Editorial – Clonal plants and environmental heterogeneity – space, time and scale

The fifth Clonal Plant Workshop entitled 'Clonal plants and environmental heterogeneity – space, time and scale' was held at the University of Wales, Bangor, from the 9th to the 14th September 1997. The workshops began in 1988, when a small group of plant scientists with different backgrounds met in the Netherlands to discuss plant clonality. This meeting was followed by workshops in 1990, 1992 and 1995 in Sweden, the Czech Republic and Hungary, respectively. The purpose of the Bangor meeting was to continue to integrate knowledge from a wide range of biological disciplines to attempt a better understanding of clonal plants in the context of the heterogeneous environments in which they occur. This special issue is a collection of a number of the presentations at the Bangor workshop. The effects of spatial and temporal environmental heterogeneity on individuals, populations and communities are, of course, diverse, and this collection of papers is not intended to provide a synthesis of the ecological consequences of environmental heterogeneity. Rather, this special issue more accurately reflects progress in various areas of clonal plant research including population dynamics of ramets and genets, mathematical modelling and molecular techniques. We wish to thank all participants of the workshop for their contribution and trust that they found the meeting as stimulating and enjoyable as we did. We are indebted to the authors and the many referees for their friendly cooperation and to Plant Ecology for publishing the proceedings. We also gratefully acknowledge the financial support of the following that made the workshop possible: The British Ecological Society, The Tansley Fund of the New Phytologist Trust, The Countryside Council for Wales, The Institute of Terrestrial Ecology (Bangor) and Skye Instruments Ltd, Wales.     

PDZ domains – glue and guide

PDZ domains are small globular building blocks that are amongst the most abundant protein interaction domains in organisms. Over the past several years an avalanche of data has implicated these modules in the clustering, targeting and routing of associating proteins. An overview is given of the types of interactions displayed by PDZ domains and how this relates to the current knowledge on their spatial structure. Furthermore, the different levels on which PDZ – ligand binding can be regulated and the consequences of PDZ domain-mediated clustering for activity, routing and targeting of interacting proteins will be addressed. Finally, some cell and animal models that illustrate the impact of PDZ domain-containing proteins on (multi-) cellular processes will be discussed.     

Lipoxygenases – Structure and reaction mechanism

Lipid oxidation is a common metabolic reaction in all biological systems, appearing in developmentally regulated processes and as response to abiotic and biotic stresses. Products derived from lipid oxidation processes are collectively named oxylipins. Initial lipid oxidation may either occur by chemical reactions or is derived from the action of enzymes. In plants this reaction is mainly catalyzed by lipoxygenase (LOXs) enzymes and during recent years analysis of different plant LOXs revealed insights into their enzyme mechanism. This review aims at giving an overview of concepts explaining the catalytic mechanism of LOXs as well as the different regio- and stereo-specificities of these enzymes.     

Aspergillus-specific antibodies – Targets and applications

Aspergillus is a fungal genus comprising several hundred species, many of which can damage the health of plants, animals and humans by direct infection and/or due to the production of toxic secondary metabolites known as mycotoxins. Aspergillus-specific antibodies have been generated against polypeptides, polysaccharides and secondary metabolites found in the cell wall or secretions, and these can be used to detect and monitor infections or to quantify mycotoxin contamination in food and feed. However, most Aspergillus-specific antibodies are generated against heterogeneous antigen preparations and the specific target remains unknown. Target identification is important because this can help to characterize fungal morphology, confirm host penetration by opportunistic pathogens, detect specific disease-related biomarkers, identify new candidate targets for antifungal drug design, and qualify antibodies for diagnostic and therapeutic applications. In this review, we discuss how antibodies are raised against heterogeneous Aspergillus antigen preparations and how they can be characterized, focusing on strategies to identify their specific antigens and epitopes. We also discuss the therapeutic, diagnostic and biotechnological applications of Aspergillus-specific antibodies.     

