The Extracellular Vesicles Containing Inorganic Polyphosphate of Candida Yeast upon Growth on Hexadecane.

The cell wall of Candida yeast grown on presence of hexadecane as a sole carbon source undergoes structural and functional changes including the formation of specific supramolecular complexes-canals. The canals contain specific polysaccharides and enzymes that provide primary oxidization of alkanes. In addition, inorganic polyphosphate (polyP) was identified in Candida maltosa canals. The aim of the work was a comparative study of the features of cell walls and extracellular structures in yeast C. maltosa, C. albicans and C. tropicalis with special attention to inorganic polyphosphates as possible part of these structures when grown on the widely used xenobiotic hexadecane (diesel fuel). Fluorescence microscopy with DAPI has shown an unusual localization of polyP on the cell surface and in the exovesicles in the three yeast species, when growing on hexadecane. Electron-scanning microscopy showed that the exovesicles were associated with the cell wall and also presented in the external environment probably as biofilm components. Treatment of hexadecane-grown cells with purified Ppx1 polyphosphatase led to the release of phosphate into the incubation medium and the disappearance of polyP in vesicles and cell wall observed using microscopic methods. The results indicate the important role of polyP in the formation of extracellular structures in the Candida yeast when consuming hexadecane and are important for the design of xenobiotic destructors based on yeast or mixed cultures.

Nanomechanical properties of SSTSAA microcrystals are dominated by the inter-sheet packing.

Amyloid fibrils have been associated with human disease for many decades, but it has also become apparent that they play a functional, non-disease-related role in e.g. bacteria and mammals. Moreover, they have been shown to possess interesting mechanical properties that can be harnessed for future man-made applications. Here, the mechanical behaviour of SSTSAA microcrystals has been investigated. The SSTSAA peptide organization in these microcrystals has been related to that in the corresponding amyloid fibrils. Using high-pressure X-ray diffraction experiments, the bulk modulus K, which is the reciprocal of the compressibility ß, has been calculated to be 2.48 GPa. This indicates that the fibrils are tightly packed, although the packing of most native globular proteins is even better. It is shown that the value of the bulk modulus is mainly determined by the compression along the c-axis, that relates to the inter-sheet distance in the fibrils. These findings corroborate earlier data obtained by AFM and molecular dynamics simulations that showed that mechanical resistance varies according to the direction of the applied strain, which can be related to packing and hydrogen bond contributions. Pressure experiments provide complementary information to these techniques and help to acquire a full mechanical characterization of biomolecular assemblies. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Changes in cell wall structure and protein set in Candida maltosa grown on hexadecane.

The yeast Candida maltosa is a model organism for studying adaptive changes in the structure and function of the cell wall when consuming water-insoluble nutrient sources. The cells of C. maltosa that utilize hydrocarbons contain supramolecular structures, so-called "canals" in the cell wall. Differences in protein profiles of culture liquids and cell wall extracts of C. maltosa grown on glucose and hexadecane were analyzed. Three proteins specific of cells grown on hexadecane were revealed using mass spectrometry: glycosyl hydrolase EPD2 in the culture liquid; a protein belonging to the cytochrome C family in the 0.5 mol/L NaCl extract; and PPIA_CANAL protein known as chaperone, in the 0.1% SDS extract. The possible role of these proteins in cell wall structures responsible for adaptation to hexadecane utilization is discussed.

A novel approach for predicting protein S-glutathionylation.

