Ultraphotostable Phosphorescent Nanosensors for Sensing the Lysosomal pH at the Single-Cell Level over Long Durations.

Ultraphotostable phosphorescent nanosensors have been designed for continuously sensing the lysosome pH over a long duration. The nanosensors exhibited excellent photostability, high accuracy, and capability to measure pH values during cell proliferation for up to 7 days. By arranging a metal-ligand complex of long phosphorescence lifetime and pH indicator in silica nanoparticles, we discover efficient Förster resonance energy transfer, which converts the pH-responsive UV-vis absorption signal of the pH indicator into a phosphorescent signal. Both the phosphorescent intensity and lifetime change at different pH values, and intracellular pH values can be accurately measured by our custom-built rapid phosphorescent lifetime imaging microscopy. The excellent photostability, high accuracy, and good biocompatibility prove that these nanosensors are a useful tool for tracing the fluctuation of pH values during endocytosis. The methodology can be easily adapted to design new nanosensors with different pKa or for different kinds of intracellular ions, as there are hundreds of pH and ion indicators readily available.

Two new bibenzyl methylglucosides as SIRT3 activators obtained through microbial transformation.

Microbial transformation of dihydroresveratrol (DHRSV) using Beauveria bassiana has produced two new methylglucosylated derivatives of DHRSV (1 and 2), whose structures were characterized as 4'-O-(4″-O-methyl-ß-D-glucopyranosyl)-dihydroresveratrol (4'-O-MG DHRSV, 1) and 3-O-(4″-O-methyl-ß-D-glucopyranosyl)-dihydroresveratrol (3-O-MG DHRSV, 2) on the basis of spectroscopic methods. They showed moderate SIRT3 agonistic activity, and compound 2 exhibited the best deacetylation of 406.63% at 10 µM. The activity of 2 increased by 3.12-fold compared with that of DHRSV, since 2 performed better in molecular docking assay (GScore -8.445).

Luminescent Silica Nanosensors for Lifetime Based Imaging of Intracellular Oxygen with Millisecond Time Resolution.

Intracellular oxygen concentration was quantitatively imaged and rapidly traced with millisecond time resolution. We have demonstrated a new kind of oxygen nanosensors based on a ruthenium complex doped solid silica nanoparticles, which showed high oxygen sensing performance (I0/I100 = 3.29, t95 < 3 s) and ease of surface functionalization. Their sensing performance can be tuned by changing types of oxygen-sensitive probes and particle morphology. The nanosensors showed excellent control in both sensor size (from 30 to 200 nm), monodispersity, morphology, surface chemistry, and batch to batch consistency. Their uniform size distribution and good biocompatibility made them suitable for intracellular studies. Because the sensor surface can be easily functionalized with arbitrary units (such as transmembrane motifs, drugs, organelle-targeting groups, imaging reagent, and multiple sensor probes), these nanosensors provide a general platform to build easy-to-use tools for intracellular applications. The ease of surface functionalization was demonstrated by modifying the sensors outer surface with morpholinopropylamine and (3-carboxypropyl) triphenyl phosphonium, to actively target intracellular lysosomes and mitochondria of the tested cell lines (HeLa, MCF-7, and MCF-10A). Applying the mitochondria-targeting oxygen nanosensor together with our custom-built rapid phosphorescent lifetime imaging system, variations of intracellular oxygen have been quantitatively imaged and traced (in millisecond intervals) in real time and in situ.

Fully Reversible Optical Sensor for Hydrogen Peroxide with Fast Response.

A fully reversible optical sensor for hydrogen peroxide with fast response is presented. The sensor was fabricated by in situ growing ultrasmall platinum nanoparticles (PtNPs) inside the pores of fibrous silica particles (KCC-1). The nanocomposite was then embedded into a hydrogel matrix and form a sensor layer, the immobilized PtNPs can catalytically convert hydrogen peroxide into molecular oxygen, which is measured via luminescent quenching based oxygen sensor underneath. Owing to the high porosity and permeability of KCC-1 and high local concentration of PtNPs, the sensor exhibits fast response (less than 1 min) and full reversibility. The measurement range of the sensor covers 1.0 µM to 10.0 mM, and a very small amount of sample is required during measurement (200 µL). Because of its high stability, excellent reversibility and selectivity, and extremely fast response, the sensor could fulfill all industry requirements for real-time measurement and fill market vacancy.

A background-subtraction strategy leads to ratiometric sensing of oxygen without recalibration.

