Function2Form Bridge—Toward synthetic protein holistic performance prediction

Protein engineering and synthetic biology stand to benefit immensely from recent advances in silico tools for structural and functional analyses of proteins. In the context of designing novel proteins, current in silico tools inform the user on individual parameters of a query protein, with output scores/metrics unique to each parameter. In reality, proteins feature multiple “parts”/functions and modification of a protein aimed at altering a given part, typically has collateral impact on other protein parts. A system for prediction of the combined effect of design parameters on the overall performance of the final protein does not exist. Function2Form Bridge (F2F-Bridge) attempts to address this by combining the scores of different design parameters pertaining to the protein being analyzed into a single easily interpreted output describing overall performance. The strategy comprises of (a) a mathematical strategy combining data from a myriad of in silico tools into an OP-score (a singular score informing on a user-defined overall performance) and (b) the F2F Plot, a graphical means of informing the wetlab biologist holistically on designed construct suitability in the context of multiple parameters, highlighting scope for improvement. F2F predictive output was compared with wetlab data from a range of synthetic proteins designed, built, and tested for this study. Statistical/machine learning approaches for predicting overall performance, for use alongside the F2F plot, were also examined. Comparisons between wetlab performance and F2F predictions demonstrated close and reliable correlations. This user-friendly strategy represents a pivotal enabler in increasing the accessibility of synthetic protein building and de novo protein design.     

Colonization of wheat roots from seed‐applied spores of Idriella (Microdochium) bolleyi: A biocontrol agent of take‐all

Wheat seedlings were grown in containers of perlite in a glasshouse, and spores of Idriella bolleyi were applied either to the seeds in alginate gel or to the perlite as aqueous suspensions. Growth and sporulation of the fungus on seeds and roots were assessed by plating methods and by retrieval of spores from water that drained from the plant containers. Idriella bolleyi sporulated heavily on seeds for up to 3 weeks when applied to them in alginate gel, andmost of the root system was infected from newly formed spores that were carried in percolating water. Removal of the inoculated seeds from seedlings at 7 days reduced the degree of root infection and temporarily reduced the number of spores in drainage water; however, spore numbers increased to control levels (seeds attached) by 21 days, indicating subsequent sporulation on the roots. When spores were applied to perlite containing young (0–3 days) seedlings I. bolleyi colonized the seeds, sporulated heavily on them and extensively colonized the roots. However, it established poorly on seeds and roots if added to the perlite when seedlings were 11 days or older. The results suggest that early growth on seeds is necessary for establishment of a high population of I. bolleyi, and that cycles of sporulation on seeds and then roots contribute to colonization of the rhizosphere. The features associated with the rhizosphere competence of I. bolleyi are compared with those for systemic colonization of the xylem by vascular wilt fungi, and suggest a new approach to the selection of root‐colonizing biocontrol agents.     

Mechanisms of reaction of hematoxylin with aluminium-treated wheat roots

Hematoxylin stain is used for localization of aluminium in plant root tissue and is the basis of a rapid assay of relative At tolerance among wheat cultivars. In the present study, mechanisms by which hematoxylin might selectively stain Al-sensitive wheat roots have been examined. The results are consistent with the idea that in Al-sensitive cultivars, hematoxylin forms complexes with Al that precipitate with phosphate as AlPO₄ in intercellular spaces: (1) Al and P are co-localized in the cell wall region of the outer cortex of Al-stressed roots by using x-ray microanalysis: (2) the molybdenum blue histochemical stain for extracellular phosphate reveals areas of stain that parallel those observed with hematoxylin; (3) in vitro, the presence of phosphate in an Al-hematoxylin reaction mixture causes formation of precipitate when the P/Al ratio exceeds 1. 0. I suggest that selective hematoxylin staining of Al-sensitive wheat cultivars is the result of direct damage by Al to root cells, leading to leakage of phosphorus into the cell wall region. Cultivars whose roots are damaged by Al in this way are likely to be judged Al-sensitive when other criteria such as growth or crop yield are used.     

Epitope Analysis of Soybean Major Allergen Gly m Bd 30K Recognized by the Mouse Monoclonal Antibody Using Overlapping Peptides

The epitopes of the major soybean allergen, Gly m Bd 30K, recognized by mouse monoclonal antibodies H6 and F5 were investigated by using synthetic peptides bound to pins. The epitopes are shown to be localized in peptide ³¹QGGCGRGWAFSATGAI-EA⁴⁸ for H6, and in ¹¹⁵ DKVTIDGYETLIMSDEST¹³² for F5.     

Variation in noxiousness of different wheat species for celiac patients

Abstract

Peptic-tryptic (PT) digested prolamins from spelt wheat Triticum aestivum ssp. spelta and landraces ERSA 6 and ERSA 8 of farro wheat T. turgidum ssp. dicoccum were found to agglutinate K562(S) cells, and exert strong toxic effects on Caco-2/TC7 cells. Cytotoxicity of spelt prolamins against Caco-2/TC7 cells was greatly reduced by 10-mer peptide QQPQDAVQPF. By contrast, the PT digests from monoccum wheat (Triticum monococcum) and farro landraces Prometeo, L5563, L5540 and L5558 did not exhibit any negative effects on K562(S) and Caco-2/TC7 cells. Toxic genotypes ERSA 6 and ERSA 8 were found to share the same gliadin pattern, which was absent in inactive landraces. Monococcum, farro and spelt wheats differed from each other in their responses to antibodies specific for 13-mer cytotoxic sequence FPGQQQPFPPQQP and 10-mer peptide QQPQDAVQPF. This latter sequence was found to occur in high amounts in common wheat line FG, Phaseoulus vulgaris, Ph. coccineus and Lens culinaria.     

Végétation marine de l'Ile de Port-Cros (Parc National). XII: Sur Acrochaetium molinieri sp. nov. et Lophosiphonia cristata Falkenberg

Abstract

Marine vegetation of Port-Cros Island (National park). XII: on Acrochaetium molinieri sp. nov. and Lophosiphonia cristata Falkenberg. – Acrochaetium molinieri sp. nov. is characterized by its bicellular base; only one of these cells originates an erect filament. Lophosiphonia cristata, rarely mentioned from the Mediterranean, is richly illustrated and described in detail     

Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs

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Responses of a sterile red fungus to soil types,wheat varieties and the presence of certain isolates ofStreptomyces

The biological activities of a sterile red fungus (SRF) capable of plant growth promotion and suppression of take-all disease were investigated in soils collected from Lancelin, Newdegate and Mt. Barker regions of Western Australia. Further, the effects of three wheat cultivars and the presence of two isolates ofStreptomyces on the biological activities of the SRF were tested using the Lancelin soil. The biological activities of the SRF were greatest in the Lancelin and Newdegate (wheat field) soils and with the wheat cultivar Gutha. In in vitro studies the soil streptomycetes tested showed either a significant increase in the exudate production by the SRF, which had antifungal and growth promoting properties, or an inhibition of growth of the fungus. Streptomycete A63 which stimulated the exudate production by the SRF in vitro, however, did not enhance disease protection in vivo. On the other hand, protection from root rot by the SRF in vivo was reduced in the presence of the streptomycete isolate Ax which is capable of inhibiting the growth of the SRF in vitro.