Electrically induced gel-to-gel phase-transition in neurons

At the end of transcardial perfusions with ice-cold physiological saline for 30 min or with isoosmotic potassium chloride for 5 min, but immediately before perfusion fixation, condenser-discharge electric shocks were administered to rats through surface electrodes pressed onto the temporal muscles of the scalped skull. As a result, striking ultrastructural compaction came about in numerous neurons thinly scattered in certain brain areas. Its features displayed a high degree of similarity to those previously observed following the in vivo administration of the same kind of electric shocks. This surprising independence from the actual state of metabolism questions whether the ultrastructural compaction, induced either in vivo or post mortem, is the result of any cascade of enzyme-mediated processes. On the other hand, a physical mechanism, phase transition propagated by non-covalent free energy stored in a cytoplasmic gel structure, which was proposed recently to explain a mechanically induced similar ultrastructural compaction, appears to apply also to the present case.     

Soil composition affects the nesting behavior of blue-tailed bee-eaters (Merops philippinus) on Kinmen Island

The blue-tailed bee-eater (Merops philippinus) is a summer migrant that breeds on Kinmen Island, located off the west coast of Taiwan, about 5 km from the southern coast of mainland China. The aim of this study was to investigate why blue-tailed bee-eaters build their nests in sandy loam and sandy clay loam, but not in clay loam. Soil chemical and physical properties, and mineralogical composition were measured for the different soil types. Clay loam had a significantly lower pH, Na, and base saturation than did sandy loam or sandy clay loam. Clay loam had a significantly higher N, cation-exchange capacity (CEC), K, and free iron (Fe_d) and aluminum oxide (Al_d) contents than the other soil types. Clay loam had significantly lower sand and higher clay content, and higher bulk density and penetration resistance than the other soil types. The correlation coefficients (r ²) between penetration resistance and Fe_d, Al_d, and clay contents were 0.997, 0.848, and 0.779, respectively. Soil strength and compaction are important criteria for bee-eaters nesting-site selection. The lower pH of clay loam would enhance the exchangeable Al and acidity, further increasing the soil aggregation. Thus, it might prevent the bee-eaters from excavating nesting burrows.     

Wetland development in early stages of volcanic succession

Abstract. Wetland vegetation developed in the crater of Mount Usu, northern Japan, soon after the 1977–1978 eruptions which destroyed the vegetation. The cover of each species was measured in 1994 in 118 50 cm × 50 cm plots situated in transects and related to environmental factors (elevation, water depth, soil texture, soil compaction, soil organic matter, and soil pH) to clarify vegetation development. Five vegetation types were recognized dominated by Eleocharis kamtschatica, Equisetum arvense, Lythrum salicaria, Juncus fauriensis and Phragmites australis respectively. Sedge/grass marsh and reed swamp dominated deep-water sites; willow swamp and wet meadow vegetation characterized shallow-water sites, indicating that vegetation zonation developed soon after the eruption. Since those wetland plants were derived neither from seed banks nor from vegetative propagules, they had to immigrate from outside the summit areas. However, except for willows, most species lack the ability for long-distance dispersal. Late successional species, such as P. australis established in the early stages of the primary succession. The water depth varied by 27.5 cm among the plots. Coarse soil particles accumulated, and pH (5.22–6.55) was low on the elevated sites. Organic matter ranged from 2.8 % to 19.1 %, and was high on the elevated sites. Water depth was responsible for the establishment of large-scale vegetation patterns, while edaphic factors, i.e. soil compaction, pH, and organic matter, were determinants of small-scale vegetation patterns. Among the edaphic factors, soil compaction appeared to have a strong influence on vegetation development.     

Folding Steps in the Fibrillation of Functional Amyloid: Denaturant Sensitivity Reveals Common Features in Nucleation and Elongation

Functional bacterial amyloids (FuBA) are intrinsically disordered proteins (IDPs) which rapidly and efficiently aggregate, forming extremely stable fibrils. The conversion from IDP to amyloid is evolutionarily optimized and likely couples folding to association. Many FuBA contain several imperfect repeat sequences which contribute to the stability of mature FuBA fibrils. Aggregation can be considered an intermolecular extension of the process of intramolecular protein folding which has traditionally been studied using chemical denaturants. Here we employ denaturants to investigate folding steps during fibrillation of CsgA and FapC. We quantify protein compactification (i.e. the extent of burial of otherwise exposed surface area upon association of proteins) during different stages of fibrillation based on the dependence of fibrillation rate constants on the denaturant concentration (m-values) determined from fibrillation curves. For both proteins, urea mainly affects nucleation and elongation (not fragmentation), consistent with the fact that these steps involve both intra- and intermolecular association. The two steps have similar m-values, indicating that activation steps in nucleation and elongation involve the same level of folding. Surprisingly, deletion of two or three repeats from FapC leads to larger m-values (i.e. higher compactification) during the activation step of fibril growth. This observation is extended by SAXS analysis of the fibrils which indicates that weakening of the amyloidogenic core caused by repeat deletions causes a larger portion of normally unstructured regions of the protein to be included into the amyloid backbone. We conclude that the sensitivity of fibrillation to denaturants can provide useful insight into molecular mechanisms of aggregation.     

