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71.
The intact O-specific caryophyllan polysaccharide of the lipopolysaccharide fraction from the bacterium Pseudomonas (Burkholderia) caryophylli was isolated for the first time. Its structure was clarified by means of chemical and spectroscopic analysis and consisted of a homopolymer of randomly acetylated caryophyllose units. The position of acetyl groups when present is not unique: all the hydroxyl-groups on the side chain of the sugar can be substituted with a slight preference for acetylation of the C-5-C-10 tail of this unusual monosaccharide 相似文献
72.
73.
Giovanna Carratu Michelangelo Melchionna Matteo Giannattasio 《Plant biosystems》2013,147(5-6):219-226
Abstract Different hydrolases were found to be present in the crude extract of dry de-embryonated wheat grains, including acid phosphatase. When the crude extract was chromatographed on a Wheat-Germ Agglutinin-Sepharose affinity column, an aliquot of acid phosphatase bound to the column and could be eluted specifically by N-acetyl-D-glucosamine solution. Some properties of the WGA-binding acid phosphatase (pH optimum, heat stability, Triton X-100 sensitivity, inhibition by some ions, molecular weight and Km) were studied. WGA appeared to have a stabilizing effect on the enzyme, while it was ineffective on the Km. 相似文献
74.
The task of gene regulatory network reconstruction from high-throughput data is receiving increasing attention in recent years. As a consequence, many inference methods for solving this task have been proposed in the literature. It has been recently observed, however, that no single inference method performs optimally across all datasets. It has also been shown that the integration of predictions from multiple inference methods is more robust and shows high performance across diverse datasets. Inspired by this research, in this paper, we propose a machine learning solution which learns to combine predictions from multiple inference methods. While this approach adds additional complexity to the inference process, we expect it would also carry substantial benefits. These would come from the automatic adaptation to patterns on the outputs of individual inference methods, so that it is possible to identify regulatory interactions more reliably when these patterns occur. This article demonstrates the benefits (in terms of accuracy of the reconstructed networks) of the proposed method, which exploits an iterative, semi-supervised ensemble-based algorithm. The algorithm learns to combine the interactions predicted by many different inference methods in the multi-view learning setting. The empirical evaluation of the proposed algorithm on a prokaryotic model organism (E. coli) and on a eukaryotic model organism (S. cerevisiae) clearly shows improved performance over the state of the art methods. The results indicate that gene regulatory network reconstruction for the real datasets is more difficult for S. cerevisiae than for E. coli. The software, all the datasets used in the experiments and all the results are available for download at the following link: http://figshare.com/articles/Semi_supervised_Multi_View_Learning_for_Gene_Network_Reconstruction/1604827. 相似文献
75.
Iina Vainio Amna Abu Khamidakh Michelangelo Paci Heli Skottman Kati Juuti-Uusitalo Jari Hyttinen Soile Nymark 《PloS one》2015,10(6)
Objective
Computational models of calcium (Ca2+) signaling have been constructed for several cell types. There are, however, no such models for retinal pigment epithelium (RPE). Our aim was to construct a Ca2+ signaling model for RPE based on our experimental data of mechanically induced Ca2+ wave in the in vitro model of RPE, the ARPE-19 monolayer.Methods
We combined six essential Ca2+ signaling components into a model: stretch-sensitive Ca2+ channels (SSCCs), P2Y2 receptors, IP3 receptors, ryanodine receptors, Ca2+ pumps, and gap junctions. The cells in our epithelial model are connected to each other to enable transport of signaling molecules. Parameterization was done by tuning the above model components so that the simulated Ca2+ waves reproduced our control experimental data and data where gap junctions were blocked.Results
Our model was able to explain Ca2+ signaling in ARPE-19 cells, and the basic mechanism was found to be as follows: 1) Cells near the stimulus site are likely to conduct Ca2+ through plasma membrane SSCCs and gap junctions conduct the Ca2+ and IP3 between cells further away. 2) Most likely the stimulated cell secretes ligand to the extracellular space where the ligand diffusion mediates the Ca2+ signal so that the ligand concentration decreases with distance. 3) The phosphorylation of the IP3 receptor defines the cell’s sensitivity to the extracellular ligand attenuating the Ca2+ signal in the distance.Conclusions
The developed model was able to simulate an array of experimental data including drug effects. Furthermore, our simulations predict that suramin may interfere ligand binding on P2Y2 receptors or accelerate P2Y2 receptor phosphorylation, which may partially be the reason for Ca2+ wave attenuation by suramin. Being the first RPE Ca2+ signaling model created based on experimental data on ARPE-19 cell line, the model offers a platform for further modeling of native RPE functions. 相似文献76.
