Computation of physicochemical parameters, namely pH, in complex (bio)chemical systems: extension to gas-liquid systems

The first model has been proposed to compute, in complex liquid (bio)chemical systems, a number of physicochemical parameters, namely pH, concentration of one of any chemical species, partition between acid-base forms, global charge, or ionic strength, assuming the physicochemical equilibrium state. The extension of the present model, described here, permits moreover the computation of gas-liquid distributions, specific gas volumes, or total pressures. The model solely requires the knowledge of existing thermodynamic constants and of the concentration of every chemical species other than the species under examination. The model elicits a unique equilibrium state. Computed values agreed with experimental measurements, thereby validating the model. Digital computer programs were prepared to use the proposed algorithms.     

Facile synthesis,physiochemical characterization and bio evaluation of sulfadimidine capped cobalt nanoparticles

Due to their less expensive, environment friendly nature, and their natural abundance of cobalt have attained more significant attention for the synthesis of cobalt nanoparticles. In the present study, we report the facile synthesis of cobalt nanoparticles using a straight forward chemical reduction approach of cobalt chloride with sodium borohydride and capping of sulfadimidine. sulfadimidine has strong capping eligibility on the surface of nanoparticles due to its chemical stability and is an applicable as stabilizer due to the existence of an amine bond. The as-synthesized sulfadimidine stabilized cobalt nanoparticles (Co-SD NPs) were characterized by using various spectroscopic and microscopic analysis like UV–Visible spectroscopy (UV–Vis), X-ray powder diffraction (XRD), scanning electron microscopy (SEM), High-Resolution Transmission electron microscopy (HR-TEM), and Fourier-transform infrared spectroscopy (FT-IR). The XRD analysis exhibited the triclinic crystal structure of the as-synthesized cobalt nanoparticles and FT-IR analysis confirmed the capping of sulfadimidine via monodentate interaction. The HR-TEM analysis displayed the size of the cobalt nanoparticles approximately 3–5 nm. The antibacterial properties of the sulfadimidine stabilized cobalt nanoparticles (Co-SD NPs) were tested against various bacterial strains such as Klebsiella pneumonia (KP), Escherichia coli (EC) and Pseudomonas syringae (PS) by using agar disc diffusion approach. The results of sulfadimidine capped cobalt nanoparticles displayed the enhanced biological properties against the tested gram-negative bacteria.     

SNOW: standard nomenclature wizard to help searching for (bio) chemical standardized names

SUMMARY: When developing bioinformatical tools dealing with enzymatic activity, metabolism or enzymatic networks, the problem of the lack of a clear nomenclature for biochemical compounds often arises. This problem leads us to develop a small web-based tool (SNOW, Standard NOmenclature Wizard) which may help to find recommended and trivial names or the correct closest spelling for a query compound name, if it exists. AVAILABILITY: Web-based interface available at http://ibb.uab.es/snow/ SUPPLEMENTARY INFORMATION: http://ibb.uab.es/snow/snow_moreinfo.html     

Water pH and metabolic parameters in silver catfish (Rhamdia quelen)

This study evaluated the effects of an acute change in water pH (from pH 7.5 to 4.0, 5.0, 6.0, 7.5, 8.0 or 9.0) on several biochemical parameters in juveniles of the silver catfish, Rhamdia quelen. Ammonia levels decreased in the liver and increased in the muscle with increasing water pH. In the kidney, lower ammonia levels were observed at neutral pH. An increase in water pH decreased the glucose, glycogen and lactate levels in the liver and kidney (except for glycogen levels in the kidney and lactate levels in the liver, which presented lower levels at neutral pH). In muscle, the glucose and glycogen levels decreased with increasing water pH, whereas lactate levels tended to be lower at neutral pH. Gill and kidney Na⁺/K⁺-ATPase activities tended to increase in alkaline water, and the highest value was observed in fish exposed to pH 9.0. The optimal levels of the analyzed biochemical parameters occurred at neutral pH. In conclusion, exposure to acidic and alkaline pH changes the metabolic parameters of silver catfish as well as gill Na⁺/K⁺-ATPase activity.     

Carbon monoxide complex of cytochrome b(5) at acidic pH

CO complex of cyt b(5) generated at acidic pH is investigated by absorption, resonance Raman (RR), and far UV CD measurements. The Soret maximum wavelength blue-shifted to 420 nm with other absorption bands observed around 540 and 570 nm for reduced cyt b(5) upon interaction with CO at acidic pH (pH 3.1-3.5). Under this condition, the iron-carbon stretching RR band was observed at 529 cm(-1) (520 cm(-1) for C(18)O), which indicated formation of a heme&bond;CO adduct with a histidine as an axial ligand. Heme dissociated from the reduced cyt b(5) protein at pH approximately 3.5, whereas its rate decreased under CO atmosphere compared with N(2) atmosphere, due to formation of a heme&bond;CO adduct with a histidine as an axial ligand.     

