Wood, bark and stem anatomy of New World species of Gnetum

Quantitative and qualitative data are presented for 11 collections of six species. The wide range of character states for the species is presented in the form of a key to emphasize their potential systematic correlations. Distinctive among these are phcllem characteristics. Fibre-tracheids are newly reported for lianoid Gnetum species. Cells previously thought to be like companion cells in secondary phloem are shown to be uniseriate rays, counterparts to uniseriate xylem rays. Laticifers are abundant in most of the species, and are newly described for secondary tissues of Gnetum. Presence of tyloses in laticifers of two species is apparently a new report for vascular plants. Tori are present in two New World Gnetum species, adding to the report in African species. Perforation plates are simple except near or in primary xylem, where they are simple or foraminate. Torus presence and foraminate perforation plate presence are features more reminiscent of Ephedra and other gymnosperms than of angiosperms. The bark of Gnetum is also very similar to that of Ephedra.     

Urban indicators for UK butterflies

Most people live in urban environments and there is a need to produce abundance indices to assist policy and management of urban greenspaces and gardens. While regional indices are produced, with the exception of birds, studies of the differences between urban and rural areas are rare. We explore these differences for UK butterflies, with the intention to describe changes that are relevant to people living in urban areas, in order to better connect people with nature in support of conservation, provide a measure relevant to human well-being, and assess the biodiversity status of the urban environment.Transects walked under the UK Butterfly Monitoring Scheme are classified as urban or rural, using a classification for urban morphological zones. We use models from the Generalised Abundance Index family to produce urban and rural indices of relative abundance for UK butterfly species. Composite indices are constructed for various subsets of species. For univoltine and bivoltine species, where we are able to fit phenomenological models, we estimate measures of phenology and identify urban/rural differences. Trends in relative abundance over the period 1995–2014 are more negative in urban areas compared to rural areas for 25 out of 28 species. For the composite indices, all trends are negative, and they are significantly more negative for urban areas than for rural areas. Analysis of phenological parameters shows butterflies tend to emerge earlier in urban than in rural areas. In addition, some fly longer in urban than in rural areas, whereas in other cases the opposite is the case, and hypotheses are proposed to account for these features.Investigating new urban/rural indicators has revealed national declines that are stronger for urban areas. For continued monitoring, there is a need for an urban butterfly indicator, and for this to be evaluated and reported annually. We explain how this may be interpreted, and the relevance for other monitoring schemes. The results of this paper, including the phenological findings, shed new light on the potentially deleterious effects of urbanisation and climate change, which require suitable monitoring and reporting to support policy and management, for example of urban greenspaces and gardens.     

The application of SIMS to nutrient tracer studies in plant physiology

Current controversies in root physiology relating to the uptake and translocation of mineral nutrients are presented. The opportunities for a SIMS contribution to resolve these controversies are discussed for each of the stable isotope tracers relevant to plant nutrition. It is concluded that for all major nutrients except phosphorus there are promising stable isotope tracers. At the same time, there are challenges to overcome in each case, with respect to background levels, peak interferences and sometimes sensitivity. Techniques of tissue preparation and handling are discussed in some detail, giving attention to the special requirements of plant tissue preparation and analysis for diffusable ions. It is suggested that adapting a preparation and transfer system, designed for production of bulk frozen-hydrated cryofractured specimens, to a secondary ion mass spectrometer would permit easy, rapid preparation. Additionally, this preparation minimizes several serious technical problems inherent to other preparative methods. Difficulties in quantitation are treated briefly, outlining some difficulties specific to plant tissue analysis. Prospects for future applications in plant mineral nutrition are evaluated, taking into account current instrumental developments.     

A new method of salt pan formation in intertidal marshes

Summary

Records of fungi occurring in the Hebrides are extended, particularly for Jura and Islay where, respectively, 40 and 47 taxa are recorded for the first time. Twenty taxa are added to the list for Rhum and 89 to that for Colonsay. Additional fungi are also reported for Hirta (St. Kilda) , Bernary, Mingulay, Barra and South Uist in the Outer Hebrides, and Eigg and Canna in the Inner Hebrides.     