Speciation of dimethyltin(IV) – and trimethyltin(IV) – carbocysteinate and – glutamate systems in aqueous media

Abstract

The formation of complex species in the dimethyltin(IV) and trimethyltin(IV)-carboxymethyl-L-cysteinate (carbocysteinate) systems in NaCl_aq, at different ionic strengths, and in a multicomponent Na⁺, K⁺, Ca²⁺ ,Mg²⁺, Cl^? and SO₄^2-? medium representative of the seawater major composition, is discussed. Experimental results give evidence for the formation of the following species (L = carbocysteinate): [(CH₃)₂Sn(L)]⁰, [(CH₃)₂Sn(HL)]⁺, [(CH₃)₂Sn(OH)(L)]^?, [(CH₃)₂Sn(OH)₂(L)]^2? in the DMT–CCYS system, and [(CH₃)₃Sn(HL)]⁰, [(CH₃)₃Sn(L)]^? and [(CH₃)₃Sn(OH)(L)]^2? in the TMT-CCYS system. The ionic strength dependence of formation constants was taken into account by an extended Debye Hückel type equation and by the SIT (Specific ion Interaction Theory). Measurements were carried out also on the dimethyltin(IV)-glutamate and trimethyltin(IV)-glutamate systems in NaCl_aq, owing the strict similarity of glutamate and carbocysteinate. Results obtained show the formation of complex species having the same stoichiometry as those formed in the DMT- and TMT-carbocysteinate systems, with very similar stability, confirming that carbocysteinate behaves as a dicarboxylic amino acid without involving the sulfur-bridge potential binding site in metal coordination.     

Journal of Ethnobiology and Ethnomedicine – achievements and perspectives

Last summer we officially launched the Journal of Ethnobiology and Ethnomedicine, published by BioMedCentral, with the aim of establishing a serious, peer-reviewed, open-access online journal that focuses on the multidisciplinary, interdisciplinary, and transdisciplinary fields of ethnobiology and ethnomedicine, drawing on approaches and methods from both the social and biological sciences. The strong start vindicates the widely held belief that the journal responds to a real need within the research community. The success of the journal has been most gratifying. The steady influx of submissions of high scientific standards illustrates the strong demand for a dynamic, proactive, and open-minded scientific journal in these research areas. Our aim has been to dedicate JEE to the "scientific communities" worldwide, particularly those in the developing countries.     

Metastatic tumor cells – genotypes and phenotypes

Background

Metastasis is the primary cause of mortality in cancer patients. Therefore, elucidating the genetics and epigenetics of metastatic tumor cells and the mechanisms by which tumor cells acquire metastatic properties constitute significant challenges in cancer research.

Objective

To summarize the current understandings of the specific genotype and phenotype of the metastatic tumor cells.

Method and Result

In-depth genetic analysis of tumor cells, especially with advances in the next-generation sequencing, have revealed insights of the genotypes of metastatic tumor cells. Also, studies have shown that the cancer stem cell (CSC) and epithelial to mesenchymal transition (EMT) phenotypes are associated with the metastatic cascade.

Conclusion

In this review, we will discuss recent advances in the field by focusing on the genomic instability and phenotypic dynamics of metastatic tumor cells.

     

Acetylcholinesterases – the structural similarities and differences

Acetylcholinesterase (AChE) is a widely spread enzyme playing a very important role in nerve signal transmission. As AChE controls key processes, its inhibition leads to the very fast death of an organism, including humans. However, when this feature is to be used for killing of unwanted organisms (i.e. mosquitoes), one is faced with the question - how much do AChEs differ between species and what are the differences? Here, a theoretical point of view was utilized to identify the structural basis for such differences. The various primary and tertiary alignments show that AChEs are very evolutionary conserved enzymes and this fact could lead to difficulties, for example, in the search for inhibitors specific for a particular species.     

Prions and Non-infectious Amyloids of Mammals – Similarities and Differences

Amyloids are highly ordered aggregates of protein fibrils exhibiting cross-β structure formed by intermolecular hydrogen bonds. Pathological amyloid deposition is associated with the development of several socially significant incurable human diseases. Of particular interest are infectious amyloids, or prions, that cause several lethal neurodegenerative diseases in humans and can be transmitted from one organism to another. Because of almost complete absence of criteria for infectious and non-infectious amyloids, there is a lack of consensus, especially, in the definition of similarities and differences between prions and non-infectious amyloids. In this review, we formulated contemporary molecular-biological criteria for identification of prions and non-infectious amyloids and focused on explaining the differences between these two types of molecules.     

