Bilirubin binding to polypeptides and chiral amines. Induced circular dichroism and fluorescence studies

Induced Cotton effects have been observed in the visible region on interaction of bilirubin with chiral mono- and diamines and poly-l-lysine. At alkaline pH distinct CD spectra are observed for bilirubin bound to the α-helical and β-sheet conformation of poly-l-lysine, which differ from that observed for the pigment bound to human serum albumin. The CD pattern observed on binding to N-acetyl-Lys-N1-methylamide in CH2Cl2 and dioxane is different from that observed in the presence of l-Ala-NH-(CH2)6-NH-l-Ala in dioxane. The latter case resembles the spectrum observed in the presence of human serum albumin. Binding to the helical polypeptide melittin and the antiparallel β-sheet peptide, gramicidin S, in aqueous solutions results in opposite signs of the bilirubin CD bands. The quenching of tryptophan fluorescence in melittin, in aqueous solution and enhancement of bilirubin fluorescence in dioxane on binding to gramicidin S have been used to monitor pigment-peptide interactions. The results suggest the utility of bilirubin as a conformational probe.

The use of temperate species in the Australian subtropics.

Temperate species and tropical crop silage are the basis for forage production for the dairy industry in the Australian subtropics. Irrigation is the key resource needed for production, with little survival of temperate species under rain-grown conditions except for lucerne. Annual ryegrass (Lolium multiflorum), fertilised with either inorganic nitrogen or grown with clovers, is the main cool season forage for the dairy industry. It is sown into fully prepared seedbeds, oversown into tropical grasses, especially kikuyu (Pennisetum clandestinum) or sown after mulching. There has been a continual improvement in the performance of annual and hybrid ryegrass cultivars over the last 25 years. In small plot, cutting experiments, yields of annual ryegrass typically range from 15 to 21 t DM/ha, with equivalent on-farm yields of 7 to 14 t DM/ha of utilised material. Rust (Puccinia coronata) remains the major concern although resistance is more stable than in oats. There have also been major improvements in the performance of perennial ryegrass (L. perenne) cultivars although their persistence under grazing is insufficient to make them a reliable forage source for the subtropics. On the other hand, tall fescue (Festuca arundinacea) and prairie grass (Bromus willdenowii) cultivars perform well under cutting and grazing, although farmer resistance to the use of tall fescue is strong. White clover (Trifolium repens) is a reliable and persistent performer although disease usually reduces its performance in the third year after sowing. Persian (Shaftal) annual clover (T. resupinatum) gives good winter production but the performance of berseem clover (T. alexandrinum) is less reliable and the sub clovers (T. subterraneum) are generally not suited to clay soils of neutral to alkaline pH. Lucerne (Medicago sativa), either as a pure stand or in mixtures, is a high producing legume under both irrigation and natural rainfall. Understanding the importance of leaf and crown diseases, and the development of resistant cultivars, have been the reasons for its reliability. Insects on temperate species are not as serious a problem in the subtropics as in New Zealand (NZ). Fungal and viral diseases, on the other hand, cause many problems and forage performance would benefit from more research into resistance.

Vanadate-stimulated NADH oxidation by xanthine oxidase: An intrinsic property

Vanadate-dependent oxidation of NADH by xanthine oxidase does not require the presence of xanthine and therefore is not due to cooxidation. Addition of NADH or xanthine had no effect on the oxidation of the other substrate. Oxidation of NADH was high at acid pH and oxidation of xanthine was high at alkaline pH. The specific activity was relatively very high with NADH. Concentration-dependent oxidation of NADH was obtained in the presence of the polymeric form of vanadate, but not orthovanadate or metavanadate. Both NADH and NADPH were oxidized, as in the nonenzymatic system. Oxidation of NADH, but not xanthine, was inhibited by KCN, ascorbate, MnCl2, cytochrome c, mannitol, Tris, epinephrine, norepinephrine, and triiodothyronine. Oxidation of NADH was accompanied by uptake of oxygen and generation of H2O2 with a stoichiometry of 1:1:1 for NADH:O2:H2O2. A 240-nm-absorbing species was formed during the reaction which was different from H2O2 or superoxide. A mechanism of NADH oxidation is suggested wherein VV and O2 receive one electron each successively from NADH followed by VIV giving the second electron to superoxide and reducing it to H2O2.