Mercapturic acids as biomarkers of exposure to electrophilic chemicals:applications to environmental and industrial chemicals

The use of mercapturic acids (N-acetyl-L-cysteine S-conjugates, MAs) in the biological monitoring of human exposure to environmental and industrial chemicals is receiving more and more attention. Mercapturic acids (MAs) are formed from glutathione (GSH) S-conjugates via the MA-pathway. Although this pathway can lead to different end-products, the formation of MAs is the predominant route in most species, including man. Two GSH S-transferases (GSTs) show genetic polymorphisms in humans and this can have major consequences for individual susceptibility to toxic effects and for MA formation. In occupational toxicology, adducts to biomacromolecules are also used as biomarkers. DNA adducts are a measure for the effective dose, while protein adducts are related to the dose at critical site. Both type of adducts are normally determined in blood, while MAs are determined in urine. Most MAs are excreted with relatively short half-lifes, allowing a direct evaluation of the occupational circumstances. For many compounds similar (linear) dose-dependency was found for MA excretion, formation of macromolecular adducts, and for various biomarkers of toxic effects. These relations together with fact that MAs relate to the electrophilic character of compounds, allows for the conclusion that MAs are biomarkers of toxicologically relevant internal doses of chemicals or their metabolites. An overview will be given here of the use of MAs in the assessment of internal human exposure to electrophilic environmental and industrial chemicals. Additionally, the formation of GSH S-conjugates, their catabolism to MAs and several of the frequently used analytical approaches are discussed. When appropriate, the influence of genetic polymorphisms on formation of MAs and on susceptibility to toxicity will be discussed for different chemicals as well.     

Optimal approximate conversions of odds ratios and hazard ratios to risk ratios

Odds ratios approximate risk ratios when the outcome under consideration is rare but can diverge substantially from risk ratios when the outcome is common. In this paper, we derive optimal analytic conversions of odds ratios and hazard ratios to risk ratios that are minimax for the bias ratio when outcome probabilities are specified to fall in any fixed interval. The results for hazard ratios are derived under a proportional hazard assumption for the exposure. For outcome probabilities specified to lie in symmetric intervals centered around 0.5, it is shown that the square-root transformation of the odds ratio is the optimal minimax conversion for the risk ratio. General results for any nonsymmetric interval are given both for odds ratio and for hazard ratio conversions. The results are principally useful when odds ratios or hazard ratios are reported in papers, and the reader does not have access to the data or to information about the overall outcome prevalence.     

Hematology and blood biochemistry in infant baboons (Papio hamadryas)

Although published normative reference standards for hematologic and clinical chemistry measures are available for adult baboons, their applicability to infants has not been addressed. We analyzed these measures in 110 infant baboons (55 females and 55 males) from a large breeding colony at the Southwest Regional Primate Research Center in San Antonio, Texas. The sample consists of olive baboons and olive/yellow baboon hybrids, 1 week to 12 months of age. We produced cross-sectional reference values and examined the effects of age, sex, and subspecies on these variables. Hematology reference ranges for infant baboons are similar to, but wider than, those for adults. Reference ranges for blood biochemistry measures are generally more dissimilar to adults, indicating that for many variables, reference ranges for adult baboons are not adequate for infants. Although sex and subspecies differences are rare, age accounts for more than 10% of the variance in many of the variables.     

Application of whole cell rhodococcal biocatalysts in acrylic polymer manufacture

Rhodococci are ubiquitous in nature and their ability to metabolise a wide range of chemicals, many of which are toxic, has given rise to an increasing number of studies into their diverse use as biocatalysts. Indeed rhodococci have been shown to be especially good at degrading aromatic and aliphatic nitriles and amides and thus they are very useful for waste clean up where these toxic chemicals are present.The use of biocatalysts in the chemical industry has in the main been for the manufacture of high-value fine chemicals, such as pharmaceutical intermediates, though investigations into the use of nitrile hydratase, amidase and nitrilase to convert acrylonitrile into the higher value products acrylamide and acrylic acid have been carried out for a number of years. Acrylamide and acrylic acid are manufactured by chemical processes in vast tonnages annually and they are used to produce polymers for applications such as superabsorbents, dispersants and flocculants. Rhodococci are chosen for use as biocatalysts on an industrial scale for the production of acrylamide and acrylic acid due to their ease of growth to high biomass yields, high specific enzyme activities obtainable, their EFB class 1 status and robustness of the whole cells within chemical reaction systems.Several isolates belonging to the genus Rhodococcus have been shown in our studies to be among the best candidates for acrylic acid preparation from acrylonitrile due to their stability and tolerance to high concentrations of this reactive and disruptive substrate. A critical part of the selection procedure for the best candidates during the screening programme was high purity product with very low residual substrate concentrations, even in the presence of high product concentrations. Additionally the nitrile and amide substrate scavenging ability which enables rhodococci to survive very successfully in the environment leads to the formation of biocatalysts which are suitable for the removal of low concentrations of acrylonitrile and acrylamide in waste streams and for the removal of impurities in manufacturing processes.     

