An electrophoretic approach to Basidiomycetes taxonomy: Intraspecific variability,varieties, ecological influences

Abstract

Basidiospores of several Basidiomycetes species were treated with electrophoretic techniques, comparing the different protein fractions of the soluble component of the spores wall. The electrophoretic data were elaborated to obtain dendrograms indicating the similarity degree. The method was set up and tested for its validity. The technique showed that the degree of variability within the observed species escaped any generalization, covering a broad range; it was possible to identify the varieties in dendrograms of species grown in the same/different geographical zones; the growing environment and the symbiotic host often influenced the electrophoretic pattern of the spore wall proteins and resulted in dendrograms reflecting the ecological conditions.

Abbreviations: ACP, acid phosphatases; EST, esterases; UPGMA, unweighed pair‐group method using arithmetical average     

Genes and generalizations: Darden's strategies and the question of context

In her recent book Lindley Darden has endeavored to reclaim for philosophy an active role in the elaboration of good science. She has done this, not by holding up some set of rational standards derived from outside of scientific practice, but rather by delving into the history of science and coming out with a set of scientific strategies. Unconcerned about whether any particular strategy wasin fact employed in a given historical case her project depends upon two claims, first that these strategiescould have been successfully deployed in the particular cases from which they were construed, and second and more importantly, that these strategies can be generalized beyond any particular context and be put to future use. It will be argued that Darden's conception of the possible context independence of scientific strategies is based upon an overly cognitivist misconstrual. An alternative account of the relationship of context dependent and context independent aspects of scientific theory formation will be offered as well as its implications for philosophy.     

Precaution,threshold risk and public deliberation

It has been argued that the precautionary principle is incoherent and thus useless as a guide for regulatory policy. In a recent paper in Bioethics, Wareham and Nardini propose a response to the ‘precautionary paradox’ according to which the precautionary principle's usefulness for decision making in policy and regulation contexts can be justified by appeal to a probability threshold discriminating between negligible and non‐negligible risks. It would be of great significance to debates about risk and precaution if there were a sound method for determining a minimum probability threshold of negligible risk. This is what Wareham and Nardini aim to do. The novelty of their approach is that they suggest that such a threshold should be determined by a method of public deliberation. In this article I discuss the merits of Wareham and Nardini’s public deliberation method for determining thresholds. I raise an epistemic worry about the public deliberation method they suggest, and argue that their proposal is inadequate due to a hidden assumption that the acceptability of a risk can be completely analysed in terms of its probability.     

Arabidopsis and cotton (Gossypium) as models for studying copia-like retrotransposon evolution

Transposable elements have likely played an important role in species evolution. Questions of transposable element evolution, therefore, are best addressed within the context of their hosts' evolutionary history. This approach requires efficient means to identify and characterize transposable elements among related species. For the copia-like retrotransposons, this has recently become possible due to the development of a polymerase chain reaction assay to identify these sequences among plants. In this paper, the evolution of copia-like retrotransposons is evaluated within the context of the evolutionary history of two plant models, Arabidopsis thaliana and cotton (Gossypium).     

Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit

Gene expression is stochastic, and noise that arises from the stochastic nature of biochemical reactions propagates through active regulatory links. Thus, correlations in gene-expression noise can provide information about regulatory links. We present what to our knowledge is a new approach to measure and interpret such correlated fluctuations at the level of single microcolonies, which derive from single cells. We demonstrated this approach mathematically using stochastic modeling, and applied it to experimental time-lapse fluorescence microscopy data. Specifically, we investigated the relationships among LuxO, LuxR, and the small regulatory RNA qrr4 in the model quorum-sensing bacterium Vibrio harveyi. Our results show that LuxR positively regulates the qrr4 promoter. Under our conditions, we find that qrr regulation weakly depends on total LuxO levels and that LuxO autorepression is saturated. We also find evidence that the fluctuations in LuxO levels are dominated by intrinsic noise. We furthermore propose LuxO and LuxR interact at all autoinducer levels via an unknown mechanism. Of importance, our new method of evaluating correlations at the microcolony level is unaffected by partition noise at cell division. Moreover, the method is first-order accurate and requires less effort for data analysis than single-cell-based approaches. This new correlation approach can be applied to other systems to aid analysis of gene regulatory circuits.     