Bacillus cereus spores and cereulide in food-borne illness

B. cereus is a gram-positive bacterium that possesses two different forms of life:the large, rod-shaped cells (ca. 0.002 mm by 0.004 mm) that are able to propagate and the small (0.001 mm), oval shaped spores. The spores can survive in almost any environment for up to centuries without nourishment or water. They are insensitive towards most agents that normally kill bacteria: heating up to several hours at 90 ºC, radiation, disinfectants and extreme alkaline (≥ pH 13) and acid (≤ pH 1) environment. The spores are highly hydrophobic and therefore make them tend to stick to all kinds of surfaces, steel, plastics and live cells. In favorable conditions the spores of B. cereus may germinate into vegetative cells capable of producing food poisoning toxins. The toxins can be heat-labile protein formed after ingestion of the contaminated food, inside the gastrointestinal tract (diarrhoeal toxins), or heat stable peptides formed in the food (emesis causing toxin, cereulide). Cereulide cannot be inactivated in foods by cooking or any other procedure applicable on food. Cereulide in consumed food causes serious illness in human, even fatalities. In this thesis, B. cereus strains originating from different kinds of foods and environments and 8 different countries were inspected for their capability of forming cereulide. Of the 1041 isolates from soil, animal feed, water, air, used bedding, grass, dung and equipment only 1.2 % were capable of producing cereulide, whereas of the 144 isolates originating from foods 24 % were cereulide producers. Cereulide was detected by two methods: by its toxicity towards mammalian cells (sperm assay) and by its peculiar chemical structure using liquid-chromatograph-mass spectrometry equipment. B. cereus is known as one of the most frequent bacteria occurring in food. Most foods contain more than one kind of B. cereus. When randomly selected 100 isolates of B. cereus from commercial infant foods (dry formulas) were tested, 11% of these produced cereulide. Considering a frequent content of 103 to 104 cfu (colony forming units) of B. cereus per gram of infant food formula (dry), it appears likely that most servings (200 ml, 30 g of the powder reconstituted with water) may contain cereulide producers. When a reconstituted infant formula was inoculated with >105 cfu of cereulide producing B. cereus per ml and left at room temperature, cereulide accumulated to food poisoning levels (> 0.1 mg of cereulide per serving) within 24 hours. Paradoxically, the amount of cereulide (per g of food) increased 10 to 50 fold when the food was diluted 4 - 15 fold with water. The amount of the produced cereulide strongly depended on the composition of the formula: most toxin was formed in formulas with cereals mixed with milk, and least toxin in formulas based on milk only. In spite of the aggressive cleaning practices executed by the modern dairy industry, certain genotypes of B. cereus appear to colonise the silos tanks. In this thesis four strategies to explain their survival of their spores in dairy silos were identified. First, high survival (log 15 min kill ≤ 1.5) in the hot alkaline (pH >13) wash liquid, used at the dairies for cleaning-in-place. Second, efficient adherence of the spores to stainless steel from cold water. Third, a cereulide producing group with spores characterized by slow germination in rich medium and well preserved viability when exposed to heating at 90 ºC. Fourth, spores capable of germinating at 8 ºC and possessing the psychrotolerance gene, cspA. There were indications that spores highly resistant to hot 1% sodium hydroxide may be effectively inactivated by hot 0.9% nitric acid. Eight out of the 14 dairy silo tank isolates possessing hot alkali resistant spores were capable of germinating and forming biofilm in whole milk, not previously reported for B. cereus. In this thesis it was shown that cereulide producing B. cereus was capable of inhibiting the growth of cereulide non-producing B. cereus occurring in the same food. This phenomenon, called antagonism, has long been known to exist between B. cereus and other microbial species, e.g. various species of Bacillus, gram-negative bacteria and plant pathogenic fungi. In this thesis intra-species antagonism of B. cereus was shown for the first time. This brother-killing did not depend on the cereulide molecule, also some of the cereulide non-producers were potent antagonists. Interestingly, the antagonistic clades were most frequently found in isolates from food implicated with human illness. The antagonistic property was therefore proposed in this thesis as a novel virulence factor that increases the human morbidity of the species B. cereus, in particular of the cereulide producers.

