The ultrastructure of topical cutaneous calcinosis

Summary Mineralized plaques, which develop at the site of repeated subcutaneous injections of 100 g KMnO₄/0.2 H₂O in rats, were investigated by electron microscopy. The newly formed, delineated, white plaque tissue at the injection site consisted of numerous, mostly unaltered fibroblasts and collagen fibers, without participation of inflammatory cells. Some signs of cell injury were found in the center of the lesions. Numerous, irregularly distributed, small, mineralized foci were seen near the fibroblasts. These were formed by aggregation of small needle-like units (50 Å in diameter and 0.05–2.0 m long). These needle-shaped units were found either in vesicular, cell derived structures, considered to be shed cell processes or cell fragments, or on collagen fibers. Intramitochondrial deposits of such needle-like units were seen frequently. Fusion of smaller mineralized foci to larger plaques occured and then needle-shaped units were seen at the periphery of the electron-dense lesions. Hypotheses concerning the mechanism of experimental cutaneous calcinosis (soft tissue mineralization) are discussed and related to the findings of this study. Probable intracellular crystal deposition and mineralization in cell-derived structures were shown for the first time in topical cutaneous calcinosis.     

The free energy folding penalty accompanying binding of intrinsically disordered α‐helical motifs

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes and preform critical roles in many cellular processes, most often through the association with globular proteins. Despite lacking a stable three‐dimensional structure by themselves, they may acquire a defined conformation upon binding globular targets. The most common type of secondary structure acquired by these binding motifs entails formation of an α‐helix. It has been hypothesized that such disorder‐to‐order transitions are associated with a significant free energy penalty due to IDP folding, which reduces the overall IDP‐target affinity. However, the exact magnitude of IDP folding penalty in α‐helical binding motifs has not been systematically estimated. Here, we report the folding penalty contributions for 30 IDPs undergoing folding‐upon‐binding and find that the average IDP folding penalty is +2.0 kcal/mol and ranges from 0.7 to 3.5 kcal/mol. We observe that the folding penalty scales approximately linearly with the change in IDP helicity upon binding, which provides a simple empirical way to estimate folding penalty. We analyze to what extent do pre‐structuring and target‐bound IDP dynamics (fuzziness) reduce the folding penalty and find that these effects combined, on average, reduce the folding cost by around half. Taken together, the presented analysis provides a quantitative basis for understanding the role of folding penalty in IDP‐target interactions and introduces a method estimate this quantity. Estimation and reduction of IDP folding penalty may prove useful in the rational design of helix‐stabilized inhibitors of IDP‐target interactions.StatementThe α‐helical binding motifs are ubiquitous among the intrinsically disordered proteins (IDPs). Upon binding their targets, they undergo a disorder‐to‐order transition, which is accompanied by a significant folding penalty whose magnitude is generally not known. Here, we use recently developed statistical‐thermodynamic model to estimate the folding penalties for 30 IDPs and clarify the roles of IDP pre‐folding and bound‐state dynamics in reducing the folding penalty.     

Quantification of microtubule stutters: dynamic instability behaviors that are strongly associated with catastrophe

Microtubules (MTs) are cytoskeletal fibers that undergo dynamic instability (DI), a remarkable process involving phases of growth and shortening separated by stochastic transitions called catastrophe and rescue. Dissecting DI mechanism(s) requires first characterizing and quantifying these dynamics, a subjective process that often ignores complexity in MT behavior. We present a Statistical Tool for Automated Dynamic Instability Analysis (STADIA) that identifies and quantifies not only growth and shortening, but also a category of intermediate behaviors that we term “stutters.” During stutters, the rate of MT length change tends to be smaller in magnitude than during typical growth or shortening phases. Quantifying stutters and other behaviors with STADIA demonstrates that stutters precede most catastrophes in our in vitro experiments and dimer-scale MT simulations, suggesting that stutters are mechanistically involved in catastrophes. Related to this idea, we show that the anticatastrophe factor CLASP2γ works by promoting the return of stuttering MTs to growth. STADIA enables more comprehensive and data-driven analysis of MT dynamics compared with previous methods. The treatment of stutters as distinct and quantifiable DI behaviors provides new opportunities for analyzing mechanisms of MT dynamics and their regulation by binding proteins.     