BACKGROUND: S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in their functions. Regulatory glutathionylation of proteins is a controllable and reversible process associated with cell response to the changing redox status. Prediction of cysteine residues that undergo glutathionylation allows us to find new target proteins, which function can be altered in pathologies associated with impaired redox status. We set out to analyze this issue and create new tool for predicting S-glutathionylated cysteine residues. RESULTS: One hundred forty proteins with experimentally proven S-glutathionylated cysteine residues were found in the literature and the RedoxDB database. These proteins contain 1018 non-S-glutathionylated cysteines and 235 S-glutathionylated ones. Based on 235 S-glutathionylated cysteines, non-redundant positive dataset of 221 heptapeptide sequences of S-glutathionylated cysteines was made. Based on 221 heptapeptide sequences, a position-specific matrix was created by analyzing the protein sequence near the cysteine residue (three amino acid residues before and three after the cysteine). We propose the method for calculating the glutathionylation propensity score, which utilizes the position-specific matrix and a criterion for predicting glutathionylated peptides. CONCLUSION: Non-S-glutathionylated sites were enriched by cysteines in - 3 and + 3 positions. The proposed prediction method demonstrates 76.6% of correct predictions of S-glutathionylated cysteines. This method can be used for detecting new glutathionylation sites, especially in proteins with an unknown structure.

Carbon nanotube sorting due to commensurate molecular wrapping.

Single-walled carbon nanotubes (SWCNTs) can be sorted by their structural parameters using organic molecules and polymers: some of which, demonstrating a profound affinity only for specific nanotubes, form dense coatings on them. Here, analyzing well-known examples of flavin group molecules and those of 2,4-dichlorophenoxyacetic acid, we show for the first time that successful formation of the considered coatings depends on the ability of molecules to wrap around the SWCNT in a commensurate way. Commensurability provides a decrease in the free energy of the resulting bilayer system and makes the coating much more stable. Concurrently, it strongly relates the nanotube chiral vector with the geometric characteristics of the adhering molecules, which leads to revealed selection rules. If they are not satisfied, the deposition of molecules does not occur or is insignificant. The proposed theory unambiguously explains known experimental results on the formation of spiral wrappings of SWCNTs by flavin group molecules and points out other organic molecules and polymers suitable for effective CNT sorting.

Effect of Extra-Framework Cations on Negative Linear Compressibility and High-Pressure Phase Transitions: A Study of KCd[Ag(CN)2]3.

The negative thermal expansion material potassium cadmium dicyanoargentate, KCd[Ag(CN)2]3, is studied at high pressure using a combination of X-ray single-crystal diffraction, X-ray powder diffraction, infrared and Raman spectroscopy, and density functional theory calculations. In common with the isostructural manganese analogue, KMn[Ag(CN)2]3, this material is shown to exhibit very strong negative linear compressibility (NLC) in the crystallographic c direction due to structure hinging. We find increased structural flexibility results in enhanced NLC and NTE properties, but this also leads to two pressure-induced phase transitions-to very large unit cells involving octahedral tilting and shearing of the structure-below 2 GPa. The presence of potassium cations has an important effect on the mechanical and thermodynamic properties of this family, while the chemical versatility demonstrated here is of considerable interest to tune unusual mechanical properties for application.

Cell wall canals formed upon growth of Candida maltosa in the presence of hexadecane are associated with polyphosphates.

Canals are supramolecular complexes observed in the cell wall of Candida maltosa grown in the presence of hexadecane as a sole carbon source. Such structures were not observed in glucose-grown cells. Microscopic observations of cells stained with diaminobenzidine revealed the presence of oxidative enzymes in the canals. 4΄,6΄-diamino-2-phenylindole staining revealed that a substantial part of cellular polyphosphate was present in the cell wall of cells grown on hexadecane in condition of phosphate limitation. The content and chain length of polyphosphates were higher in hexadecane-grown cells than in glucose grown ones. The treatment of cells with yeast polyphosphatase PPX1 resulted in the decrease of the canal size. These data clearly indicated that polyphosphates are constituents of canals; they might play an important role in the canal structure and functioning.

Incommensurate atomic density waves in the high-pressure IVb phase of barium.