An ellipsometry study on the effect of aluminium chloride and ferric chloride formulations on mucin layers adsorbed at hydrophobic surfaces

Ellipsometry was used to investigate the effect of polyaluminium chloride (PAC) formulations of different degrees of hydrolysation on an adsorbed mucin film. The results were compared to the effect of aluminium chloride (AlCl₃) and ferric chloride. A compaction of the mucin film took place upon addition of the formulations and this occurred to different extents and at different concentrations for the different formulations. The compaction of PAC of a low degree of hydrolysis behaved similarly to AlCl₃. PAC of a high degree of hydrolysis showed a greater compaction effect than the other aluminium formulations. The initial compaction concentration was found to be 0.001 mM which is less than previously found for aluminium–mucin complex formation in bulk. The reversibility of the compaction was also investigated. The compaction of the mucin film was found to be partly reversible for AlCl₃ and PAC of low degree of hydrolysis. No reversibility was observed for the formulations of PAC of high hydrolysis grade or for ferric chloride. The results are consistent with previously observed effects of PAC of a low degree of hydrolysis on bacterial surfaces where a compaction of surface polymers was indicated by the reduced range of repulsive steric interactions.     

The Reaction Products of Epoxydon with Thiols,Ethylmercaptan and Cysteamine

We isolated a yeast from air, strain S-2, which produces raw starch-digesting α-amylase, xylanase, and polygalacturonase. The fermentation ability was negative, and D.B.B., urease, and DNase tests were positive. The major ubiquinone was Q-10 and the mol% G + C content of nuclear DNA was 67. The cells were oval to ellipsoidal; no true mycelium, pseudomycelium, or teliospores were observed; and it contained a large amount of xylose (19.7 mol%) in the whole-cell hydrolyzates. From these characters, strain S-2 was assigned to the genus Cryptococcus.     

Exploring biodiversity in a metropolitan area in the Mediterranean region: The urban and suburban flora of Rome (Italy)

This work provides an overview of plant diversity in the municipality of Rome (Italy) through an assessment of the flora in urban and suburban sectors of the city. It is aimed at providing the knowledge required to support proactive action for plant conservation. On the basis of a literature-derived catalogue and of an extensive survey campaign, the flora was investigated in terms of conservation interest; habitat types and locations that require protection measures were identified according to the occurrence of valuable native plants. Valuable species exclusive of the urban sector are threatened by the compaction trend affecting the urban fabric. Such species occur mainly in ruderal environments and fallows of archaeological sites and urban parks, near river courses and in remnants of natural forests. Valuable species exclusive of the suburban sector are threatened by urban sprawl. They occur prevalently in wet environments of the subcoastal strip and in coastal sands, Mediterranean maquis, tuffaceous gorges, sulphur springs and archaeological sites. The results highlight the need to preserve the complexity of the land mosaic, especially within the urban matrix, and to strengthen the existing environmental protection tools in the suburban area against foreseeable land cover changes.     

Ligand‐Induced Compaction of the PEX5 Receptor‐Binding Cavity Impacts Protein Import Efficiency into Peroxisomes

Peroxisomes entirely rely on the import of their proteome across the peroxisomal membrane. Recognition efficiencies of peroxisomal proteins vary by more than 1000‐fold, but the molecular rationale behind their subsequent differential import and sorting has remained enigmatic. Using the protein cargo alanine‐glyoxylate aminotransferase as a model, an unexpected increase from 34 to 80% in peroxisomal import efficiency of a single‐residue mutant has been discovered. By high‐resolution structural analysis, we found that it is the recognition receptor PEX5 that adapts its conformation for high‐affinity binding rather than the cargo protein signal motif as previously thought. During receptor recognition, the binding cavity of the receptor shrinks to one third of its original volume. This process is impeded in the wild‐type protein cargo because of a bulky side chain within the recognition motif, which blocks contraction of the PEX5 binding cavity. Our data provide a new insight into direct protein import efficiency by removal rather than by addition of an apparent specific sequence signature that is generally applicable to peroxisomal matrix proteins and to other receptor recognition processes.      

DNA compaction by mononuclear platinum cancer drug cisplatin and the trisplatinum anticancer agent BBR3464: Differences and similarities

Cisplatin, a mononuclear platinum compound, which is known as a cancer drug for long time, can exhibit considerable side effects and is also not effective in many types of cancer. Therefore, the alternative platinum anticancer agents that can act at a much lower dose limit compared to the dose relevant for cisplatin treatment have been searched for. BBR3464, a trinuclear platinum compound, is found to exhibit cytotoxic effects at 10 to 1000 times lower dose limit, even in cisplatin-resistant cancer cells. The primary cellular target for cisplatin and BBR3464 is thought to be DNA. Herein, we report the nature of DNA structural changes that are induced by cisplatin and BBR3464, considering the same DNA sequence and similar sample deposition methods for comparison purpose. We have applied high-resolution atomic force microscopy (AFM) in order to obtain an idea about the molecular basis of BBR3464's effectiveness at the lower dose limit. We show from the molecularly resolved AFM images that both the compounds can compact the whole dsDNA molecules, though the degree of compaction in case of BBR3464 treatment is significantly higher. Furthermore, local compaction in terms of loop structure formation could be induced by both BBR3464 and cisplatin, though BBR3464 generated microloops and macroloops both, whereas cisplatin could generate primarily the microloops. It is a significant observation that BBR3464 could induce relatively drastic DNA structural changes in terms of loop formation as well as overall DNA compaction at a molar ratio, which is 50 times less than that applied for cisplatin treatment. Implications of such structural changes in cytotoxic effects of the platinum anticancer agents will be mentioned.