Silicon and phosphorus linkage with iron via oxygen in the amorphous matrix of Gallionella ferruginea stalks

Bacterial species belonging to the genus Gallionella are Fe-oxidizing bacteria that produce uniquely twisted extracellular stalks consisting of iron-oxide-encrusted inorganic/organic fibers in aquatic environments. This paper describes the degree of crystallinity of Gallionella stalks and the chemical linkages of constituent elements in the stalk fibers. Transmission electron microscopy revealed that the matrix of the fiber edge consisted of an assembly of primary particles of approximately 3 nm in diameter. Scanning transmission electron microscopy revealed the rough granular surfaces of the fibers, which reflect the disordered assembly of the primary particles, indicating a high porosity and large specific surface area of the fibers. This may provide the surface with broader reactive properties. X-ray diffractometry, selected-area electron diffraction, and high-resolution transmission electron microscopy together showed that the primary particles had an amorphous structure. Furthermore, energy-dispersive X-ray analysis and Fourier transform infrared spectroscopy detected the bands characteristic of the vibrational modes assigned to O-H, Fe-O-H, P-O-H, Si-O-H, Si-O-Fe, and P-O-Fe bonds in the stalks, suggesting that the minor constituent elements P and Si could affect the degree of crystallinity of the fibers by linking with Fe via O. This knowledge about the mutual associations of these elements provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.     

The ultrastructure of chemolithoautotrophic Gallionella ferruginea and Thiobacillus ferrooxidans as revealed by chemical fixation and freeze-etching

By using sodium thioglycolate to dissolve the high amount of excreted stalk material in axenic cultures of the chemolithoautotrophic iron bacterium Gallionella ferruginea, the ultrastructure of Gallionella cells from pure cell suspensions could be studied without any loss of viability or disturbance by dense ferric stalk fibers, and compared with Thiobacillus ferrooxidans, also grown chemolithoautotrophically with ferrous iron as energy source. Both organisms were chemically fixed or freeze-etched. Particular structural differences between these iron-bacteria could be ascertained. G. ferruginea possesses intracytoplasmic membranes and soluble d-ribulose-1,5-bisphosphate-carboxylase, whereas T. ferrooxidans contains carboxysomes but no intracytoplasmic membranes; Gallionella forms poly--hydroxybutyrate and glycogen as storage material; T. ferrooxidans produces only glycogen. Both organisms also differ from each other with respect to the freeze fracture behaviour of the cell envelope layers. Whereas the cells of T. ferrooxidans exhibit a characteristic double cleavage, exposing the plasmic fracture face and exoplasmic fracture face of the outer membrane and cytoplasmic membrane, the exceptionally thin multilayered cell envelope of G. ferruginea revealed a particularly intimate association between the layers, resulting in a visualisation of the supramolecular organisation of only the inner fracture face of the cytoplasmic membrane. The results are discussed predominantly in relation to the extremely distinct environments of both organisms.     

Atomistic simulation of the sol formation during synthesis of organic/inorganic hybrid materials

Atomistic modelling was employed to investigate interactions between the precursors used in preparation of organic/inorganic polymer hybrids. Three molecular systems composed of different kinds of organofunctionalised silanes and an organic polymer in aqueous solution have been simulated, representing various model stages of the hydrolysis reaction during the sol/gel processing. The equilibrium configurations obtained by Molecular Dynamics were analysed in order to elucidate the extent of the hydrogen bonding network and clustering of components within the systems. Diffusion coefficients were obtained to estimate the mobility of the components and the stability of the molecular associations. It has been concluded that the molecular mechanism of the initial stages of the sol/gel process used for preparation of the organic/inorganic hybrids involves clustering of the organofunctionalysed inorganic components as a first step and then progressive hydrolysis as consequent steps. The organic polymer component plays a role of the cluster "wrap" and thus prevents the particles from unlimited growth and precipitation from the solution.     