The host-guest structures of elements at high pressure discovered a decade ago still leave many open questions due to the lack of precise models based on full exploitation of the diffraction data. This concerns in particular Ba IV, which is stable in the range 12-45 GPa. With the example of phase Ba IVb, which is characterized here for the first time, a systematic analysis is presented of possible host-guest structure models based on high-quality single-crystal diffraction data obtained with synchrotron radiation at six different pressures between 16.5 and 19.6 GPa. It is shown that a new incommensurately modulated (IM) structure model better fits the experimental data. Unlike the composite models which are commonly reported for the Ba IV phases, the IM model reveals a density wave and its pressure-dependent evolution. The crucial role played by the selected model in the interpretation of structure evolution under pressure is discussed. The findings give a new experimental basis for a better understanding of the nature of host-guest structures.

Ultrasound-Guided Ureteral Stent Removal in Women.

OBJECTIVES: The purpose of this study was to develop a fast, comfortable, and safe method of ureteral stent removal in women. METHODS: From February 2014 to July 2015, a retrospective multicenter controlled study including 82 female outpatients was conducted. The control group was composed of 46 patients who underwent stent removal using a 22F cystoscope. The experimental group was composed of 36 patients who underwent stent removal under ultrasound guidance with a 15F spiral-ending device. Exclusion criteria were pelvic organ prolapse quantification stage II or higher and complicated stents (with migration or encrustation). RESULTS: All studied patients had successful ureteral stent removal. No complications were seen in both groups. Differences between mean visual analog pain scale scores and stent removal durations were statistically significant in favor of the experimental group (P = .0077 and .0075, respectively). CONCLUSIONS: The proposed method for ureteral stent removal in women under ultrasound guidance was shown to be faster and to have lower visual analog pain scale scores, in comparison with removal by a cystoscope, which makes it an attractive option for outpatient urologic praxis in uncomplicated cases, and because it is free of the risk of ionizing radiation and more comfortable, it can be used in pregnant patients.

A new multipurpose diffractometer PILATUS@SNBL.

The diffraction beamline BM01A at the European Synchrotron Radiation Facility (CRG Swiss-Norwegian beamlines) has been successfully operational for 20 years. Recently, a new multifunctional diffractometer based on the Dectris Pilatus 2M detector has been constructed, commissioned and offered to users. The diffractometer combines a fast and low-noise area detector, which can be tilted and moved horizontally and vertically, together with flexible goniometry for sample positioning and orientation. The diffractometer is controlled by a user-friendly and GUI-based software Pylatus which is also used to control various auxiliary equipment. The latter includes several heating and cooling devices, in situ cells and complimentary spectroscopic tools.

Modifications of the cell wall of yeasts grown on hexadecane and under starvation conditions.

Electron-microscopic examinations have demonstrated local modifications in the cell wall of the yeast Candida maltosa grown on hexadecane. In our earlier studies, these modified sites, observed in other yeasts grown on oil hydrocarbons, were conventionally called 'canals'. The biochemical and cytochemical studies of C. maltosa have revealed a correlation between the formation of 'canals' and decrease in the amount of cell wall polysaccharides, glucan and mannan. The ultrathin sections and surface replicas have shown that the 'canals' are destroyed by pronase, thus indicating that a significant proportion of their content is represented by proteins. This finding was compatible with our earlier data on the localization of oxidative enzymes in 'canals' and possible participation of the 'canals' in the primary oxidation of hydrocarbons. A completely unexpected and intriguing phenomenon has been the appearance of 'canals' in the yeast C. maltosa under starvation conditions. Unlike the yeasts grown on hexadecane, mannan almost disappears in starving cells, while the quantity of glucan first decreases and then is restored to its initial level. The role of 'canals' in starving cells is as yet unclear; it is assumed that they acquire exoenzymes involved in the utilization of products of cell lysis in the starving population. In the future, 'canals' of starving cells will be studied in connection with their possible participation in apoptosis.

Manganese tolerance in yeasts involves polyphosphate, magnesium, and vacuolar alterations.