Recommendations for the routine sampling of diatoms for water quality assessments in Europe

Many methods for using diatoms for routine monitoring of water quality have been developed in Europe and, in some countries, these are being used to enforce environmental legislation. In order to facilitate their wider use, particularly with respect to European Union legislation, steps are being taken to harmonize methodology. In this paper, the principles and practice of sampling are described in relation to the main habitat types encountered in Europe. Although details of methods and sampling programmes have to be tailored to particular circumstances and the overall objectives of the monitoring, a number of generalizations can be made. Where available, rocks and other hard surfaces are the preferred substrates and methods for sampling these are described. If such substrata are not available, then introduced ('artificial') substrata have many applications. Various types of introduced substrata can be used successfully, so long as some basic precautions are described. Other types of substrata such as macrophytes and macroalgae may also be useful under certain circumstances, although there is less consensus in the literature on the most appropriate methods, and of the validity of comparisons between indices computed from epiphytic and epilithic communities. When designing surveys, it is recommended that as far as possible, extremes of non-water quality factors (e.g. shade, current speed, etc) are avoided, unless these are characteristic of the system under investigation. Detailed guidelines for sampling epilithon are described. Along with the recommendations for sampling other substrata, it is hoped that these provide a framework that can be adapted to most river types in Europe. This revised version was published online in June 2006 with corrections to the Cover Date.     

Fibronectin and integrin alpha 5 play requisite roles in cardiac morphogenesis

Fibronectin and its major receptor, integrin α5β1 are required for embryogenesis. These mutants have similar phenotypes, although, defects in integrin α5-deficient mice are milder. In this paper, we examined heart development in those mutants, in which the heart is formed, and discovered that both fibronectin and integrin α5 were required for cardiac morphogenesis, and in particular, for the formation of the cardiac outflow tract. We found that Isl1⁺ precursors are specified and migrate into the heart in fibronectin- or integrin α5-mutant embryos, however, the hearts in these mutants are of aberrant shape, and the cardiac outflow tracts are short and malformed. We show that these defects are likely due to the requirement for cell adhesion to fibronectin for proliferation of myocardial progenitors and for Fgf8 signaling in the pharyngeal region.     

Requirements on bacterial polyesters as future substitute for conventional plastics for consumer goods

Bacterial polyesters such as polyhydroxybutyrate (PHB) or polyhydroxyalkanoates (PHAs) have to pass the following requirements to be accepted on a large scale: (i) they have to fulfil an urgent market need: (ii) they require that new and efficient composting systems are installed in urban areas; (iii) they have to complete with the present plastics as far as quality and processing performance are concerned; (iv) they have to meet the requirement for the registration as food packages; and (v) they have to meet competitive price limits. (i) Some 30% of the plastics in the municipal waste originates from goods which are less than 1 year in use and tend to be heavily soiled by food and feed residues. This part is difficult and expensive to dispose of. Biodegradable alternatives could replace a large part of it. The waste could be diverted from landfills and incineration to composting sites near the end user. The savings in costs and frustrations are the source of a pressing demand for biopolymers, especially for producing goods which do not demand longevity and which are likely to end up soiled with organic matters. (ii) Composting infrastructures exist in rural areas. In urban areas new systems for collecting and composting ‘garden and kitchen wastes’ are being installed for reducing landfill problems, especially in Austria, Denmark, Germany and the Netherlands. These installations give biopolymers a competitive edge in the disposal discussion. (iii) Bacterial polyesters meet various quality and processing performances. They are water-resistant, and goods made of the polyesters are water-tight. The material can be processed by injection and by blow moulding. However, the esters are not flexible enough for forming films or foils. They also tend to become brittle and to lose their vapour barrier properties. It is expected that these limits will be overcome by improving blend formulations. (iv) Bacterial polyesters are not yet allowed for use as food package material. Since the esters represent a novel product, the procedure for the registration poses serious, but no insoluble problems. They require long and costly tests. There are no indications that bacterial polyesters would not attain the requirements. However, they are not expected to serve as food packages in the near future. (v) The present prices for bacterial polyesters are far too high to be accepted on a large scale by the processing and packaging industry. Costs are high mainly because of the raw material prices and to the small-scale production units. They can be lowered to accepted levels by investing in larger units in countries where inexpensive raw materials are available. Thus they will be able to meet the price limits. Since bacterial polyesters increasingly meet the requirements for the penetration of a mass market and since more and more consumers accept composting as an environmentally sound way of recycling organic materials, the polyesters are expected to penetrate a significant part of the short-lived and contaminated plastic products markets by the turn of the century.     