Autophagy regulation by inorganic,organic, and organic/inorganic hybrid nanoparticles: Organelle damage,regulation factors,and potential pathways

The rapid development of nanotechnology requires a more thorough understanding of the potential health effects caused by nanoparticles (NPs). As a programmed cell death, autophagy is one of the biological effects induced by NPs, which maintain intracellular homeostasis by degrading damaged organelles and removing aggregates of defective proteins through lysosomes. Currently, autophagy has been shown to be associated with the development of several diseases. A significant number of research have demonstrated that most NPs can regulate autophagy, and their regulation of autophagy is divided into induction and blockade. Studying the autophagy regulation by NPs will facilitate a more comprehensive understanding of the toxicity of NPs. In this review, we will illustrate the effects of different types of NPs on autophagy, including inorganic NPs, organic NPs, and organic/inorganic hybrid NPs. The potential mechanisms by which NPs regulate autophagy are highlighted, including organelle damage, oxidative stress, inducible factors, and multiple signaling pathways. In addition, we list the factors influencing NPs-regulated autophagy. This review may provide basic information for the safety assessment of NPs.     

Growth of Iron-Oxidizing Bacteria Gallionella ferruginea and Leptothrix cholodnii in Oligotrophic Environments: Ca,Mg, and C as Limiting Factors and G. ferruginea Necromass as C-Source

Abstract

Iron-oxidizing bacteria (FeOB) can successively populate low-nutrient aquatic environments and adapt to a broad concentration range of alkaline earth metals, with optimum conditions widely differing from one species to another. For the most abundant known FeOB genera Gallionella and Leptothrix, there is a lack of reports on substrate affinity for calcium and magnesium and necromass assimilability. Single nutrient and combined affinity for Ca and Mg of a wild Gallionella ferruginea isolate and a Leptothrix cholodnii strain as well as growth of heterotrophic L. cholodnii on necromass of autotrophic G. ferruginea were determined by cell density measurements. G. ferruginea responds with Monod-shaped preferences and thus favors waters rich in Ca and Mg. Maximum growth occurred at Ca concentrations five times above those of commonly used modified mineral Wolfe’s medium. L. cholodnii showed a Monod-shaped preference in the low concentration range and an inhibitory response to increasing hardness: concentrations >2?mM Ca or >0.6?mM Mg allow only 50 or 75%, respectively, of maximum specific cell densities. Considering the concentration range with a Monod-shaped response (for L. cholodnii only lower concentration range), both FeOB show a type I independent colimitation for Ca and Mg with lower requirements of Mg than Ca. On a C-limited medium containing G. ferruginea necromass as the only C-source, L. cholodnii cell counts were higher by two orders of magnitude compared to pyruvate medium. Thus, the necromass may serve as a primary C-source for heterotrophic FeOB and other heterotrophic bacteria with technical and economical relevance.     

Synthesis and characterization of novel organic/inorganic hybrid material with short peptide brushes generated on the surface

A novel route to synthesize an organic/inorganic hybrid material containing short peptide chains attached on the surface (e.g., oligo(S-benzyl-L-cysteine)) was developed. Poly[N-(beta-aminoethylene)acrylamide] (PAEA) adsorbed onto silica particles surface (main diameter between 15 and 40 microm) was irreversibly fixed by the reaction between the accessible primary amino groups of the PAEA and 3,3',4,4'-benzophenone tetracarboxylic dianhydride (BTCDA). After the deposition of PAEA from a salt-free aqueous solution onto microporous silica particles and stabilization by a cross-linking reaction with BTCDA, five repeated coupling reactions of boc-S-benzyl-L-cysteine were performed. Changes in surface charges during the polyelectrolyte adsorption were studied by electrokinetic measurements. The cross-linking degree was a tool to control the surface charge of the PAEA/silica hybrid particles. X-ray photoelectron spectroscopy (XPS) was employed to obtain information about the amount of the adsorbed polyelectrolyte as well as the amount of the amino acid S-benzyl-L-cysteine that was covalently bound to the hybrid particle surface and polycondensed there. In the XPS spectra, the sulfur peaks (S 2p3/2, S 2p1/2, and S 2s) qualitatively and quantitatively indicated the presence of the amino acid on the hybrid material surface. After each step of coupling, the intensity of the S 2s peak was increased by a constant value. This indicates the oligopeptide growth. The novel hybrid material offers possibilities for subsequent derivatization reactions such as coupling other amino acids, peptides, obtaining hybrid ion exchange resins, and so forth.     

