Global biostratigraphic comparison and correlation of an early Cisuralian palynoflora from Bolivia

This paper presents new data about Early Permian (Cisuralian) strata, palynostratigraphy and absolute dating from the Copacabana Formation in central Bolivia. Recent stratigraphic and palynologic data from marine and transitional rocks at Apillapampa refine the age of Cisuralian palynomorphs in South America. Twelve samples interbedded with five volcanic ashes (processed and productive) yielded 94 palynomorph species arranged in two informal palynoassemblages: the lower assemblage Vittatina costabilis corresponds to one sample near the base of the Copacabana Formation and the upper Lueckisporites virkkiae assemblage occurs in overlying marine and coal-bearing transitional intervals. Ages were also independently refined by a modern review of conodonts, fusulinids, along with those U–Pb radiometric ages (Isotope Dilution Thermal Ionization Mass Spectrometry [ID-TIMS] of zircon-bearing interbedded tuffs). These data suggest that the lower marine member of the Copacabana Formation at this location is Asselian and Sakmarian. Lueckisporites virkkiae is a key species of palynomorph utilised in South American and global Permian biostratigraphic reconstructions. Hence, a thorough global comparison of these palynofloras and correlations is addressed in this contribution, considering first appearances of mainly cosmopolitan diagnostic taxa. Correlations are established with many similar Permian palynofloras, some also constrained with radiometric data, in South America (Brazil, Uruguay and Argentina) and elsewhere.     

Synthesis and FTIR Conformational Studies of Peptides From the Basic Region of c-Jun: a Critical Analysis on the Basis of CD and NMR Data

Abstract

The peptide (35 residues) corresponding to the basic subdomain (bSD) of c-Jun (residues 252–281) and its fragments NP (N-terminal peptide, 1–19) and CP (C-terminal peptide, 1635) were synthesized in stepwise solid-phase using the tert-butyloxycarbonyl/benzyl strategy. In a previous paper, we have shown that during its binding to the DNA site CRE (cAMP- responsive element) the bSD structure was converted into α-helix from an initial random coil conformation [Krebs, D., Dahmani, B., El Antri, S., Monnot, M., Convert, O., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem. 231, 370–380 (1995)]. Our results suggested both a high flexibility and a helical potential in bSD, these two properties seeming crucial for the accommodation of the basic subdomain of c-Jun to its specific DNA targets. In this work, we assessed the conformational variability of bSD through the study of the secondary structures of its NP and CP fragments in trifluoroethanol (TFE)/²H₂O mixtures, using Fourier transform infrared (FTIR) spectroscopy. The IR results were critically analyzed in light of our previously reported circular dichroism (CD) and NMR data [Krebs, D., Dahmani, B., Monnot, M., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem. 235, 699–712 (1996)]. Upon addition of TFE, the relative areas of the seven components of the amide I band (1700–1620 cm^?1) reflected the conversion of a large amount of random coil conformation into α-helix for the two fragments and bSD. This effect was accompanied by more subtle variations of the less populated structures, in agreement with the results of CD and NMR experiments. The IR results stipulated the conservation of the parent bSD secondary structures in both fragments; however, NP and CP peptides did not display similar random-to-α-helix stabilization pattern upon additions of TFE to aqueous solutions. The profile from CD signal at 222 nm was found sigmoidal for NP and almost linear for CP, while that corresponding to the parent peptide bSD was just in between those of its fragments. Thus, the present study confirms the high flexibility and helix propensity of the c-Jun basic subdomain and suggests that the N- and C-terminal parts of the peptide do not follow the same random-to-helix conversion profile during their complexation with DNA.     

Texture perception through direct and indirect touch: An analysis of perceptual space for tactile textures in two modes of exploration

Considerable information about the texture of objects can be perceived remotely through a probe. It is not clear, however, how texture perception with a probe compares with texture perception with the bare finger. Here we investigate the perception of a variety of textured surfaces encountered daily (e.g., corduroy, paper, and rubber) using the two scanning modes—direct touch through the finger and indirect touch through a probe held in the hand—in two tasks. In the first task, subjects rated the overall pair-wise dissimilarity of the textures. In the second task, subjects rated each texture along three continua, namely, perceived roughness, hardness, and stickiness of the surfaces, shown previously as the primary dimensions of texture perception in direct touch. From the dissimilarity judgment experiment, we found that the texture percept is similar though not identical in the two scanning modes. From the adjective rating experiments, we found that while roughness ratings are similar, hardness and stickiness ratings tend to differ between scanning conditions. These differences between the two modes of scanning are apparent in perceptual space for tactile textures based on multidimensional scaling (MDS) analysis. Finally, we demonstrate that three physical quantities, vibratory power, compliance, and friction carry roughness, hardness, and stickiness information, predicting perceived dissimilarity of texture pairs with indirect touch. Given that different types of texture information are processed by separate groups of neurons across direct and indirect touch, we propose that the neural mechanisms underlying texture perception differ between scanning modes.     

Another call for the end of invasion biology

The restriction of invasion biology to non‐native species has been laid down as one founding principle of the discipline by many researchers. However, this split between native and non‐native species is highly controversial. Using a phenomenological approach and a more pragmatic examination of biological invasions, the present paper discusses how this dichotomy has restricted the relevance of the field, both from theoretical and practical viewpoints. We advocate the emergence of a broader disciplinary field.     