A green protocol for room temperature synthesis of silver nanoparticles in seconds

We describe here a rapid, energy-efficient, green and economically scalable room temperature protocol for the synthesis of silver nanoparticles. Tannic acid, a polyphenolic compound derived from plant extracts is used as the reducing agent. Silver nanoparticles of mean size ranging from 3.3 to 22.1 nm were synthesized at room temperature by the addition of silver nitrate to tannic acid solution maintained at an alkaline pH. The mean size was tuned by varying the molar ratio of tannic acid to silver nitrate. We also present proof of concept results demonstrating its suitability for room temperature continuous flow processing.

Process variables in biomimetic synthesis of silver nanoparticles by aqueous extract of Azadirachta indica (Neem) leaves

Owing to widespread applications, synthesis and characterization of silver nanoparticles is recently attracting considerable attention. Increasing environmental concerns over chemical synthesis routes have resulted in attempts to develop biomimetic approaches. One of them is synthesis using plant parts, which eliminates the elaborate process of maintaining the microbial culture and often found to be kinetically favourable than other bioprocesses. The present study deals with investigating the effect of process variables like reductant concentrations, reaction pH, mixing ratio of the reactants and interaction time on the morphology and size of silver nanoparticles synthesized using aqueous extract of Azadirachta indica (Neem) leaves. The formation of crystalline silver nanoparticles was confirmed using X-ray diffraction analysis. By means of UV spectroscopy, Scanning and Transmission Electron Microscopy techniques, it was observed that the morphology and size of the nanoparticles were strongly dependent on the process parameters. Within 4 h interaction period, nanoparticles below 20-nm-size with nearly spherical shape were produced. On increasing interaction time (ageing) to 66 days, both aggregation and shape anisotropy (ellipsoidal, polyhedral and capsular) of the particles increased. In alkaline pH range, the stability of cluster distribution increased with a declined tendency for aggregation of the particles. It can be inferred from the study that fine tuning the bioprocess parameters will enhance possibilities of desired nano-product tailor made for particular applications.

Chemical modification of sheep plasma glycoprotein

Glycoprotein isolated from sheep plasma was chemically modified, and the effect of chemical modification on biological activities and immunological cross reactions has been studied. The removal of sialic acid resulted in a change in the “overall conformation” of the glycoprotein as evidenced by a decrease in viscosity of the glycoprotein solution and an increased susceptibility of the glycoprotein to proteolytic enzymes. Sialic acid-free glycoprotein no longer inhibited the tryptic activity or prolonged the clotting time of plasma. However, it could react with the antiserum to sheep plasma glycoprotein. The periodate oxidation of sheep plasma glycoprotein resulted in a complete loss of inhibition of trypsin activity, prolongation of plasma clotting time, and the ability to cross-react with the rabbit antiserum. The significance of periodate oxidation in relation to the possible sequence of sugars in the carbohydrate prosthetic group in the glycoprotein is discussed. Iodination and heating in buffers of acid and alkaline pH values of sheep plasma glycoprotein resulted in complete loss of trypsin activity and ability to prolong plasma clotting time. Iodination of the glycoprotein did not affect the immunological cross-reactivity.

Studies on interaction of colloidal Ag nanoparticles with Bovine Serum Albumin (BSA)

Biofunctionalization of noble metal nanoparticles like Ag, Au is essential to obtain biocompatibility for specific biomedical applications. Silver nanciparticles are being increasingly used in bio-sensing applications owing to excellent optoelectronic properties. Among the serum albumins, the most abundant proteins in plasma, a wide range of physiological functions of Bovine Serum Albumin (BSA) has made it a model system for biofunctionalization. In absence of adequate prior reports, this study aims to investigate the interaction between silver nanoparticles and BSA. The interaction of BSA [0.05-0.85% concentrations] with Ag nanoparticles [50 ppm concentration] in aqueous dispersion was Studied through UV-vis spectral changes, morphological and surface structural changes. At pH 7, which is More than the isoelectric point of BSA, a decrease in absorbance at plasmon peak of uninteracted nanciparticles (425 mn) was noted till 0.45% BSA, beyond that a blue shift towards 410 urn was observed. The blue shift may be attributed to enhanced electron density on the particle surfaces. Increasing pH to 12 enhanced the blue shift further to 400 rim. The conformational changes in BSA at alkaline pH ranges and consequent hydrophobic interactions also played an important role. The equilibrium adsorption data fitted better to Freundlich isotherm compared to Langmuir Curve. The X-ray diffraction study revealed complete coverage of Ag nanoparticles by BSA. The scanning electron microscopic study of the interacted nanoparticles was also carried Out to decipher morphological changes. This study established that tailoring the concentration of BSA and pH of the interaction it was possible to reduce aggregation of nanoparticles. Biofunctionalized Ag nanoparticles with reduced aggregation will be more amenable towards bio-sensing applications. (C) 2009 Elsevier B.V. All rights reserved.