Luminescence-quenching based optical oxygen sensors have wide applications in many fields, which have already replaced almost 40% of the commercial market share dominated previously by the Clark oxygen electrode. The majority of optical oxygen sensors are based on lifetime measurement, which are precise, but are relatively expensive, and require high-speed electronics and detecting circuits. Alternatively, oxygen concentration can be measured via a luminescence intensity change, which is a referenced approach according to the Stern-Volmer equation. However, luminescence intensity based measurement tends to be highly influenced by background light. At a given sensor composition, different instrumentation setups, sensor surface roughnesses and thicknesses, and environmental light will result in significantly different calibration curves and sensitivities. This makes luminescence-intensity based optical sensors almost impossible to use practically, because each sensor needs to be recalibrated before use, and the calibration curve each time is quite different. We have solved this problem by introducing a new background-subtraction strategy. After background subtraction, oxygen sensors with different probe concentrations, instrumentation setups, surface roughnesses, supporting matrixes, and at different temperatures present identical calibration curves. This could greatly reduce the calibration task during practical use. Combined with the advantages of low price and a simple optical configuration, the new method will significantly promote wider applications of optical oxygen sensors.

Silicon nitride O-band (de)multiplexers with low thermal sensitivity.

In this paper, four-channel cascaded Mach-Zehnder interferometer-based wavelength (de)multiplexers in the O-band are demonstrated experimentally by utilizing silicon nitride (SiN) optical waveguides. By reference to the commonly used 100 Gigabit Ethernet standards, two types of (de)multiplexer devices with different channel spacings are designed and fabricated. Both the devices exhibit low insertion loss and flat passbands. The lower thermo-optical coefficient provided by SiN brings benefits of reduction in thermal sensitivity. The fabricated (de)multiplexers show a temperature-dependent wavelength shift of about 18.5 pm/°C, which is reduced by 75% compared to the standard silicon-based devices.

Transmission of 2.86 Tb/s data stream in silicon subwavelength grating waveguides.

In this paper, we perform an investigation of terabit-scale data transmission in silicon subwavelength grating (SWG) waveguides for wavelength-division multiplexing (WDM) optical signals. Silicon SWG waveguide is capable of decreasing the light confinement in silicon core by engineering the geometry, leading to relatively lower optical nonlinearity compared to silicon wire waveguide. We demonstrate ultrahigh-bandwidth 2.86 Tb/s data transmission through the fabricated 2-mm-long silicon SWG waveguide over a wide range of launch powers. In the experiment, 75 WDM channels are utilized with each carrying 38.12 Gb/s orthogonal frequency-division multiplexing (OFDM) 16-ary quadrature amplitude modulation (16-QAM) signal. With the benefit of efficient reduction on optical nonlinearity, the optimum launch power is increased by 8 dB in SWG waveguide, indicating higher tolerance to the nonlinear impairments, compared to a silicon wire waveguide with identical length. With the optimum launch power, all 75 channels exhibit bit-error rate (BER) values less than 4e-5 after SWG waveguide transmission. We also evaluate the terabit-scale data transmission performance through four silicon SWG waveguides with different lengths (1 mm, 2 mm, 4 mm and 12 mm). The required optical signal-to-noise ratios (OSNRs) to achieve BER level of 1e-3 are around 15.27, 15.47, 16.66 and 20.38 dB, respectively.

Structure of the Legionella Effector, lpg1496, Suggests a Role in Nucleotide Metabolism.

Pathogenic Gram-negative bacteria use specialized secretion systems that translocate bacterial proteins, termed effectors, directly into host cells where they interact with host proteins and biochemical processes for the benefit of the pathogen. lpg1496 is a previously uncharacterized effector of Legionella pneumophila, the causative agent of Legionnaires disease. Here, we crystallized three nucleotide binding domains from lpg1496. The C-terminal domain, which is conserved among the SidE family of effectors, is formed of two largely α-helical lobes with a nucleotide binding cleft. A structural homology search has shown similarity to phosphodiesterases involved in cleavage of cyclic nucleotides. We have also crystallized a novel domain that occurs twice in the N-terminal half of the protein that we term the KLAMP domain due to the presence of homologous domains in bacterial histidine kinase-like ATP binding region-containing proteins and S-adenosylmethionine-dependent methyltransferase proteins. Both KLAMP structures are very similar but selectively bind 3',5'-cAMP and ADP. A co-crystal of the KLAMP1 domain with 3',5'-cAMP reveals the contribution of Tyr-61 and Tyr-69 that produces π-stacking interactions with the adenine ring of the nucleotide. Our study provides the first structural insights into two novel nucleotide binding domains associated with bacterial virulence.