Synthesis and characterization of three novel inorganic/organic hybrid materials based on polyoxomolybdate clusters: an investigation into the structural consequences of steric effect of the organoimine ligands

Hydrothermal means have been employed in isolating three new compounds, [Cu₂Mo₄O₁₃(C₅H₆N₂)₂·3H₂O] (1), [Cu₂Mo₄O₁₃(C₆H₈N₂)₂] (2) and [CuMo₆O₁₉(C₁₈H₂₄N₂)] (3) from mixtures of CuNO₃/CuSO₄, the corresponding ligands (methylpyrazine, dimethylpyrimidine and ditertiarybutyl-2,2′-bipyridine) and MoO₃ at temperatures from 120 to 160 °C. The structures of these compounds range from three-dimensional in the case of 1 to ‘zero-dimensional’ or molecular in the case of 3 in accordance with the extent of steric hindrance presented by the ligand.     

Benefits associated with the stalk of Gallionella ferruginea,evaluated by comparison of a stalk-forming and a non-stalk-forming strain and biofilm studies in situ

Factors that regulate and induce stalk formation by the iron-oxidizing and stalk-forming bacterium Gallionella ferruginea were studied in laboratory cultures and in situ. A stalk-forming strain, Sta⁺, and a non-stalk-forming strain, Sta^-, were used for comparative studies of the benefits associated with the stalk. Two different growth media were used: a ferrous sulfide medium (FS-medium), with slow oxidation of iron giving high concentrations of toxic oxygen radicals and a ferrous carbonate medium (FC-medium), with fast iron oxidation giving low concentration of the toxic oxygen radicals. It was found that Sta⁺ cells grown in the FS-medium survived 3 weeks longer than Sta^- cells grown in the FS-medium. When each strain was grown in the FC-medium, the Sta^- cells had an advantage and survived 8 weeks longer than the Sta⁺ cells. No difference in survival was found for Sta⁺ cells grown in FS-medium compared to growth in FC-medium. In laboratory cultures, the average stalk length per cell values were 7–2.5 times higher (92 h and 150–300 h growth, respectively) in a medium with 620 m iron than in a medium with 290 m iron. Gallionella ferruginea Sta⁺ outcompeted Sta^- cells when inoculated as mixed populations in FC-medium. It has previously been suggested that stalk formation in vitro is induced by oxygen. To confirm this observation, biofilm development in natural waters was studied in two wells, one with trace amounts of oxygen (LH) and one without (TH). A dense biofilm developed on surfaces exposed to flowing well LH water, but no biofilm developed in well TH. Stalks were formed in water samples from both wells when allowed to make contact with air. This work demonstrates for the first time that the stalk has a protecting function against the toxic oxygen radicals formed during the chemical iron oxidation. It also shows that it is the oxidation rate of the ferrous iron and not its concentration that is harmful to the cells. The stalk gives G. ferruginea a unique possibility to colonize and survive in habitats with high contents of iron, inaccessible for bacteria without a defense system against the oxidation of iron. Correspondence to: L. Hallbeck     

New immobilization method for enzyme stabilization involving a mesoporous material and an organic/inorganic hybrid gel

