Target specificity analysis of the Abl kinase using peptide microarray data

Protein kinases play an important role in cellular signalling. The reliable prediction of their substrates is of high importance for the deciphering of signalling pathways. A recently developed peptide microarray technology for the charcterisation of protein kinases delivers data on the individual phosphorylation status of each single member of a large peptide library. This data can be used to approximate the substrate specificity of the investigated kinase. We present an approach to process the collected information using a combination of a weight matrix approach and a nearest neighbor approach. Experiments with the protein-tyrosine kinase Abl are conducted to validate the results. Randomly selected peptides (1433) are used to estimate the substrate preferences of the kinase. The obtained prediction results are compared with standard methods. The new approach is tested further on bona fide Abl phosphorylation sites.     

Common patterns in type II restriction enzyme binding sites

Restriction enzymes are among the best studied examples of DNA binding proteins. In order to find general patterns in DNA recognition sites, which may reflect important properties of protein–DNA interaction, we analyse the binding sites of all known type II restriction endonucleases. We find a significantly enhanced GC content and discuss three explanations for this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking energy. These features make RR/YY steps particularly accessible for specific protein–DNA interactions. Finally, we show that the recognition sites of type II restriction enzymes are underrepresented in host genomes and in phage genomes.     

Eye lens proteomics: from global approach to detailed information about phakinin and gamma E and F crystallin genes

Exploration of the lenticular proteome poses a challenging and worthwhile undertaking as cataracts, the products of a disease phenotype elicited by this proteome, remains the leading cause of vision impairment worldwide. The complete ten day old lens proteome of Mus musculus C57BL/6J was resolved into 900 distinct spots by large gel carrier ampholyte based 2-DE. The predicted amino acid sequences of all 16 crystallins ubiquitous in mammals were corroborated by mass spectrometry (MS). In detailed individual spot analyses, the primary structure of the full murine C57BL/6J beaded filament component phakinin CP49 was sequenced by liquid chromatography/electrospray ionization-tandem MS and amended at two positions. This definitive polypeptide sequence was aligned to the mouse genome, thus identifying the entire C57BL/6J genomic coding region. Also, two murine C57/6J polypeptides, both previously classified as gamma F crystallin, were clearly distinguished by MS and electrophoretic mobility. Both were assigned to their respective genes, one of the polypeptides was reclassified as C57BL/6J gamma E crystallin. Building on these data and previous investigations an updated crystallin reference map was put forth and several non crystallin lenticular components were examined. These results represent the first part of a comprehensive investigation of the mouse lens proteome (http://www.mpiib-berlin.mpg.de/2D-PAGE) with emphasis on understanding genetic effects on proteins and disease development.     

Life Cycle Assessment of Novel Aircraft Interior Panels Made from Renewable or Recyclable Polymers with Natural Fiber Reinforcements and Non‐Halogenated Flame Retardants

A comprehensive life cycle assessment of panels for aircraft interiors was conducted, including both a conventional glass fiber‐reinforced panel and different novel sustainable panels. The conventional panel is made of a glass fiber‐reinforced thermoset composite with halogenated flame retardant, whereas the sustainable panels are made of renewable or recyclable polymers, natural fiber reinforcements, and nonhalogenated flame retardants. Four different sustainable panels were investigated: a geopolymer‐based panel; a linseed‐oil–based biopolymer panel; and two thermoplastic panels, one with polypropylene (PP) and another with polylactic acid (PLA). All of the sustainable panels were developed to fulfil fire resistance requirements and to be lighter than the conventional panels in order to reduce fuel consumption and air pollutant emissions from the aircraft. The environmental impacts associated with energy consumption and air emissions were assessed, as well as other environmental impacts resulting from the extraction and processing of materials, transportation of materials and waste, panel manufacturing, use, maintenance, and end of life (EoL). All the sustainable panels showed better environmental performance than the conventional panel. The overall impacts of the sustainable panels were offset by the environmental benefits in the use stage attributed to weight reduction. One square meter of the novel panels could save to 6,000 kilograms of carbon dioxide equivalents. The break‐even point (in months) at which the use of sustainable panels would yield an environmental benefit relative to the impacts arising in production and EoL was as follows: 1.2 for the geopolymer panel; 1.7 for the biopolymer panel; 10.4 for the PLA panel; and 54.5 for the PP panel.     

The effect of environmental gradients on the bed site selection of roe deer (<Emphasis Type="Italic">Capreolus capreolus</Emphasis>)

A wildlife species’ selection of bedding sites is often characterised by strong trade-offs, as habitat quality, predator avoidance and foraging needs should be achieved simultaneously. Human activities often represent major threats in addition. In areas of intensive agriculture, e.g. mowing is one of the main causes of mortality of roe deer (Capreolus capreolus) fawns due their hiding strategy. For a species’ offspring, the selection of bedding sites is particularly crucial and thus, identifying how and when animals use such habitats is important for management. We used a long-term dataset of marked roe deer fawns in Switzerland (1971–2015) to reveal the characteristics of optimal bedding sites within the first two weeks of a fawn’s life in three contrasting landscapes and the potential trade-offs that may occur. We hypothesised that roe deer adjust the selection of bedding sites to current environmental conditions and available habitat to achieve sufficient levels of predator avoidance and thermoregulation necessary for the fawn’s survival, as well as the availability of sufficient food resources for the mother doe. We found that, in general, grassland habitats with medium vegetation height (20–50 cm) and habitats in close proximity to the edge of the forest were favoured to achieve those basic requirements. However, the use of bed site habitats differed between the three contrasting landscapes in dependence of elevation and hence vegetation phenology. Our results provide essential information to reduce mortality rates caused by mowing and improve the reproductive success of this species.