A novel strategy for ratiometric determination of o-phenylenediamine via in-situ fluorogenic reaction and generation of metal nanoparticles.

Herein, a novel ratiometric strategy for ultra-sensitive detection of o-phenylenediamine (OPD) was proposed based on combinatorial reactions of in-situ fluorogenic reaction and in-situ formation of red fluorescent dithiothreitol-copper nanoparticles (DTT-CuNPs). Here, Cu2+ is used both as an oxidant and as a precursor. Dehydroascorbic acid (DHAA) is formed via redox reaction of AA and Cu2+. Then, DHAA reacts with OPD to yield blue fluorescent quinoxaline (OXD) with emission peak at 434 nm through in-situ fluorogenic reaction. Red emitting DTT-CuNPs with emission peak at 666 nm is instantly generated due to the coordination reaction between DTT and the residual Cu2+ which is not consumed by AA. The fluorescence intensity (FI) of OXD at 434 nm is closely relied on the concentration of OPD, which can be used as a response signal for OPD detection. Meanwhile, FI of DTT-CuNPs at 666 nm has no significant change, which can be used as a reference signal for OPD detection. Thus, the ratio (F434/F666) of the Cu2+/AA/DTT sensing system is successfully employed to quantify OPD, exhibiting a wide linear range from 0.2 µM to 60 µM, with LOD of 0.09 µM.

Construction of nanohybrid Tb@CDs/GSH-CuNCs as a ratiometric probe to detect phosphate anion based on aggregation-induced emission and FRET mechanism.

The simple preparation of a nanohybrid of terbium-doped carbon dots/glutathione-capped copper nanoclusters (Tb@CDs/GSH-CuNCs) was for the first time developed for ratiometric detection of phosphate anion (Pi). Blue-emission of Tb@CDs can trigger non-luminescence of GSH-CuNCs for aggregation-induced emission (AIE) performance due to the strong reserved coordination capacity of Tb3+. Thus, Tb@CDs/GSH-CuNCs rapidly generated dual-emission signals at 630 nm and 545 nm by directly mixing the two individual materials via the AIE effect, alongside fluorescence resonance energy transfer (FRET) process. However, by the introduction of Pi, both AIE and FRET processes were blocked because of the stronger binding affinity of Tb3+ and Pi than that of Tb3+ and -COOH on Tb@CDs, thus realizing successful ratiometric detection of Pi. The linear concentration range was 0-16 µM, with the limit of detection (LOD) of 0.32 µM. The proposed method provided new ideas for designing nanohybrid of CDs and nanoclusters (MNCs) as ratiometric fluorescent probes for analytical applications.

Ce4+/Ce3+ as the switch of AIE-copper nanoclusters for highly selective detection of ascorbic acid in soft drinks.

An ultrasimple "turn-on" sensor for indirectly detecting ascorbic acid (AA) was prepared using N-acetyl-L-cysteine stabilized copper nanoclusters (NAC-CuNCs) via the AIE (aggregation-induced emission) effect controlled by Ce4+/Ce3+ redox reaction. This sensor fully utilizes the different properties of Ce4+ and Ce3+. Non-emissive NAC-CuNCs were synthesized by a facile reduction method. NAC-CuNCs easily aggregate in the presence of Ce3+ due to AIE, resulting in fluorescence enhancement. However, this phenomenon cannot be observed in the presence of Ce4+. Ce4+ possesses strong oxidizing ability and produces Ce3+ by reacting with AA via a redox reaction, followed by switching on the luminescence of NAC-CuNCs. Moreover, the fluorescence intensity (FI) of NAC-CuNCs increases with the concentration of AA in the range of 4-60 µM, with the limit of detection (LOD) as low as 0.26 µM. This probe with excellent sensitivity and selectivity was successfully used in the determination of AA in soft drinks.

Ce3+-induced Fluorescence Amplification of Copper Nanoclusters Based on Aggregation-induced Emission for Specific Sensing 2,6-pyridine Dicarboxylic Acid.