Using celluloses to reinforce the optimized alginate film in wet state: Effect of cellulose types and cooking treatment.

Alginate (Alg) as co-extruded casing is of interest to the meat industry as replacers for natural sausage casing. However, these studies on the mechanical reinforcement of Alg-based film are still limited in the wet state (e.g. co-extrusion process). In this work, Alg-D with the highest viscosity-average molecular weight (1.12 × 105) was selected from four types of alginates based on the results of the viscosity of Alg solutions and film strength. Next, three celluloses (cellulose nanocrystals (CNC), cellulose nanofibers (CNF) and microfibrillated fiber (MFC)) were added to the Alg-D matrix at different concentrations. SEM showed that the cross section of the Alg-based films became more compact and uniform when the size of celluloses decreased. The tensile test revealed that the strength (TS) of Alg-based films exhibited an initial increase followed by a subsequent drop as the cellulose content rose. The best mechanical strengthening effect was the Alg-CNC film (1.16 MPa), which increased by 93.33 % compared with that of pure Alg. Cooking treatment could further enhance this trend. The opacity increased gradually with the increase of cellulose content, while these films were still transparent enough for food packaging. These findings would have potential applications in food packaging, especially co-extruded sausage casings.

Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1.

The Nrd1-Nab3-Sen1 (NNS) complex carries out the transcription termination of non-coding RNAs (ncRNAs) by RNA polymerase II (Pol II) in yeast, although the detailed interactions among its subunits remain obscure. Here we have identified three sequence motifs in Sen1 that mediate direct interactions with the Pol II CTD interaction domain (CID) of Nrd1, determined the crystal structures of these Nrd1 interaction motifs (NIMs) bound to the CID, and characterized the interactions in vitro and in yeast. Removal of all three NIMs abolishes NNS complex formation and gives rise to ncRNA termination defects.

Highly Sensitive Dissolved Oxygen Sensor with a Sustainable Antifouling, Antiabrasion, and Self-Cleaning Superhydrophobic Surface.

Long-term sensing of dissolved oxygen in aqueous solution always suffers from adherence of algae, barnacles, and clams and formation of biofilms on the sensor surface, which strongly influences the diffusion of oxygen into the sensor film. Metabolism of these adhered species consumes oxygen and causes bias on sensor readout. Therefore, commercial sensors are equipped with mechanical brushes to constantly clean the sensor surface, which significantly complicates the sensor design and causes damage to the sensor surface. In addition, extra energy storage and mechanical structures are required, which make an optical sensor bulky and limit its service life. We have developed a robust and highly sensitive dissolved oxygen sensor with good mechanical stability and self-cleaning capability. The sensor was fabricated by doping oxygen-sensitive probe PtTFPP with superhydrophobic coating. The 3 to 5 nm micro/nanostructures formed from silica sol were solidified with silicone resin, which endowed the sensor film with excellent mechanical stability. The sensor film exhibits antifouling, antiabrasion, and self-cleaning properties. There is no need of mechanical brushes to clean sensor surfaces, which greatly simplifies the sensor design. Owing to the porous structure, the sensor shows high quenchability, with I 0/I 100 of 77. All these features guarantee that the sensor could be used in harsh and dirty conditions for long-term monitoring of dissolved oxygen concentration.

Synthesis of highly stable cyanine-dye-doped silica nanoparticle for biological applications.

Cyanine dyes are widely used in biological labeling and imaging because of their narrow near infrared emission, good brightness and high flexibility in functionalization, which not only enables multiplex analysis and multi-color imaging, but also greatly reduces autofluorescence from biological matter and increases signal-to-noise ratio. Unfortunately, their poor chemical- and photo-stability strongly limits their applications. The incorporation of cyanine dyes in silica nanoparticles provides a solution to the problem. On one hand, the incorporation of cyanine dyes in silica matrix can enhance their chemical- and photo-stability and increase brightness of the nanomaterials. On the other hand, silica matrix provides an optimized condition to host the dye, which helps to maintain their fluorescent properties during application. In addition, the well-established silane technique provides numerous functionalities for diverse applications. However, commercially available cyanine dyes are not very stable at high alkaline conditions, which will gradually lose their fluorescence over time. Our results showed that cyanine dyes are very vulnerable in the reverse micelle system, in which they will lose their fluorescence in less than half an hour. The existence of surfactant could greatly promote degradation of cyanine dyes. Fluorescent silica nanoparticles cannot be obtained at the high alkaline condition with the existence of surfactant. In contrast, the cyanine dyes are relatively stable in Stöber media. Owing to the fast formation of silica particles in Stöber media, the exposure time of cyanine dye in alkaline solution was greatly reduced, and highly fluorescent particles with good morphology and size distribution could be obtained via Stöber approach. However, the increasing water content in the Stöber could reduce the stability of cyanine dyes, which should be avoided. This research here provides a clear guidance on how to successfully synthesize cyanine dye-doped silica nanoparticles with good morphology, size distribution, stability and brightness.

Molecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation.

Histone H3 lysine 36 methylation (H3K36me) is critical for epigenetic regulation and mutations at or near H3K36 are associated with distinct types of cancers. H3K36M dominantly inhibits H3K36me on wild-type histones, whereas H3G34R/V selectively affects H3K36me on the same histone tail. Here we report the crystal structures of SETD2 SET domain in complex with an H3K36M peptide and SAM or SAH. There are large conformational changes in the substrate binding regions of the SET domain, and the K36M residue interacts with the catalytic pocket of SETD2. H3G34 is surrounded by a very narrow tunnel, which excludes larger amino acid side chains. H3P38 is in the trans configuration, and the cis configuration is incompatible with SETD2 binding. Finally, mutations of H3G34 or H3P38 alleviate the inhibitory effects of H3K36M on H3K36me, demonstrating that the stable interaction of H3K36M with SETD2 is critical for its inhibitory effects.

NMR Signal Quenching from Bound Biradical Affinity Reagents in DNP Samples.

We characterize the effect of specifically bound biradicals on the NMR spectra of dihydrofolate reductase from E. coli. Dynamic nuclear polarization methods enhance the signal-to-noise of solid state NMR experiments by transferring polarization from unpaired electrons of biradicals to nuclei. There has been recent interest in colocalizing the paramagnetic polarizing agents with the analyte of interest through covalent or noncovalent specific interactions. This experimental approach broadens the scope of dynamic nuclear polarization methods by offering the possibility of selective signal enhancements and the potential to work in a broad range of environments. Paramagnetic compounds can have other effects on the NMR spectroscopy of nearby nuclei, including broadening of nuclear resonances due to the proximity of the paramagnetic agent. Understanding the distance dependence of these interactions is important for the success of the technique. Here we explore paramagnetic signal quenching due to a bound biradical, specifically a biradical-derivatized trimethoprim ligand of E. coli dihydrofolate reductase. Biradical-derivatized trimethoprim has nanomolar affinity for its target, and affords strong and selective signal enhancements in dynamic nuclear polarization experiments. In this work, we show that, although the trimethoprim fragment is well ordered, the biradical (TOTAPOL) moiety is disordered when bound to the protein. The distance dependence in bleaching of NMR signal intensity allows us to detect numerous NMR signals in the protein. We present the possibility that static disorder and electron spin diffusion play roles in this observation, among other contributions. The fact that the majority of signals are observed strengthens the case for the use of high affinity or covalent radicals in dynamic nuclear polarization solid state NMR enhancement.

Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA.

The Arabidopsis protein FPA controls flowering time by regulating the alternative 3'-end processing of the FLOWERING LOCUS (FLC) antisense RNA. FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3'-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain.

Ionic liquids modified graphene oxide composites: a high efficient adsorbent for phthalates from aqueous solution.

In 2015, more than 30% of erasers were found to contain a PAE content that exceeded the 0.1% limit established by the Quality and Technology Supervision Bureau of Jiangsu Province in China. Thus, strengthening the supervision and regulation of the PAE content in foods and supplies, in particular, remains necessary. Graphene oxide (GO) and its composites have drawn great interests as promising adsorbents for polar and nonpolar compounds. However, GO-based adsorbents are typically restricted by the difficult separation after treatment because of the high pressure in filtration and low density in centrifugation. Herein, a series of novel ionic liquids modified graphene oxide composites (GO-ILs) were prepared as adsorbents for phthalates (PAEs) in eraser samples, which overcame the conventional drawbacks. These novel composites have a combination of the high surface area of graphene oxide and the tunability of the ionic liquids. It is expected that the GO-ILs composites can be used as efficient adsorbents for PAEs from aqueous solution. This work also demonstrated a new technique for GO-based materials applied in sample preparation.