Characterization of mitochondrial neutral protease activity and the response of lysosomal enzymes to clofibrate feeding in rat liver

The phosphate-inhibitable neutral protease activity of the heavy mitochondrial fraction of rat liver is of lysosomal origin. The activity is essentially due to the thiol proteinases of the lysosomes. Digitonin treatment of the mitochondrial fraction results in the release of about 85 per cent of the neutral protease activity and the residual activity has an alkaline pH optimum and is not inhibited by phosphate. Clofibrate feeding at 0.5 per cent level in the diet results in enhanced levels of lysosomal enzymes. The increase is however restricted to the lysosome-rich fraction such that the activities associated with the heavy mitochondrial fraction show a significant decrease. It is suggested that clofibrate inhibits engulfment of mitochondria by lysosomes and this results in enhanced mitochondrial protein content.

Identification and characterization of cysteine proteinases of Trypanosoma evansi

Trypanosoma evansi is a causative agent of `surra', a common haemoprotozoan disease of livestock in India causing high morbidity and mortality in disease endemic areas. The proteinases released by live and dead trypanosomes entail immunosuppression in the infected host, which immensely contribute in disease pathogenesis. Cysteine proteinases are identified in the infectious cycle of trypanosomes such as cruzain from Trypanosoma cruzi, rhodesain or brucipain from Trypanosoma brucei rhodesiense and congopain from Trypanosoma congelense. These enzymes localised in lysosome-like organelles, flagellar pocket and on cell surface, which play a critical role in the life cycle of protozoan parasites, viz. in host invasion, nutrition and alteration of the host immune response. The paper describes the identification of cysteine proteinases of T. evansi lysate, activity profile at different pH optima and inhibition pattern using a specific inhibitor, besides the polypeptide profile of an antigen. Eight proteinases of T. evansi were identified in the molecular weight (MW) ranges of 28-170 kDa using gelatin substrate-polyacrylamide gel electrophoresis (GS-PAGE), and of these proteinases, six were cysteine proteinases, as they were inhibited by L-3-carboxy-2,3-transepoxypropionyl-lecuylamido (4-guanidino)-butane (E-64), a specific inhibitor. These proteolytic enzymes were most reactive in acidic pH between 3.0 and 5.5 in the presence of dithiothreitol and completely inactive at alkaline pH 10.0. Similarly, the GS-PAGE profile of the serum samples of rats infected with T. evansi revealed strong proteolytic activity only at the 28-kDa zone at pH 5.5, while no proteolytic activity was observed in serum samples of uninfected rats. Further, the other zones of clearance, which were evident in T. evansi antigen zymogram, could not be observed in the serum samples of rats infected with T. evansi. The polypeptide pattern of the whole cell lysate antigen revealed 12-15 polypeptide bands ranging from 28 to 81 kDa along with five predominant polypeptides bands (MW of 81, 66, 62, 55 and 45 kDa), which were immunoreactive with hyperimmune serum (HIS) and serum of experimentally infected rabbits with T. evansi infection. The immunoblot recognised antibodies in experimentally infected rabbits and against HIS as well, corresponding to the zone of clearances at lower MW ranges (28-41 kDa), which may be attributed to the potential of these proteinases in the diagnosis of T. evansi infection. Since these thiol-dependent enzymes are most active in acidic pH and considering their inhibition characteristics, these data suggest that they resemble to the mammalian lysosomal cathepsin B and L.

