Characterization of tryptophan environments in glutamate dehydrogenases from temperature-dependent phosphorescence

Tryptophan room temperature phosphorescence in solution was detected in glutamic dehydrogenase from bovine liver and Escherichia coli with lifetimes of 1.2 and 0.65 s, respectively. Although these enzymes possess three and five tryptophanyl residues per polypeptide chain, respectively, the temperature dependence of the phosphorescence quantum yield estimates that the room temperature emission is due, in either case, to a single residue. Long triplet-state lifetimes and very small rates of O2 quenching indicate that these tryptophanyl side chains are embedded in a highly inflexible internal region of the macromolecule. Aided by sequence homology with dehydrogenases of known structure and theoretical predictions of secondary structure [Wootton, J.C. (1974) Nature (London) 252, 542-546; Brett, M., Chambers, G.K., Holder, A. A., Fincham, J.R.S., & Wootton, J.C. (1976) J. Mol. Biol. 106, 1-22], the phosphorescing tryptophans have been tentatively placed in the catalytic coenzyme binding domain of each enzyme. The particular sensitivity of the triplet-state lifetime in probing local changes in conformation provides a strong indication that within the time window of phosphorescence measurements the six subunits in the hexameric enzymes are equivalent. Furthermore, while in the bovine enzyme this parameter is markedly affected by the interaction with ligands which have a functional role, the constancy of the phosphorescence lifetime at various degrees of polymerization suggests that the association process is not accompanied by important conformational changes in the macromolecule.     

Eye factors and lens-forming transformations of outer cornea in Xenopus laevis larvae

Outer cornea of lensectomized Xenopus laevis tadpoles at state 50 (according to Nieuwkoop, P.D. and Faber, J., ('56) Normal Table of Xenopus laevis, Daudin, North-Holland, Amsterdam, pp. 1-243) was removed 3, 7 and 10 days after lensectomy and implanted between the outer and the inner cornea of larvae of the same species at stage 51-52. In these conditions, the implanted outer cornea remained isolated from the retinal factor of the vitreous chamber, although it received the nutritional factors normally reaching the outer cornea. Results show that lens-forming transformation process of the outer cornea is arrested, and lens-forming structures undergo regression at speed which increases with increasing precocity of the stage of lens-forming transformation undergone by the implanted cornea. These data suggest that the process of lens-forming transformation is not a single-step process, but a sequence of interactions extending over a long period of time requiring the continuous presence of the retinal factor in the vitreous chamber until complete differentiation of the lens is achieved.     

Heterogeneity of protein conformation in solution from the lifetime of tryptophan phosphorescence

The decay of Trp phosphorescence of proteins in fluid solutions was shown to provide a sensitive tool for probing the conformational homogeneity of these macromolecules in the millisecond to second time scale. Upon examination of 15 single Trp emitting proteins multiexponential decays were observed in 12 cases, a demonstration that the presence of slowly interconverting conformers in solution is more the norm rather than an exception. The amplitude of preexponential terms, from which the conformer equilibrium is derived, was found to be a sensitive function of solvent composition (buffer, pH, ionic strength and glycerol cosolvent), temperature, and complex formation with substrates and cofactors. In many cases, raising the temperature, a point is reached at which the decay becomes practically monoexponential, meaning that conformer interconversion rates have become commensurate with the triplet lifetime. Estimation of activation free energy barriers to interconversion shows that the large values of DeltaG* are rather similar among polypeptides and that the protein substates involved are sufficiently long-lived to display individual binding/catalytic properties.     

Native tree regeneration in native tree plantations: understanding the contribution of Araucaria angustifolia to biodiversity conservation in the threatened Atlantic Forest in Argentina

Deforestation is a global process that has strongly affected the Atlantic Forest in South America, which has been recognised as a threatened biodiversity hotspot. An important proportion of deforested areas were converted to forest plantations. Araucaria angustifolia is a native tree to the Atlantic Forest, which has been largely exploited for wood production and is currently cultivated in commercial plantations. An important question is to what extent such native tree plantations can be managed to reduce biodiversity loss in a highly diverse and vulnerable forest region . We evaluated the effect of stand age, stand basal area, as a measure of stand density, and time since last logging on the density and richness of native tree regeneration in planted araucaria stands that were successively logged over 60 years, as well as the differences between successional groups in the response of plant density to stand variables. We also compared native tree species richness in planted araucaria stands to neighbouring native forest. Species richness was 71 in the planted stands (27 ha sampled) and 82 in native forest (18 ha sampled) which approximate the range of variation in species richness found in the native forests of the study area. The total abundance and species richness of native trees increased with stand age and time since last logging, but ecological groups differed in their response to such variables. Early secondary trees increased in abundance with stand age 3–8 times faster than climax or late secondary trees. Thus, the change in species composition is expected to continue for a long term. The difference in species richness between native forest and planted stands might be mainly explained by the difference in plant density. Therefore, species richness in plantations can contribute to local native tree diversity if practices that increase native tree density are implemented.     

