Development of models and methods to simulate peptide-assisted nucleation and growth of calcium-minerals

In den vergangenen Jahren wurden einige bislang unbekannte Phänomene experimentell beobachtet, wie etwa die Existenz unterschiedlicher Prä-Nukleations-Strukturen. Diese haben zu einem neuen Verständnis von Prozessen, die auf molekularer Ebene während der Nukleation und dem Wachstum von Kristallen auftreten, beigetragen. Die Auswirkungen solcher Prä-Nukleations-Strukturen auf den Prozess der Biomineralisation sind noch nicht hinreichend verstanden. Die Mechanismen, mittels derer biomolekulare Modifikatoren, wie Peptide, mit Prä-Nukleations-Strukturen interagieren und somit den Nukleationsprozess von Mineralen beeinflussen könnten, sind vielfältig. Molekulare Simulationen sind zur Analyse der Formation von Prä-Nukleations-Strukturen in Anwesenheit von Modifikatoren gut geeignet. Die vorliegende Arbeit beschreibt einen Ansatz zur Analyse der Interaktion von Peptiden mit den in Lösung befindlichen Bestandteilen der entstehenden Kristalle mit Hilfe von Molekular-Dynamik Simulationen.rnUm informative Simulationen zu ermöglichen, wurde in einem ersten Schritt die Qualität bestehender Kraftfelder im Hinblick auf die Beschreibung von mit Calciumionen interagierenden Oligoglutamaten in wässrigen Lösungen untersucht. Es zeigte sich, dass große Unstimmigkeiten zwischen etablierten Kraftfeldern bestehen, und dass keines der untersuchten Kraftfelder eine realistische Beschreibung der Ionen-Paarung dieser komplexen Ionen widerspiegelte. Daher wurde eine Strategie zur Optimierung bestehender biomolekularer Kraftfelder in dieser Hinsicht entwickelt. Relativ geringe Veränderungen der auf die Ionen–Peptid van-der-Waals-Wechselwirkungen bezogenen Parameter reichten aus, um ein verlässliches Modell für das untersuchte System zu erzielen. rnDas umfassende Sampling des Phasenraumes der Systeme stellt aufgrund der zahlreichen Freiheitsgrade und der starken Interaktionen zwischen Calciumionen und Glutamat in Lösung eine besondere Herausforderung dar. Daher wurde die Methode der Biasing Potential Replica Exchange Molekular-Dynamik Simulationen im Hinblick auf das Sampling von Oligoglutamaten justiert und es erfolgte die Simulation von Peptiden verschiedener Kettenlängen in Anwesenheit von Calciumionen. Mit Hilfe der Sketch-Map Analyse konnten im Rahmen der Simulationen zahlreiche stabile Ionen-Peptid-Komplexe identifiziert werden, welche die Formation von Prä-Nukleations-Strukturen beeinflussen könnten. Abhängig von der Kettenlänge des Peptids weisen diese Komplexe charakteristische Abstände zwischen den Calciumionen auf. Diese ähneln einigen Abständen zwischen den Calciumionen in jenen Phasen von Calcium-Oxalat Kristallen, die in Anwesenheit von Oligoglutamaten gewachsen sind. Die Analogie der Abstände zwischen Calciumionen in gelösten Ionen-Peptid-Komplexen und in Calcium-Oxalat Kristallen könnte auf die Bedeutung von Ionen-Peptid-Komplexen im Prozess der Nukleation und des Wachstums von Biomineralen hindeuten und stellt einen möglichen Erklärungsansatz für die Fähigkeit von Oligoglutamaten zur Beeinflussung der Phase des sich formierenden Kristalls dar, die experimentell beobachtet wurde.

