Visualizing the DNA repair process by a photolyase at atomic resolution.

Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.

Application of Visual Recognition Based on BP Neural Network in Architectural Design Optimization.

In order to establish the mapping relationship between architectural design parameters and building performance and optimize architectural design parameters, an architectural design optimization method based on BP neural network is proposed. The selected main design parameters of building ventilation include spacing coefficient, air outlet area, and height from the bottom of the window sill to the ground. Take the comprehensive performance of building ventilation design as the main optimization objective to optimize the building design. First, nine groups of samples of building optimization design are obtained through uniform experimental design. Then, based on the architectural design sample data obtained by BP neural network training, the mapping relationship between architectural design parameters and building performance is established, and based on this mapping, the optimal design parameters of the building are calculated. The research results have a certain reference value for architectural design optimization.

Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme.

Flavin coenzymes are universally found in biological redox reactions. DNA photolyases, with their flavin chromophore (FAD), utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD•- isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine-aspartate salt bridge allows proton transfer from arginine to FAD•-. Our molecular videos demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis.

Shape stable poly(vinyl alcohol) hydrogels with immobilized metal hexacyanoferrates for cesium removal from waters.

The metal hexacyanoferrates with transition metal ions to replace ferric ions in the face center cubic structure of Prussian blue (PB) crystals are candidate adsorbents for radioactive cesium ions in waters. This study for the first time synthesized the shape stable poly(vinyl alcohol) (PVA) hydrogels with immobilized metal hexacynoferrate (PB analogue) that can be stored at dry and can efficiently adsorb cesium ions from waters after rewetting. A total of eight PB analogue particles in two families M3[Fe(III)(CN)6]2 (MFe(III)) or M4[Fe(II)(CN)6]2 (MFe(II)) with M=Zn, Ni, Cu, or Co were synthesized and were immobilized in the PVA hydrogels following boric acid and sulfate crosslinking. The produced PVA-PB analogue hydrogels are all stable in shape after dry and rewet, and the rewet hydrogels can adsorb cesium ions from waters at much higher rates. As predicted by the diffusion-reaction model, the apparent reaction constants for cesium ion adsorption are 4.2×10-4 1/s, 3.4×10-4 1/s, 3.9×10-4 1/s, 4.1×10-4 1/s, 4.1×10-4 1/s, 3.8×10-4 1/s, 1.1×10-3 1/s, and 9.6×10-4 1/s, for ZnFe(III), ZnFe(II), NiFe(III), NiFe(II), CuFe(III), CuFe(II), CoFe(III), and CoFe(II), respectively. The corresponding maximum adsorption capacities based on Langmuir isotherm model at 25 °C are 232.6 mg/g, 389.0 mg/g, 193.9 mg/g, 256.8 mg/g, 388.2 mg/g, 395.1 mg/g, 297.3 mg/g, and 391.2 mg/g, respectively. The use of PVA-CoFe(III) is the candidate for enhanced Cs removal from waters comparing the use of other PB analogues as adsorbent.

Vibrio cholerae biofilm scaffolding protein RbmA shows an intrinsic, phosphate-dependent autoproteolysis activity.

Vibrio cholerae is the causative agent of the diarrheal disease cholera, for which biofilm communities are considered to be environmental reservoirs. In endemic regions, and after algal blooms, which may result from phosphate enrichment following agricultural runoff, the bacterium is released from biofilms resulting in seasonal disease outbreaks. However, the molecular mechanism by which V. cholerae senses its environment and switches lifestyles from the biofilm-bound state to the planktonic state is largely unknown. Here, we report that the major biofilm scaffolding protein RbmA undergoes autocatalytic proteolysis via a phosphate-dependent induced proximity activation mechanism. Furthermore, we show that RbmA mutants that are defective in autoproteolysis cause V. cholerae biofilms to grow larger and mechanically stronger, correlating well with the observation that RbmA stability directly affects microbial community homeostasis and rheological properties. In conclusion, our biophysical study characterizes a novel phosphate-dependent breakdown pathway of RbmA, while microbiological data suggest a new, sensory role of this biofilm scaffolding element.

The Glutamate Receptor-Like Protein GLR3.7 Interacts With 14-3-3ω and Participates in Salt Stress Response in Arabidopsis thaliana.