Lysozyme: A model protein for amyloid research

Ever since lysozyme was discovered by Fleming in 1922, this protein has emerged as a model for investigations on protein structure and function. Over the years, several high-resolution structures have yielded a wealth of structural data on this protein. Extensive studies on folding of lysozyme have shown how different regions of this protein dynamically interact with one another. Data is also available from numerous biotechnological studies wherein lysozyme has been employed as a model protein for recovering active recombinant protein from inclusion bodies using small molecules like L-arginine. A variety of conditions have been developed in vitro to induce fibrillation in hen lysozyme. They include (a) acidic pH at elevated temperature, (b) concentrated solutions of ethanol, (c) moderate concentrations of guanidinium hydrochloride at moderate temperature, and (d) alkaline pH at room temperature. This review aims to bring together similarities and differences in aggregation mechanisms, morphology of aggregates, and related issues that arise using the different conditions mentioned above to improve our understanding. The alkaline pH condition (pH 12.2), discovered and studied extensively in our lab, shall receive special attention. More than a decade ago, it was revealed that mutations in human lysozyme can cause accumulation of large quantities of amyloid in liver, kidney, and other regions of gastrointestinal tract. Understanding the mechanism of lysozyme aggregation will probably have therapeutic implications for the treatment of systemic nonneuropathic amyloidosis. Numerous studies have begun to focus attention on inhibition of lysozyme aggregation using antibody or small molecules. The enzymatic activity of lysozyme presents a convenient handle to quantify the native population of lysozyme in a sample where aggregation has been inhibited. The rich information available on lysozyme coupled with the multiple conditions that have been successful in inducing/inhibiting its aggregation in vitro makes lysozyme an ideal model protein to investigate amyloidogenesis.

Synthesis and Characterization of Fly Ash Geopolymer Sand

Geopolymers are an alternative binder to portland cement in the manufacture of mortars and concrete, as its three-dimensional aluminosilicate network imparts excellent mechanical properties. Use of geopolymers in place of ordinary portland cement is favored owing to the possible energy and carbon dioxide savings. River sand is another construction industry material that needs development of a sustainable alternate in India. Geopolymerization of fly ash amorphous silica mixtures is employed to produce fine aggregates as a possible replacement to river sand. Geopolymerization of fly ash amorphous silica mixtures in 10M NaOH solution at 100 degrees C for 7days produced fine aggregates termed fly ash geopolymer sand (FAPS)] that had comparable grain size distribution, specific gravity, and improved frictional resistance with river sand. The FAPS particles exhibited more alkaline pH (12.5) and higher total dissolved solids (TDS) concentration (TDS=747 mg/L) in comparison to the river sand specimen (pH=7.9 and TDS=32.5 mg/L). However, when used as fine aggregate in mortar, FAPS-mortar specimens develop similar pH, lower TDS, similar compressive strength, and modulus in relation to river sand-mortar specimens. The experimental results suggest that FAPS particles have the potential to replace river sand in the manufacture of mortar and concrete.

Iodide Retention by Modified Kaolinite in the Context of Safe Disposal of High Level Nuclear Waste

Bentonite clay is identified as potential buffer in deep geological repositories (DGR) that store high level radioactive wastes (HLW) as the expansive clay satisfies the expected mechanical and physicochemical functions of the buffer material. In the deep geological disposal of HLW, iodine-129 is one of the significant nuclides, attributable to its long half-life (half life 1⁄4 1:7 × 107 years). However, the negative charge on the basal surface of bentonite particles precludes retention of iodide anions. To render the bentonite effective in retaining hazardous iodide species in DGR, improvement of the anion retention capacity of bentonite becomes imperative. The iodide retention capac-ity of bentonite is improved by admixing 10 and 20% Ag-kaolinite (Ag-K) with bentonite (B) on a dry mass basis. The present study produced Ag-kaolinite by heating silver nitrate-kaolinite mixes at 400°C. Marginal release of iodide retained by Ag-kaolinite occurred under extreme acidic (pH 1⁄4 2:5) and alkaline (pH 1⁄4 12:5) conditions. The swell pressure and iodide etention results of the B-Ag-K specimens bring out that mixing Ag-K with bentonite does not chemically modify the expansive clay; the mixing is physical in nature and Ag-K presence only contributes to iodide retention of the admixture. DOI: 10.1061/(ASCE)HZ.2153-5515.0000121. © 2012 American Society of Civil Engineers.