Horseradish peroxidase (HRP) was immobilized in a mesoporous material (folded sheets mesoporous materials, FSM-16) and then entrapped in organic/inorganic hybrid gel comprising various molar ratios of dimethyldimethoxysilane (DMDMOS)/tetramethoxysilane (TMOS). When pore size of FSM-16 materials is much larger than the diameters of horseradish peroxidase (HRP), the residual enzymatic activity after thermal treatment (70°C, 60 min) increased from 73 to 99%, and the oxidative conversion yield of 1,2-diaminobenzene in an organic solvent increased from 59 to 79% after 4 h and the level of leakage of immobilized HRP decreased from 6 to 1.5% on washing by secondary hybrid gel entrapment comprising a molar ratio of DMDMOS/TMOS=1:3. When pore size of FSM-16 materials just matches the diameter of the enzyme, the conversion yield in an organic solvent and the level of leakage of immobilized HRP did not change so much.     

Program for the visualization of inorganic crystals

A program has been developed to manipulate images of inorganic structures and organic molecules on ALLIANT VFX/40 using the PHIGS + standard. This article reviews algorithms for representing spheres, ellipsoids and various polyhedrons involved in inorganic chemistry. The program also supports the display and manipulation of animated frames from dynamics simulations. Many graphical facilities have been implemented and we discuss their interest in the field of molecular graphics.     

Covalent structural analysis of yeast inorganic pyrophosphatase.

The present paper describes the amino acid sequence analysis of the internal and COOH-terminal cyanogen bromide fragments of yeast inorganic pyrophosphatase (Sterner, R., Noyes, C., and Heinrikson, R.L. (1974) Biochemistry 13, 91-99). This information coupled with that derived from earlier structural studies of the enzyme (Sterner, R., AND Heinrikson, R.L. (1975) Arch. Biochem. Biophys. 165, 693-703) provides the complete covalent structure of the pyrophosphatase subunit. The majority of the sequence data was derived from automated Edman degradation of the intact cyanogen bromide fragments and the large tryptic peptides obtained from citraconylated derivates in which cleavages were restricted to arginyl residues. The structural determination was completed by analysis of tryptic and chymotryptic peptides from the decitraconylated fragments. The monomer peptide chain contains 285 amino acid residues and the molecular weight calculated from the sequence analysis is 32,042.     

Conductometric immunoassay for interleukin-6 in human serum based on organic/inorganic hybrid membrane-functionalized interface

Various sensor-based immunoassay methods have been extensively developed for the detection of interleukin-6 (IL6), but most often exhibit low detection signals and low detection sensitivity, and are unsuitable for routine use. The aim of this work is to develop a simple and sensitive conductometric immunoassay for IL6 in human serum by using an organic/inorganic hybrid membrane-functionalized interface. Initially, thionine-bound 3,4,9,10-perylenetetracarboxylic acid was doped into colloidal alumina, then nanogold particles were immobilized onto the thionine surface, and then horseradish peroxidase-labeled anti-IL6 antibodies were conjugated on the nanogold surface. The organic/inorganic hybrid membrane provides a good microenvironment for the immobilization of biomolecules, enhanced the surface coverage of protein, and improved the sensitivity of the immunosensor. The performance and factors influencing the performance of the immunosensor were evaluated. The detection is based on the change in local conductivity before and after the antigen-antibody interaction in 0.02 M phosphate buffer solution (pH 6.8) containing 50 μM H₂O₂, 0.01 M KI and 0.15 M NaC1. Under optimal conditions, the proposed immunosensor exhibited a wide linear range from 25 to 400 pg/ml towards IL6 with a relatively low detection limit of 5 pg/ml (S/N = 3). The stability, reproducibility and precision of the immunosensor were acceptable. 37 serum specimens were assayed by the developed immunosensor and standard enzyme-linked immunosorbent assay, respectively, and the results obtained were almost consistent. More importantly, the detection methodology provides a promising approach for other proteins or biosecuritys.     

