@article {49599, title = {BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.}, volume = {30}, year = {2014}, month = {2014 May 1}, pages = {1214-9}, abstract = {

MOTIVATION: Base-calling of sequencing data produced by high-throughput sequencing platforms is a fundamental process in current bioinformatics analysis. However, existing third-party probabilistic or machine-learning methods that significantly improve the accuracy of base-calls on these platforms are impractical for production use due to their computational inefficiency.

RESULTS: We directly formulate base-calling as a blind deconvolution problem and implemented BlindCall as an efficient solver to this inverse problem. BlindCall produced base-calls at accuracy comparable to state-of-the-art probabilistic methods while processing data at rates 10 times faster in most cases. The computational complexity of BlindCall scales linearly with read length making it better suited for new long-read sequencing technologies.

}, keywords = {algorithms, High-Throughput Nucleotide Sequencing, HUMANS, Probability, Reproducibility of Results, Sequence Analysis, DNA, software, Time factors}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btu010}, author = {Ye, Chengxi and Hsiao, Chiaowen and Corrada Bravo, Hector} } @article {49739, title = {Distinct Rap1 activity states control the extent of epithelial invagination via α-catenin.}, journal = {Dev Cell}, volume = {25}, year = {2013}, month = {2013 May 13}, pages = {299-309}, abstract = {

Localized cell shape change initiates epithelial folding, while neighboring cell invagination determines the final depth of an epithelial fold. The mechanism that controls the extent of invagination remains unknown. During Drosophila gastrulation, a higher number of cells undergo invagination to form the deep posterior dorsal fold, whereas far fewer cells become incorporated into the initially very similar anterior dorsal fold. We find that a decrease in α-catenin activity causes the anterior fold to invaginate as extensively as the posterior fold. In contrast, constitutive activation of the small GTPase Rap1 restricts invagination of both dorsal folds in an α-catenin-dependent manner. Rap1 activity appears spatially modulated by Rapgap1, whose expression levels are high in the cells that flank the posterior fold but low in the anterior fold. We propose a model whereby distinct activity states of Rap1 modulate α-catenin-dependent coupling between junctions and actin to control the extent of epithelial invagination.

}, keywords = {Actins, alpha Catenin, Animals, Cell Adhesion, Cell Adhesion Molecules, Cell Membrane, Cell Shape, Drosophila, Drosophila Proteins, Embryo, Nonmammalian, Enzyme Activation, Epithelial Cells, Genes, Insect, Green Fluorescent Proteins, GTP Phosphohydrolases, GTPase-Activating Proteins, Intercellular Junctions, RNA Interference, Time factors, Time-Lapse Imaging}, issn = {1878-1551}, doi = {10.1016/j.devcel.2013.04.002}, author = {Wang, Yu-Chiun and Khan, Zia and Wieschaus, Eric F} } @article {38143, title = {Carbonic anhydrase III: the phosphatase activity is extrinsic}, journal = {Archives of biochemistry and biophysicsArchives of biochemistry and biophysics}, volume = {377}, year = {2000}, note = {http://www.ncbi.nlm.nih.gov/pubmed/10845711?dopt=Abstract}, type = {10.1006/abbi.2000.1793}, abstract = {The carbonic anhydrases reversibly hydrate carbon dioxide to yield bicarbonate and hydrogen ion. They have a variety of physiological functions, although the specific roles of each of the 10 known isozymes are unclear. Carbonic anhydrase isozyme III is particularly rich in skeletal muscle and adipocytes, and it is unique among the isozymes in also exhibiting phosphatase activity. Previously published studies provided evidence that the phosphatase activity was intrinsic to carbonic anhydrase III, that it had specificity for tyrosine phosphate, and that activity was regulated by reversible glutathionylation of cysteine186. To study the mechanism of this phosphatase, we cloned and expressed the rat liver carbonic anhydrase III. The purified recombinant had the same specific activity as the carbonic anhydrase purified from rat liver, but it had virtually no phosphatase activity. We attempted to identify an activator of the phosphatase in rat liver and found a protein of approximately 14 kDa, the amount of which correlated with the phosphatase activity of the carbonic anhydrase III fractions. It was identified as liver fatty acid binding protein, which was then purified to test for activity as an activator of the phosphatase and for protein-protein interaction, but neither binding nor activation could be demonstrated. Immunoprecipitation experiments established that carbonic anhydrase III could be separated from the phosphatase activity. Finally, adding additional purification steps completely separated the phosphatase activity from the carbonic anhydrase activity. We conclude that the phosphatase activity previously considered to be intrinsic to carbonic anhydrase III is actually extrinsic. Thus, this isozyme exhibits only the carbon dioxide hydratase and esterase activities characteristic of the other mammalian isozymes, and the phosphatase previously shown to be activated by glutathionylation is not carbonic anhydrase III.}, keywords = {Animals, Carbonic Anhydrases, Chromatography, High Pressure Liquid, Cloning, Molecular, Enzyme Activation, Glutathione, Kinetics, Liver, Male, Muscles, Phosphoric Monoester Hydrolases, Precipitin Tests, Rabbits, Rats, Rats, Inbred F344, Recombinant Proteins, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Time factors}, author = {Kim, G. and J. Selengut and Levine, R. L.} } @article {38220, title = {The effect of calprotectin on the nucleation and growth of struvite crystals as assayed by light microscopy in real-time}, journal = {The Journal of urologyThe Journal of urology}, volume = {159}, year = {1998}, note = {http://www.ncbi.nlm.nih.gov/pubmed/9507889?dopt=Abstract}, abstract = {PURPOSE: To use light microscopy to observe the urease-induced growth of struvite crystals in real-time, and to compare the effects of various proteins on that growth. MATERIALS AND METHODS: Artificial urine, with and without citrate, and a minimal urine solution containing only urea and the components of struvite and apatite were incubated with urease and test proteins in the depressions of culture slides. The number and size of rectangular and X-shaped struvite crystals were recorded using a low-power phase contrast microscope. RESULTS: The formation of crystalline struvite appears to occur after the formation of an amorphous calcium- and magnesium-containing phase. The extent of this amorphous phase is dependent on the presence of calcium and citrate, both of which strongly promote its formation over the crystalline phase. alpha-globulin, gamma-globulin and chymotrypsin inhibitor all result in the same amount of crystalline struvite as bovine serum albumin which is used as a control. Calprotectin, on the other hand, causes consistent and significant reductions in the number and size of struvite crystals under a wide range of conditions. No changes in the morphology of the struvite crystals were observed. CONCLUSIONS: Calprotectin, the dominant protein of infection stone matrix, has distinctive properties which affect the formation and growth of struvite crystals. The presence of citrate in synthetic urine dramatically reduces the number of struvite crystals observed. The present method for observing the effects of putative infection stone inhibitors appears to have merit.}, keywords = {Crystallization, Dose-Response Relationship, Drug, Leukocyte L1 Antigen Complex, Magnesium Compounds, Neural Cell Adhesion Molecules, Phosphates, Time factors}, author = {Asakura, H. and J. Selengut and Orme-Johnson, W. H. and Dretler, S. P.} }