ALBERT

Description: Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specificity allowing cleavage of degenerate ‘star’ sites. Additionally, uncharacterized restriction endonucleases and engineered variants present novel activities. Traditionally, restriction endonuclease activity is assayed on simple substrates such as plasmids and synthesized oligonucleotides. We present and use high-throughput Illumina sequencing-based strategies to assay the sequence specificity and flanking sequence preference of restriction endonucleases. The techniques use fragmented DNA from sequenced genomes to quantify restriction endonuclease cleavage on a complex genomic DNA substrate in a single reaction. By mapping millions of restriction site–flanking reads back to the Escherichia coli and Drosophila melanogaster genomes we were able to quantitatively characterize the cognate and star site activity of EcoRI and MfeI and demonstrate genome-wide decreases in star activity with engineered high-fidelity variants EcoRI-HF and MfeI-HF, as well as quantify the influence on MfeI cleavage conferred by flanking nucleotides. The methods presented are readily applicable to all type II restriction endonucleases that cleave both strands of double-stranded DNA.

Description: Author(s): G. D. Dracoulis, G. J. Lane, H. Watanabe, R. O. Hughes, N. Palalani, F. G. Kondev, M. P. Carpenter, R. V. F. Janssens, T. Lauritsen, C. J. Lister, D. Seweryniak, S. Zhu, P. Chowdhury, W. Y. Liang, Y. Shi, and F. R. Xu Deep-inelastic reactions and γ -ray spectroscopy have been used to study excited states in 195 Au. A three-quasiparticle isomer with a mean-life of 18.6(3) μ s has been assigned at 2461+ Δ keV, with decays into newly identified structures. Possible configurations for the isomer are discussed including a... [Phys. Rev. C 87, 014326] Published Tue Jan 22, 2013

Description: A bstract Onset of maturity in trilobites is generally considered to occur when the last trunk segment is released into the thorax, marking the start of the holaspid stage. Here we describe striking morphological changes that occur within the holaspid ontogeny of Lonchopygella megaspina Zhou in Zhou et al., 1977 , which include the effacement of dorsal furrows, the rapid and complete degeneration of pygidial lateral spines, and the increasing prominence of a pygidial axial spine. These notable changes, which are not coincident with the onset of the holaspid phase, emphasize that the onset of maturity in trilobites should be viewed on a character-by-character basis before assessing whether the exoskeleton as a whole can be described as mature. The holaspid pygidial condition in L. megaspina may represent an intermediate step in an evolutionary transition in the number, form, and allocation of segments in the tsinaniid trunk. Pygidial transition from a dynamically changing complement of segments in the meraspid phase to a static complement in the holaspid phase was accompanied by a marked change in the extent to which segment boundaries defined pygidial structure. Attaining this static complement allowed subsequent pygidial development to emphasize its structure as an integrated unit in which internal segmental boundaries became diffuse, a continuous margin to become prominent, and an elongated terminal spine, first evident at onset of epimorphic growth, to develop allometrically. Trilobite body development suggests that while the segmented construction placed constraints on how morphology varied, the influence of these constraints diminished following completion of thoracic segment construction. Selective premium for a distinct posterior tagma might favor the early ontogenetic acquisition of such a structure, and could have been a driver of the repeated trend toward caudalization witnessed among derived trilobite clades.

Description: In this paper we investigate the performance of an algorithm for automatic segmentation of full polarimetric, synthetic aperture radar (SAR) sea ice scenes. The algorithm uses statistical and polarimetric properties of the backscattered radar signals to segment the SAR image into a specified number of classes. This number was determined in advance from visual inspection of the SAR image and by available in situ measurements. The segmentation result was then compared to ice charts drawn by ice service analysts. The comparison revealed big discrepancies between the charts of the analysts, and between the manual and the automatic segmentations. In the succeeding analysis, the automatic segmentation chart was labeled into ice types by sea ice experts, and the SAR features used in the segmentation were interpreted in terms of physical sea ice properties. Utilizing polarimetric information in sea ice charting will increase the efficiency and exactness of the maps. The number of classes used in the segmentation has shown to be of significant importance. Thus, studies of automatic and robust estimation of the number of ice classes in SAR sea ice scenes will be highly relevant for future work.

Description: In this paper we investigate the performance of an algorithm for automatic segmentation of full polarimetric, synthetic aperture radar (SAR) sea ice scenes. The algorithm uses statistical and polarimetric properties of the backscattered radar signals to segment the SAR image into a specified number of classes. This number was determined in advance from visual inspection of the SAR image and by available in-situ measurements. The segmentation result was then compared to ice charts drawn by ice service analysts. The comparison revealed big discrepancies between the charts of the analysts, and between the manual and the automatic segmentations. In the succeeding analysis, the automatic segmentation chart was labeled into ice types by sea ice experts, and the SAR features used in the segmentation were interpreted in terms of physical sea ice properties. Studies of automatic and robust estimation of the number of ice classes in SAR sea ice scenes will be highly relevant for future work.