Basidiomycetous and ascomycetous yeast species were tested for manganese tolerance. Basidiomycetous Cryptococcus humicola, Cryptococcus terricola, Cryptococcus curvatus and ascomycetous Candida maltosa, Kluyveromyces marxianus, Kuraishia capsulata, Lindnera fabianii and Sacharomyces cerevisiae were able to grow at manganese excess (2.5 mmol/L), while the growth of basidiomycetous Rhodotorula bogoriensis was completely suppressed. The lag phase duration increased and the exponential growth rate decreased at manganese excess. The increase of cell size and enlargement of vacuoles were characteristics for the cells grown at manganese excess. The alterations in inorganic polyphosphate content and cellular localization were studied. L. fabianii, K. capsulata, C. maltosa, and Cr. humicola accumulated the higher amounts of inorganic polyphosphates, while Cr. terricola and Cr. curvatus demonstrated no such accumulation. The polyphosphate content in the cell wall tested by DAPI staining increased in all species under the study; however, this effect was more pronounced in Cr. terricola and Cr. curvatus. The accumulation of Mg(2+) in the cell wall under Mn(2+) excess was observed in Cr. humicola, Cr. curvatus and Cr. terricola. The accumulation of polyphosphate and magnesium in the cell wall was supposed to be a factor of manganese tolerance in yeasts.

Exploration of the mechanical behavior of metal organic frameworks UiO-66(Zr) and MIL-125(Ti) and their NH2 functionalized versions.

The structural behaviour under mechanical stimuli of two metal organic frameworks, UiO-66(Zr) and MIL-125(Ti) and their amino-functionalized derivatives has been investigated by high-pressure powder X-ray diffraction up to 3.5 GPa. All these solids showed a gradual pressure-induced reversible decrease of their crystallinity and UiO-66(Zr)_NH2 material has been revealed as one of the most resilient MOFs reported so far corresponding to a very high bulk modulus. The mechanical behaviors of these MOFs have been correlated to their chemical and geometric features including the metal-oxygen coordination number, the nature of the organic linker, the porosity as well as their crystal density.

Cytoplasmic inorganic polyphosphate participates in the heavy metal tolerance of Cryptococcus humicola.

The basidiomycetous yeast Cryptococcus humicola was shown to be tolerant to manganese, cobalt, nickel, zinc, lanthanum, and cadmium cations at a concentration of 2.5 mmol/L, which is toxic for many yeasts. The basidiomycetous yeast Cryptococcus terreus was sensitive to all these ions and did not grow at the above concentration. In the presence of heavy metal cations, С. humicola, as opposed to C. terreus, was characterized by the higher content of acid-soluble inorganic polyphosphates. In vivo 4',6'-diamino-2-phenylindole dihydrochloride staining revealed polyphosphate accumulation in the cell wall and cytoplasmic inclusions of С. humicola in the presence of heavy metals. In C. terreus, polyphosphates in the presence of heavy metals accumulate mainly in vacuoles, which results in morphological changes in these organelles and, probably, disturbance of their function. The role of polyphosphate accumulation and cellular localization as factors of heavy metal tolerance of Cryptococcus humicola is discussed.

Adaptation of Saccharomyces cerevisiae to toxic manganese concentration triggers changes in inorganic polyphosphates.

The ability of Saccharomyces cerevisiae to adapt to toxic Mn(2+) concentration (4 mM) after an unusually long lag phase has been demonstrated for the first time. The mutants lacking exopolyphosphatase PPX1 did not change the adaptation time, whereas the mutants lacking exopolyphosphatase PPN1 reduced the lag period compared with the wild-type strains. The cell populations of WT and ΔPPN1 in the stationary phase at cultivation with Mn(2+) contained a substantial number of enlarged cells with a giant vacuole. The adaptation correlated with the triggering of polyphosphate metabolism: the drastic increase in the rate and chain length of acid-soluble polyphosphate. The share of this fraction, which is believed to be localized in the cytoplasm, increased to 76%. Its average chain length increased to 200 phosphate residues compared with 15 at the cultivation in the absence of manganese. DAPI-stained inclusions in the cytoplasm were accumulated in the lag phase during the cultivation with Mn(2+).

