648 research outputs found

    Probing hydrogen-bonding in binary liquid mixtures with terahertz time-domain spectroscopy: a comparison of Debye and absorption analysis.

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    Terahertz time-domain spectroscopy is used to explore hydrogen bonding structure and dynamics in binary liquid mixtures, spanning a range of protic-protic, protic-aprotic and aprotic-aprotic systems. A direct absorption coefficient analysis is compared against more complex Debye analysis and we observed good agreement of the two methods in determining the hydrogen bonding properties when at least one of the mixture components is protic. When both components are aprotic, we show that the trend in absorption coefficients match well with the theoretical trend in strength of hydrogen bond interactions predicted based on steric and electronic properties of the components.The authors would like to acknowledge funding provided by EPSRC Grant EP/G011397/1.This is the final published version. It first appeared at http://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/c4cp04477k#!divAbstract

    Free Radical Generation from High-Frequency Electromechanical Dissociation of Pure Water

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    We reveal a unique mechanism by which pure water can be dissociated to form free radicals without requiring catalysts, electrolytes, or electrode contact by means of high-frequency nanometer-amplitude electromechanical surface vibrations in the form of surface acoustic waves (SAWs) generated on a piezoelectric substrate. The physical undulations associated with these mechanical waves, in concert with the evanescent electric field arising from the piezoelectric coupling, constitute half-wavelength "nanoelectrochemical cells" in which liquid is trapped within the SAW potential minima with vertical dimensions defined by the wave amplitude (∼10 nm), thereby forming highly confined polarized regions with intense electric field strengths that enable the breakdown of water. The ions and free radicals that are generated rapidly electromigrate under the high field intensity in addition to being convectively transported away from the cells by the bulk liquid recirculation generated by the acoustic excitation, thereby overcoming mass transport limitations that lead to ion recombination.A.R.R., N.C., and L.Y.Y. acknowledge funding support from the Australian Research Council through Discovery Project (DP180102110); Future Fellowship (FT140100834); and Linkage, Infrastructure, Equipment & Facilities (LE170100023) grant

    A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

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    Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal

    Mass spectrometry protein expression profiles in colorectal cancer tissue associated with clinico-pathological features of disease

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    Background: Studies of several tumour types have shown that expression profiling of cellular protein extracted from surgical tissue specimens by direct mass spectrometry analysis can accurately discriminate tumour from normal tissue and in some cases can sub-classify disease. We have evaluated the potential value of this approach to classify various clinico-pathological features in colorectal cancer by employing matrix-assisted laser desorption ionisation time of-flight-mass spectrometry (MALDI-TOF MS). Methods: Protein extracts from 31 tumour and 33 normal mucosa specimens were purified, subjected to MALDI-Tof MS and then analysed using the `GenePattern' suite of computational tools (Broad Institute, MIT, USA). Comparative Gene Marker Selection with either a t-test or a signal-to-noise ratio (SNR) test statistic was used to identify and rank differentially expressed marker peaks. The k-nearest neighbours algorithm was used to build classification models either using separate training and test datasets or else by using an iterative, `leave-one-out' cross-validation method. Results: 73 protein peaks in the mass range 1800-16000Da were differentially expressed in tumour verses adjacent normal mucosa tissue (P <= 0.01, false discovery rate <= 0.05). Unsupervised hierarchical cluster analysis classified most tumour and normal mucosa into distinct cluster groups. Supervised prediction correctly classified the tumour/normal mucosa status of specimens in an independent test spectra dataset with 100\% sensitivity and specificity (95\% confidence interval: 67.9-99.2\%). Supervised prediction using `leave-one-out' cross validation algorithms for tumour spectra correctly classified 10/13 poorly differentiated and 16/18 well/moderately differentiated tumours (P = < 0.001; receiver-operator characteristics - ROC - error, 0.171); disease recurrence was correctly predicted in 5/6 cases and disease-free survival (median follow-up time, 25 months) was correctly predicted in 22/23 cases (P = < 0.001; ROC error, 0.105). A similar analysis of normal mucosa spectra correctly predicted 11/14 patients with, and 15/19 patients without lymph node involvement (P = 0.001; ROC error, 0.212). Conclusions: Protein expression profiling of surgically resected CRC tissue extracts by MALDI-TOF MS has potential value in studies aimed at improved molecular classification of this disease. Further studies, with longer follow-up times and larger patient cohorts, that would permit independent validation of supervised classification models, would be required to confirm the predictive value of tumour spectra for disease recurrence/patient survival
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