Depletion of the heaviest stable N isotope is associated with NH4 +/NH3 toxicity in NH4 +-fed plants

Background: In plants, nitrate (NO(3)(-)) nutrition gives rise to a natural N isotopic signature (delta(15)N), which correlates with the delta(15)N of the N source. However, little is known about the relationship between the delta(15)N of the N source and the (14)N/(15)N fractionation in plants under ammonium (NH(4)(+)) nutrition. When NH(4)(+) is the major N source, the two forms, NH(4)(+) and NH(3), are present in the nutrient solution. There is a 1.025 thermodynamic isotope effect between NH(3) (g) and NH(4)(+)(aq) which drives to a different delta(15)N. Nine plant species with different NH(4)(+)-sensitivities were cultured hydroponically with NO(3)(-) or NH(4)(+) as the sole N sources, and plant growth and delta(15)N were determined. Short-term NH(4)(+)/NH(3) uptake experiments at pH 6.0 and 9.0 (which favours NH(3) form) were carried out in order to support and substantiate our hypothesis. N source fractionation throughout the whole plant was interpreted on the basis of the relative transport of NH(4)(+) and NH(3). -- Results: Several NO(3)(-)-fed plants were consistently enriched in (15)N, whereas plants under NH(4)(+) nutrition were depleted of (15)N. It was shown that more sensitive plants to NH(4)(+) toxicity were the most depleted in (15)N. In parallel, N-deficient pea and spinach plants fed with (15)NH(4)(+) showed an increased level of NH(3) uptake at alkaline pH that was related to the (15)N depletion of the plant. Tolerant to NH(4)(+) pea plants or sensitive spinach plants showed similar trend on (15)N depletion while slight differences in the time kinetics were observed during the initial stages. The use of RbNO(3) as control discarded that the differences observed arise from pH detrimental effects. -- Conclusions: This article proposes that the negative values of delta(15)N in NH(4)(+)-fed plants are originated from NH(3) uptake by plants. Moreover, this depletion of the heavier N isotope is proportional to the NH(4)(+)/NH(3) toxicity in plants species. Therefore, we hypothesise that the low affinity transport system for NH(4)(+) may have two components: one that transports N in the molecular form and is associated with fractionation and another that transports N in the ionic form and is not associated with fractionation.

Protein-protein recognition: The neonatal Fe receptor and immunoglobulin G

The neonatal Fe receptor (FeRn) binds the Fe portion of immunoglobulin G (IgG) at the acidic pH of endosomes or the gut and releases IgG at the alkaline pH of blood. FeRn is responsible for the maternofetal transfer of IgG and for rescuing endocytosed IgG from a default degradative pathway. We investigated how FeRn interacts with IgG by constructing a heterodimeric form of the Fe (hdFc) that contains one FeRn binding site. This molecule was used to characterize the interaction between one FeRn molecule and one Fe and to determine under what conditions FeRn forms a dimer. The hdFc binds one FeRn molecule at pH 6.0 with a K_d of 80 nM. In solution and with FeRn anchored to solid supports, the heterodimeric Fe does not induce a dimer of FeRn molecules. FcRnhdFc complex crystals were obtained and the complex structure was solved to 2.8 Å resolution. Analysis of this structure refined the understanding of the mechanism of the pH-dependent binding, shed light on the role played by carbohydrates in the Fe binding, and provided insights on how to design therapeutic IgG antibodies with longer serum half-lives. The FcRn-hdFc complex in the crystal did not contain the FeRn dimer. To characterize the tendency of FeRn to form a dimer in a membrane we analyzed the tendency of the hdFc to induce cross-phosphorylation of FeRn-tyrosine kinase chimeras. We also constructed FeRn-cyan and FeRn-yellow fluorescent proteins and have analyzed the tendency of these molecules to exhibit fluorescence resonance energy transfer. As of now, neither of these analyses have lead to conclusive results. In the process of acquiring the context to appreciate the structure of the FcRn-hdFc interface, we developed a study of 171 other nonobligate protein-protein interfaces that includes an original principal component analysis of the quantifiable aspects of these interfaces.