonist, with partial agonists exhibiting greater sensitivity to the effects of GDP than full agonists. The relative efficacy of partial agonists was greater at the lower GDP concentrations. Concentration-response experiments were performed for a range of agonists at the two [S-35]GTPgammaS concentrations and with different concentrations of GDP. At 0.1 nM [S-35]GTPgammaS, the potency of both full and partial agonists was dependent on the GDP concentration in the assays. At 10 nM [S-35]GTPgammaS, the potency of full agonists exhibited a greater dependence on the GDP concentration, whereas the potency of partial agonists was virtually independent of GDP. We concluded that at the lower [S-35]GTPgammaS concentration, the rate-determining step in G protein activation is the binding of [S-35]GTPgammaS to the G protein. At the higher [S-35]GTPgammaS concentration, for full agonists, [S-35]GTPgammaS binding remains the slowest step, whereas for partial agonists, another (GDP-independent) step, probably ternary complex breakdown, becomes rate-determining.

A novel Bayesian approach to drug design with simple and complex enzymes: Use with lens aldehyde dehydrogenase and the glyoxalase pathway

Purpose: Acquiring details of kinetic parameters of enzymes is crucial to biochemical understanding, drug development, and clinical diagnosis in ocular diseases. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. Methods: We have developed Bayesian utility functions to minimise kinetic parameter variance involving differentiation of model expressions and matrix inversion. These have been applied to the simple kinetics of the enzymes in the glyoxalase pathway (of importance in posttranslational modification of proteins in cataract), and the complex kinetics of lens aldehyde dehydrogenase (also of relevance to cataract). Results: Our successful application of Bayesian statistics has allowed us to identify a set of rules for designing optimum kinetic experiments iteratively. Most importantly, the distribution of points in the range is critical; it is not simply a matter of even or multiple increases. At least 60 % must be below the KM (or plural if more than one dissociation constant) and 40% above. This choice halves the variance found using a simple even spread across the range.With both the glyoxalase system and lens aldehyde dehydrogenase we have significantly improved the variance of kinetic parameter estimation while reducing the number and costs of experiments. Conclusions: We have developed an optimal and iterative method for selecting features of design such as substrate range, number of measurements and choice of intermediate points. Our novel approach minimises parameter error and costs, and maximises experimental efficiency. It is applicable to many areas of ocular drug design, including receptor-ligand binding and immunoglobulin binding, and should be an important tool in ocular drug discovery.

Conservation strategy maps: a tool to facilitate biodiversity action planning illustrated using the heath fritillary butterfly

1. The UK Biodiversity Action Plan (UKBAP) identifies invertebrate species in danger of national extinction. For many of these species, targets for recovery specify the number of populations that should exist by a specific future date but offer no procedure to plan strategically to achieve the target for any species. 2. Here we describe techniques based upon geographic information systems (GIS) that produce conservation strategy maps (CSM) to assist with achieving recovery targets based on all available and relevant information. 3. The heath fritillary Mellicta athalia is a UKBAP species used here to illustrate the use of CSM. A phase 1 habitat survey was used to identify habitat polygons across the county of Kent, UK. These were systematically filtered using relevant habitat, botanical and autecological data to identify seven types of polygon, including those with extant colonies or in the vicinity of extant colonies, areas managed for conservation but without colonies, and polygons that had the appropriate habitat structure and may therefore be suitable for reintroduction. 4. Five clusters of polygons of interest were found across the study area. The CSM of two of them are illustrated here: the Blean Wood complex, which contains the existing colonies of heath fritillary in Kent, and the Orlestone Forest complex, which offers opportunities for reintroduction. 5. Synthesis and applications. Although the CSM concept is illustrated here for the UK, we suggest that CSM could be part of species conservation programmes throughout the world. CSM are dynamic and should be stored in electronic format, preferably on the world-wide web, so that they can be easily viewed and updated. CSM can be used to illustrate opportunities and to develop strategies with scientists and non-scientists, enabling the engagement of all communities in a conservation programme. CSM for different years can be presented to illustrate the progress of a plan or to provide continuous feedback on how a field scenario develops.