PGR forum: serving the crop wild relative user community

The Euro-Mediterranean region is an important centre for the diversity of crop wild relatives. Crops, such as oats (Avena sativa), sugar beet (Beta vulgaris), apple (Malus domestica), annual meadow grass (Festuca pratensis), white clover (Trifolium repens), arnica (Arnica montana), asparagus (Asparagus officinalis), lettuce (Lactuca sativa), and sage (Salvia officinalis) etc., all have wild relatives in the region. The European Community funded project, PGR Forum (www.pgrforum.org) is building an online information system to provide access to crop wild relative data to a broad user community; including plant breeders, protected area managers, policy-makers, conservationists, taxonomists and the wider public. The system will include data on uses, geographical distribution, biology, population and habitat information, threats (including IUCN Red List assessments) and conservation actions. This information is vital for the continued sustainable utilisation and conservation of crop wild relatives. Two major databases have been utilised as the backbone to a Euro-Mediterranean crop wild relative catalogue, which forms the core of the information system: Euro+Med PlantBase (www.euromed.org.uk) and Mansfeld’s World Database of Agricultural and Horticultural Crops (http://mansfeld.ipk-gatersleben.de). By matching the genera found within the two databases, a preliminary list of crop wild relatives has been produced. Around 20,000 of the 30,000+ species listed in Euro+Med PlantBase can be considered crop wild relatives, i.e. those species found within the same genus as a crop. The list is currently being refined by implementing a priority ranking system based on the degree of relatedness of taxa to the associated crop.

Aligning sequences to structures

Most newly sequenced proteins are likely to adopt a similar structure to one which has already been experimentally determined. For this reason, the most successful approaches to protein structure prediction have been template-based methods. Such prediction methods attempt to identify and model the folds of unknown structures by aligning the target sequences to a set of representative template structures within a fold library. In this chapter, I discuss the development of template-based approaches to fold prediction, from the traditional techniques to the recent state-of-the-art methods. I also discuss the recent development of structural annotation databases, which contain models built by aligning the sequences from entire proteomes against known structures. Finally, I run through a practical step-by-step guide for aligning target sequences to known structures and contemplate the future direction of template-based structure prediction.

Managing threatened species: the ecological toolbox, evolutionary theory and declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviour-based models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley's declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

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.

Direct detection of chlorosilylene and time resolved study of some of its reactions in the gas-phase using a new photochemical precursor

Chlorosilylene, ClSiH, was prepared by 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene in the gas phase. ClSiH was monitored in real time at 457.9 nm using a CW argon ion laser. The kinetics of reactions of ClSiH with C2H4, CH2 = CHCMe3, C2H2, Me2O, SO2, HCl, MeSiH3, Me2SiH2, Me3SiH, MeGeH3, MeGeH3 and precursor have been studied at ambient temperatures for the first time. Addition reactions of ClSiH and reactions with lone pair donors are faster than insertion reactions. Surprisingly ClSiH inserts faster into Si-H than Ge-H bonds. ClSiH is intermediate in reactivity between SiH2 and SiCI2. Relative reactivities of CISiH and SiH2 vary considerably. (c) 2005 Elsevier B.V. All rights reserved.

The synthesis and characterisation of two new iron thioantimonates: [Fe(en)(3)](2)Sb2S5 center dot 0.55H(2)O and [Fe(en)(3)](2)Sb4S8

Two new iron thioantimonates, [Fe(en)(3)](2)Sb2S5 (.) 0.55H(2)O (1) and [Fe(en)(3)](2)Sb4S8 (2). were synthesised under solvothermal conditions from the reactions of Sb2S3, FeCl2 and S in the presence of ethylenediamine at 413 and 438 K, respectively. The products were characterised by single-crystal X-ray diffraction, elemental analysis and SQUID magnetometry. Compound 1 is unusual in containing isolated Sb2S54- anions formed from two corner-sharing SbS33- trigonal pyramids. These units are arranged in rippled layers, 4 A apart, parallel to the bc-plane. Octahedrally coordinated [Fe(en)(3)](2+) cations lie in depressions within these anionic layers. In compound (2), repeated corner linking of SbS33- trigonal pyramids generates SbS2- chains, which may be considered as a polymerised form of the Sb2S54- anions in 1. The SbS2- chains are separated by [Fe(en)(3)](2+) cations. In both compounds, there is an extensive network of hydrogen bonds between the nitrogen atoms of the ethylenediamine ligands and the sulfur atoms of the anions and, in the case of 1, the uncoordinated water molecule. (c) 2005 Elsevier Ltd. All rights reserved.

Preliterate phonological awareness and early literacy skills in Turkish

The role of preschool phonological awareness in early reading and spelling skills was investigated in the transparent orthography of Turkish. Fifty-six preschool children (mean age=5.6 years) were followed into Grade 2 (mean age=7.6 years). While preschool phonological awareness failed to make any reliable contribution to future reading skills, it was the strongest longitudinal correlate of spelling skills measured at the end of Grades 1 and 2. Overall findings suggested that phonological awareness may be differentially related to reading and spelling, and that spelling is a more sensitive index of phonological processing skills. In this study, verbal short-term memory emerged as the most powerful and consistent longitudinal correlate of reading speed. This finding raised important questions about the component processes of reading speed, and the role of memory and morphosyntactic skills in an agglutinative and transparent orthography such as Turkish.

