Analysis of red and yellow ochre samples from Clearwell Caves and Catalhoyuk by vibrational spectroscopy and other techniques

Ochre samples excavated from the neolithic site at Qatalhoyuk, Turkey have been compared with "native" ochres from Clearwell Caves, UK using infrared spectroscopy backed up by Raman spectroscopy, scanning electron microscopy (with energy-dispersive X-rays (EDX) analysis), powder X-ray diffraction, diffuse reflection UV-Vis and atomic absorption spectroscopies. For the Clearwell Caves ochres, which range in colour from yellow-orange to red-brown, it is shown that the colour is related to the nature of the chromophore present and not to any differences in particle size. The darker red ochres contain predominantly haematite while the yellow ochre contains only goethite. The ochres from Qatalhoyuk contain only about one-twentieth of the levels of iron found in the Clearwell Caves ochres. The iron oxide pigment (haematite in all cases studied here) has been mixed with a soft lime plaster which also contains calcite and silicate (clay) minerals. (C) 2003 Elsevier B.V. All rights reserved.

Iron Uptake and Homeostasis in Microorganisms

Preface. Iron is considered to be a minor element employed, in a variety of forms, by nearly all living organisms. In some cases, it is utilised in large quantities, for instance for the formation of magnetosomes within magnetotactic bacteria or during use of iron as a respiratory donor or acceptor by iron oxidising or reducing bacteria. However, in most cases the role of iron is restricted to its use as a cofactor or prosthetic group assisting the biological activity of many different types of protein. The key metabolic processes that are dependent on iron as a cofactor are numerous; they include respiration, light harvesting, nitrogen fixation, the Krebs cycle, redox stress resistance, amino acid synthesis and oxygen transport. Indeed, it is clear that Life in its current form would be impossible in the absence of iron. One of the main reasons for the reliance of Life upon this metal is the ability of iron to exist in multiple redox states, in particular the relatively stable ferrous (Fe2+) and ferric (Fe3+) forms. The availability of these stable oxidation states allows iron to engage in redox reactions over a wide range of midpoint potentials, depending on the coordination environment, making it an extremely adaptable mediator of electron exchange processes. Iron is also one of the most common elements within the Earth’s crust (5% abundance) and thus is considered to have been readily available when Life evolved on our early, anaerobic planet. However, as oxygen accumulated (the ‘Great oxidation event’) within the atmosphere some 2.4 billion years ago, and as the oceans became less acidic, the iron within primordial oceans was converted from its soluble reduced form to its weakly-soluble oxidised ferric form, which precipitated (~1.8 billion years ago) to form the ‘banded iron formations’ (BIFs) observed today in Precambrian sedimentary rocks around the world. These BIFs provide a geological record marking a transition point away from the ancient anaerobic world towards modern aerobic Earth. They also indicate a period over which the bio-availability of iron shifted from abundance to limitation, a condition that extends to the modern day. Thus, it is considered likely that the vast majority of extant organisms face the common problem of securing sufficient iron from their environment – a problem that Life on Earth has had to cope with for some 2 billion years. This struggle for iron is exemplified by the competition for this metal amongst co-habiting microorganisms who resort to stealing (pirating) each others iron supplies! The reliance of micro-organisms upon iron can be disadvantageous to them, and to our innate immune system it represents a chink in the microbial armour, offering an opportunity that can be exploited to ward off pathogenic invaders. In order to infect body tissues and cause disease, pathogens must secure all their iron from the host. To fight such infections, the host specifically withdraws available iron through the action of various iron depleting processes (e.g. the release of lactoferrin and lipocalin-2) – this represents an important strategy in our defence against disease. However, pathogens are frequently able to deploy iron acquisition systems that target host iron sources such as transferrin, lactoferrin and hemoproteins, and thus counteract the iron-withdrawal approaches of the host. Inactivation of such host-targeting iron-uptake systems often attenuates the pathogenicity of the invading microbe, illustrating the importance of ‘the battle for iron’ in the infection process. The role of iron sequestration systems in facilitating microbial infections has been a major driving force in research aimed at unravelling the complexities of microbial iron transport processes. But also, the intricacy of such systems offers a challenge that stimulates the curiosity. One