Selective backbone labelling of ILV methyl labelled proteins

Adding the ¹³C labelled 2-keto-isovalerate and 2-oxobutanoate precursors to a minimal medium composed of ¹²C labelled glucose instead of the commonly used (²D, ¹³C) glucose leads not only to the ¹³C labelling of (I, L, V) methyls but also to the selective ¹³C labelling of the backbone C_α and CO carbons of the Ile and Val residues. As a result, the backbone (¹H, ¹⁵N) correlations of the Ile and Val residues and their next neighbours in the (i + 1) position can be selectively identified in HN(CA) and HN(CO) planes. The availability of a selective HSQC spectrum corresponding to the sole amide resonances of the Ile and Val residues allows connecting them to their corresponding methyls by the intra-residue NOE effect, and should therefore be applicable to larger systems.     

Soil decomposition of wheat internodes of different maturity stages: relative impact of the soluble and structural fractions

The aim of this study was to clarify the importance of the soluble fraction on cell wall decomposition. Wheat plant was chosen as a model and was harvested at three stages of maturity: anthesis (A stage), 20 days after anthesis (B stage) and physiological maturity (PM stage). Wheat third internode (numbered down from the ear) were selected for this study. Internode age influenced the cumulative CO(2) kinetics with internodes from wheat stem harvested at anthesis mineralizing 62.1%+/-2.2 of added residue C whereas those harvested at the B and PM stages mineralized 58.8%+/-1.4 and 51.6%+/-1.7, respectively of the added C. Chemical analyses revealed that maturation of the selected internodes mainly altered residue quality by modifying the proportion of soluble to cell wall fractions rather than the quality of these fractions. The hexose to pentose ratios were good biomarkers of microbial sugars for both soluble and cell wall fractions, as were the uronic acids, which are not commonly determined in soil decomposition studies. This study clearly demonstrated that the contents of the internode soluble fraction did not affect the extent of cell wall C mineralization. Therefore, the soluble content of crop residues would not regulate the soil microbial populations able to mineralize cell wall C. However, this needs to be validated on a broader range of residue types with different nature of cell wall C or soluble compounds.     

Enhanced perception in savant syndrome: patterns,structure and creativity

According to the enhanced perceptual functioning (EPF) model, autistic perception is characterized by: enhanced low-level operations; locally oriented processing as a default setting; greater activation of perceptual areas during a range of visuospatial, language, working memory or reasoning tasks; autonomy towards higher processes; and superior involvement in intelligence. EPF has been useful in accounting for autistic relative peaks of ability in the visual and auditory modalities. However, the role played by atypical perceptual mechanisms in the emergence and character of savant abilities remains underdeveloped. We now propose that enhanced detection of patterns, including similarity within and among patterns, is one of the mechanisms responsible for operations on human codes, a type of material with which savants show particular facility. This mechanism would favour an orientation towards material possessing the highest level of internal structure, through the implicit detection of within- and between-code isomorphisms. A second mechanism, related to but exceeding the existing concept of redintegration, involves completion, or filling-in, of missing information in memorized or perceived units or structures. In the context of autistics'' enhanced perception, the nature and extent of these two mechanisms, and their possible contribution to the creativity evident in savant performance, are explored.     

Reduced modeling and state observation of an activated sludge process

This article first proposes a reduction strategy of the activated sludge process model with alternated aeration. Initiated with the standard activated sludge model (ASM1), the reduction is based on some biochemical considerations followed by linear approximations of nonlinear terms. Two submodels are then obtained, one for the aerobic phase and one for the anoxic phase, using four state variables related to the organic substrate concentration, the ammonium and nitrate‐nitrite nitrogen, and the oxygen concentration. Then, a two‐step robust estimation strategy is used to estimate both the unmeasured state variables and the unknown inflow ammonium nitrogen concentration. Parameter uncertainty is considered in the dynamics and input matrices of the system. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Nitric oxide donor-mediated inhibition of phosphorylation shows that light-mediated degradation of photosystem II D1 protein and phosphorylation are not tightly linked

An outcome of the photochemistry during oxygenic photosynthesis is the rapid turn over of the D1 protein in the light compared to the other proteins of the photosystem II (PS II) reaction center. D1 is a major factor of PS II instability and its replacement a primary event of the PS II repair cycle. D1 also undergoes redox-dependent phosphorylation prior to its degradation. Although it has been suggested that phosphorylation modulates D1 metabolism, reversible D1 phosphorylation was reported not to be essential for PS II repair in Arabidopsis. Thus, the involvement of phosphorylation in D1 degradation is controversial. We show here that nitric oxide donors inhibit in vivo phosphorylation of the D1 protein in Spirodela without inhibiting degradation of the protein. Thus, D1 phosphorylation is not tightly linked to D1 degradation in the intact plant.     

Association of sugar content QTL and PQL with physiological traits relevant to frost damage resistance in pea under field and controlled conditions

To increase yield in pea (Pisum sativum L.), autumn sowing would be preferable. Hence, frost tolerance of pea became a major trait of interest for breeders. In order to better understand the cold acclimation in pea, Champagne a frost tolerant line and Terese, a frost sensitive line, and their recombinant inbred lines (RIL) were studied. RIL frost tolerance was evaluated by a frost damage scale under field as well as controlled conditions. A quantitative trait loci (QTL) approach was used to identify chromosomal regions linked to frost tolerance. The detected QTL explained from 6.5 to 46.5% of the phenotypic variance. Amongst them, those located on linkage groups 5 and 6 were consistent with over all experiments, in field as well as in controlled environments. In order to improve the understanding of the frost tolerance mechanisms, several cold acclimation key characters such as concentration of sugars, electrolyte leakage, osmotic pressure, and activity of RuBisCO were assessed. Some of these physiological QTL colocalised with QTL for frost damage, in particular two raffinose QTL on LG5 and LG6 and one RuBisCO activity QTL on LG6, explaining 8.8 to 27.0% of the phenotypic variance. In addition, protein quantitative loci were mapped; some of them colocalised with frost damage and physiological QTL on LG5 and LG6, explaining 16.0–43.6% of the phenotypic variance. Raffinose metabolism and RuBisCO activity and its effect on photosynthesis might play a major role in cold acclimation of pea. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of the C1q-binding Sites of Human C1r and C1s: A REFINED THREE-DIMENSIONAL MODEL OF THE C1 COMPLEX OF COMPLEMENT*