Distribution of metals in several vineyards of North Italy: from soil to wine

Nowadays we live in densely populated regions and this leads to many environmental issues. Among all pollutants that human activities originate, metals are relevant because they can be potentially toxic for most of living beings. We studied the fate of Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn in a vineyard environment analysing samples of plant, wine and soil. Sites were chosen considering the type of wine produced, the type of cultivation (both organic and conventional agriculture) and the geographic location. We took vineyards that cultivate the same grape variety, the Trebbiano). We investigated 5 vineyards located in the Ravenna district (Italy): two on the Lamone Valley slopes, one in the area of river-bank deposits near Ravenna city, then a farm near Lugo and one near Bagnacavallo in interfluve regions. We carried out a very detailed characterization of soils in the sites, including the analysis of: pH, electric conductivity, texture, total carbonate and extimated content of dolomite, active carbonate, iron from ammonium oxalate, Iron Deficiency Chlorosis Index (IDCI), total nitrogen and organic carbon, available phosphorous, available potassium and Cation Exchange Capacity (CEC). Then we made the analysis of the bulk chemical composition and a DTPA extraction to determine the available fraction of elements in soils. All the sites have proper ground to cultivate, with already a good amount of nutrients, such as not needing strong fertilisations, but a vineyard on hills suffers from iron deficiency chlorosis due to the high level of active carbonate. We found some soils with much silica and little calcium oxide that confirm the marly sandstone substratum, while other soils have more calcium oxide and more aluminium oxide that confirm the argillaceous marlstone substratum. We found some critical situations, such as high concentrations of Chromium, especially in the farm near Lugo, and we noticed differences between organic vineyards and conventional ones: the conventional ones have a higher enrichment in soils of some metals (Copper and Zinc). Each metal accumulates differently in every single part of grapevines. We found differences between hill plants and lowland ones: behaviors of plants in metal accumulations seems to have patterns. Metals are more abundant in barks, then in leaves or sometimes in roots. Plants seem trying to remove excesses of metal storing them in bark. Two wines have excess of acetic acid and one conventional farm produces wine with content of Zinc over the Italian law limit. We already found evidence of high values relating them with uncontaminated environments, but more investigations are suggested to link those values to their anthropogenic supplies.

Orientation dependent molecular friction on organic layer compound crystals

High resolution friction force maps of the benzylammonium terminated crystalline surface of a layer compound are presented. The lateral force map acquired with an atomic force microscope, reveals a significant contrast between different molecular orientations yielding molecular rows which differ from their neighboring ones. The single crystals are formed by stacks of copper oxalate sheets sandwiched between stereoregular organic cations, resulting in highly organized surface structures. Single molecular defects are observed at small loads. The experimental results are compared with numerical calculations which indicate a transition from an unperturbed state at small loads to a distorted state at higher loads. (C) 2011 American Institute of Physics.

Pathophysiology and diagnosis of nephrocalcinosis

Nephrocalcinosis is the result of a myriad of hereditary or acquired diseases in the calcium, phosphate or oxalate metabolism that lead to deposition of calcium containing precipitates within the kidney. Nephrocalcinosis and nephrolithiasis are pathophysiologically tightly related and often co-exist. In the case of recurrent nephrolithiasis, nephrocalcinosis has to be excluded. Stone analysis can yield important clues to the underlying disease process. The best way to diagnose nephrocalcinosis and an accompanying nephrolithiasis is by native computer tomography scans. Untreated, nephrocalcinosis will lead to a progressive decline in renal function and eventually to end stage renal disease. Thus, for each case, the underlying disease process has to be determined and a causative therapy initiated.

Isolated extraordinary daytime urinary frequency of childhood: a case series of 26 children in Switzerland

BACKGROUND: The term 'isolated extraordinary daytime urinary frequency' designates an abnormally increased diurnal frequency of painless urination in a completely toilet-trained child with normal urinalysis. METHODS: We report the history of 26 children (16 boys and 10 girls; aged between 4.1 and 10 years) who were referred to us between 2002 and 2006 and subsequently diagnosed with this condition. RESULTS: Possible psychosocial problems, or recent emotional stressors, were disclosed in the majority of the children: recent (36 months or less) asylum seekers (n = 9), school-related problems (n = 4), parental divorce (n = 2) or death of the mother (n = 1). Possible dietary causes were observed in 9 patients: oxalate-rich beverages (n = 5) and liberal ingestion of 'acidic' juices (n = 4). A diet low in oxalates was recommended when children were consuming large quantities of oxalate-rich beverages; and a diet low in acidic juice was recommended in those liberally ingesting acidic juices. Reassurance and observation were the approach in the remaining cases. The median duration of the symptoms was 5 months. A longer (p < 0.05) duration was noted in children of asylum seekers. CONCLUSIONS: This functional condition is easily identifiable, but often under- or misdiagnosed. Confounding the condition might result in redundant investigation.