such challenge is to understand how balanced levels of free iron within the cytosol are achieved in a way that avoids toxicity whilst providing sufficient levels for metabolic purposes – this is a requirement that all organisms have to meet. Although the systems involved in achieving this balance can be highly variable amongst different microorganisms, the overall strategy is common. On a coarse level, the homeostatic control of cellular iron is maintained through strict control of the uptake, storage and utilisation of available iron, and is co-ordinated by integrated iron-regulatory networks. However, much yet remains to be discovered concerning the fine details of these different iron regulatory processes. As already indicated, perhaps the most difficult task in maintaining iron homeostasis is simply the procurement of sufficient iron from external sources. The importance of this problem is demonstrated by the plethora of distinct iron transporters often found within a single bacterium, each targeting different forms (complex or redox state) of iron or a different environmental condition. Thus, microbes devote considerable cellular resource to securing iron from their surroundings, reflecting how successful acquisition of iron can be crucial in the competition for survival. The aim of this book is provide the reader with an overview of iron transport processes within a range of microorganisms and to provide an indication of how microbial iron levels are controlled. This aim is promoted through the inclusion of expert reviews on several well studied examples that illustrate the current state of play concerning our comprehension of how iron is translocated into the bacterial (or fungal) cell and how iron homeostasis is controlled within microbes. The first two chapters (1-2) consider the general properties of microbial iron-chelating compounds (known as ‘siderophores’), and the mechanisms used by bacteria to acquire haem and utilise it as an iron source. The following twelve chapters (3-14) focus on specific types of microorganism that are of key interest, covering both an array of pathogens for humans, animals and plants (e.g. species of Bordetella, Shigella, , Erwinia, Vibrio, Aeromonas, Francisella, Campylobacter and Staphylococci, and EHEC) as well as a number of prominent non-pathogens (e.g. the rhizobia, E. coli K-12, Bacteroides spp., cyanobacteria, Bacillus spp. and yeasts). The chapters relay the common themes in microbial iron uptake approaches (e.g. the use of siderophores, TonB-dependent transporters, and ABC transport systems), but also highlight many distinctions (such as use of different types iron regulator and the impact of the presence/absence of a cell wall) in the strategies employed. We hope that those both within and outside the field will find this book useful, stimulating and interesting. We intend that it will provide a source for reference that will assist relevant researchers and provide an entry point for those initiating their studies within this subject. Finally, it is important that we acknowledge and thank wholeheartedly the many contributors who have provided the 14 excellent chapters from which this book is composed. Without their considerable efforts, this book, and the understanding that it relays, would not have been possible. Simon C Andrews and Pierre Cornelis

Introduction of 4-chloro-alpha-cyanocinnamic acid liquid matrices for high sensitivity UV-MALDI MS

Matrix-assisted laser desorption/ionization (MALDI) is a key ionization technique in mass spectrometry (MS) for the analysis of labile macromolecules. An important area of study and improvements in relation to MALDI and its application in high-sensitivity MS is that of matrix design and sample preparation. Recently, 4-chloro-alpha-cyanocinnamic acid (ClCCA) has been introduced as a new rationally designed matrix and reported to provide an improved analytical performance as demonstrated by an increase in sequence coverage of protein digests obtained by peptide mass mapping (PMM) (Jaskolla, T. W.; et al. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 12200-12205). This new matrix shows the potential to be a superior alternative to the commonly used and highly successful alpha-cyano-4-hydroxycinnamic acid (CHCA). We have taken this design one step further by developing and optimizing an ionic liquid matrix (ILM) and liquid support matrix (LSM) using ClCCA as the principle chromophore and MALDI matrix compound. These new liquid matrices possess greater sample homogeneity and a simpler morphology. The data obtained from our studies show improved sequence coverage for BSA digests compared to the traditional CHCA crystalline matrix and for the ClCCA-containing ILM a similar performance to the ClCCA crystalline matrix down to 1 fmol of BSA digest prepared in a single MALDI sample droplet with current sensitivity levels in the attomole range. The LSMs show a high tolerance to contamination such as ammonium bicarbonate, a commonly used buffering agent.