Report of the Alpine Section, 1958

Background: Over 10,000 island endemic angiosperms are highly threatened by extinction. Yet, few of these species have the temporal change in their range documented and quantified, particularly within a potentially informative context of a long period of botanical study.

Aim: Here, we used Roussea simplex a mono-specific genus endemic to Mauritius, itself an island with long botanical history and advanced habitat destruction extent, to investigate how the distribution and population of this model oceanic island plant changed through time.

Methods: All known localities and population size estimates were compiled from published literature, herbarium specimens, surveys and personal communications to estimate changes in population size, extent of occurrence and area of occupancy and investigate main distribution patterns.

Results: Roussea simplex survives in nine high elevation sites. Since the 1930s, its range halved relative to its maximum known distribution and its population size decreased much faster than direct habitat loss would predict. It now qualifies as Endangered according to the IUCN Red List categories.

Conclusions: Even in an extremely deforested island, endemic plant population decline may be driven more by diminishing habitat quality than diminishing habitat extent. This renders habitat protection alone insufficient, therefore addressing ecological interactions is vital to stem population decline.     

A note on the measurement of genetic diversity within genebank accessions of lettuce (Lactuca sativa L.) using AFLP markers

This paper discusses a statistical approach for measuring genetic diversity within genebank accessions of a self-fertilising species. This approach is applied to lettuce (Lactuca sativa L.), using AFLP marker data on a set of 1,390 accessions, representing six different lettuce types. Knowledge of the within-accession genetic diversity is important for decisions about the way accessions have to be maintained by genebanks. It is argued that if the within-accession diversity is small, as can be expected for a self-fertilising species like L. sativa, the best approach is to sample as many accessions as possible with only two plants per accession and estimate the within-accession diversity by the proportion of accessions of which the individuals are different.     

Electromagnetic fields: activities in the European Commission with a focus on research projects and the Scientific Committee of Emerging and Newly Identified Health Risks (SCENIHR)

Abstract

The article summarizes the main activities of the European Commission concerning electromagnetic fields. It explains also the regulatory context, with a special focus on past and current research projects funded by the European Union and the role of the SCENIHR in assessing risks related to EMF. Main conclusions of the SCENIHR opinion adopted in 2015 on EMF are reported.     

Fluxes of energy,water, and carbon dioxide from mountain ecosystems at Niwot Ridge,Colorado

Background: The eddy covariance (EC) technique provides a direct measure of water vapour and carbon dioxide fluxes between ecosystems and the atmosphere.

Aims: This review article highlights the findings of various studies that have integrated EC observations into basic meteorological, hydrological and ecological research questions in two ecosystems near Niwot Ridge, Colorado, and synthesises these studies into a catchment-scale model of water and carbon cycling, within the context of regional disturbance and environmental change.

Methods: EC was implemented continuously over subalpine forest and alpine tundra vegetation at Niwot Ridge, and resulting data were compared with discrete measurements and modelling studies.

Results: Sensible heat fluxes were generally in excess of latent heat fluxes, indicating that the forest and tundra ecosystems were moisture limited. Snow cover regulated the annual sum of primary productivity in the forest, and beneath-snow respiration represented a significant portion of ecosystem respiration at both locations.

Conclusions: Changes in the magnitude, timing, or spatial distribution of snow are likely to have the greatest impact on ecological processes in these semi-arid mountain catchments, but possibly in compensatory ways. Ultimately, the degree to which net carbon losses from alpine tundra offset forest carbon sequestration will determine the future magnitude of the Western United States carbon sink.     

Managing genetic testing: the relative powerlessness of actors in stable practices

Abstract

Genetics is a field in which ethical and social problems have been most pressing. Despite this, new tests often are introduced almost immediately after the isolation of a new gene. Considerations of whether a particular test should be introduced at all seem to have little effect on the development and introduction of new tests. This paper explores how this lack of social and ethical assessment can be understood. In order to do so, the sociohistorical context of clinical genetics and the way in which this practice came about will be analysed in this paper with respect to the Dutch service for clinical genetics. It will be argued that the fragmented way in which tasks and responsibility have become distributed within clinical genetics services has led to a situation in which actors seem to have no control over the introduction of genetic tests.     