A comparison of organic and inorganic nitrates/nitrites

Although both organic and inorganic nitrates/nitrites mediate their principal effects via nitric oxide, there are many important differences. Inorganic nitrate and nitrite have simple ionic structures and are produced endogenously and are present in the diet, whereas their organic counterparts are far more complex, and, with the exception of ethyl nitrite, are all medicinally synthesised products. These chemical differences underlie the differences in pharmacokinetic properties allowing for different modalities of administration, particularly of organic nitrates, due to the differences in their bioavailability and metabolic profiles. Whilst the enterosalivary circulation is a key pathway for orally ingested inorganic nitrate, preventing an abrupt effect or toxic levels of nitrite and prolonging the effects, this is not used by organic nitrates. The pharmacodynamic differences are even greater; while organic nitrates have potent acute effects causing vasodilation, inorganic nitrite's effects are more subtle and dependent on certain conditions. However, in chronic use, organic nitrates are considerably limited by the development of tolerance and endothelial dysfunction, whereas inorganic nitrate/nitrite may compensate for diminished endothelial function, and tolerance has not been reported. Also, while inorganic nitrate/nitrite has important cytoprotective effects against ischaemia-reperfusion injury, continuous use of organic nitrates may increase injury. While there are concerns that inorganic nitrate/nitrite may induce carcinogenesis, direct evidence of this in humans is lacking. While organic nitrates may continue to dominate the therapeutic arena, this may well change with the increasing recognition of their limitations, and ongoing discovery of beneficial effects and specific advantages of inorganic nitrate/nitrite.     

MolMovDB: analysis and visualization of conformational change and structural flexibility

The Database of Macromolecular Movements (http://MolMovDB.org) is a collection of data and software pertaining to flexibility in protein and RNA structures. The database is organized into two parts. Firstly, a collection of 'morphs' of solved structures representing different states of a molecule provides quantitative data for flexibility and a number of graphical representations. Secondly, a classification of known motions according to type of conformational change (e.g. 'hinged domain' or 'allosteric') incorporates textual annotation and information from the literature relating to the motion, linking together many of the morphs. A variety of subsets of the morphs are being developed for use in statistical analyses. In particular, for each subset it is possible to derive distributions of various motional quantities (e.g. maximum rotation) that can be used to place a specific motion in context as being typical or atypical for a given population. Over the past year, the database has been greatly expanded and enhanced to incorporate new structures and to improve the quality of data. The 'morph server', which enables users of the database to add new morphs either from their own research or the PDB, has also been enhanced to handle nucleic acid structures and multi-chain complexes.     

Effects of organic and inorganic polyamine cations on the structure of human serum albumin

The presence of several high affinity binding sites on human serum albumin (HSA) makes it a possible target for many organic and inorganic molecules. Organic polyamines are widely distributed in living cells and their biological roles have been associated with their physical and chemical interactions with proteins, nucleic acids, and lipids. This study is designed to examine the effects of spermine, spermidine, putrescine, and cobalt [Co(III)]-hexamine cations on the solution structure of HSA using Fourier transform IR, UV-visible, and circular dichroism (CD) spectroscopic methods. The spectroscopic results show that polyamine cations are located along the polypeptide chains with no specific interaction. The order of perturbations is associated with the number of positive charges of the polyamine cation: spermine > Co(III)-hexamine > spermidine > putrescine. The overall binding constants are 1.7 x 10(4), 1.1 x 10(4), 5.4 x 10(3), and 3.9 x 10(3)M(-1), respectively. The protein conformation is altered (IR and CD data) with reductions of alpha helices from 60 to 55% for free HSA to 50-40% and with increases of beta structures from 22 to 15% for free HSA to 33-23% in the presence of polyamine cations.     