The C1 complex of complement is assembled from a recognition protein C1q and C1s-C1r-C1r-C1s, a Ca²⁺-dependent tetramer of two modular proteases C1r and C1s. Resolution of the x-ray structure of the N-terminal CUB₁-epidermal growth factor (EGF) C1s segment has led to a model of the C1q/C1s-C1r-C1r-C1s interaction where the C1q collagen stem binds at the C1r/C1s interface through ionic bonds involving acidic residues contributed by the C1r EGF module (Gregory, L. A., Thielens, N. M., Arlaud, G. J., Fontecilla-Camps, J. C., and Gaboriaud, C. (2003) J. Biol. Chem. 278, 32157–32164). To identify the C1q-binding sites of C1s-C1r-C1r-C1s, a series of C1r and C1s mutants was expressed, and the C1q binding ability of the resulting tetramer variants was assessed by surface plasmon resonance. Mutations targeting the Glu¹³⁷-Glu-Asp¹³⁹ stretch in the C1r EGF module had no effect on C1 assembly, ruling out our previous interaction model. Additional mutations targeting residues expected to participate in the Ca²⁺-binding sites of the C1r and C1s CUB modules provided evidence for high affinity C1q-binding sites contributed by the C1r CUB₁ and CUB₂ modules and lower affinity sites contributed by C1s CUB₁. All of the sites implicate acidic residues also contributing Ca²⁺ ligands. C1s-C1r-C1r-C1s thus contributes six C1q-binding sites, one per C1q stem. Based on the location of these sites and available structural information, we propose a refined model of C1 assembly where the CUB₁-EGF-CUB₂ interaction domains of C1r and C1s are entirely clustered inside C1q and interact through six binding sites with reactive lysines of the C1q stems. This mechanism is similar to that demonstrated for mannan-binding lectin (MBL)-MBL-associated serine protease and ficolin-MBL-associated serine protease complexes.The classical pathway of complement, a major component of innate immune defense against pathogens and altered self, is triggered by C1, a 790-kDa Ca²⁺-dependent complex assembled from a recognition protein C1q and C1s-C1r-C1r-C1s, a tetramer of two modular proteases, C1r and C1s, that respectively mediate activation and proteolytic activity of the complex (1–3). C1q has the overall shape of a bunch of tulips and comprises six heterotrimeric collagen-like triple helices that assemble through their N-terminal moieties to form a “stalk” and then diverge to form individual “stems,” each prolonged by a C-terminal globular recognition domain (4). C1r and C1s are homologous modular proteases each comprising, starting from the N-terminal end, a C1r/C1s, sea urchin EGF² (uEGF), bone morphogenetic protein (CUB) module (5), an EGF-like module (6), a second CUB module, two complement control protein modules (7), and a serine protease domain. This modular structure is shared by the mannan-binding lectin-associated serine proteases (MASPs), a group of enzymes that associate with mannan-binding lectin (MBL) and the ficolins and thereby trigger activation of the lectin pathway of complement (8).Assembly of the C1s-C1r-C1r-C1s tetramer involves Ca²⁺-dependent heterodimeric C1r-C1s interactions between the CUB₁-EGF segments of each protease (9–12). Similarly, MASP-1, MASP-2, MASP-3, and mannan-binding lectin-associated protein 19 (MAp19), an alternative splicing product of the MASP-2 gene comprising the N-terminal CUB₁-EGF segment of MASP-2, all associate as homodimers through their N-terminal CUB₁-EGF moieties (13–15). The structures of human C1s CUB₁-EGF, human MAp19, human MASP-1/3 CUB₁-EGF-CUB₂, and rat MASP-2 CUB₁-EGF-CUB₂ have been solved by x-ray crystallography (16–19), revealing that these domains all associate as head-to-tail homodimers through a highly conserved interface involving interactions between the CUB₁ module of one monomer and the EGF module of its counterpart. In addition, all CUB modules contained in these structures were found to contain a hitherto unrecognized Ca²⁺-binding site involving three conserved acidic residues (Glu⁴⁵, Asp⁵³, and Asp⁹⁸ in C1s), defining a novel CUB module subset diverging from the type originally described in the spermadhesins (20).Mutagenesis studies have recently established that assembly of the MBL- and ficolin-MASP complexes involves a major electrostatic interaction between two acidic Ca²⁺ ligands from the MASP CUB modules and a conserved lysine located in the collagen fibers of MBL and ficolins (16, 18, 21, 22). In the case of C1, a hypothetical model of the C1q/C1r/C1s interface, involving interaction between acidic residues mainly contributed by the C1r EGF module and unmodified lysine residues also located in the collagen-like stems of C1q, was derived from the x-ray structure of the C1s CUB₁-EGF interaction domain (16, 23). The aim of this work was to use site-directed mutagenesis to delineate the sites of C1r and C1s involved in the interaction between C1s-C1r-C1r-C1s and C1q. Our data rule out our previous interaction model and provide evidence that C1 assembly involves the same basic Ca²⁺-dependent mechanism as demonstrated in the case of MBL-MASP and ficolin-MASP complexes.