Microwave activation of the electro-oxidation of glucose in alkaline media

The oxidation of glucose is a complex process usually requiring catalytically active electrode surfaces or enzyme modified electrodes. In this study the effect of high intensity microwave radiation on the oxidation of glucose in alkaline solution at Au, Cu, and Ni electrodes is reported. Calibration experiments with the Fe(CN)(6)(3-/4-) redox system in aqueous 0.1 M NaOH indicate that strong thermal effects occur at both 50 and 500 mu m diameter electrodes with temperatures reaching 380 K. Extreme mass transport effects with mass transport coefficients of k(mt) > 0.01 m s(-1) (or k(mt) > 1.0 cm s(-1)) are observed at 50 mu m diameter electrodes in the presence of microwaves. The electrocatalytic oxidation of glucose at 500 mu m diameter Au, Cu, or Ni electrodes immersed in 0.1 M NaOH and in the presence of microwave radiation is shown to be dominated by kinetic control. The magnitude of glucose oxidation currents at Cu electrodes is shown to depend on the thickness of a pre-formed oxide layer. At 50 mu m diameter Au, Cu, or Ni electrodes microwave enhanced current densities are generally higher, but only at Au electrodes is a significantly increased rate for the electrocatalytic oxidation of glucose to gluconolactone observed. This rate enhancement appears to be independent of temperature but microwave intensity dependent, and therefore non-thermal in nature. Voltammetric currents observed at Ni electrodes in the presence of microwaves show the best correlation with glucose concentration and are therefore analytically most useful.

Electrochemical determination of plant-derived leuco-indigo after chemical reduction by glucose

Electrochemical determination of redox active dye species is demonstrated in indigo samples contaminated with high levels of organic and inorganic impurities. The use of a hydrodynamic electrode system based on a vibrating probe (250 Hz, 200 mu m lateral amplitude) allows time-independent diffusion controlled signals to be enhanced and reliable concentration data to be obtained under steady state conditions at relatively fast scan rates up to 4 V s-1In this work the indigo content of a complex plant-derived indigo sample (dye content typically 30%) is determined after indigo is reduced by addition of glucose in aqueous 0.2 M NaOH. The soluble leuco-indigo is measured by its oxidation response at a vibrating electrode. The vibrating electrode, which consisted of a laterally vibrating 500 mu m diameter gold disc, is calibrated with Fe(CN)(6) 3-/4- in 0.1 M KCl and employed for indigo determination at 55, 65, and 75 C in 0.2 M NaOH. Determinations of the indigo content of 25 different samples of plant-derived indigo are compared with those obtained by conventional spectrophotometry. This comparison suggests a significant improvement by the electrochemical method, which appears to be less sensitive to impurities.

Electrochemical and sonoelectrochemical monitoring of indigo reduction by glucose