Anaerotruncus colihominis gen. nov., sp. nov., from human faeces

Phenotypic and phylogenetic studies were performed on two isolates of an unidentified Gram-positive, anaerobic, non-spore-forming, rod-shaped bacterium that was isolated from human faeces. The organisms were catalase-negative, produced acetic and butyric acids as end products of metabolism and possessed a DNA G+C content of approximately 54 mol%. Comparative 16S rRNA gene sequencing demonstrated that the two isolates were related closely to each other and formed a hitherto unknown sublineage within the Clostridium leptum rRNA cluster of organisms. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium should be classified in a novel genus as Anaerotruncus colihominis gen. nov., so. nov. The type strain of Anaerotruncus colihominis is WAL 14565(T) = CCUG 45055(T) = CIP 107754(T).

A randomised clinical trial to assess the effect of total enteral and total parenteral nutritional support on metabolic, inflammatory and oxidative markers in patients with predicted severe acute pancreatitis (APACHE II >= 66)

Background: Total enteral nutrition (TEN) within 48 h of admission has recently been shown to be safe and efficacious as part of the management of severe acute pancreatitis. Our aim was to ascertain the safety of immediate TEN in these patients and the effect of TEN on systemic inflammation, psychological state, oxidative stress, plasma glutamine levels and endotoxaemia. Methods: Patients admitted with predicted severe acute pancreatitis (APACHE II score 15) were randomised to total enteral (TEN; n = 8) or total parenteral nutrition (TPN; n = 9). Measurements of systemic inflammation (C-reactive protein), fatigue ( visual analogue scale), oxidative stress ( plasma thiobarbituric acid- reactive substances), plasma glutamine and anti-endotoxin IgG and IgM antibody concentrations were made on admission and repeated on days 3 and 7 thereafter. Clinical progress was monitored using APACHE II score. Organ failure and complications were recorded. Results: All patients tolerated the feeding regime well with few nutrition-related complications. Fatigue improved in both groups but more rapidly in the TEN group. Oxidative stress was high on admission and rose by similar amounts in both groups. Plasma glutamine concentrations did not change significantly in either group. In the TPN group, 3 patients developed respiratory failure and 3 developed non-respiratory single organ failure. There were no such complications in the TEN group. Hospital stay was shorter in the TEN group [ 7 (4-14) vs. 10 (7-26) days; p = 0.05] as was time to passing flatus and time to opening bowels [1 (0-2) vs. 2 (1-5) days; p = 0.01]. The cost of TEN was considerably less than of TPN. Conclusion: Immediate institution of nutritional support in the form of TEN is safe in predicted severe acute pancreatitis. It is as safe and as efficacious as TPN and may be beneficial in the clinical course of this disease. Copyright (C) 2003 S. Karger AG, Basel and IAP.

The art of conversation is coordination: common ground and the coupling of eye movements during dialogue

When two people discuss something they can see in front of them, what is the relationship between their eye movements? We recorded the gaze of pairs of subjects engaged in live, spontaneous dialogue. Cross-recurrence analysis revealed a coupling between the eye movements of the two conversants. In the first study, we found their eye movements were coupled across several seconds. In the second, we found that this coupling increased if they both heard the same background information prior to their conversation. These results provide a direct quantification of joint attention during unscripted conversation and show that it is influenced by knowledge in the common ground.

The locally twisted cubes

This paper introduces a new variant of the popular n-dimensional hypercube network Q(n), known as the n-dimensional locally twisted cube LTQ(n), which has the same number of nodes and the same number of connections per node as Q(n). Furthermore. LTQ(n) is similar to Q(n) in the sense that the nodes can be one-to-one labeled with 0-1 binary sequences of length n. so that the labels of any two adjacent nodes differ in at most two successive bits. One advantage of LTQ(n) is that the diameter is only about half of the diameter of Q(n) We develop a simple routing algorithm for LTQ(n), which creates a shortest path from the source to the destination in O(n) time. We find that LTQ(n) consists of two disjoint copies of Q(n) by adding a matching between their nodes. On this basis. we show that LTQ(n) has a connectivity of n.

Vertical velocity variance and skewness in clear and cloud-topped boundary layers as revealed by Doppler lidar

In this paper, observations by a ground-based vertically pointing Doppler lidar and sonic anemometer are used to investigate the diurnal evolution of boundary-layer turbulence in cloudless, cumulus and stratocumulus conditions. When turbulence is driven primarily by surface heating, such as in cloudless and cumulus-topped boundary layers, both the vertical velocity variance and skewness follow similar profiles, on average, to previous observational studies of turbulence in convective conditions, with a peak skewness of around 0.8 in the upper third of the mixed layer. When the turbulence is driven primarily by cloud-top radiative cooling, such as in the presence of nocturnal stratocumulus, it is found that the skewness is inverted in both sign and height: its minimum value of around −0.9 occurs in the lower third of the mixed layer. The profile of variance is consistent with a cloud-top cooling rate of around 30Wm−2. This is also consistent with the evolution of the thermodynamic profile and the rate of growth of the mixed layer into the stable nocturnal boundary layer from above. In conditions where surface heating occurs simultaneously with cloud-top cooling, the skewness is found to be useful for diagnosing the source of the turbulence, suggesting that long-term Doppler lidar observations would be valuable for evaluating boundary-layer parametrization schemes. Copyright c 2009 Royal Meteorological Society

Measuring gametic disequilibrium from multilocus data

We describe a Bayesian approach to analyzing multilocus genotype or haplotype data to assess departures from gametic (linkage) equilibrium. Our approach employs a Markov chain Monte Carlo (MCMC) algorithm to approximate the posterior probability distributions of disequilibrium parameters. The distributions are computed exactly in some simple settings. Among other advantages, posterior distributions can be presented visually, which allows the uncertainties in parameter estimates to be readily assessed. In addition, background knowledge can be incorporated, where available, to improve the precision of inferences. The method is illustrated by application to previously published datasets; implications for multilocus forensic match probabilities and for simple association-based gene mapping are also discussed.