CH/π interactions of π-system of acetylacetonato chelate ring: Comparison of CH/π interactions of Ni(II)-acetylacetonato chelate and benzene rings

The calculations have been done for CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring. The results show that there is an attractive electrostatic interaction, while dispersion component is a major source of attractive interacting energies. The interaction was compared with CH/π interaction between two benzene rings. The comparison shows that two interactions are quite similar, enabling to estimate the energy of CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring to be about 10.5 kJ/mol. The results indicate that CH/π interactions of chelate ring in various molecular systems can be as important as CH/π interactions of phenyl ring.     

p-aminohippuric acid transport at renal apical membrane mediated by human inorganic phosphate transporter NPT1

Organic anions are secreted into urine via organic anion transporters across the renal basolateral and apical membranes. However, no apical membrane transporter for organic anions such as p-aminohippuric acid (PAH) has yet been identified. In the present study, we showed that human NPT1, which is present in renal apical membrane, mediates the transport of PAH. The K(m) value for PAH uptake was 2.66 mM and the uptake was chloride ion sensitive. These results are compatible with those reported for the classical organic anion transport system at the renal apical membrane. PAH transport was inhibited by various anionic compounds. Human NPT1 also accepted uric acid, benzylpenicillin, faropenem, and estradiol-17beta-glucuronide as substrates. Considering its chloride ion sensitivity, Npt1 is expected to function for secretion of PAH from renal proximal tubular cells. This is the first molecular demonstration of an organic anion transport function for PAH at the renal apical membrane.     

Dimorphic and yeast-like mutants of the genusCephalosporium Cda

A series of mutants, in which the mycelial type of growth gradually changes to the dimorphic and permanent yeast-like forms, were isolated from cultures ofCephalosporium sp. subjected to UV radiation. The intermediate stage between the mycelial and dimorphic strains (mutants 2/29 and 2/R) is characterized by the absence of aerial hyphae, ability to form conidiophores inside agar and by polymorphism of conidia. The Y-M transformation of two dimorphic mutants obtained from the 2/R mutant depends on temperature. Another mutant isolated from the 2/29 strain was found to form the mycelial phase only when osmolarity of the medium increased. At 22°C the transformation of all three dimorphic strains was influenced by the carbon source: the Y phase predominated in glucose-containing media, the M phase predominated in media with amino acids or citrate serving as carbon sources. Another mutant (2/7R) was found to grow permanently in the Y phase and was not influenced by temperature, osmolarity of the medium and by the carbon source. It is assumed that the dimorphism of the mutants is caused by a conformational mutation inhibiting the apical growth. This mutation can be phenotypically reversed by some factors of the environment.     

Key Elements in a Framework for Land Use Impact Assessment Within LCA (11 pp)

Background, Aim and Scope Land use by agriculture, forestry, mining, house-building or industry leads to substantial impacts, particularly on biodiversity and on soil quality as a supplier of life support functions. Unfortunately there is no widely accepted assessment method so far for land use impacts. This paper presents an attempt, within the UNEP-SETAC Life Cycle Initiative, to provide a framework for the Life Cycle Impact Assessment (LCIA) of land use. Materials and Methods: This framework builds from previous documents, particularly the SETAC book on LCIA (Lindeijer et al. 2002), developing essential issues such as the reference for occupation impacts; the impact pathways to be included in the analysis; the units of measure in the impact mechanism (land use interventions to impacts); the ways to deal with impacts in the future; and bio-geographical differentiation. Results: The paper describes the selected impact pathways, linking the land use elementary flows (occupation; transformation) and parameters (intensity) registered in the inventory (LCI) to the midpoint impact indicators and to the relevant damage categories (natural environment and natural resources). An impact occurs when the land properties are modified (transformation) and also when the current man-made properties are maintained (occupation). Discussion: The size of impact is the difference between the effect on land quality from the studied case of land use and a suitable reference land use on the same area (dynamic reference situation). The impact depends not only on the type of land use (including coverage and intensity) but is also heavily influenced by the bio-geographical conditions of the area. The time lag between the land use intervention and the impact may be large; thus land use impacts should be calculated over a reasonable time period after the actual land use finishes, at least until a new steady state in land quality is reached. Conclusions: Guidance is provided on the definition of the dynamic reference situation and on methods and time frame to assess the impacts occurring after the actual land use. Including the occupation impacts acknowledges that humans are not the sole users of land. Recommendations and Perspectives: The main damages affected by land use that should be considered by any method to assess land use impacts in LCIA are: biodiversity (existence value); biotic production potential (including soil fertility and use value of biodiversity); ecological soil quality (including life support functions of soil other than biotic production potential). Bio-geographical differentiation is required for land use impacts, because the same intervention may have different consequences depending on the sensitivity and inherent land quality of the environment where it occurs. For the moment, an indication of how such task could be done and likely bio-geographical parameters to be considered are suggested. The recommendation of indicators for the suggested impact categories is a matter of future research.     

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.