Projection Methods for the Analysis of Complex Motions in Macromolecules

Abstract

In studies of macromolecular dynamics it is often desirable to analyze complex motions in terms of a small number of coordinates. Only for simple types of motion, e.g., rigid-body motions, these coordinates can be easily constructed from the Cartesian atomic coordinates. This article presents an approach that is applicable to infinitesimal or approximately infinitesimal motions, e.g., Cartesian velocities, normal modes, or atomic fluctuations. The basic idea is to characterize the subspace of interesting motions by a set of (possibly linearly dependent) vectors describing elementary displacements, and then project the dynamics onto this subspace. Often the elementary displacements can be found by physical intuition. The restriction to small displacements facilitates the study of complicated coupled motions and permits the construction of collective-motion subspaces that do not correspond to any set of generalized coordinates.

As an example for this technique, we analyze the low-frequency normal modes of proteins up to ≈ 20 THz (600 cm^?1) in order to see what kinds of motions occupy which frequency range. This kind of analysis is useful for the interpretation of spectroscopic measurements on proteins, e.g., inelastic neutron scattering experiments.     

Athalamia hyalina (Sommerf.) S.Hatt. in Scotland,new to the British Isles

Abstract

The liverwort Athalamia hyalina (Sommerf.) S.Hatt. and the family Cleveaceae are reported as new to the British Isles from the eastern Scottish Highlands. The Scottish plants are described and illustrated and the significance of the discovery is assessed. In Scotland, Athalamia hyalina occurs on thin soil on eroding limestone ledges in a montane habitat with a continental climate. It is in active growth in the winter months, producing spores in spring. Its range is restricted but it occurs within a protected area and is not threatened at present. The species is widespread in the northern hemisphere.     

Reinterpreting Responsiveness for Health Systems Research in Low and Middle‐Income Countries

The ethical concept of responsiveness has largely been interpreted in the context of international clinical research. In light of the increasing conduct of externally funded health systems research (HSR) in low‐ and middle‐income countries (LMICs), this article examines how responsiveness might be understood for such research and how it can be applied. It contends that four features (amongst others) set HSR in LMICs apart from international clinical research: a focus on systems; being context‐driven; being policy‐driven; and being closely linked to development objectives. These features support reinterpreting responsiveness for HSR in LMICs as responsiveness to systems needs, where health system performance assessments can be relied upon to identify systems needs, and/or responsiveness to systems priorities, which entails aligning research with HSR priorities set through country‐owned processes involving national and sub‐national policymakers from host countries. Both concepts may be difficult to achieve in practice. Country ownership is not an established fact for many countries and alignment to their priorities may be meaningless without it. It is argued that more work is, therefore, needed to identify strategies for how the responsiveness requirement can be ethically fulfilled for HSR in LMICs under non‐ideal conditions such as where host countries have not set HSR priorities via country‐owned processes. Embeddedness is proposed as one approach that could be the focus of further development.     

Social diversity and changes in the form and appearance of the Qatari house

This article examines the relationship between house form and appearance and social diversity. The metamorphosis of two features of the Qatari house which operate as loci of communication between occupants and non‐occupants, the majlis (guest reception area) and the exterior ornamentation, is described within the context of increasing social diversity between the 1960s and the 1990s. The manner in which each of these features conveys information to the new range of audiences within the diverse population of Qatar is examined. The article supports the view that differences in the use of a house to signify status are related to the character of social networks and demonstrates that in a dual social system where networks coexist but rarely overlap methods and media of communication through the built environment can be similarly bifurcated.     

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis‐regulatory, rather than the coding, regions of developmental genes. This “cis‐regulatory hypothesis” has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis‐regulatory hypothesis. We then test the empirical support for the cis‐regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis‐regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis‐regulatory changes published annually is rapidly increasing. Above the species level, cis‐regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis‐regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question “Do coding or cis‐regulatory mutations cause more phenotypic evolution?” hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.     