A morphological, karyological and chemical study of the Apteranthes (Caralluma) europaea complex

The Apteranthes europaea complex (Apocynaceae–Asclepiadoideae–Ceropegieae–Stapeliinae) distributed from Morocco/southern Spain along the North African coast of the Mediterranean Sea up to Sinai, Negev and southern Jordan is studied with emphasis on stem and flower morphology by SEM, chromosome sizes and flavonoid compounds. Apteranthes europaea was found to be rich in rather uncommon flavone glycosides. Of these, luteolin 4'-neohesperidoside represents the major flavonoid of all samples; luteolin-3'- O -(6'- O -sinapoylglucoside)-4'- O -neohesperidoside and luteolin-3'- O -(6'- O -feruloylglucoside)-4'- O -neohesperidoside are reported here for the first time. Flavonol glycosides also occur, but in much smaller quantities. The different flower morphs, variation in stem and corolla epidermal structures, slight variations in the length of the 2 n  = 22 chromosomes and in quantitative flavonoid composition are taxonomically best reflected by subdividing the complex into a western var. europaea (Europe and Africa) and an eastern var. judaica (Sinai, Arabia).  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 149 , 419–432.     

Cellulose as a (bio)affinity carrier: properties,design and applications

This contribution presents a framework for the rational design of affinity sorbents based on cellulose materials as a support. A three-level evaluation procedure, utilizing the knowledge of physical, chemical and engineering theories, is discussed, which integrates the design of support, affinity sorbent and chromatographic contactor. The principal support properties, such as morphological, diffusional, hydrodynamic, mechanical or ligand-binding properties, are presented and literature data on them are surveyed.     

Iteroparity in complex mating systems of steelhead Oncorhynchus mykiss (Walbaum)

This study investigated diverse reproductive types in complex mating systems of steelhead Oncorhynchus mykiss . Postspawned steelhead (kelts) were sampled during attempted downstream migration over Lower Granite Dam on the Snake River, U.S.A. Multilocus microsatellite genotypes (14 loci) were used to assign unknown origin, kelt individuals to upstream populations of origin. Results indicated that iteroparity is a life-history trait that remains in several tributaries of the Snake River basin despite strong selection against downstream adult passage because of hydroelectric dams. The largest populations of steelhead in the Snake River, however, were only weakly represented (Clearwater River = 7·5% and Salmon River = 9·4%, respectively) in the kelt steelhead mixture relative to the Grande Ronde River (18·2%), Imnaha River (17·4%), Pahsimeroi Hatchery (25·2%) and Asotin Creek (22·2%). A lack of correlation between population escapement size and kelt proportions ( P > 0·05) suggests that iteroparity was not uniformly expressed across populations, but was significantly negatively correlated with body size ( P < 0·05). Iteroparity may be a valuable source of genetic variability and a conservation priority, especially in years with poor recruitment or in recently bottlenecked populations.     

Verbascoside — A review of its occurrence, (bio)synthesis and pharmacological significance

Phenylethanoid glycosides are naturally occurring water-soluble compounds with remarkable biological properties that are widely distributed in the plant kingdom. Verbascoside is a phenylethanoid glycoside that was first isolated from mullein but is also found in several other plant species. It has also been produced by in vitro plant culture systems, including genetically transformed roots (so-called ‘hairy roots’). Verbascoside is hydrophilic in nature and possesses pharmacologically beneficial activities for human health, including antioxidant, anti-inflammatory and antineoplastic properties in addition to numerous wound-healing and neuroprotective properties. Recent advances with regard to the distribution, (bio)synthesis and bioproduction of verbascoside are summarised in this review. We also discuss its prominent pharmacological properties and outline future perspectives for its potential application.     

Catalytic mechanism of the tryptophan synthase alpha(2)beta(2) complex. Effects of pH, isotopic substitution, and allosteric ligands.

The mechanism of the tryptophan synthase alpha(2)beta(2) complex from Salmonella typhimurium is explored by determining the effects of pH, of temperature, and of isotopic substitution on the pyridoxal phosphate-dependent reaction of L-serine with indole to form L-tryptophan. The pH dependence of the kinetic parameters indicates that three ionizing groups are involved in substrate binding and catalysis with pK(a)1 = 6.5, pK(a)2 = 7.3, and pK(a)3 = 8.2-9. A significant primary isotope effect (approximately 3.5) on V and V/K is observed at low pH (pH 7), but not at high pH (pH 9), indicating that the base that accepts the alpha-proton (betaLys-87) is protonated at low pH, slowing the abstraction of the alpha-proton and making this step at least partially rate-limiting. pK(a)2 is assigned to betaLys-87 on the basis of the kinetic isotope effect results and of the observation that the competitive inhibitors glycine and oxindolyl-L-alanine display single pK(i) values of 7.3. The residue with this pK(a) (betaLys-87) must be unprotonated for binding glycine or oxindolyl-L-alanine, and, by inference, L-serine. Investigations of the temperature dependence of the pK(a) values support the assignment of pK(a)2 to betaLys-87 and suggest that the ionizing residue with pK(a)1 could be a carboxylate, possibly betaAsp-305, and that the residue associated with a conformational change at pK(a)3 may be betaLys-167. The occurrence of a closed to open conformational conversion at high pH is supported by investigations of the effects of pH on reaction specificity and on the equilibrium distribution of enzyme-substrate intermediates.     