Projection structure of a member of the amino acid/polyamine/organocation transporter superfamily

The L-arginine/agmatine antiporter AdiC is a key component of the arginine-dependent extreme acid resistance system of Escherichia coli. Phylogenetic analysis indicated that AdiC belongs to the amino acid/polyamine/organocation (APC) transporter superfamily having sequence identities of 15-17% to eukaryotic and human APC transporters. For functional and structural characterization, we cloned, overexpressed, and purified wild-type AdiC and the point mutant AdiC-W293L, which is unable to bind and consequently transport L-arginine. Purified detergent-solubilized AdiC particles were dimeric. Reconstitution experiments yielded two-dimensional crystals of AdiC-W293L diffracting beyond 6 angstroms resolution from which we determined the projection structure at 6.5 angstroms resolution. The projection map showed 10-12 density peaks per monomer and suggested mainly tilted helices with the exception of one distinct perpendicular membrane spanning alpha-helix. Comparison of AdiC-W293L with the projection map of the oxalate/formate antiporter from Oxalobacter formigenes, a member from the major facilitator superfamily, indicated different structures. Thus, two-dimensional crystals of AdiC-W293L yielded the first detailed view of a transport protein from the APC superfamily at sub-nanometer resolution.

Prevalence of nephrolithiasis in patients with ileal bladder substitutes

OBJECTIVES: To assess the effect of ileal bladder substitutes with preservation of the ileocecal valve and distal 25 cm of ileum on nephrolithiasis. METHODS: We reviewed a consecutive series of 518 patients (44 women and 474 men) with ileal orthotopic bladder substitution in whom 55 to 65 cm of ileum was resected but with preservation of the ileocecal valve and distal 25 cm of ileum, to determine prevalence of nephrolithiasis as well as bicarbonate, base excess, creatinine levels, and urinary pH at time of stone diagnosis and 2 years before it. RESULTS: Four male patients with a median age of 66 years (range, 50 to 70 years) developed nephrolithiasis after ileal bladder substitute, for a total of five calculi. The prevalence of nephrolithiasis in this retrospective cohort is thus 1% (5 of 518). They developed the calculi after a median follow-up of 8 years (range, 4 to 17 years). The four patients were diagnosed with calculi at 2.3, 3, 10, 10.3, and 14 years after bladder substitute. Two of the stones were uric acid calculi; the remaining three were calcium oxalate. None of our patients were acidotic or had elevated serum creatinines at time of stone formation. Urinary pH determined once in spontaneously voided urine at the time of stone diagnosis was pH 6.0 for the two uric acid calculi and pH 7.0 for the remaining calculi. CONCLUSIONS: The present study demonstrates a low prevalence of calculi in our cohort.

[Osteoporosis diet]

Bone requires a wide variety of nutrients to develop normally and to maintain itself after growth. Most important--in the sense that bony abnormalities are associated with their deficiencies--are protein, calcium, phosphorus, vitamin D, C and K, zinc, manganese and copper. The nutrients most likely to be deficient in citizens of industrialized countries are calcium and vitamin D. In this review of the current literature about nutritional aspects of osteoporosis, we have focused on factors influencing calcium requirement: the principal interacting nutrients are sodium, protein, caffeine, fiber, oxalate, phytate, and the acid/alkaline ash character of the overall diet. Fiber and caffeine decrease calcium absorption from the gut and typically exert relatively minor effects, while sodium, protein and the acid/alkaline balance of the diet increase urinary excretion of calcium and are of much greater significance for the calcium homeostasis. Alkali buffers, whether vegetables or fruits reverse this urinary calcium loss. As long as accompanied by adequate calcium intake, protein-rich diet is not deleterious to bone: a calcium-to-protein ratio of 20:1 (mg calcium/g protein) is recommended. Whether a nutrition-based therapeutic approach to osteoporosis is feasible in the near future is yet unclear: at least there are some recent promising data from in-vitro as well as from rat studies showing that extracts taken from various vegetables, mainly from the onion family inhibit bone resorption in a dose-dependent manner.

Glutamic acid inducing kidney stone biomimicry by a brushite/gelatin composite

Brushite is a well known precursor of calcium oxalate monohydrate, the main mineral found in kidney stones having a monoclinic crystal structure. Here, we present a new method for biomimicking brushite using a single tube diffusion technique for gel growth. Brushite crystals were grown by precipitation of calcium hydrogen phosphate hydrate in a gelatin/glutamic acid network. They are compared with those produced in gel in the presence of urea. The aggregates were analyzed by scanning electron microscopy (SEM), X-ray diffraction (XRD), infrared spectroscopy (IR) and thermal gravimetric analysis (TGA). SEM revealed a change of morphology by glutamic acid from spherulitic growth to plate-shaped and mushroom-like forms consisting of crystal plates and highly ordered prismatic needles, respectively. Furthermore, brushite crystals grown in a gelatin/glutamic acid/urea network showed needle-shaped morphology being different from other brushite growth forms. The XRD method showed that cell parameters for brushite specimens were slightly larger than those of the American Mineral Society reference structure. The mushroom-like biomimetic composite bears a strong resemblance to the brushite kidney stones which may open up new future treatment options for crystal deposition diseases. Hence, suitable diets from glutamic acid rich foods could be recommended to inhibit and control brushite kidney stones.

