Cell-Derived N/P/S-Codoped Fluorescent Carbon Nanodots with Intrinsic Targeting Ability for Tumor-Specific Phototheranostics.

Combining targeting ability, imaging function, and photothermal/photodynamic therapy into a single agent is highly desired for cancer theranostics. Herein, we developed a one-for-all nanoplatform with N/P/S-codoped fluorescent carbon nanodots (CNDs) for tumor-specific phototheranostics. The CNDs were prepared via a one-pot hydrothermal process using cancer cells as sources of carbon, nitrogen, phosphorus, and sulfur. The obtained N/P/S-codoped CNDs exhibit wide light absorption in the range of 200-900 nm and excitation-dependent emission with high photostability. Importantly, the cancer cell-derived N/P/S-codoped CNDs have outstanding biocompatibility and naturally intrinsic targeted ability for cancer cells as well as dual photothermal/photodynamic effects under 795 nm laser irradiation. Moreover, the photothermal conversion efficiency and singlet oxygen (1O2) generation efficiency were calculated to be 52 and 34%, respectively. These exceptional properties enable CNDs to act as fine theranostic agents for targeted imaging and photothermal-photodynamic synergistic therapy within the NIR therapeutic window. The CNDs prepared in this work are promising for construction as a universal tumor phototheranostic platform.

Exploring the Charge Storage Dynamics in Donor-Acceptor Covalent Organic Frameworks Based Supercapacitors by Employing Ionic Liquid Electrolyte.

Two donor-acceptor type tetrathiafulvalene (TTF)-based covalent organic frameworks (COFs) are investigated as electrodes for symmetric supercapacitors in different electrolytes, to understand the charge storage and dynamics in 2D COFs. Till-date, most COFs are investigated as Faradic redox pseudocapacitors in aqueous electrolytes. For the first time, it is tried to enhance the electrochemical performance and stability of pristine COF-based supercapacitors by operating them in the non-Faradaic electrochemically double layer capacitance region. It is found that the charge storage mechanism of ionic liquid (IL) electrolyte based supercapacitors is dependent on the micropore size and surface charge density of the donor-acceptor COFs. The surface charge density alters due to the different electron acceptor building blocks, which in turn influences the dense packing of the IL near its pore. The micropores induce pore confinement of IL in the COFs by partial breaking of coulomb ordering and rearranging it. The combination of these two factors enhance the charge storage in the highly microporous COFs. The density functional theory calculations support the same. At 1 A g-1 , TTF-porphyrin COF provides capacitance of 42, 70, and 130 F g-1 in aqueous, organic, and IL electrolyte respectively. TTF-diamine COF shows a similar trend with 100 F g-1 capacitance in IL.

High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize.

Maize (Zea mays) is one of the most important crops in the world. However, few agronomically important maize genes have been cloned and used for trait improvement, due to its complex genome and genetic architecture. Here, we integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition. After low-cost barcode-based deep sequencing, 412 edited sequences covering 118 genes were precisely identified from individuals showing clear phenotypic changes. The profiles of the associated gene-editing events were similar to those identified in human cell lines and consequently are predictable using an existing algorithm originally designed for human studies. We observed unexpected but frequent homology-directed repair through endogenous templates that was likely caused by spatial contact between distinct chromosomes. Based on the characterization and interpretation of gene function from several examples, we demonstrate that the integration of forward and reverse genetics via a targeted mutagenesis library promises rapid validation of important agronomic genes for crops with complex genomes. Beyond specific findings, this study also guides further optimization of high-throughput CRISPR experiments in plants.

Investigation of Anti-Alzheimer's Mechanisms of Sarsasapogenin Derivatives by Network-Based Combining Structure-Based Methods.