Cell surface proteins and malignant transformation

Many of the altered properties of malignant cells are thought to involve alterations in cell surface functions. In order to understand these alterations it is necessary to know more about the molecular structure of the surface. Methods for analyzing surface proteins are discussed and their application to normal and transformed tissue culture cells are reviewed. A number of surface proteins are observed to be altered by transformation. Most of the alterations are reductions in amounts of particular species, although a few proteins do increase. Evidence concerning the reasons for these alterations and the possible functions of some of the molecules is reviewed. Working hypotheses arising from these data are presented and prospects for understanding the physiological changes in terms of molecular effects are discussed. Particular emphasis is placed on the idea that surface molecules are associated in specific-non-covalent complexes which are important for their functions.     

Stability of complex spike timing-dependent plasticity in cerebellar learning

Dynamics of spike-timing dependent synaptic plasticity are analyzed for excitatory and inhibitory synapses onto cerebellar Purkinje cells. The purpose of this study is to place theoretical constraints on candidate synaptic learning rules that determine the changes in synaptic efficacy due to pairing complex spikes with presynaptic spikes in parallel fibers and inhibitory interneurons. Constraints are derived for the timing between complex spikes and presynaptic spikes, constraints that result from the stability of the learning dynamics of the learning rule. Potential instabilities in the parallel fiber synaptic learning rule are found to be stabilized by synaptic plasticity at inhibitory synapses if the inhibitory learning rules are stable, and conditions for stability of inhibitory plasticity are given. Combining excitatory with inhibitory plasticity provides a mechanism for minimizing the overall synaptic input. Stable learning rules are shown to be able to sculpt simple-spike patterns by regulating the excitability of neurons in the inferior olive that give rise to climbing fibers.     

Structure and genetics of Shigella O antigens

This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.     

Why Alcoholics Ought to Compete Equally for Liver Transplants

Some philosophers and physicians have argued that alcoholic patients, who are responsible for their liver failure by virtue of alcoholism, ought to be given lower priority for a transplant when donated livers are being allocated to patients in need of a liver transplant. The primary argument for this proposal, known as the Responsibility Argument, is based on the more general idea that patients who require scarce medical resources should be given lower priority for those resources when they are responsible for needing them and when they are competing with patients who need the same resources through no fault of their own. Since alcoholic patients are responsible for needing a new liver and are in direct competition with other patients who need a new liver through no fault of their own, it follows that alcoholic patients ought to be given lower priority for a transplant. In this article, I argue against the Responsibility Argument by suggesting that in order for it to avoid the force of plausible counter examples, it must be revised to say that patients who are responsible for needing a scarce medical resource due to engaging in behavior that is not socially valuable ought to be given lower priority. I'll then argue that allocating organs according to social value is inconsistent or in tension with liberal neutrality on the good life. Thus, if one is committed to liberal neutrality, one ought to reject the Responsibility Argument.     

Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins

The prediction of protein 3D structures close to insertions and deletions or, more generally, loop prediction, is still one of the major challenges in homology modeling projects. In this article, we developed ranking criteria and selection filters to improve knowledge-based loop predictions. These criteria were developed and optimized for a test data set containing 678 insertions and deletions. The examples are, in principle, predictable from the used loop database with an RMSD < 1 A and represent realistic modeling situations. Four noncorrelated criteria for the selection of fragments are evaluated. A fast prefilter compares the distance between the anchor groups in the template protein with the stems of the fragments. The RMSD of the anchor groups is used for fitting and ranking of the selected loop candidates. After fitting, repulsive close contacts of loop candidates with the template protein are used for filtering, and fragments with backbone torsion angles, which are unfavorable according to a knowledge-based potential, are eliminated. By the combined application of these filter criteria to the test set, it was possible to increase the percentage of predictions with a global RMSD < 1 A to over 50% among the first five ranks, with average global RMSD values for the first rank candidate that are between 1.3 and 2.2 A for different loop lengths. Compared to other examples described in the literature, our large numbers of test cases are not self-predictions, where loops are placed in a protein after a peptide loop has been cut out, but are attempts to predict structural changes that occur in evolution when a protein is affected by insertions and deletions.     