Robustness of a meta-network to alternative habitat loss scenarios

Studying how habitat loss affects the tolerance of ecological networks to species extinction (i.e. their robustness) is key for our understanding of the influence of human activities on natural ecosystems. With networks typically occurring as local interaction networks interconnected in space (a meta-network), we may ask how the loss of specific habitat fragments affects the overall robustness of the meta-network. To address this question, for an empirical meta-network of plants, herbivores and natural enemies we simulated the removal of habitat fragments in increasing and decreasing order of area, age and connectivity for plant extinction and the secondary extinction of herbivores, natural enemies and their interactions. Meta-network robustness was characterized as the area under the curve of remnant species or interactions at the end of a fragment removal sequence. To pinpoint the effects of fragment area, age and connectivity, respectively, we compared the observed robustness for each removal scenario against that of a random sequence. The meta-network was more robust to the loss of old (i.e. long-fragmented), large, connected fragments than of young (i.e. recently fragmented), small, isolated fragments. Thus, young, small, isolated fragments may be particularly important to the conservation of species and interactions, while contrary to our expectations larger, more connected fragments contribute little to meta-network robustness. Our findings highlight the importance of young, small, isolated fragments as sources of species and interactions unique to the regional level. These effects may largely result from an unpaid extinction debt, whereby younger fragments are likely to lose species over time. Yet, there may also be more long-lasting effects from cultivated lands (e.g. water, fertilizers and restricted cattle grazing) and network complexity in small, isolated fragments. Such fragments may sustain important biological diversity in fragmented landscapes, but maintaining their conservation value may depend on adequate restoration strategies.     

Diversity in proteinase specificity of thermophilic lactobacilli as revealed by hydrolysis of dairy and vegetable proteins

Ability of industrially relevant species of thermophilic lactobacilli strains to hydrolyze proteins from animal (caseins and β-lactoglobulin) and vegetable (soybean and wheat) sources, as well as influence of peptide content of growth medium on cell envelope-associated proteinase (CEP) activity, was evaluated. Lactobacillus delbrueckii subsp. lactis (CRL 581 and 654), L. delbrueckii subsp. bulgaricus (CRL 454 and 656), Lactobacillus acidophilus (CRL 636 and 1063), and Lactobacillus helveticus (CRL 1062 and 1177) were grown in a chemically defined medium supplemented or not with 1 % Casitone. All strains hydrolyzed mainly β-casein, while degradation of α_s-caseins was strain dependent. Contrariwise, κ-Casein was poorly degraded by the studied lactobacilli. β-Lactoglobulin was mainly hydrolyzed by CRL 656, CRL 636, and CRL 1062 strains. The L. delbrueckii subsp. lactis strains, L. delbrueckii subsp. bulgaricus CRL 656, and L. helveticus CRL 1177 degraded gliadins in high extent, while the L. acidophilus and L. helveticus strains highly hydrolyzed soy proteins. Proteinase production was inhibited by Casitone, the most affected being the L. delbrueckii subsp. lactis species. This study highlights the importance of proteolytic diversity of lactobacilli for rational strain selection when formulating hydrolyzed dairy or vegetable food products.     

Caudal Brainstem Raphe Nuclei: Neural Substrate for their Involvement in the Expression of Some Biological Rhythms

Nucleus raphe pallidus (RPa) lies ventrally in the caudal brainstem, where it is coextensive rostrally with the nucleus raphe magnus (RMg) and caudally with the nucleus raphe obscurus (ROb). Retrograde neuronal tracing studies of our laboratory, carried out in rats and presented elsewhere, with fluorogold, true-blue or fast-blue, iontophoretically injected or by crystalline deposit, along the RPa extent, displayed many labeled pericaria at the preoptic area (POA), as well as lateral (LH) and dorsomedial (DMH) hypothalamus; paraventricular nucleus (PVN) and dorsal (DR) and median (MnR) raphe nuclei among others structures. In addition, RPa, which projects to the intermediolateral column, has been demonstrated to bear relation to many of the somatic-visceral functions also reported for POA. Iontophoretic injections of PHA-L, an anterograde tracer, in the POA subnuclei, presented terminal and varicose labeled fibers in RPa, as well as in the RMg, ROb, paraventricular thalamic (PVA), PVN and supraoptic nucleus (SO), LH, subparaventricular zone (sPVZ) and locus coeruleus (LC). Interestingly, POA, PVA, PVN, LH and SO have been described as retino- and suprachiasmatic-recipients. Taken together, these neuronal connections between brainstem raphe nuclei and POA, the similarity of functions to which they are related, as well as connections with other retino-suprachiasmatic-recipient structures, suggest that these caudal brainstem raphe nuclei could be part of the output system for the expression of some biological rhythms.     

Achillea ligustica: composition and antimicrobial activity of essential oils from the leaves, flowers and some pure constituents

The composition of the essential oils obtained from the leaves and the flowers of Achillea ligustica (Asteraceae) growing in Sicily has been studied. The main constituents of the leaves were 4-terpineol (19.3%), carvone (8.9%), γ-terpinene (7.2%) and β-phellandrene (6.8%). 4-terpineol (12.0%), carvone (10.0%), and β-phellandrene (5.4%), along with linalool (20.4%) and cedrol (4.3%) were detected in the flower’s oil. Furthermore, the antimicrobial activity of the essential oils and of some of the main constituents were assayed on bacteria and fungi. In memory of Prof. Ivano Morelli (1940–2005)