Volatile sensation: The chemical ecology of the earthy odorant geosmin

Geosmin may be the most familiar volatile compound, as it lends the earthy smell to soil. The compound is a member of the largest family of natural products, the terpenoids. The broad distribution of geosmin among bacteria in both terrestrial and aquatic environments suggests that this compound has an important ecological function, for example, as a signal (attractant or repellent) or as a protective specialized metabolite against biotic and abiotic stresses. While geosmin is part of our everyday life, scientists still do not understand the exact biological function of this omnipresent natural product. This minireview summarizes the current general observations regarding geosmin in prokaryotes and introduces new insights into its biosynthesis and regulation, as well as its biological roles in terrestrial and aquatic environments.     

Inferring landscape resistance to gene flow when genetic drift is spatially heterogeneous

In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the ‘true’ cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the ‘true’ costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the ‘true’ scenario (cost distance Mantel correlations), but this ‘true’ scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the ‘true’ scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data.     

Recherches cytogénétiques sur les solanum,section tuberarium

Résumé Il ressort de divers essais de traitement de graines deS. Antipoviczii, par la colchicine, que la concentration optima est de l'ordre de 0,2%. La durée de l'immersion doit être d'environ 6 heures, s'il s'agit de graines prégermées; de 5 à 6 jours, s'il s'agit de graines sèches. Des observations analogues ont été faites, après traitements semblables, chezS. verrucosum etS. longipedicellatum.Le traitement, dans les conditions précitées, de graines deS. tuberosum, variétés Flava et Katahdin, a donné des plantes octoploïdes réduites, à feuilles coriaces, à pigmentation très foncée, terminalement ramifiées (Flava) ou non ramifiées (Katahdin); elles se sont montrées entièrement stériles pendant deux années consécutives, après avoir végété pendant 9 à 10 mois; leurs tubercules sont petits et peu nombreux.

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Summary Various colchicine treatments of seeds, inS. Antipoviczii, have shown that the optimum concentration of the solution is 0,2%. Pre-germinated seeds should be soaked for about 6 hours and dry seeds 5 or 6 days, as is indicated through cytological analysis at various steps of the treatment. The same result have been obtained withS. verrucosum andS. longipedicellatum.After such a treatment, octoploids plants ofS. tuberosum var. Flava and var. Katahdin have been produced, which remain small and form thick dark-green leaves; the stem is thick, but very flexible, with dense terminal ramification (Flava) or without ramification (Katahdin). They produce a few small tubers but are completely sterible; in 1953 and in 1954, no flower has appeared even after a vegetative period of 9–10 months each year.

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Samenvatting Een vergelijking van verschillende colchicine-concentraties, waarin zaden vanSolanum antipoviczii geweekt werden, heeft aangetoond dat de optimum-concentratie van de oplossing 0.2% bedraagt. Voorgekiemde zaden verlangen een onderdompeling van ongeveer zes uur, droge zaden vereisen vijf tot zes dagen, zoals bleek uit een cytologische analyse op verschillende tijdstippen tijdens de behandeling. Dezelfde resultaten werden verkregen metS. verrucosum en metS. longipedicellatum.Na zulk een behandeling werden octoploide planten vanS. tuberosum var. Flava en var. Katahdin verkregen, welke planten klein blijven en donkergroene, leerachtige bladeren vormen; de stengel is dik, maar goed buigbaar, met een dichte terminale vertakking (Flava) of onvertakt (Katahdin). Deze planten bleken twee jaar lang (1953 en 1954) volkomen steriel te zijn, in deze zin, dat ze na een vegetatieve groeitijd van 9–10 maanden niet tot bloei zijn gekomen. Wel produceerden ze talrijke kleine knolletjes.

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Recherches subsidiées par le Fonds National de la Recherche Scientifique (Crédits aux Chercheurs).     

A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana.

This work proposes a model of the metabolic branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana which involves kinetic competition for phosphohomoserine between the allosteric enzyme threonine synthase and the two-substrate enzyme cystathionine gamma-synthase. Threonine synthase is activated by S-adenosylmethionine and inhibited by AMP. Cystathionine gamma-synthase condenses phosphohomoserine to cysteine via a ping-pong mechanism. Reactions are irreversible and inhibited by inorganic phosphate. The modelling procedure included an examination of the kinetic links, the determination of the operating conditions in chloroplasts and the establishment of a computer model using the enzyme rate equations. To test the model, the branch-point was reconstituted with purified enzymes. The computer model showed a partial agreement with the in vitro results. The model was subsequently improved and was then found consistent with flux partition in vitro and in vivo. Under near physiological conditions, S-adenosylmethionine, but not AMP, modulates the partition of a steady-state flux of phosphohomoserine. The computer model indicates a high sensitivity of cystathionine flux to enzyme and S-adenosylmethionine concentrations. Cystathionine flux is sensitive to modulation of threonine flux whereas the reverse is not true. The cystathionine gamma-synthase kinetic mechanism favours a low sensitivity of the fluxes to cysteine. Though sensitivity to inorganic phosphate is low, its concentration conditions the dynamics of the system. Threonine synthase and cystathionine gamma-synthase display similar kinetic efficiencies in the metabolic context considered and are first-order for the phosphohomoserine substrate. Under these conditions outflows are coordinated.     

The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences.

In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with the observed ones to appraise the behaviour of a known x-ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time-consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined. A simulation of hydrophobic effects in an aqueous environment is also proposed which seems to provide a better approximation of the observed solution structure of the protein.     

Replication of macrophage-tropic and T-cell-tropic strains of human immunodeficiency virus type 1 is augmented by macrophage-endothelial cell contact.

Macrophages perform a central role in the pathogenesis of human immunodeficiency virus type 1 (HIV-1) infection and have been implicated as the cell type most prominent in the development of central nervous system impairment. In this study, we evaluated the effect of interaction between macrophages and endothelial cells on HIV-1 replication. Upregulation of HIV-1 replication was consistently observed in monocyte-derived macrophages (hereafter called macrophages) cocultured with either umbilical vein endothelial cells or brain microvascular endothelial cells. HIV-1 p24 antigen production of laboratory-adapted strains and patient-derived isolates was increased 2- to 1,000-fold in macrophage-endothelial cocultures, with little or no detectable replication in cultures containing endothelial cells only. The upregulation of HIV-1 in macrophage-endothelial cocultures was observed not only for viruses with the non-syncytium-inducing, macrophage-tropic phenotype but also for viruses previously characterized as syncytium inducing and T-cell tropic. In contrast, cocultures of macrophages with glioblastoma, astrocytoma, cortical neuronal, fibroblast, and placental cells failed to increase HIV-1 replication. Enhancement of HIV-1 replication in macrophage-endothelial cocultures required cell-to-cell contact; conditioned media from endothelial cells or macrophage-endothelial cocultures failed to augment HIV-1 replication in macrophages. Additionally, antibody to leukocyte function-associated antigen (LFA-1), a macrophage-endothelial cell adhesion molecule, inhibited the enhanced HIV-1 replication in macrophage-endothelial cell cocultures. Thus, these data indicate that macrophage-endothelial cell contact enhances HIV-1 replication in macrophages for both macrophage-tropic and previously characterized T-cell-tropic strains and that antibody against LFA-1 can block the necessary cell-to-cell interaction required for the observed upregulation. These findings may have important implications for understanding the ability of HIV-1 to replicate efficiently in tissue macrophages, including those in the brain and at the blood-brain barrier.