Evaluation of preparation methods for MS‐based analysis of intestinal epithelial cell proteomes

The gut epithelium formed between an organism and the environment plays an essential role in host–microbe interactions, yet remains one of the least characterized mammalian tissues. Especially the membrane proteins, which are critical to bacterial adhesion, are understudied, because these proteins are low in abundance, and large amounts of sample is needed for their preparation and for undertaking MS‐based analysis. The aim of this study was to evaluate three different methods for isolation and preparation of pig intestinal epithelial cells for MS‐based analysis of the proteome. Samples were analyzed by LC and electrospray QTOF‐MS. The methods were evaluated according to efficiency, purity, transmembrane protein recovery, as well as for suitability to large‐scale preparations. Our data clearly demonstrate that mucosal shaving is by far the best‐suited method for in‐depth MS analysis in terms of ease and speed of sample preparation, as well as protein recovery. In comparison, more gentle methods where intestinal epithelial cells are harvested by shaking are more time consuming, result in lower protein yield, and are prone to increased technical variation due to multiple steps involved.     

Covariance between relatives for X-chromosomal loci in a population in disequilibrium

Summary According to Hardy-Weinberg, for a single autosomal locus, a population achieves equilibrium in one generation of random mating if allelic frequency is the same in the sexes, or in two generations if the frequency is not. For a single X-chromosomal locus, however, the approach to equilibrium oscillates and is gradual. Covariances between relatives for autosomal and for X-chromosomal loci are in the literature for a random mating population in equilibrium. Although assumption of equilibrium is defensible for an autosomal locus, it is less defensible for an X-chromosomal locus. Covariances between collateral and between lineal relatives are derived for X-chromosomal loci in a random mating population not in equilibrium. Collateral relatives such as sibs are of the same generation, and lineal relatives such as parent-offspring are of different generations. Coefficient of co-ancestry between relatives, based on identity by descent, was used in this development. Results are applicable to crossbreeding in livestock and poultry, and also to haplo-diploid organisms, such as the honeybee, in which the entire genome is equivalent to being X-chromosomal.Supported in part by the Illinois Agricultural Experiment Station, Hatch Project 35-0367     

A general approach to the concept of varietal ability for synthetic varieties

Summary Genetic effects for varietal value are defined at the level of the population of k-parent synthetic varieties. A simple expression for the total variance among synthetics arises directly from these definitions. A general expression for the covariance among related synthetics is given. Genetic effects are also defined in a completely general way so as to allow for any system of testing and used to derive an expression for the genetic advance in recurrent selection for varietal value. Covariances between relatives evaluated in the system of testing and in varietal combination are introduced, allowing a direct expression of the genetic advance in varietal development when parents are selected either individually or in groups. Some general implications for plant breeding are outlined.Dedicated to Professor F.W. Schnell on the occasion of his 65th birthday     

The public's knowledge of and support for conservation of Australia's tree-kangaroos and other animals

After providing background on Dendrolagus species in Australia, two consecutive surveys ofBrisbane's residents are used to assess public knowledge of tree-kangaroos and the stated degree of supportfor their conservation in Australia. The responses of participants in Survey I are based on their pre-surveyknowledge of wildlife. The same set of participants completed Survey II after being provided with additionalinformation on all thewildlife speciesmentioned in Survey I.Changes in the attitudes of respondents and theirdegree of support for the protection and conservation of Australia's tree-kangaroos are measured, includingchanges in their contingent valuations and stated willingness to provide financial support for such conservation.Reasons for wanting to protect tree-kangaroos are specified and analysed. Furthermore, changesthat occur in the relative importance of these reasons with increased knowledge are also examined. Supportfor the conservation of tree-kangaroos is found to rise with the additional knowledge supplied about allspecies and is compared with variations in support for protection of other mammals. Support for the conservationof Australia's less well known tropical mammals is found to increase relative to better knownmammals (icons) present in temperate areas, such as koalas and red kangaroos. Possible implications of theresults for government conservation policies in Australia are examined.