Protein profiling of organic stone matrix and urine from dogs with urolithiasis

Two-thirds of the organic matrix in urinary stones consists of proteins. Their relationship to calculogenesis remains controversial with regard to their effect as inhibitors or promoters during stone formation. The purpose of the present study was to determine the differences in peptide and protein pattern between the urine of stone formers (n = 23) and control dogs (n = 12), as well as between organic matrix of different urinary stones (struvite n = 11, calcium oxalate n = 8, uric acid n = 4) using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. Specific differences in protein and peptide profiles were found in the organic matrix of different mineral compositions. Characteristic differences were also found in urinary peptide and protein pattern especially in molecular masses below 20 kDa between affected and healthy dogs. Based on the obtained molecular masses they were in some cases tentatively identified as proteins that are known to be involved in stone formation in humans. The study shows that in dogs, specific-urinary peptides and proteins might be associated with urolithiasis. It indicates the importance to further characterize those proteins for possible diagnostic purposes in prognosis and therapy

Levels of retinol and retinyl esters in plasma and urine of dogs with urolithiasis

Vitamin A (VA) deficiency and Tamm-Horsfall glycoprotein (THP), a protein that binds retinol and retinyl esters in canine urine, might be involved in the pathogenesis of urolithiasis in dogs. In the present study, we assessed levels of retinol, retinyl esters, retinol-binding protein (RBP) and THP in plasma and urine of dogs with a history of urolithiasis (n = 25) compared with clinically healthy controls (n = 18). Plasma retinol concentrations were higher in dogs with uroliths of struvit (P < 0.01), calcium oxalate (P < 0.05), urate (P < 0.01) and cysteine, but there were no differences in the concentrations of plasma RBP and retinyl esters. Excretion of urinary retinol and retinyl esters were tentatively, but not significantly higher in the stone-forming groups, which was accompanied by increased levels of urinary RBP (P < 0.01) and lower excretions in THP (P < 0.01). The results show that VA deficiency may be excluded as a potential cause for canine urolithiasis. However, the occurrence of RBP and a concomitant reduction of THP in urine indicates a disturbed kidney function as cause or consequence of stone formation in dogs.

The Exploitation of Versatile Building Blocks for the Self-Assembly of Novel Molecular Magnets

Using molecular building blocks to self-assemble lattices supporting long-range magnetic order is currently an active area of solid-state chemistry. Consequently, it is the realm of supramolecular chemistry that synthetic chemists are turning to in order to develop techniques for the synthesis of structurally well-defined supramolecular materials. In recent years we have investigated the versatility and usefulness of two classes of molecular building blocks, namely, tris-oxalato transition-metal (M. Pilkington and S. Decurtins, in “Magnetoscience—From Molecules to Materials,” Wiley–VCH, 2000), and octacyanometalate complexes (Pilkington and Decurtins, Chimia 54, 593 (2001)), for applications in the field of molecule-based magnets. Anionic, tris-chelated oxalato building blocks are able to build up two-dimensional honeycomb-layered structural motifs as well as three-dimensional decagon frameworks. The discrimination between the crystallization of the two- or three-dimensional structures relies on the choice of the templating counterions (Decurtins, Chimia 52, 539 (1998); Decurtins et al. Mol. Cryst. Liq. Cryst. 273, 167 (1995); New J. Chem. 117 (1998)). These structural types display a range of ferro, ferri, and antiferromagnetic properties (Pilkington and Decurtins, in “Magnetoscience—From Molecules to Materials”). Octacyanometalate building blocks self-assemble to afford two new classes of cyano-bridged compounds namely, molecular clusters and extended three dimensional networks (J. Larionova et al., Angew. Chem. Int. Ed. 39, 1605 (2000); Pilkington et al., in preparation). The molecular cluster with a MnII9MoV6 core has the highest ground state spin value, S=51/2, reported to-date (Larionova et al., Angew. Chem. Int. Ed. 39, 1605 (2000)). In the high-temperature regime, the magnetic properties are characterized by ferromagnetic intracluster coupling. In the magnetic range below 44 K, the magnetic cluster signature is lost as possibly a bulk behavior starts to emerge. The three-dimensional networks exhibit both paramagnetic and ferromagnetic behavior, since the magnetic properties of these materials directly reflect the electronic configuration of the metal ion incorporated into the octacyanometalate building blocks (Pilkington et al., in preparation). For both the oxalate- and cyanide-bridged materials, we are able to manipulate the magnetic properties of the supramolecular assemblies by tuning the electronic configurations of the metal ions incorporated into the appropriate molecular building blocks (Pilkington and Decurtins, in “Magnetoscience—From Molecules to Materials,” Chimia 54, 593 (2000)).

