The deactivation pathways of the excited-states of the mycosporine-like amino acids shinorine and porphyra-334 in aqueous solution.

In vitro studies on the structurally related mycosporine-like amino acids (MAAs) porphyra-334 and shinorine in aqueous solutions were carried out aiming at their full photochemical and photophysical characterization and expanding the evidence on the assigned UV-photoprotective role of the molecules in vivo. The experiments on shinorine confirmed a high photostability and a poor fluorescence quantum yield, in concordance with previous results on porphyra-334. The estimation of triplet production quantum yields for both MAAs was achieved by laser-flash photolysis measurements. In particular, photosensitization experiments on porphyra-334 support the participation of the triplet state in the photodecomposition mechanism yielding a more precise value of [capital Phi](T). As well, photoacoustic calorimetry experiments allowed the first direct quantification of the nonradiative relaxation pathways of the excited MAAs in solution, corroborating that the vast majority (ca. 97%) of the absorbed energy is promptly delivered to the surroundings as heat, consistently with the low photodecomposition and emission yields observed.     

The ability of rufous hummingbirds Selasphorus rufus to dilute and concentrate urine

Most terrestrial animals face the challenge of having to conserve water in a desiccating environment. Not surprisingly, the ability to produce concentrated urine has been relatively well studied in birds. Nectar-feeding birds are unusual among terrestrial animals in that they often ingest and excrete prodigious water volumes to obtain adequate energy. Thus, they confront the unusual challenge of having to conserve electrolytes. The diluting abilities of birds and the renal mechanisms that may correlate with them have been relatively neglected. To elucidate diluting and concentrating abilities in nectar-feeding birds, we fed rufous hummingbirds Selasphorus rufus an electrolyte-free nectar and a nectar containing a range of NaCl concentrations. Hummingbirds had a spectacular (and possibly unique) diluting ability: when fed on electrolyte-free food they produced excreta containing less than 0.5 mM l⁻¹ each of sodium and potassium. Hummingbirds also had a poor concentrating ability, retaining sodium and chloride when their food (0.632 M l⁻¹ sucrose) contained more than 35 mM l⁻¹ of NaCl. The kidneys of hummingbirds do not appear to be suited for concentrating urine, and possibly contain structural features that give them a unique diluting ability compared with those of birds that do not feed on nectar.     

Evaluation of coupling conditions for the incorporation of Nα-Fmoc-Tyr(PO3H2)-OH in solid-phase peptide synthesis

Summary In order to minimise the formation of the pyrophosphate derivative of the target peptide when side-chain-unprotected phopshotyrosine is used in solid-phase peptide synthesis, this building block can be incorporated using benzotriazolyloxy-tris-(dimethylamino)phosphonium hexafluorophosphate/1-hydroxybenzotriazole/N-methylmorpholine (1:1:2.3) in the presence of a chaotropic salt (0.4 M LiCl in N-methyl-2-pyrrolidinone).Abbreviations BOP benzotriazolyloxy-tris-(dimethylamino)phosphonium hexafluorophosphate - DIEA diisopropylethylamine - Fmoc 9-fluorenylmethoxycarbony - HATU N-[(dimethylamino)1H-1,2,3-triazolo[4,5-b]pyridin-1-ylmethylene]-N-methylmethan-aminium hexafluorophosphate N-oxide - HOBt 1-hydroxybenzotriazole - HPLC high-performance liquid chromatography - MALDI-TOF matrix-assisted laser-desorption ionization time-of-flight mass spectrometry - NMM N-methylmorpholine - NMP N-methyl-2-pyrrolidinone - Pmc 2,2,5,7,8-pentamethyl-chroman-6-sulfonyl - ® solid support - TFA trifluoroacetic acid - TPTU 2-(2-pyridon-1-yl)-1,1,3,3-tetramethyluroniumfluoroborate. Abbreviations used for amino acids follow the recommendations of the IUPAC-IUB Commission of Biochemical Nomenclature [Eur. J. Biochem., 138 (1984) 9]     

Phase labeling of C−H and C−C spin-system topologies: Application in PFG-HACANH and PFG-HACA(CO)NH triple-resonance experiments for determining backbone resonance assignments in proteins

Summary Triple-resonance experiments can be designed to provide useful information on spin-system topologies. In this paper we demonstrate optimized proton and carbon versions of PFG-CT-HACANH and PFG-CT-HACA(CO)NH straight-through triple-resonance experiments that allow rapid and almost complete assignments of backbone H, ¹³C, ¹⁵N and H^N resonances in small proteins. This work provides a practical guide to using these experiments for determining resonance assignments in proteins, and for identifying both intraresidue and sequential connections involving glycine residues. Two types of delay tunings within these pulse sequences provide phase discrimination of backbone Gly C and H resonances: (i) C–H phase discrimination by tuning of the refocusing period _{a_f}; (ii) C–C phase discrimination by tuning of the ¹³C constant-time evolution period 2T_c. For small proteins, C–C phase tuning provides better S/N ratios in PFG-CT-HACANH experiments while C–H phase tuning provides better S/N ratios in PFG-CT-HACA(CO)NH. These same principles can also be applied to triple-resonance experiments utilizing ¹³C-¹³C COSY and TOCSY transfer from peripheral side-chain atoms with detection of backbone amide protons for classification of side-chain spin-system topologies. Such data are valuable in algorithms for automated analysis of resonance assignments in proteins.     

