Metal Ion-Regulated Fluorescent Sensor Array Based on Gold Nanoclusters for Physiological Phosphate Sensing

The detection of physiological phosphates (PPs) is of great importance due to their essential roles in numerous biological processes, but the efficient detection of different PPs simultaneously remains challenging. In this work, we propose a fluorescence sensor array for detecting PPs based on metal-ion-regulated gold nanoclusters (AuNCs) via an indicator-displacement assay. Zn2+ and Eu3+ are selected to assemble with two different AuNCs, resulting in quenching or enhancing their fluorescence. Based on the competitive interaction of metal ions with AuNCs and PPs, the fluorescence of AuNCs will be recovered owing to the disassembly of AuNC-metal ion ensembles. Depending on different PPs’ distinct fluorescence responses, a four-channel sensor array was established. The array not only exhibits good discrimination capability for eight kinds of PPs (i.e., ATP, ADP, AMP, GTP, CTP, UTP, PPi, and Pi) via linear discriminant analysis but also enables quantitative detection of single phosphate (e.g., ATP) in the presence of interfering PPs mixtures. Moreover, potential application of the present sensor array for the discrimination of different PPs in real samples (e.g., cell lysates and serum) was successfully demonstrated with a good performance. This work illustrates the great potential of a metal ion-regulated sensor array as a new and efficient sensing platform for differential sensing of phosphates as well as other disease-related biomolecules

DataSheet2.XLSX

<p>Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches.</p

Presentation1.PDF

<p>Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches.</p

GGCMs participating in the study, model type and key references, as well as nutrients considered in crop model simulations (N: nitrogen, P: phosphorus, K: potassium).

<p>GGCMs participating in the study, model type and key references, as well as nutrients considered in crop model simulations (N: nitrogen, P: phosphorus, K: potassium).</p

CV of global maize, wheat, rice, and soybean productivity (%) over 28 years (1981–2008) of the 10 individual GGCMs, their ensemble median and FAO statistics [39].

<p>Data are shown for actual, unlimited (uWN), unlimited nutrients (uN) and unlimited water (uW) conditions and have been detrended prior to computing CVs. FAO data is only available for actual conditions. For better readability, the lowest CVs per model (rows) are colored green, highest are colored orange.</p

Yield dent (see text) for maize under actual (a) conditions and differences in yield dent for uWN-actual (b), uW-actual (c), and uN-actual (d) for all grid cells with at least 100ha maize cropland [38] and a minimum yield of 0.5 tDM ha^-1.

<p>Yield dent (see text) for maize under actual (a) conditions and differences in yield dent for uWN-actual (b), uW-actual (c), and uN-actual (d) for all grid cells with at least 100ha maize cropland [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198748#pone.0198748.ref038" target="_blank">38</a>] and a minimum yield of 0.5 tDM ha^-1.</p

Global distribution of relative (%) temporal yield variability per production system (actual, uW, uN, uWN) and GGCM per grid cell for maize.

<p>Colored bars show the interquartile range of yield CVs across all grid cells with at least 100ha maize cropland [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198748#pone.0198748.ref038" target="_blank">38</a>] and a minimum yield of 0.5 tDM ha^-1. Black lines within the bars show the median, dashed whiskers extend to the maximum value with 1.5 times the interquartile range and values outside this range are classified as outliers and depicted as dots. Yield CV of more than 100% are not shown.</p

Changes in CV from purely rainfed to fully irrigated systems with current nitrogen (uW-rf).

<p>The CV can increase in regions where different growing seasons are specified for irrigated and rainfed systems [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198748#pone.0198748.ref015" target="_blank">15</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198748#pone.0198748.ref038" target="_blank">38</a>]. Maps show data of the GGCM ensemble median for all grid cells with at least 100ha maize cropland [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198748#pone.0198748.ref038" target="_blank">38</a>] and a minimum yield of 0.5 tDM ha^-1.</p

A Unique Approach to Design Potent and Selective Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (CBP) Inhibitors

The epigenetic regulator CBP/P300 presents a novel therapeutic target for oncology. Previously, we disclosed the development of potent and selective CBP bromodomain inhibitors by first identifying pharmacophores that bind the KAc region and then building into the LPF shelf. Herein, we report the “hybridization” of a variety of KAc-binding fragments with a tetrahydroquinoline scaffold that makes optimal interactions with the LPF shelf, imparting enhanced potency and selectivity to the hybridized ligand. To demonstrate the utility of our hybridization approach, two analogues containing unique Asn binders and the optimized tetrahydroquinoline moiety were rapidly optimized to yield single-digit nanomolar inhibitors of CBP with exquisite selectivity over BRD4(1) and the broader bromodomain family

Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice

A series of trisubstituted hydroxylactams was identified as potent enzymatic and cellular inhibitors of human lactate dehydrogenase A. Utilizing structure-based design and physical property optimization, multiple inhibitors were discovered with <10 μM lactate IC₅₀ in a MiaPaca2 cell line. Optimization of the series led to <b>29</b>, a potent cell active molecule (MiaPaca2 IC₅₀ = 0.67 μM) that also possessed good exposure when dosed orally to mice