Homologous critical behavior in the molecular frameworks Zn(CN)2 and Cd(imidazolate)2.

Using a combination of single-crystal and powder X-ray diffraction measurements, we study temperature- and pressure-driven structural distortions in zinc(II) cyanide (Zn(CN)2) and cadmium(II) imidazolate (Cd(im)2), two molecular frameworks with the anticuprite topology. Under a hydrostatic pressure of 1.52 GPa, Zn(CN)2 undergoes a first-order displacive phase transition to an orthorhombic phase, with the corresponding atomic displacements characterized by correlated collective tilts of pairs of Zn-centered tetrahedra. This displacement pattern sheds light on the mechanism of negative thermal expansion in ambient-pressure Zn(CN)2. We find that the fundamental mechanical response exhibited by Zn(CN)2 is mirrored in the temperature-dependent behavior of Cd(im)2. Our results suggest that the thermodynamics of molecular frameworks may be governed by considerations of packing efficiency while also depending on dynamic instabilities of the underlying framework topology.

Giant negative linear compressibility in zinc dicyanoaurate.

The counterintuitive phenomenon of negative linear compressibility (NLC) is a highly desirable but rare property exploitable in the development of artificial muscles, actuators and next-generation pressure sensors. In all cases, material performance is directly related to the magnitude of intrinsic NLC response. Here we show the molecular framework material zinc(II) dicyanoaurate(I), Zn[Au(CN)(2)](2), exhibits the most extreme and persistent NLC behaviour yet reported: under increasing hydrostatic pressure its crystal structure expands in one direction at a rate that is an order of magnitude greater than both the typical contraction observed for common engineering materials and also the anomalous expansion in established NLC candidates. This extreme behaviour arises from the honeycomb-like structure of Zn[Au(CN)(2)](2) coupling volume reduction to uniaxial expansion, and helical Au…Au 'aurophilic' interactions accommodating abnormally large linear strains by functioning as supramolecular springs.

In situ Raman spectroscopic study of the pressure induced structural changes in ammonia borane.

The effect of static compression up to 65 GPa at ambient temperature on ammonia borane, BH(3)NH(3), has been investigated using in situ Raman spectroscopy in a diamond anvil cells. Two phase transitions were observed at approximately 12 GPa and previously not reported transition at 27 GPa. It was demonstrated that ammonia borane behaves differently under compression at quasi-hydrostatic and non-hydrostatic conditions. The ability of BH(3)NH(3) to generate second harmonic of the laser light observed up to 130 GPa suggests that the non-centrosymmetric point group symmetry is preserved in the material up to very high pressures.

Accumulation of phosphate and polyphosphate by Cryptococcus humicola and Saccharomyces cerevisiae in the absence of nitrogen.

The search for new phosphate-accumulating microorganisms is of interest in connection with the problem of excess phosphate in environment. The ability of some yeast species belonging to ascomycetes and basidiomycetes for phosphate (P (i) ) accumulation in nitrogen-deficient medium was studied. The ascomycetous Saccharomyces cerevisiae and Kuraishia capsulata and basidiomycetous Cryptococcus humicola, Cryptococcus curvatus, and Pseudozyma fusiformata were the best in P (i) removal. The cells of Cryptococcus humicola and S. cerevisiae took up 40% P (i) from the media containing P (i) and glucose (5 and 30 mM, respectively), and up to 80% upon addition of 5 mM MgSO(4) (.) The cells accumulated P (i) mostly in the form of polyphosphate (PolyP). In the presence of Mg(2+) , the content of PolyP with longer average chain length increased in both yeasts; they both had numerous inclusions fluorescing in the yellow region of the spectrum, typical of DAPI-PolyP complexes. Among the yeast species tested, Cryptococcus humicola is a new promising model organisms to study phosphorus removal from the media and biomineralization in microbial cells.