Alzheimer's disease (AD), a neurodegenerative disease with no cure, affects millions of people worldwide and has become one of the biggest healthcare challenges. Some investigated compounds play anti-AD roles at the cellular or the animal level, but their molecular mechanisms remain unclear. In this study, we designed a strategy combining network-based and structure-based methods together to identify targets for anti-AD sarsasapogenin derivatives (AAs). First, we collected drug-target interactions (DTIs) data from public databases, constructed a global DTI network, and generated drug-substructure associations. After network construction, network-based models were built for DTI prediction. The best bSDTNBI-FCFP_4 model was further used to predict DTIs for AAs. Second, a structure-based molecular docking method was employed for rescreening the prediction results to obtain more credible target proteins. Finally, in vitro experiments were conducted for validation of the predicted targets, and Nrf2 showed significant evidence as the target of anti-AD compound AA13. Moreover, we analyzed the potential mechanisms of AA13 for the treatment of AD. Generally, our combined strategy could be applied to other novel drugs or compounds and become a useful tool in identification of new targets and elucidation of disease mechanisms. Our model was deployed on our NetInfer web server (http://lmmd.ecust.edu.cn/netinfer/).

Pyrene-Based Covalent Organic Frameworks for Photocatalytic Hydrogen Peroxide Production.

Four highly porous covalent organic frameworks (COFs) containing pyrene units were prepared and explored for photocatalytic H2 O2 production. The experimental studies are complemented by density functional theory calculations, proving that the pyrene unit is more active for H2 O2 production than the bipyridine and (diarylamino)benzene units reported previously. H2 O2 decomposition experiments verified that the distribution of pyrene units over a large surface area of COFs plays an important role in catalytic performance. The Py-Py-COF though contains more pyrene units than other COFs which induces a high H2 O2 decomposition due to a dense concentration of pyrene in close proximity over a limited surface area. Therefore, a two-phase reaction system (water-benzyl alcohol) was employed to inhibit H2 O2 decomposition. This is the first report on applying pyrene-based COFs in a two-phase system for photocatalytic H2 O2 generation.

Synthesis of Renal-Clearable Multicolor Fluorescent Silicon Nanodots for Tumor Imaging and In Vivo H2O2 Profiling.

Fluorescent silicon nanodots have shown great prospects for bioimaging and biosensing applications. Although various fluorescent silicon-containing nanodots (SiNDs) have been developed, there are few reports about renal-clearable multicolor SiNDs. Herein, renal-clearable multicolor fluorescent SiNDs are synthesized by using silane molecules and organic dyes through a facile one-step hydrothermal method. The fluorescence of the resulting SiNDs can be tuned to blue (bSiNDs), green (gSiNDs), and red (rSiNDs) by simply changing the categories of silane reagents or dye molecules. The as-prepared SiNDs exhibit strong fluorescence with a quantum yield up to 72%, excellent photostability, and good biocompatibility with 12 h renal clearance rate as high as 86% ID. These properties enabled the SiNDs for tumor fluorescence imaging and H2O2 imaging in living cells and tissue through in situ reduction reaction-lighted fluorescence of the nanoprobe. Our results provide an invaluable methodology for the synthesis of renal-clearable multicolor SiNDs and their potential applications for fluorescence imaging and biomarker sensing. These SiNDs are also promising for various biological and biomedical applications.

Creation of Exclusive Artificial Cluster Defects by Selective Metal Removal in the (Zn, Zr) Mixed-Metal UiO-66.

The differentiation between missing linker defects and missing cluster defects in MOFs is difficult, thereby limiting the ability to correlate materials properties to a specific type of defects. Herein, we present a novel and easy synthesis strategy for the creation of solely "missing cluster defects" by preparing mixed-metal (Zn, Zr)-UiO-66 followed by a gentle acid wash to remove the Zn nodes. The resulting material has the reo UiO-66 structure, typical for well-defined missing cluster defects. The missing clusters are thoroughly characterized, including low-pressure Ar-sorption, iDPC-STEM at a low dose (1.5 pA), and XANES/EXAFS analysis. We show that the missing cluster UiO-66 has a negligible number of missing linkers. We show the performance of the missing cluster UiO-66 in CO2 sorption and heterogeneous catalysis.

A Plasmon-Enhanced SnSe2 Photodetector by Non-Contact Ag Nanoparticles.