Genome‐scale metabolic reconstruction and constraint‐based modelling of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125
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Marco Fondi Isabel Maida Elena Perrin Alessandra Mellera Stefano Mocali Ermenegilda Parrilli Maria Luisa Tutino Pietro Liò Renato Fani 《Environmental microbiology》2015,17(3):751-766
The Antarctic strain Pseudoalteromonas haloplanktis TAC125 is one of the model organisms of cold‐adapted bacteria and is currently exploited as a new alternative expression host for numerous biotechnological applications. Here, we investigated several metabolic features of this strain through in silico modelling and functional integration of –omics data. A genome‐scale metabolic model of P. haloplanktis TAC125 was reconstructed, encompassing information on 721 genes, 1133 metabolites and 1322 reactions. The predictive potential of this model was validated against a set of experimentally determined growth rates and a large dataset of growth phenotypic data. Furthermore, evidence synthesis from proteomics, phenomics, physiology and metabolic modelling data revealed possible drawbacks of cold‐dependent changes in gene expression on the overall metabolic network of P. haloplanktis TAC125. These included, for example, variations in its central metabolism, amino acid degradation and fatty acid biosynthesis. The genome‐scale metabolic model described here is the first one reconstructed so far for an Antarctic microbial strain. It allowed a system‐level investigation of variations in cellular metabolic fluxes following a temperature downshift. It represents a valuable platform for further investigations on P. haloplanktis TAC125 cellular functional states and for the design of more focused strategies for its possible biotechnological exploitation. 相似文献
77.
Ugutz Unzueta Felicitas Vázquez Giulia Accardi Rosa Mendoza Verónica Toledo-Rubio Maria Giuliani Filomena Sannino Ermenegilda Parrilli Ibane Abasolo Simo Schwartz Jr. Maria L. Tutino Antonio Villaverde José L. Corchero Neus Ferrer-Miralles 《Applied microbiology and biotechnology》2015,99(14):5863-5874
78.
Dott. Michelangelo Minio 《Plant biosystems》2013,147(1):216-218
Abstract The use of the mini-plug system for the production of container seedlings is relatively new, so there is little information on the potential impact of method on the quality of planting stock. The objective in this study was to evaluate the impact of mini-plug growing method on quality of Pinus brutia seedlings, and compare the performance of this stock type with that of standard container nursery stock. Seedling survival, growth and physiological status (root growth potential, shoot electrolyte leakage) were measured after pre-cultivation in mini-plugs, at the end of the first growing season in standard containers and after field transplanting. Our results showed that mini-plug transplants of P. brutia seedlings performed as well as the standard planting stock currently used in nursery operation in Greece. For the pre-cultivation of P. brutia seedlings in mini-plugs, the use of peat and a density of 2000 mini-plugs m?2 are recommended. 相似文献
79.
Giuseppe Perugino Pierpaolo Falcicchio Maria Michela Corsaro Ikuo Matsui Michelangelo Parrilli Mose’ Rossi 《Biocatalysis and Biotransformation》2013,31(1-2):23-29
The β-glycosidase from the hyperthermophilic Archaeon Pyrococcus horikoshii (Phoβ-gly) is a monomeric enzyme with wide substrate specificity belonging to family 1 of glycoside hydrolases classification. Inspection of the three-dimensional structure of the enzyme, recently resolved, showed that Phoβ-gly is membrane bound and that the residues putatively involved in the catalytic activity are Glu155 and Glu324 working as the general acid/base and the nucleophile of the reaction, respectively. We show here that mutation of the latter completely eliminated the activity of the enzyme and that it could be reactivated in the presence of sodium formate. Analysis of the products obtained in the presence of sodium formate buffer pH 4.0 at 75°C showed that the Glu324Gly mutant acts as a hyperthermophilic glycosynthase. 相似文献
80.
Morphogenesis takes place against a background of organism-to-organism and environmental variation. Therefore, fundamental questions in the study of morphogenesis include: How are the mechanical processes of tissue movement and deformation affected by that variability, and in turn, how do the mechanic of the system modulate phenotypic variation? We highlight a few key factors, including environmental temperature, embryo size and environmental chemistry that might perturb the mechanics of morphogenesis in natural populations. Then we discuss several ways in which mechanics-including feedback from mechanical cues-might influence intra-specific variation in morphogenesis. To understand morphogenesis it will be necessary to consider whole-organism, environment and evolutionary scales because these larger scales present the challenges that developmental mechanisms have evolved to cope with. Studying the variation organisms express and the variation organisms experience will aid in deciphering the causes of birth defects. 相似文献