A comparison of the strength of biodiversity effects across multiple functions

In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.     

Water stress impact on young seedling growth of Acacia arabica

Drought is the major constraint in arid regions throughout the world and identification of drought-resistant plants is therefore of crucial importance. Since young seedling stage is especially sensitive to water stress, the present work analyzed the physiological behavior of seedling from Acacia arabica issued from a dry area, grown under controlled environmental conditions and subjected to progressive soil drying. Although soil gravimetric water content (g H₂O g^?1 soil dry weight) dropped from 80 % to less than 35 %, most plants remained alive until the end of the water stress. Seedlings were able to efficiently close their stomata to reduce water losses and accumulated high amounts of proline. Despite osmotic adjustment, turgor pressure decreased in stressed plants and could explain the stress-induced inhibition of plant growth. Decrease in net photosynthesis was related to stress-induced decrease in stomatal conductance and not to any impact on chlorophyll concentration or fluorescence-related parameter: both PSII efficiency and photochemical quenching remained unaffected by water stress while drought-induced increase in non-photochemical quenching should be regarded as a strategy to avoid over-energisation of the photosynthetic apparatus. Instantaneous water use efficiency increased in stressed plants comparative to controls. Oxidative stress estimated by malondialdehyde concentration was recorded only at the end of the treatment, suggesting that stressed plants remained able to cope with reactive oxygen species. Water stress induced an increase in anthocyanins, while aglycone flavonols decreased. Those compounds were not involved in the management of oxidative stress. It is concluded that A. arabica is a promising drought-resistant plant species for rehabilitation of dry areas.     

Solid-state NMR Study Reveals Collagen I Structural Modifications of Amino Acid Side Chains upon Fibrillogenesis

In vivo, collagen I, the major structural protein in human body, is found assembled into fibrils. In the present work, we study a high concentrated collagen sample in its soluble, fibrillar, and denatured states using one and two dimensional {¹H}-¹³C solid-state NMR spectroscopy. We interpret ¹³C chemical shift variations in terms of dihedral angle conformation changes. Our data show that fibrillogenesis increases the side chain and backbone structural complexity. Nevertheless, only three to five rotameric equilibria are found for each amino acid residue, indicating a relatively low structural heterogeneity of collagen upon fibrillogenesis. Using side chain statistical data, we calculate equilibrium constants for a great number of amino acid residues. Moreover, based on a ¹³C quantitative spectrum, we estimate the percentage of residues implicated in each equilibrium. Our data indicate that fibril formation greatly affects hydroxyproline and proline prolyl pucker ring conformation. Finally, we discuss the implication of these structural data and propose a model in which the attractive force of fibrillogenesis comes from a structural reorganization of 10 to 15% of the amino acids. These results allow us to further understand the self-assembling process and fibrillar structure of collagen.     

A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION*

Oligopeptidases impose a size limitation on their substrates, the mechanism of which has long been under debate. Here we present the structure of a hexameric serine protease, an oligopeptidase from Pyrococcus horikoshii (PhAAP), revealing a complex, self-compartmentalized inner space, where substrates may access the monomer active sites passing through a double-gated “check-in” system, first passing through a pore on the hexamer surface and then turning to enter through an even smaller opening at the monomers'' domain interface. This substrate screening strategy is unique within the family. We found that among oligopeptidases, a residue of the catalytic apparatus is positioned near an amylogenic β-edge, which needs to be protected to prevent aggregation, and we found that different oligopeptidases use different strategies to achieve such an end. We propose that self-assembly within the family results in characteristically different substrate selection mechanisms coupled to different multimerization states.     

Monosaccharide precursors for boosting chondroitin-like capsular polysaccharide production

Chondroitin sulfate is a well-known bioactive molecule, widely used as an anti-osteoarthritis drug, that is nowadays mainly produced by animal tissue sources with unsafe extraction procedures. Recent studies have explored an integrated biotechnological–chemical strategy to obtain a chondroitin sulfate precursor from Escherichia coli K4 capsular polysaccharide, demonstrating the influence of environmental and growth conditions on capsule synthesis. In this research work, the flexibility of the strain biosynthetic machinery was investigated to enhance the K4 capsular polysaccharide production by supplementing the growth medium with the monosaccharides (glucuronic acid, galactosamine and fructose) that constitute the chain. Shake flask experiments were performed by adding the sugars singularly or together, by testing monosaccharide different concentrations and times of addition and by observing the bacterial sugar consumption. A K4 capsular polysaccharide production enhancement, compared to the control, was observed in all cases of supplementation and, in particular, significant 68 and 57 % increases were observed when adding 0.385 mM glucuronic acid plus galactosamine or 0.385 mM fructose, respectively. Increased expression levels of the gene kfoC, coding for a K4 polymerase, evaluated in different growth conditions, confirmed the results at the molecular level. Furthermore, batch fermentations, performed in lab-scale reactors (2 L), allowed to double the K4 capsular polysaccharide production values obtained in shake flask conditions, by means of a strict control of the growth parameters.