The 2D layered materials are promising candidates for broadband, low-cost photodetectors. One deficiency of 2D materials is the relatively low absorbance of light, limiting the applications of the 2D photodetectors. Doping of plasmonic nanoparticles into 2D materials may enhance the optical absorbance owing to the localized surface plasmonic resonance (LSPR) effect; however, considerable defects may be introduced into the 2D materials at the same time, resulting in certain degradation of device performance. Here, a novel design of 2D photodetectors with enhanced photoresponsivity by non-contact plasmonic nanoparticles (NPs) is proposed, consisting of a hybrid structure of few-layer SnSe2 transferred a fused silica (SiO2 ) plate with embedded Ag NPs. The system of Ag NPs-in-SiO2 shows strong LSPR effect with significantly enhanced optical absorption, acting on SnSe2 in a non-contact configuration. Benefiting from well-preserved intrinsic features of SnSe2 and LSPR effect, the responsivity of the photodetector is enhanced by 881 times with the bias voltage of 0.1 V, which is superior to previously reported results of plasmon-enhanced 2D photodetectors. Moreover, the SiO2 with embedded Ag NPs is recyclable and can be easy to be recombined with different 2D materials. This work offers additional strategy for development of efficient, low-cost 2D photodetectors by using plasmonic NPs.

Toward Unusual-High Hole Mobility of p-Channel Field-Effect-Transistors.

The relative low hole mobility of p-channel building block device challenges the continued miniaturization of modern electronic chips. Metal-semiconductor junction is always an efficient strategy to control the carrier concentration of channel semiconductor, benefiting the carrier mobility regulation of building block device. In this work, complementary metal oxide semiconductor (CMOS)-compatible metals are selected to deposit on the surface of the important p-channel building block of GaSb nanowire field-effect-transistors (NWFETs), demonstrating the efficient strategy of hole mobility enhancement by metal-semiconductor junction. When deposited with lower work function metal of Al, the peak hole mobility of GaSb NWFET can be enhanced to as high as ≈3372 cm2 V-1 s-1 , showing three times than the un-deposited one. The as-studied metal-semiconductor junction is also efficient for the hole mobility enhancement of other p-channel devices, such as GaAs NWFET, GaAs film FET, and WSe2 FET. With the enhanced mobility, the as-constructed CMOS inverter shows good invert characteristics, showing a relatively high gain of ≈18.1. All results may be regarded as important advances to the next-generation electronics.

Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize.

Alternative splicing (AS) enhances transcriptome diversity and plays important roles in regulating plant processes. Although widespread natural variation in AS has been observed in plants, how AS is regulated and contribute to phenotypic variation is poorly understood. Here, we report a population-level transcriptome assembly and genome-wide association study to identify splicing quantitative trait loci (sQTLs) in developing maize (Zea mays) kernels from 368 inbred lines. We detected 19,554 unique sQTLs for 6570 genes. Most sQTLs showed small isoform usage changes without involving major isoform switching between genotypes. The sQTL-affected isoforms tend to display distinct protein functions. We demonstrate that nonsense-mediated mRNA decay, microRNA-mediated regulation, and small interfering peptide-mediated peptide interference are frequently involved in sQTL regulation. The natural variation in AS and overall mRNA level appears to be independently regulated with different cis-sequences preferentially used. We identified 214 putative trans-acting splicing regulators, among which ZmGRP1, encoding an hnRNP-like glycine-rich RNA binding protein, regulates the largest trans-cluster. Knockout of ZmGRP1 by CRISPR/Cas9 altered splicing of numerous downstream genes. We found that 739 sQTLs colocalized with previous marker-trait associations, most of which occurred without changes in overall mRNA level. Our findings uncover the importance of AS in diversifying gene function and regulating phenotypic variation.

Near infrared imaging of intracellular GSH by AuNCs@MnO2 core-shell nanoparticles based on the absorption competition mechanism.