New guinea salt fern (Asplenium acrobryum complex): Identity,distribution, and chemical composition of its salt

Fronds of a fern of theAsplenium acrobryum complex were traditionally used as a source of salt in the inland areas of Papua New Guinea. All previously published reports of the use of fern salt in the botanical and ethnobotanical literature had erroneously identified the species involved asAsplenium nidus, one of the common bird’s-nest ferns. A chemical analysis of the salts contained in the ash of the salt fern as well as those species related toAsplenium nidus revealed that the bulk of the inorganic component was potassium, calcium and chloride. These results are comparable to those published for the salt-yielding grass,Coix gigantean. There is no obvious chemical reason why onlyAsplenium acrobryum should be used for salt production in preference toAsplenium nidus and related species. In view of the low levels of consumption of such salt it is unlikely that there will be any cases of potassium toxicity attributable to the use of these plants.     

Luminescent pH sensing and DNA binding properties of a novel ruthenium(II) complex

A new Ru(II) complex, [Ru(bpy)(2)(dhipH3)](ClO4)(2) (in which bpy=2,2'-bipyridine, dhipH(3)=3,4-dihydroxy-imidado[4,5-f][1,10]-phenanthroline), was synthesized and characterized, and the pH effect on the emission spectra of the complex was studied. The interaction of the complex with calf thymus DNA was investigated by UV-visible and emission spectroscopy, and viscosity measurements. The results suggest that the complex acted as a sensitive luminescent pH sensor and a strong ct-DNA intercalator with an intrinsic binding constant of (4.0+/-0.7) x 10(5) M(-1) in buffered 50 mM NaCl.     

Use of a bioelectrochemical cell for the synthesis of (bio)chemicals

A bioelectrochemical cell containing either d-glucose oxidase (β-d-glucose:oxygen 1-oxidoreductase, EC 1.1.3.4) or xanthine oxidase (xanthine:oxygen oxidoreductase, EC 1.2.3.2) plus dichlorophenol-indophenol as electron acceptor in one half-cell, and chloroperoxidase (chloride:hydrogen-peroxide oxidoreductase, EC 1.11.1.10) in the other half-cell is described. Due to a combination of chemical, biochemical and electrochemical reactions, electricity and specific (bio)chemicals can be produced in the cell simultaneously and in both compartments. Furthermore, the oxidases in a bioelectrochemical cell are not inactivated by H₂O₂ and as a result the operational lifetimes of the oxidases were increased about five-fold.     

Odor and (bio)diversity: single enantiomers of chiral fragrant substances

Our sense of smell is enantioselective. This review reports interesting examples of single stereoisomers of natural and synthetic odorants, prepared via bioorganic routes, that support this statement. This article is the summary of a talk given at the Flavours & Fragrances 2004 conference in Manchester at the MCC/UMIST, 12-14 May, 2004.     

pH effects on optical and DNA binding properties of a thiophene-containing ruthenium(II) complex

A new ruthenium(II) complex, [Ru(bpy)₂(Htip)]Cl₂ {where bpy = 2,2′-bipyridine and Htip = 2-(thiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}, has been synthesized and characterized by ¹H NMR spectroscopy, elemental analysis, and mass spectrometry. The pH effects on UV-Vis absorption and emission spectra of the complex have been studied, and the ground- and excited-state acidity ionization constant values have been derived. The calf thymus (ct) DNA binding properties of the complex have been investigated with UV-Vis absorption and luminescence titrations, steady-state emission quenching by [Fe(CN)₆]⁴⁻, DNA competitive binding with ethidium bromide, DNA melting experiments, and viscosity measurements. The molecular structures and electronic properties of [Ru(bpy)₂(Htip)]²⁺ and deprotonated form [Ru(bpy)₂(tip)]⁺ have also been investigated by means of density functional theory calculations in an effort to understand the DNA binding properties. The results suggest that the complex undergo three-step successive protonation/deprotonation reactions with one of which occurring over physiological pH region, and act as a ct-DNA intercalator with an intrinsic DNA binding constant value on 10⁵ M⁻¹ order of magnitude that is insensitive to pH.