The Design and Synthesis of Versatile Molecular Building Blocks: Working Towards the Controlled Self-Assembly of Novel Functional Materials

Our research goals are focused on the preparation of novel molecule-based materials that possess specifically designed properties in solution or in the solid state e.g. self-assembly, magnetism, conductivity and spin crossover phenomena. Most of our systems incorporate paramagnetic transition metal ions and the search for new molecule-based magnetic materials is a prominent theme. Specific areas of research include the preparation and study of oxalate based 2D and 3D magnets, probing the versatility of octacyanometalate building blocks as precursors for new molecular magnets, and the preparation of new tetrathiafulvalene (TIF) derivatives for applications in molecular and supramolecular chemistry.

Early renal failure after domino hepatic transplantation using the liver from a compound heterozygous patient with primary hyperoxaluria.

BACKGROUND To cover the shortage of cadaveric organs, new approaches to expand the donor pool are needed. Here we report on a case of domino liver transplantation (DLT) using an organ harvested from a compound heterozygous patient with primary hyperoxaluria (PHO), who underwent combined liver and kidney transplantation. The DLT recipient developed early renal failure with oxaluria. The time to the progression to oxalosis with renal failure in such situations is unknown, but, based on animal data, we hypothesize that calcineurin inhibitors may play a detrimental role. METHODS A cadaveric liver and kidney transplantation was performed in a 52-year-old male with PHO. His liver was used for a 64-year-old patient with a non-resectable, but limited cholangiocarcinoma. RESULTS While the course of the PHO donor was uneventful, in the DLT recipient early post-operative, dialysis-dependent renal failure with hyperoxaluria developed. Histology of a kidney biopsy revealed massive calcium oxalate crystal deposition as the leading aetiological cause. CONCLUSIONS DLT using PHO organs for marginal recipients represents a possible therapeutic approach regarding graft function of the liver. However, it may negatively alter the renal outcome of the recipient in an unpredictable manner, especially with concomitant use of cyclosporin. Therefore, we suggest that, although DLT should be promoted, PHO organs are better excluded from such procedures.

Stand scale variability of topsoil organic matter composition in a high-elevation Norway spruce forest ecosystem

Our knowledge about the effect of single-tree influence areas on the physicochemical properties of the underlying mineral soil in forest ecosystems is still limited. This restricts our ability to adequately estimate future changes in soil functioning due to forest management practices. We studied the stand scale spatial variation of different soil organic matter species investigated by 13C NMR spectroscopy, lignin phenol and neutral sugar analysis under an unmanaged mountainous high-elevation Norway spruce (Picea abies L.) forest in central Europe. Multivariate geostatistical approaches were applied to relate the spatial patterns of the different soil organic matter species to topographic parameters, bulk density, oxalate- and dithionite-extractable iron, pH, and the impact of tree distribution. Soil samples were taken from the mineral top soil. Generally, the stand scale distribution patterns of different soil organic matter compounds could be divided into two groups: Those compounds, which were significantly spatially correlated with topography/altitude and those with small scale spatial pattern (range ≤ 10 m) that was closely related to tree distribution. The concentration of plant-derived soil organic matter components, such as lignin, at a given sampling point was significantly spatially related to the distance of the nearest tree (p ≤ 0.05). In contrast, the spatial distribution of mainly microbial-derived compounds (e.g. galactose and mannose) could be attributed to the dominating impact of small-scale topography and the contribution of poorly crystalline iron oxides that were significantly larger in the central depression of the study site compared to crest and slope positions. Our results demonstrate that topographic parameters dominate the distribution of overall topsoil organic carbon (OC) stocks at temperate high-elevation forest ecosystems, particularly in sloped terrain. However, trees superimpose topography-controlled OC biogeochemistry beneath their crown by releasing litter and changing soil conditions in comparison to open areas. This may lead to distinct zones with different mechanisms of soil organic matter degradation and also stabilization in forest stands.