The reduction of indigo (dispersed in water) to leuco-indigo (dissolved in water) is an important industrial process and investigated here for the case of glucose as an environmentally benign reducing agent. In order to quantitatively follow the formation of leuco-indigo two approaches based on (i) rotating disk voltammetry and (ii) sonovoltammetry are developed. Leuco-indigo, once formed in alkaline solution, is readily monitored at a glassy carbon electrode in the mass transport limit employing hydrodynamic voltammetry. The presence of power ultrasound further improves the leuco-indigo determination due to additional agitation and homogenization effects. While inactive at room temperature, glucose readily reduces indigo in alkaline media at 65 degrees C. In the presence of excess glucose, a surface dissolution kinetics limited process is proposed following the rate law d eta(leuco-indigo)/dt = k x c(OH-) x S-indigo where eta(leuco-indigo) is the amount of leuco-indigo formed, k = 4.1 x 10(-9) m s(-1) (at 65 degrees C, assuming spherical particles of I gm diameter) is the heterogeneous dissolution rate constant,c(OH-) is the concentration of hydroxide, and Sindigo is the reactive surface area. The activation energy for this process in aqueous 0.2 M NaOH is E-A = 64 U mol(-1) consistent with a considerable temperature effects. The redox mediator 1,8-dihydroxyanthraquinone is shown to significantly enhance the reaction rate by catalysing the electron transfer between glucose and solid indigo particles. (c) 2006 Elsevier Ltd. All fights reserved.

Extracellular disulfide exchange and the regulation of cellular function

An emerging concept is that disulfide bonds can act as a dynamic scaffold to present mature proteins in different conformational and functional states on the cell surface. Two examples are the conversion of the receptor, integrin a alpha(IIb)beta(3), from a low affinity to a high affinity state, and the interaction of CD4 receptor with the HIV-1 envelope glycoprotein gp120 to promote virus-cell fusion. In both of these cases there is a remodeling of the protein disulfide bonding pattern. The formation and rearrangement of disulfide bonds is modulated by a family of enzymes known as the thiol isomerases, which include protein disulfide isomerase (PDI), ERp5, ERp57, and ERp72. While these enzymes were reported originally to be restricted in location to the endoplasmic reticulum, in some cells thiol isomerases are found on the cell surface. This may indicate a wider role for these enzymes in cell function. In platelets it has been shown that reagents that react with cell surface sulfhydryl groups are capable of blocking a number of functional responses, including integrin-mediated aggregation, adhesion, and granule secretion. Furthermore, the use of function blocking antibodies to either PDI or ERp5 causes inhibition of these functional responses. This review summarizes current knowledge of the extracellular regulation of disulfide exchange and the implications of this in the regulation of cell function.

A rotating disc voltammetry study of the 1,8-dihydroxyanthraquinone mediated reduction of colloidal indigo

Colloidal indigo is reduced to an aqueous solution of leuco-indigo in a mediated two-electron process converting the water-insoluble dye into the water-soluble leuco form. The colloidal dye does not interact directly with the electrode surface, and to employ an electrochemical process for this reduction, the redox mediator 1,8-dihydroxyanthraquinone (1,8-DHAQ) is used to transfer electrons from the electrode to the dye. The mediated reduction process is investigated at a (500-kHz ultrasound-assisted) rotating disc electrode, and the quantitative analysis of voltammetric data is attempted employing the Digisim numerical simulation software package. At the most effective temperature, 353 K, the diffusion coefficient for 1,8-DHAQ is (0.84 +/- 0.08)x10(-9) m(2) s(-1), and it is shown that an apparently kinetically controlled reaction between the reduced form of the mediator and the colloidal indigo occurs within the diffusion layer at the electrode surface. The apparent bimolecular rate constant k (app)=3 mol m(-3) s(-1) for the rate law d[leuco-indigo]/dt = k(app) x [mediator] x [indigo] is determined and attributed to a mediator diffusion controlled dissolution of the colloid particles. The average particle size and the number of molecules per particles are estimated from the apparent bimolecular rate constant and confirmed by scanning electron microscopy.