Dynamically monitoring intracellular glutathione (GSH), a crucial biomarker of oxidative stress, is of significance for the diagnosis and treatment of certain diseases. Although manganese dioxide (MnO2) based GSH fluorescent sensors have exhibited high sensitivity and good selectivity owing to the specific reactivity between GSH and MnO2, near-infrared (NIR) MnO2 based nanoprobes for GSH detection are scarce. Herein, we have developed a NIR activatable fluorescence nanoprobe for the imaging and determination of intracellular GSH based on a core-shell nanoparticle, consisting of NIR emitted gold nanocluster doped silica as the fluorescent core and manganese dioxide as the GSH-responsive shell (named AuNCs@MnO2). Due to the absorption competition mechanism, the outer MnO2 shell rather than the inner AuNCs core preferentially absorbed the excitation light, thus leading to fluorescence quenching of the inner AuNCs core. Upon addition of GSH, the fluorescence of the nanoprobe restored along with the reduction of MnO2 to Mn2+ because of the absorption competition disappearance-induced emission. The activatable fluorescence linearly increased upon changing the GSH concentration in the range of 2 to 5000 µM with a detection limit of 0.67 µM. The cytotoxicity test shows that the AuNCs@MnO2 nanoprobes have a good biocompatibility. After entering the cancer cells, the intracellular GSH degraded the outermost MnO2 shell and initiated the NIR fluorescence restoration of AuNCs, which can be used to monitor the dynamic change of intracellular GSH. This strategy provides an NIR-activatable way to detect GSH levels in living cells and offers a promising platform for the diagnosis and treatment of GSH-related diseases.

Ambipolar transport in Ni-catalyzed InGaAs nanowire field-effect transistors for near-infrared photodetection.

Weak n-type characteristics or poor p-type characteristics are limiting the applications of binary semiconductors based on ambipolar field-effect transistors (FETs). In this work, a ternary alloy of In0.2Ga0.8As nanowires (NWs) is successfully prepared using a Ni catalyst during a typical solid-source chemical-vapor-deposition process to balance the weak n-type conduction behavior in ambipolar GaAs NWFETs and the poor p-type conduction behavior in ambipolar InAs NWFETs. The presence of ambipolar transport, contributed by a native oxide shell and the body defects of the prepared In0.2Ga0.8As NWs, is confirmed by the constructed back-gated NWFETs. As demonstrated by photoluminescence, the bandgap of the prepared In0.2Ga0.8As NWs is 1.28 eV, offering the promise of application in near-infrared (NIR) photodetection. Under 850 nm laser illumination, the fabricated ambipolar NWFETs show extremely low dark currents of 50 pA and 0.5 pA when positive and negative gate voltages are applied, respectively. All the results demonstrate that with careful design of the surface oxide layer and the body defects, NWs are suitable for use in next-generation optoelectronic devices.

Defect-engineered three-dimensional vanadium diselenide microflowers/nanosheets on carbon cloth by chemical vapor deposition for high-performance hydrogen evolution reaction.

In the past decades, defect engineering has become an effective strategy to significantly improve the hydrogen evolution reaction (HER) efficiency of electrocatalysts. In this work, a facile chemical vapor deposition (CVD) method is firstly adopted to demonstrate defect engineering in high-efficiency HER electrocatalysts of vanadium diselenide nanostructures. For practical applications, the conductive substrate of carbon cloth (CC) is selected as the growth substrate. By using a four-time CVD method, uniform three-dimensional microflowers with defect-rich small nanosheets on the surface are prepared directly on the CC substrate, displaying a stable HER performance with a low Tafel slope value of 125 mV dec-1and low overpotential voltage of 295 mV at a current density of 10 mA cm-2in alkaline electrolyte. Based on the results of x-ray photoelectron spectra and density functional theory calculations, the impressive HER performance originates from the Se vacancy-related active sites of small nanosheets, while the microflower/nanosheet homoepitaxy structure facilitates the carrier flow between the active sites and conductive substrate. All the results present a new route to achieve defect engineering using the facile CVD technique, and pave a novel way to prepare high-activity layered electrocatalysts directly on a conductive substrate.