Monovalent protein-degraders – Insights and future perspectives

The therapeutic potential of interfering with dysregulated proteins by inducing its selective degradation has been pursued using different mechanisms. In the present article, we review representative examples of monovalent protein-degraders that, contrary to the proteolysis targeting chimeras, achieve target degradation without displaying recognition motifs for the recruitment of E3 ubiquitin ligases. We also highlight new technologies and assays that may brought to bear on the discovery of common elements that could predict and enable the selective degradation of pathogenic targets by monovalent protein-degraders. The successful application of these methods would pave the way to the advancement of new drugs with unique efficacy and tolerability properties.     

Non-covalent interactions – QTAIM and NBO analysis

MP2(full)/6-311++G(3df,3pd) calculations were carried out on complexes linked through various non-covalent Lewis acid – Lewis base interactions. These are: hydrogen bond, dihydrogen bond, hydride bond and halogen bond. The quantum theory of ´atoms in molecules´ (QTAIM) as well as the natural bond orbitals (NBO) method were applied to analyze properties of these interactions. It was found that for the A-H…B hydrogen bond as well as for the A-X…B halogen bond (X designates halogen) the complex formation leads to the increase of s-character in the A-atom hybrid orbital aimed toward the H or X atom. In opposite, for the A…H-B hydride bond, where the H-atom possesses negative charge, the decrease of s-character in the B-atom orbital is observed. All these changes connected with the redistribution of the electron charge being the effect of the complex formation are in line with Bent´s rule. The numerous correlations between energetic, geometrical, NBO and QTAIM parameters were also found.

Potassium in agriculture – Status and perspectives

In this review we summarize factors determining the plant availability of soil potassium (K), the role of K in crop yield formation and product quality, and the dependence of crop stress resistance on K nutrition. Average soil reserves of K are generally large, but most of it is not plant-available. Therefore, crops need to be supplied with soluble K fertilizers, the demand of which is expected to increase significantly, particularly in developing regions of the world. Recent investigations have shown that organic exudates of some bacteria and plant roots play a key role in releasing otherwise unavailable K from K-bearing minerals. Thus, breeding for genotypes that have improved mechanisms to gain access to this fixed K will contribute toward more sustainable agriculture, particularly in cropping systems that do not have access to fertilizer K. In K-deficient crops, the supply of sink organs with photosynthates is impaired, and sugars accumulate in source leaves. This not only affects yield formation, but also quality parameters, for example in wheat, potato and grape. As K has beneficial effects on human health, its concentration in the harvest product is a quality parameter in itself. Owing to its fundamental roles in turgor generation, primary metabolism, and long-distance transport, K plays a prominent role in crop resistance to drought, salinity, high light, or cold as well as resistance to pests and pathogens. Despite the abundance of vital roles of K in crop production, an improvement of K uptake and use efficiency has not been a major focus of conventional or transgenic breeding in the past. In addition, current soil analysis methods for K are insufficient for some common soils, posing the risk of imbalanced fertilization. A stronger prioritization of these areas of research is needed to counter declines in soil fertility and to improve food security.     

Colorimetry and prime colours – a theorem

Human colour vision is the result of a complex process involving topics ranging from physics of light to perception. Whereas the diversity of light entering the eye in principle span an infinite-dimensional vector space in terms of the spectral power distributions, the space of human colour perceptions is three dimensional. One important consequence of this is that a variety of colours can be visually matched by a mixture of only three adequately chosen reference lights. It has been observed that there exists one particular set of monochromatic reference lights that, according to a certain definition, is optimal for producing colour matches. These reference lights are commonly denoted prime colours. In the present paper, we intend to rigorously show that the existence of prime colours is not particular to the human visual system as sometimes stated, but rather an algebraic consequence of the manner in which a kind of colorimetric functions called colour-matching functions are defined and transformed. The solution is based on maximisation of a determinant determining the gamut size of the colour space spanned by the prime colours. Cramer’s rule for solving a set of linear equations is an essential part of the proof. By means of examples, it is shown that mathematically the optimal set of reference lights is not unique in general, and that the existence of a maximum determinant is not a necessary condition for the existence of prime colours.