Ti-Cp functionalization by deposition of organic/inorganic silica nanoparticles

In orthopaedics and cardiovascular surgery, titanium has become the metal of choice, due to its excellent mechanical properties and biocompatibility. In many surgical operations, chemicals and/or biomolecules (such as antibiotics or growth factors) are used in conjunction with prostheses, so as to avoid or stimulate targeted biological events. Often, immobilization instead of release of such molecules is preferred to optimize their effects, thus avoiding ectopic transformations. A versatile method for the functionalization of pure Ti is shown here, which allows the covalent immobilization of polypeptides. In order to avoid the hydrolysable Ti-O-Si bond found in directly silanized Ti, we use organic/inorganic silica colloids, derived from commercially available 25 nm Ludox silica nanoparticles. Prior to deposition onto Ti-Cp, the silica nanoparticles are functionalized by a propylsemicarbazide moiety by silanization. After spin-coating onto the Ti substrates, the colloids were shown by SEM to form a uniform layer, and to be very strongly adsorbed; the reactivity of the supported semicarbazide (Sc) functionalities being maintained. Chemoselective reaction of semicarbazide groups on the surface with aldehyde moieties present on the polypeptide of interest was chosen in this work due to its efficiency, to its compatibility with the proteinogenic amino acids and in particular cystein and to the use of mild experimental conditions. Aldehyde groups are also easily introduced onto polypeptides by synthesis, oxidation of N-terminal Ser residue or polysaccharide moieties of glycoproteins. Biological assays with MC3T3-E1 osteoblasts revealed an excellent cytocompatibility as shown by the assessment of cell viability, vitality and morphology.     

辣椒秸秆对滇黄精及其根际微生物群落的影响

【背景】根际微生物直接或间接影响药用植物的生长发育和品质形成,通过改善土壤理化性质来提高益生菌多样性,促进植物病虫害的生物防治和提高植物产量、品质。【目的】探究栽培土壤中添加辣椒秸秆对滇黄精生长质量和根际细菌群落结构的影响。【方法】收集种植滇黄精无处理土壤(CK)、添加腐熟辣椒秸秆改良肥土壤(X)、添加商品复合肥土壤(Y)的根际附着土样,测量滇黄精生长质量,并通过高通量测序对其根际细菌群落进行功能和结构解析。【结果】X处理的滇黄精生长质量显著优于CK处理,而且与Y处理无显著差异,其中多糖含量和根系活力明显提高,分别较Y处理提高了24.48%和56.98%。同时显著增加了种植土壤的有机质和孔隙度。在根际细菌群落分析中,相对丰度最高的是变形菌门(Proteobacteria),占比分别为CK的34.8%、X的34.6%、Y的41.3%,其中Y处理显著高于其他处理。其次是绿弯菌门(Chloroflexi),X处理为10.2%,高于CK处理(8.7%)和Y处理(5.8%)。t检验中秸秆处理蓝细菌门Cyanobacteria丰度显著高于对照,芽单胞菌门(Gemmatimonadetes)和脱硫杆...     

Hydrothermal synthesis and crystal structure of one-dimensional organic/inorganic hybrid material: [Mo4O12(2,2′-bpy)3]n

A new polyoxomolybdenum compound [Mo₄O₁₂(2,2′-bpy)₃]_n (1) (2,2′-bpy = 2,2′-bipyridine) has been hydrothermally synthesized and characterized by elemental analysis, IR spectroscopy, TG analysis, and single crystal X-ray diffraction. The solid state structure is a 1D chain with a repeat unit of three corner-sharing {MoO₄N₂} octahedra and one {MoO₄} tetrahedron.     

A novel inorganic and organic mixture cations templated indium phosphate: Synthesis and crystal structure

A novel mixture cations templated indium phosphates, Li(C₂N₂H₁₀)[In₂(HPO₄)₃(PO₄)], has been synthesized under mild hydrothermal conditions and characterized by elemental analysis and FT-IR spectrum. The crystal structure of title compound was determined by single crystal X-ray diffraction data. It belongs to monoclinic, space group P2/n with unit cell dimension a = 9.4692(13) Å, b = 9.1622(12) Å, c = 9.7063(14) Å, β = 117.5620(10)°. Its structure is characterized as a three-dimensional open-framework with 8-membered ring channels along a axis, where the inorganic lithium cation and organic double-protonated ethylenediamine cation are located and interact with the framework both electrostatically and via hydrogen bonds of N-H?O.