Twin drug design, synthesis and evaluation of diosgenin derivatives as multitargeted agents for the treatment of vascular dementia.

A novel series of multitargeted molecules were designed and synthesized by combining the pharmacological role of cholinesterase inhibitor and antioxidant of steroid as potential ligands for the treatment of Vascular Dementia (VD). The oxygen-glucose deprivation (OGD) model was used to evaluate these molecules, among which the most potent compound ML5 showed the highest activity. Firstly, ML5 showed appropriate inhibition of cholinesterases (ChEs) at orally 15 mg/kg in vivo. The further test revealed that ML5 promoted the nuclear translocation of Nrf2. Furthermore, ML5 has significant neuroprotective effect in vivo model of bilateral common carotid artery occlusion (BCCAO), significantly increasing the expression of Nrf2 protein in the cerebral cortex. In the molecular docking research, we predicted the ML5 combined with hAChE and Keap1. Finally, compound ML5 displayed normal oral absorption and it was nontoxic at 500 mg/kg, po, dose. We can draw the conclusion that ML5 could be considered as a new potential compound for VD treatment.

Nanomediator-Effector Cascade Systems for Amplified Protein Kinase Activity Imaging and Phosphorylation-Induced Drug Release In Vivo.

Protein kinases constitute a rich pool of biomarkers and therapeutic targets of tremendous diseases including cancer. However, sensing kinase activity in vivo while implementing treatments according to kinase hyperactivation remains challenging. Herein, we present a nanomediator-effector cascade system that can in situ magnify the subtle events of kinase-catalyzed phosphorylation via DNA amplification machinery to achieve kinase activity imaging and kinase-responsive drug release in vivo. In this cascade, the phosphorylation-mediated disassembly of DNA/peptide complex on the nanomediators initiated the detachment of fluorescent hairpin DNAs from the nanoeffectors via hybridization chain reaction (HCR), leading to fluorescence recovery and therapeutic cargo release. We demonstrated that this nanosystem simultaneously enabled trace protein kinase A (PKA) activity imaging and on-demand drug delivery for inhibition of tumor cell growth both in vitro and in vivo, affording a kinase-specific sense-and-treat paradigm for cancer theranostics.

CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes.

SUMMARY: CRISPR-Local is a high-throughput local tool for designing single-guide RNAs (sgRNAs) in plants and other organisms that factors in genetic variation and is optimized to generate genome-wide sgRNAs. CRISPR-Local outperforms other sgRNA design tools in the following respects: (i) designing sgRNAs suitable for non-reference varieties; (ii) screening for sgRNAs that are capable of simultaneously targeting multiple genes; (iii) saving computational resources by avoiding repeated calculations from multiple submissions and (iv) running offline, with both command-line and graphical user interface modes and the ability to export multiple formats for further batch analysis or visualization. We have applied CRISPR-Local to 71 public plant genomes, using both CRISPR/Cas9 and CRISPR/cpf1 systems. AVAILABILITY AND IMPLEMENTATION: CRISPR-Local can be freely downloaded from http://crispr.hzau.edu.cn/CRISPR-Local/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks.

Differential network analysis has become an important approach in identifying driver genes in development and disease. However, most studies capture only local features of the underlying gene-regulatory network topology. These approaches are vulnerable to noise and other changes which mask driver-gene activity. Therefore, methods are urgently needed which can separate the impact of true regulatory elements from stochastic changes and downstream effects. We propose the differential network flow (DNF) method to identify key regulators of progression in development or disease. Given the network representation of consecutive biological states, DNF quantifies the essentiality of each node by differences in the distribution of network flow, which are capable of capturing comprehensive topological differences from local to global feature domains. DNF achieves more accurate driver-gene identification than other state-of-the-art methods when applied to four human datasets from The Cancer Genome Atlas and three single-cell RNA-seq datasets of murine neural and hematopoietic differentiation. Furthermore, we predict key regulators of crosstalk between separate networks underlying both neuronal differentiation and the progression of neurodegenerative disease, among which APP is predicted as a driver gene of neural stem cell differentiation. Our method is a new approach for quantifying the essentiality of genes across networks of different biological states.