Microwave activation of the electro-oxidation of glucose in alkaline media

The oxidation of glucose is a complex process usually requiring catalytically active electrode surfaces or enzyme-modified electrodes. In this study the effect of high intensity microwave radiation on the oxidation of glucose in alkaline solution at Au, Cu, and Ni electrodes is reported. Calibration experiments with the Fe(CN)63–/4– redox system in aqueous 0.1 M NaOH indicate that strong thermal effects occur at both 50 and 500 µm diameter electrodes with temperatures reaching 380 K. Extreme mass transport effects with mass transport coefficients of kmt > 0.01 m s–1(or kmt > 1.0 cm s–1) are observed at 50 µm diameter electrodes in the presence of microwaves. The electrocatalytic oxidation of glucose at 500 µm diameter Au, Cu, or Ni electrodes immersed in 0.1 M NaOH and in the presence of microwave radiation is shown to be dominated by kinetic control. The magnitude of glucose oxidation currents at Cu electrodes is shown to depend on the thickness of a pre-formed oxide layer. At 50 µm diameter Au, Cu, or Ni electrodes microwave enhanced current densities are generally higher, but only at Au electrodes is a significantly increased rate for the electrocatalytic oxidation of glucose to gluconolactone observed. This rate enhancement appears to be independent of temperature but microwave intensity dependent, and therefore non-thermal in nature. Voltammetric currents observed at Ni electrodes in the presence of microwaves show the best correlation with glucose concentration and are therefore analytically most useful.

The mechanism of bacterial indigo reduction

The reduction of water-insoluble indigo by the recently isolated moderate thermophile, Clostridium isatidis, has been studied with the aim of developing a sustainable technology for industrial indigo reduction. The ability to reduce indigo was not shared with C. aurantibutyricum, C. celatum and C. papyrosolvens, but C. papyrosolvens could reduce indigo carmine (5,5-indigosulfonic acid), a soluble indigo derivative. The supernatant from cultures of C. isatidis, but not from cultures of the other bacteria tested, decreased indigo particle size to one-tenth diameter. Addition of madder powder, anthraquinone-2,6-disulfonic acid, and humic acid all stimulated indigo reduction by C. isatidis. Redox potentials of cultures of C. isatidis were about 100 mV more negative than those of C. aurantibutyricum, C. celatum and C. papyrosolvens, and reached –600 mV versus the SCE in the presence of indigo, but potentials were not consistently affected by the addition of the quinone compounds, which probably act by modifying the surface of the bacteria or indigo particles. It is concluded that C. isatidis can reduce indigo because (1) it produces an extracellular factor that decreases indigo particle size, and (2) it generates a sufficiently reducing potential.

Protein-disulfide isomerase-mediated reduction of two disulfide bonds of HIV envelope glycoprotein 120 occurs post-CXCR4 binding and is required for fusion

The human immunodeficiency virus (HIV) envelope (Env) glycoprotein (gp) 120 is a highly disulfide-bonded molecule that attaches HIV to the lymphocyte surface receptors CD4 and CXCR4. Conformation changes within gp120 result from binding and trigger HIV/cell fusion. Inhibition of lymphocyte surface-associated protein-disulfide isomerase (PDI) blocks HIV/cell fusion, suggesting that redox changes within Env are required. Using a sensitive assay based on a thiol reagent, we show that (i) the thiol content of gp120, either secreted by mammalian cells or bound to a lymphocyte surface enabling CD4 but not CXCR4 binding, was 0.5-1 pmol SH/pmol gp120 (SH/gp120), whereas that of gp120 after its interaction with a surface enabling both CD4 and CXCR4 binding was raised to 4 SH/gp120; (ii) PDI inhibitors prevented this change; and (iii) gp120 displaying 2 SH/gp120 exhibited CD4 but not CXCR4 binding capacity. In addition, PDI inhibition did not impair gp120 binding to receptors. We conclude that on average two of the nine disulfides of gp120 are reduced during interaction with the lymphocyte surface after CXCR4 binding prior to fusion and that cell surface PDI catalyzes this process. Disulfide bond restructuring within Env may constitute the molecular basis of the post-receptor binding conformational changes that induce fusion competence.

