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  • 1
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    FORMATION OF 0.84 NM HYDRATED KAOLINITE AS AN ENVIRONMENTALLY FRIENDLY PRECURSOR OF A KAOLINITE INTERCALATION COMPOUND (2014)
    Clay Minerals Society
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    Publication Date: 2014-01-11
    Description: Creating an environmentally friendly precursor to form a kaolinite intercalation compound is important for promoting the applications of nanohybrid kaolinite in electrochemical sensors, low- or zero-toxicity drug carriers, and clay-polymer nanocompounds. In the present study, a stable hydrated kaolinite precursor with d 001 = 0.84 nm was prepared successfully by heating the transition phase, the as-prepared kaolinite-hydrazine intercalate, at temperatures between 40 and 70°C. The structure of the hydrated kaolinite was characterized by X-ray diffraction and infrared spectroscopy. The morphology was examined using scanning electron microscopy. The results showed that the hydrated hydrazine of the transition phase was easy to decompose to hydrazines and water molecules in the interlayer at 40–70°C. Hydrazine molecules de-intercalated gradually, and water molecules remained in the ditrigonal holes of the silicate layer with sufficient stability, finally forming the stable 0.84 nm hydrated kaolinite in the system with a success rate of 80–90%. The 0.84 nm hydrated kaolinite may become an excellent precursor for the preparation of other kaolinite intercalates. A degree of intercalation of ~100% was obtained for the kaolinite-ethylene glycol intercalate, and a degree of intercalation of~80% was obtained for the kaolinite-glycine intercalate from the 0.84 nm hydrated kaolinite precursor.
    Print ISSN: 0009-8604
    Electronic ISSN: 1552-8367
    Topics: Geosciences
    Published by Clay Minerals Society
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  • 2
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    UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing (2014)
    Oxford University Press
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    Publication Date: 2014-02-28
    Description: Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better performance compared with earlier developed algorithms such as TopHat and MapSplice. To improve detection of splice junctions, TrueSight uses information on statistical patterns of nucleotide ordering in intronic and exonic DNA. This line of research led to yet another new algorithm, UnSplicer, designed for eukaryotic species with compact genomes where functional alternative splicing is likely to be dominated by splicing noise. Genome-specific parameters of the new algorithm are generated by GeneMark-ES, an ab initio gene prediction algorithm based on unsupervised training. UnSplicer shares several components with TrueSight; the difference lies in the training strategy and the classification algorithm. We tested UnSplicer on RNA-Seq data sets of Arabidopsis thaliana , Caenorhabditis elegans , Cryptococcus neoformans and Drosophila melanogaster . We have shown that splice junctions inferred by UnSplicer are in better agreement with knowledge accumulated on these well-studied genomes than predictions made by earlier developed tools.
    Keywords: Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit (2013)
    Oxford University Press
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    Publication Date: 2013-08-09
    Description: Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant bacterial strain. Our qualitative mass spectrometry data indicate that L28, L16, L33, L36 and L35 are dramatically underrepresented in the 45S particles. This protein spectrum shows interesting similarity to many qualitatively analyzed 50S precursors from different genetic background, indicating the presence of global rate-limiting steps in the late-stage assembly of 50S subunit. Our structural data reveal two major intermediate states for the 45S particles. Consistently, both states severally lack those proteins, but they also differ in the stability of the functional centers of the 50S subunit, demonstrating that they are translationally inactive. Detailed analysis indicates that the orientation of H38 accounts for the global conformational differences in these intermediate structures, and suggests that the reorientation of H38 to its native position is rate-limiting during the late-stage assembly. Especially, H38 plays an essential role in stabilizing the central protuberance, through the interaction with the 5S rRNA, and the correctly orientated H38 is likely a prerequisite for further maturation of the 50S subunit.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    HYDROTHERMAL SYNTHESIS OF MESOPOROUS MAGADIITE PLATES VIA HETEROGENEOUS NUCLEATION (2014)
    Clay Minerals Society
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    Publication Date: 2014-03-28
    Description: The conventional cauliflower-like shape of magadiite imposes serious limitations on its applications in adsorption, catalysis, ion exchange, etc . To overcome this problem, a method to prepare it with plate-like structures was developed. This novel approach is based on an interface-controlled heterogeneous nucleation process. Zirconia grinding balls with diameters of 2.0 mm were dispersed in the starting solution to provide solid–liquid interfaces. Then the starting solution with a SiO 2 :NaOH:H 2 O molar ratio of 9:2:75 was subjected to hydrothermal treatment at 433 K for 96 h. The presence of the solid–liquid interface improved the crystallization yield and controlled the morphology and specific surface area of the crystals. With the zirconia balls, the yield and sizes of the plate-like magadiite were 52 wt.% and 1–3 μm, respectively. In the absence of zirconia balls, the yield was smaller (45 wt.%) and magadiite shaped like cauliflower was formed. The plate-like magadiite had a specific surface area of 66 m 2 g –1 and a pore-size distribution between 4 and 5 nm, compared with a surface area of 28 m 2 g –1 for the cauliflower-like magadiite. In addition, the plate-like magadiite was a more effective ion exchanger than the cauliflower-like magadiite with a cation exchange capacity of 64.5 mmol/100 g (compared to 53.8 mmol/100 g for the cauliflower-like form) and it had a faster sorption rate for calcium ions.
    Print ISSN: 0009-8604
    Electronic ISSN: 1552-8367
    Topics: Geosciences
    Published by Clay Minerals Society
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  • 5
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    A comprehensive analysis of GATA-1-regulated miRNAs reveals miR-23a to be a positive modulator of erythropoiesis (2013)
    Oxford University Press
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    Publication Date: 2013-04-14
    Description: miRNAs play important roles in many biological processes, including erythropoiesis. Although several miRNAs regulate erythroid differentiation, how the key erythroid regulator, GATA-1, directly orchestrates differentiation through miRNA pathways remains unclear. In this study, we identified miR-23a as a key regulator of erythropoiesis, which was upregulated both during erythroid differentiation and in GATA-1 gain-of-function experiments, as determined by miRNA expression profile analysis. In primary human CD34+ hematopoietic progenitor cells, miR-23a increased in a GATA-1-dependent manner during erythroid differentiation. Gain- or loss-of-function analysis of miR-23a in mice or zebrafish demonstrated that it was essential for normal morphology in terminally differentiated erythroid cells. Furthermore, a protein tyrosine phosphatase, SHP2, was identified as a downstream target of miR-23a that mediated its regulation of erythropoiesis. Taken together, our data identify a key GATA-1–miRNA axis in erythroid differentiation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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