Ultrahigh Hole Mobility of Sn-Catalyzed GaSb Nanowires for High Speed Infrared Photodetectors.

Owing to the relatively low hole mobility, the development of GaSb nanowire (NW) electronic and photoelectronic devices has stagnated in the past decade. During a typical catalyst-assisted chemical vapor deposition (CVD) process, the adopted metallic catalyst can be incorporated into the NW body to act as a slight dopant, thus regulating the electrical properties of the NW. In this work, we demonstrate the use of Sn as a catalyst and dopant for GaSb NWs in the surfactant-assisted CVD growth process. The Sn-catalyzed zinc-blende GaSb NWs are thin, long, and straight with good crystallinity, resulting in a record peak hole mobility of 1028 cm2 V-1 s-1. This high mobility is attributed to the slight doping of Sn atoms from the catalyst tip into the NW body, which is verified by the red-shifted photoluminescence peak of Sn-catalyzed GaSb NWs (0.69 eV) compared with that of Au-catalyzed NWs (0.74 eV). Furthermore, the parallel array NWs also show a high peak hole mobility of 170 cm2 V-1 s-1, a high responsivity of 61 A W-1, and fast rise and decay times of 195.1 and 380.4 µs, respectively, under the illumination of 1550 nm infrared light. All of the results demonstrate that the as-prepared Sn-catalyzed GaSb NWs are promising for application in next-generation electronics and optoelectronics.

Age determination in echinoderms: first evidence of annual growth rings in holothuroids.

While age is fundamental in animal biology, forming the basis of critical concepts such as life-history strategies, longevity and population structures, measuring this variable in some taxa remains problematic. Such is the case of holothuroid echinoderms, which play key roles in marine benthic communities from the shore to the abyss, and which are extensively fished in many regions across the globe. Here, we present and validate a promising ageing technique using the cold-water species Psolus fabricii. The method involves the extraction of the oldest dermal plates (largest dorsal ossicles) to preserve their original pigments and structure. While plates initially appear to have a uniform texture, polishing and dying them reveals layered ring patterns. A study of laboratory-reared juveniles, from settlement to 40 months of age, confirmed that one layer is added annually, making plates both larger and thicker, and generating successive light and dark rings, the latter representing the transition (overlap) between two layers. Therefore, each pair of rings represents an annual growth band. Size-at-age data obtained using this method revealed that growth of P. fabricii is slow and that wild individuals collected at diving depths had reached an age of several decades.

Active buoyancy adjustment increases dispersal potential in benthic marine animals.

While the study of dispersal and connectivity in the ocean typically centres on pelagic species and planktonic larval stages of benthic species, the present work explores an overlooked locomotor means in post-settlement benthic stages that redefines their dispersal potential. Members of the echinoderm class Holothuroidea colonize a diversity of marine environments world-wide, where they play key ecological and economical roles, making their conservation a priority. Holothuroids are commonly called sea cucumbers or sea slugs to reflect their slow movements and are assumed to disperse chiefly through pelagic larvae. The present study documents and explores their unexpected ability to actively modify their buoyancy, leading them to tumble or float at speeds orders of magnitudes faster than through benthic crawling. Two focal species representing different taxonomic orders, geographic distributions and reproductive strategies were studied over several years. Active buoyancy adjustment (ABA) was achieved through a rapid increase in water-to-flesh ratio by up to 740%, leading to bloating, and simultaneously detachment from the substrate. It occurred as early as 6 months post settlement in juveniles and was recorded in wild adult populations. In experimental trials, ABA was triggered by high conspecific density, decreasing salinity and increasing water turbidity. Based on field video footage, ABA-assisted movements generated speeds of up to 90 km/day. These findings imply that displacement during planktonic larval stages may not supersede the locomotor capacity of benthic stages, challenging the notion of sedentarity. Combining the present results and anecdotal reports, ABA emerges as a generalized means of dispersal among benthic animals, with critical implications for world-wide management and conservation of commercially and ecologically significant species.