A CHARMm Based Force Field for Carbohydrates Using the CHEAT Approach: Carbohydrate Hydroxyl Groups Represented by Extended Atoms

Abstract

Computational studies of carbohydrates that do not consider explicit solvent molecules suffer from the strong tendency of the carbohydrate pendant hydroxyl groups to form intramolecular hydrogen bonds that are unlikely to be present in protic media. In this paper a novel approach towards molecular modelling of carbohydrates is described. The average effect of intra- and intermolecular hydrogen bonding is introduced into the potential energy function by adding a new (extended) atom type representing a carbohydrate hydroxyl group to the CHARMm force field; we coin the name CHEAT (Carbohydrate Hydroxyls represented by Extended AToms) for the resulting force field. As a training set for the parametrisation of CHEAT we used ethylene glycol, 10 cyclohexanols, 5 inositols, and 12 glycopyranoses for which in total 64 conformational energy differences were estimated using a set of steric interaction energies between hydroxyl and/or methyl groups on six-membered ring compounds as derived by Angyal (Angew. Chem., 8, 172-182, (1969)). The root-mean-square deviation between the estimated energy differences and the corresponding values obtained by our CHEAT approach amounts to 0.37 kcal/mol (n = 64). The CHEAT approach, which is claimed to calculate aqueous state compatible energetical and conformational properties of carbohydrates, is computationally very efficient and facilitates the calculation of nanosecond range MD trajectories as well as systematic conformational searches of oligosaccharides.     

Regulatory roles of thioredoxin in oxidative stress-induced cellular responses

Abstract

Thioredoxin (TRX) is a small ubiquitous and multifunctional protein having a redox-active dithiol/disulfide within the conserved active site sequence –Cys–Gly–Pro–Cys–. TRX is induced by a variety of oxidative stimuli, including UV irradiation, inflammatory cytokines and chemical carcinogens, and has been shown to play crucial roles in the regulation of cellular responses such as gene expression, cell proliferation and apoptosis. Overexpression of TRX protects cells from cytotoxicity elicited by oxidative stress in both in vitro and in vivo models. The regulatory mechanism of TRX expression and activity is also being elucidated. Recently, TRX binding protein-2 (TBP-2)/vitamin D3 up-regulated protein 1 (VDUP1) was identified as a negative regulator of TRX. The analysis of TRX promoter region has revealed putative regulatory elements responsible for oxidative stress. Thus, the modulation of TRX functions may be a new therapeutic strategy for the treatment of oxidative stress-mediated diseases.     

Atom-based 3D-QSAR,induced fit docking,and molecular dynamics simulations study of thieno[2,3-b]pyridines negative allosteric modulators of mGluR5

Atom-based three dimensional-quantitative structure–activity relationship (3D-QSAR) model was developed on the basis of 5-point pharmacophore hypothesis (AARRR) with two hydrogen bond acceptors (A) and three aromatic rings for the derivatives of thieno[2,3-b]pyridine, which modulates the activity to inhibit the mGluR5 receptor. Generation of a highly predictive 3D-QSAR model was performed using the alignment of predicted pharmacophore hypothesis for the training set (R²?=?0.84, SD?=?0.26, F?=?45.8, N?=?29) and test set (Q²?=?0.74, RMSE?=?0.235, Pearson-R?=?0.94, N?=?9). The best pharmacophore hypothesis AARRR was selected, and developed three dimensional-quantitative structure activity relationship (3D-QSAR) model also supported the outcome of this study by means of favorable and unfavorable electron withdrawing group and hydrophobic regions of most active compound 42d and least active compound 18b. Following, induced fit docking and binding free energy calculations reveals the reliable binding orientation of the compounds. Finally, molecular dynamics simulations for 100?ns were performed to depict the protein–ligand stability. We anticipate that the resulted outcome could be supportive to discover potent negative allosteric modulators for metabotropic glutamate receptor 5 (mGluR5).     

Molecular set theory: A mathematical representation for chemical reaction mechanisms

The present investigation is part of a program aimed at examining the mathematical basis of reaction rate theory (Bartholomay,Bull. Math. Biophys. 20, 1958) from the point of view of individual molecular events. Certain inconsistencies resulting from the classical procedure of using stoichiometric “chemical equations” to represent the kinds of mechanisms involved are pointed out and remedies are suggested by the introduction of set-theoretic notation within the framework of a so-calledMolecular Set Theory. It is concluded that whereas ordinary algebra is a suitable basis for stoichiometry, in discussing mechanisms of chemical reactions,molecular set theory is more appropriate. This is a theory of material transformations which is patterned afterabstract set theory: the individual molecules of a chemical species and chemical transformations from one species to another correspond to the abstract concepts of elements or points of a set and their mappings into other sets respectively. The new notions ofexact molecular sequences andequivalence classes of molecules arising from this study of chemical reactions may be of purely mathematical interest when referred back to the context of abstract set theory.