Redox-Bohr effect in the tetrahaem cytochrome c3 from Desulfovibrio vulgaris: a model for energy transduction mechanisms

 Using potentiometric titrations, two protons were found to participate in the redox-Bohr effect observed for cytochrome c ₃ from Desulfovibrio vulgaris (Hildenborough). Within the framework of the thermodynamic model previously presented, this finding supports the occurrence of a concerted proton-assisted 2e^– step, ideally suited for the coupling role of cytochrome c ₃ to hydrogenase. Furthermore, at physiological pH, it is shown that when sulfate-reducing bacteria use H₂ as energy source, cytochrome c ₃ can be used as a charge separation device, achieving energy transduction by energising protons which can be left in the acidic periplasmic side and transferring deenergised electrons to sulfate respiration. This mechanism for energy transduction, using a full thermodynamic data set, is compared to that put forward to explain the proton-pumping function of cytochrome c oxidase.     

The vegetable rennet of Cynara cardunculus L. contains two proteinases with chymosin and pepsin-like specificities

The flowers of cardoon (genus Cynara) are traditionally used in Portugal for cheese making. In this work the vegetable rennet of the species Cynara cardunculus L. was characterized in terms of enzymic composition and proteolytic specificity of its proteinases (cardosin A and cardosin B). Cardosin A was found to cleave insulin B chain at the bonds Leu15-Tyr16, Leu17-Val18 and Phe25-Tyr26. In addition to the bonds mentioned cardosin B cleaves also Glu13-Ala14, Ala14-Leu15 and Phe24-Phe25 indicating that it has a broader specificity. The kinetic parameters for the hydrolysis of the synthetic peptide Leu-Ser-Phe(NO₂)-Nle-Ala-Leu-oMe were also determined and compared to those of chymosin and pepsin. The results obtained indicate that in terms of specificity and kinetic parameters cardosin A is similar to chymosin whereas cardosin B is similar to pepsin. It appears therefore that the enzyme composition of cardoon rennet closely resembles that of calf rennet.     

Changes in the origin and quality of soil organic matter after pasture introduction in Rondônia (Brazil)

We examined the effects of the conversion of tropical forest to pasture on soil organic matter (SOM) origin and quality along a chronosequence of sites, including a primary forest and six pastures. Bulk soil samples received a physical size-fractionation treatment to assess the contribution of each compartment to total SOM pool. Besides a general increase in total C and N stocks along the chronosequence, we observed a reduction of the relative contribution of the coarser fractions to total soil C content, and an increased concentration in the finer fractions. The origin of the C in each size fraction was established from measurements of¹³C abundance. After 80 years about 93% of the C in the least humified fraction of the top 10 cm of soil was of pasture origin, while in the most humified it was 82%. Chemical analyses indicated that the fine silt and coarse clay fractions contained the most refractory carbon.     

Age structure,growth and reproduction ofRutilus lemmingii in an intermittent stream of the Guadalquivir river basin,southern Spain

The age, growth and reproduction ofRutilus lemmingii (Steindachner, 1866), an endemic cyprinid from the Iberian Peninsula, was studied for over a period of two years in a small seasonal tributary of the Guadalquivir river basin. Approximately 65 % of the total growth in length occured in the first year of life. Males reached a maximum age of 3+ yr (Fork Length, F.L. = 114 mm) and females 4+ yr (F.L. = 144 mm). Both sexes matured during their second year of life (1 +). The overall sex ratio (334 males to 389 females) differed significantly from unity. Somatic condition decreased markedly during the reproductive period of March to May.R. lemmingii is a multiple spawner and releases two batches of eggs per female each year. Mean egg diameter of the first batch was larger than the second one. The regression between fecundity and Fork Length (mm) was: Fec = 0.014 F.L.Z.^2.858 Compared with available information, thisR. lemmingii population, located at a lower latitude, is characterized by fast growth, early maturity, high level of reproductive effort, and a short life-span. These life-history characteristices are typical of species in unstable environments, where adult mortality is high, variable or unpredictable.     

Monte Carlo Study of Structural and Thermodynamic Properties of Liquid Chloroform Using a Five Site Model

A five site potential model combining Lennard–Jones plus Coulomb potential functions has been developed for chloroform molecule. The partial charges needed for Coulombic interactions were derived using the chelpg procedure implemented in the gaussian 92 program. These calculations were performed at the MP2 level with MC-311G* basis set for Cl and 6-311G** for C and H atoms. The parameters for the Lennard–Jones potentials were optimized to reproduce experimental values for the density and enthalpy of vaporization of the pure liquid at 298 K and 1 atm. The statistical mechanics calculations were performed with the Monte Carlo method in the isothermic and isobaric (NpT) ensemble. Besides the values obtained for density, ρ, and molar enthalpy of vaporization at constant pressure, Δ H_V, for liquid chloroform, results for molar volume, V_m, molar heat capacity, C_p, isobaric thermal expansivity, α_p, and isothermal compressibility, κ_T, for this pure liquid are also in very good agreement with experimental observations. Size effects on the values of thermodynamic properties were investigated. The potential model was also tested by computing the free energy for solvating one chloroform molecule into its own liquid at 298 K using a statistical perturbation approach. The result obtained compares well with the experimental value. Site–site pair correlation functions were calculated and are in good accordance with theoretical results available in the literature. Dipole–dipole correlation functions for the present five site model were also calculated at different carbon–carbon distances. These correlations were compared to those obtained using the four site model reported in the literature. An investigation of the solvent dependence of the relative free energy for cis/trans conversion of a hypothetical solute in TIP4P water and chloroform was accomplished. The results show strong interaction of water and chloroform molecules with the gauche conformer. The value obtained for the free energy barrier for cis/trans rotation in TIP4P water is higher than that for chloroform. This result is in agreement with the continuous theory for solvation as the conformer with higher dipole moment is more favoured by the solvent with higher dieletric constant. The results also show an increase in entropy as the solute goes from the cis to the trans geometry and this result is more appreciable in the aqueous solution. This revised version was published online in June 2006 with corrections to the Cover Date.