Global iron-dependent gene regulation in Escherichia coli - A new mechanism for iron homeostasis

Organisms generally respond to iron deficiency by increasing their capacity to take up iron and by consuming intracellular iron stores. Escherichia coli, in which iron metabolism is particularly well understood, contains at least 7 iron-acquisition systems encoded by 35 iron-repressed genes. This Fe-dependent repression is mediated by a transcriptional repressor, Fur ( ferric uptake regulation), which also controls genes involved in other processes such as iron storage, the Tricarboxylic Acid Cycle, pathogenicity, and redox-stress resistance. Our macroarray-based global analysis of iron- and Fur-dependent gene expression in E. coli has revealed several novel Fur-repressed genes likely to specify at least three additional iron- transport pathways. Interestingly, a large group of energy metabolism genes was found to be iron and Fur induced. Many of these genes encode iron- rich respiratory complexes. This iron- and Fur-dependent regulation appears to represent a novel iron-homeostatic mechanism whereby the synthesis of many iron- containing proteins is repressed under iron- restricted conditions. This mechanism thus accounts for the low iron contents of fur mutants and explains how E. coli can modulate its iron requirements. Analysis of Fe-55-labeled E. coli proteins revealed a marked decrease in iron- protein composition for the fur mutant, and visible and EPR spectroscopy showed major reductions in cytochrome b and d levels, and in iron- sulfur cluster contents for the chelator-treated wild-type and/or fur mutant, correlating well with the array and quantitative RT-PCR data. In combination, the results provide compelling evidence for the regulation of intracellular iron consumption by the Fe2+-Fur complex.

Insights into the effects on metal binding of the systematic substitution of five key glutamate ligands in the ferritin of Escherichia coli

Ferritins are nearly ubiquitous iron storage proteins playing a fundamental role in iron metabolism. They are composed of 24 subunits forming a spherical protein shell encompassing a central iron storage cavity. The iron storage mechanism involves the initial binding and subsequent O-2-dependent oxidation of two Fe2+ ions located at sites A and B within the highly conserved dinuclear "ferroxidase center" in individual subunits. Unlike animal ferritins and the heme-containing bacterioferritins, the Escherichia coli ferritin possesses an additional iron-binding site (site C) located on the inner surface of the protein shell close to the ferroxidase center. We report the structures of five E. coli ferritin variants and their Fe3+ and Zn2+ (a redox-stable alternative for Fe2+) derivatives. Single carboxyl ligand replacements in sites A, B, and C gave unique effects on metal binding, which explain the observed changes in Fe2+ oxidation rates. Binding of Fe2+ at both A and B sites is clearly essential for rapid Fe2+ oxidation, and the linking of Fe-B(2+) to Fe-C(2+) enables the oxidation of three Fe2+ ions. The transient binding of Fe2+ at one of three newly observed Zn2+ sites may allow the oxidation of four Fe2+ by one dioxygen molecule.

Surface modification of nylon 6,6 using a carbene insertion approach

The diazirine functionalised fluorenone, 3-[3-(trifluoromethyl)diazirin-3-yl]phenyl-9-oxo-9H-fluorene-2-carboxyla te was synthesised to act as a model compound capable of modifying a wide variety of polymeric substrates. Photochemical activation of the diazirine moiety of the fluorenone derivative was utilised to afford highly reactive carbenes capable of insertion into or addition to a wide variety of functionalities. In this paper the photoinduced attachment of a fluorenone derivative to nylon 6,6 has been studied using UV-visible spectroscopic analysis. Incorporation of the fluorenone chromophore onto the backbone of nylon at different loading levels and after different coating cycles has been investigated and is detailed in this paper.

Ligand bridging of the DNA Holliday junction: molecular recognition of a stacked-X four-way junction by a small molecule

Planning a Holliday: A new mode of binding to a stacked-X, four-way Holliday junction is described in which a chromophore molecule binds across the center of the junction and two adenine residues are replaced by the acridine chromophores at either side of the crossover. This binding mode is specific for the Holliday junction and does not cause unwinding of the DNA helices.