A straightforward, cost-effective and biocompatible reduction approach was applied to fabricate soluble but non-luminous glutathione-stabilized copper nanocluster (GSH-CuNCs). Surprisingly, as high as 1 × 103 times fluorescence enhancement was acquired when Ce3+ was injected at an extremely low concentration of only 18 µM. Ce3+ outperformed other rare-earth metal ions in terms of inducing fluorescence amplification of the non-luminous GSH-CuNCs. Furthermore, Ce3+ was employed as inducer for aggregation-induce emission (AIE) effect as well as reactant to coordinate with target of 2,6-pyridine dicarboxylic acid (DPA) due to the stronger coordination ability between Ce3+ and DPA than that of Ce3+ and GSH. As a result, the Ce3+/GSH-CuNCs ensemble was developed as a novel sensor to detect DPA in the "on-off" mode. When DPA was introduced into the sensor, Ce3+ failed to interact with GSH and detached from the surface of GSH-CuNCs, leading to fluorescence quenching. In addition, static quenching process and internal filtration effect (IFE) between Ce3+/GSH-CuNCs and DPA were also responsible for fluorescence quenching effect. A good linear relationship was obtained from 0.3 µM to 18 µM, with a limit of detection (LOD) of 0.19 µM. The as-proposed probe displayed high specificity to DPA and provided a simple, fast rapid and cheap method for construction this type of ensemble sensors to detect other targets.

Scaling dictates the decoder structure.

Despite fluctuations in embryo size within a species, the spatial gene expression pattern and hence the embryonic structure can nonetheless maintain the correct proportion to the embryo size. This is known as the scaling phenomenon. For morphogen-induced patterning of gene expression, the positional information encoded in the local morphogen concentrations is decoded by the downstream genetic network (the decoder). In this paper, we show that the requirement of scaling sets severe constraints on the geometric structure of such a local decoder, which in turn enables deduction of mutants' behavior and extraction of regulation information without going into any molecular details. We demonstrate that the Drosophila gap gene system achieves scaling in the way consistent with our theory-the decoder geometry required by scaling correctly accounts for the observed gap gene expression pattern in nearly all maternal morphogen mutants. Furthermore, the regulation logic and the coding/decoding strategy of the gap gene system can also be revealed from the decoder geometry. Our work provides a general theoretical framework for a large class of problems where scaling output is achieved by non-scaling inputs and a local decoder, as well as a unified understanding of scaling, mutants' behavior, and gene regulation for the Drosophila gap gene system.

Finding gene network topologies for given biological function with recurrent neural network.

Searching for possible biochemical networks that perform a certain function is a challenge in systems biology. For simple functions and small networks, this can be achieved through an exhaustive search of the network topology space. However, it is difficult to scale this approach up to larger networks and more complex functions. Here we tackle this problem by training a recurrent neural network (RNN) to perform the desired function. By developing a systematic perturbative method to interrogate the successfully trained RNNs, we are able to distill the underlying regulatory network among the biological elements (genes, proteins, etc.). Furthermore, we show several cases where the regulation networks found by RNN can achieve the desired biological function when its edges are expressed by more realistic response functions, such as the Hill-function. This method can be used to link topology and function by helping uncover the regulation logic and network topology for complex tasks.

The STING phase-separator suppresses innate immune signalling.

Biomolecular condensates (biocondensates) formed via liquid-liquid phase-separation of soluble proteins have been studied extensively. However, neither the phase-separation of endoplasmic reticulum (ER) transmembrane protein nor a biocondensate with organized membranous structures has been reported. Here, we have discovered a spherical ER membranous biocondensate with puzzle-like structures caused by condensation of the ER-resident stimulator of interferon genes (STING) in DNA virus-infected or 2'3'-cGAMP (cyclic GMP-AMP)-treated cells, which required STING transmembrane domains, an intrinsically disordered region (IDR) and a dimerization domain. Intracellular 2'3'-cGAMP concentrations determined STING translocation or condensation. STING biocondensates constrained STING and TBK1 (TANK binding protein 1) to prevent innate immunity from overactivation, presumably acting like a 'STING-TBK1-cGAMP sponge'. Cells expressing STING-E336G/E337G showed notably enhanced innate immune responses due to impaired STING condensation after viral infection at later stages. Microtubule inhibitors impeded the STING condensate gel-like transition and augmented type I-interferon production in DNA virus-infected cells. This membranous biocondensate was therefore named the STING phase-separator.