4,280 research outputs found

    Protein-RNA interactions: a structural analysis

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    A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level

    Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

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    A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set

    Maternal serum, an isolation and expansion tool for umbilical cord matrix mesenchymal stromal cells

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    The umbilical cord offers a source of readily available mesenchymal stromal cells for use in research and ultimately therapeutic application. However, methods of isolating these cells vary between investigators, and no standard method has been adopted. The aims of this work were to i) develop a methodology for the isolation of umbilical cord matrix cells without the use of enzymatic digestion or complicated dissection; ii) investigate the use of pooled maternal serum as a media supplement; and iii) to demonstrate that the cells isolated were mesenchymal stromal cells. We have demonstrated that incubating tissue explants of less than 2mm3 in serum for an hour, followed by the gradual addition of serum containing culture medium can increase cell yield compared to incubation in serum containing culture medium alone. More importantly, our method demonstrated that the use of pooled serum from women > 37 weeks pregnant (pooled maternal serum) yields higher cell numbers than the use of fetal bovine serum or pooled umbilical cord serum. Irrespective of the type of serum used the isolated cells were mesenchymal stromal cells according to the minimal criteria set out by the Mesenchymal and Tissue Stem Cell Committee of the International Society for Cellular Therapy. In conclusion, maternal serum has the potential to be used as an alternative to FBS for isolation and expansion of umbilical cord MSCs for clinical purposes

    The impact of AlphaFold2 one year on

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    The greatly improved prediction of protein 3D structure from sequence achieved by the second version of AlphaFold in 2020 has already had a huge impact on biological research, but challenges remain; the protein folding problem cannot be considered solved. We expect fierce competition to improve the method even further and new applications of machine learning to help illuminate proteomes and their many interactions

    An exploratory study on the effect of positive (warmth appeal) and negative (guilt appeal) print imagery on donation behaviour in animal welfare

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    Very few studies in social marketing empirically compare the effectiveness of positive and negative appeals. This study examines the effect of positive (warmth appeal) and negative (guilt appeal) print imagery on donation behaviour to an animal welfare organisation. A quasiexperimental design was used to test the appeals, using a convenience sample of 282 university students, with each experimental group being exposed to only one type of appeal. The results indicated that negative imagery which evoked guilt was more effective than positive imagery which evoked warmth, on intention to donate money and time to the animal welfare organisation

    Augustana Seniors Fall 1883: Gustaf Sven Swenson

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    Gustaf Swenson was a senior at Augustana College, Rock Island, Illinois, in the fall of 1883. His name appears in the college catalog of 1883 – 1884, along with his birthplace, the year of his birth, and a few other facts. From this start, we researched the genealogy and family history of Gustaf Swenson. This paper contains a short biography of Gustaf Swenson, a report on his ancestors, a report on his descendants, and some open questions for further research
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