Ionotropic glutamate receptors (iGluRs) are ligand-gated cation channels that mediate fast excitatory neurotransmission in the mammalian central nervous system. In the model plant Arabidopsis thaliana, a family of 20 glutamate receptor-like proteins (GLRs) shares similarities to animal iGluRs in sequence and predicted secondary structure. However, the function of GLRs in plants is little known. In the present study, a serine site (Ser-860) of AtGLR3.7 phosphorylated by a calcium-dependent protein kinase (CDPK) was identified and confirmed by an in vitro kinase assay. Using a bimolecular fluorescence complementation and quartz crystal microbalance analyses, the physical interaction between AtGLR3.7 and the 14-3-3ω protein was confirmed. The mutation of Ser-860 to alanine abolished this interaction, indicating that Ser-860 is the 14-3-3ω binding site of AtGLR3.7. Compared with wild type, seed germination of the glr3.7-2 mutant was more sensitive to salt stress. However, the primary root growth of GLR3.7-S860A overexpression lines was less sensitive to salt stress than that of the wild-type line. In addition, the increase of cytosolic calcium ion concentration by salt stress was significantly lower in the glr3.7-2 mutant line than in the wild-type line. Moreover, association of 14-3-3 proteins to microsomal fractions was less in GLR3.7-S860A overexpression lines than in GLR3.7 overexpression line under 150 mM NaCl salt stress condition. Overall, our results indicated that GLR3.7 is involved in salt stress response in A. thaliana by affecting calcium signaling.

Angular color variation in micron-scale light-emitting diode arrays.

A simulation scheme was developed to explore the light distribution of full-color micron-scale light-emitting diode (LED) arrays. The influences of substrate thickness, patterning, and cutting angle of the substrate on several important features, such as light field pattern, light extraction efficiency, and color variation, were evaluated numerically. An experiment was conducted; the results were consistent with simulation results for a 225 × 125 µm2 miniLED and those for an 80 × 80 µm2 microLED. Based on the simulation results, the light extraction efficiency of LED devices with a substrate increases by 67.75% over the extraction efficiency of those without a substrate. The light extraction efficiency of LED devices with a substrate increases by 113.55% when an additional patterned design is used on green and blue chips. The calculated large angle Δu'v' can be as low as 0.015 for miniLED devices.

Shape stable poly(vinyl alcohol) hydrogels with immobilized activated sludge at repeated dry-rewet cycles.

The poly(vinyl alcohol) (PVA) hydrogels can be used as a non-toxic and inexpensive immobilization matrix for microbial cells with capability of degrading organic or inorganic pollutants in wastewaters. This study for the first time produced the PVA hydrogels with immobilized cells by two-stage crosslinking which have high shape stability at dry-rewet cycles and, when recovered after sequentially three 24-hr cultivations, reveal high bioactivity in wastewater treatment. The [B(OH)3][SO42-] cores inside the PVA-boric acid-sulfate hydrogels are proposed to support the immobilized cells with sufficient structure flexibility and strength to maintain hydrogel structural integrity and of sufficient recalcitrance to biological attack. Conversely, neither the PVA-boric acid hydrogels nor the PVA-borate hydrogels can be applied as organic pollutant degraders with dry storage capability. The PVA-boric acid-sulfate hydrogels are proposed as ideal matrix that can be produced and stored in dry, massive quantity and then applied latter at the same or different sites.

High-resolution light-scattering imaging with two-dimensional hexagonal illumination patterns: system implementation and image reconstruction formulations.

Structured illumination microscopy (SIM) was recently adapted to coherent imaging, named structured oblique-illumination microscopy (SOIM), to improve the contrast and resolution of a light-scattering image. Herein, we present high-resolution laterally isotropic SOIM imaging with 2D hexagonal illuminations. The SOIM is implemented in a SIM fluorescence system based on a spatial-light modulator (SLM). We design an SLM pattern to generate diffraction beams at 0° and ± 60.3° simultaneously to form a 2D hexagonal illumination, and undertake calculations to obtain optimal SLM shifts at 19 phases to yield a reconstructed image correctly. Beams of linear and circular polarizations are used to show the effect of polarization on the resolution improvement. We derive the distributions of the electric field of the resultant hexagonal patterns and work out the formulations of the corresponding coherent-scattering imaging for image reconstruction. The reconstructed images of gold nanoparticles (100 nm) confirm the two-fold improvement of resolution and reveal the effect of polarization on resolving adjacent nanoparticles. To demonstrate biological applications, we present the cellular structures of a label-free fixed HeLa cell with improved contrast and resolution. This work enables one to perform high-resolution dual-mode - fluorescence and light-scattering - imaging in a system, and is expected to broaden the applications of SOIM.

A type III ACC synthase, ACS7, is involved in root gravitropism in Arabidopsis thaliana.

Ethylene is an important plant hormone that regulates developmental processes in plants. The ethylene biosynthesis pathway is a highly regulated process at both the transcriptional and post-translational level. The transcriptional regulation of these ethylene biosynthesis genes is well known. However, post-translational modifications of the key ethylene biosynthesis enzyme 1-aminocyclopropane-1-carboxylate (ACC) synthase (ACS) are little understood. In vitro kinase assays were conducted on the type III ACS, AtACS7, fusion protein and peptides to determine whether the AtACS7 protein can be phosphorylated by calcium-dependent protein kinase (CDPK). AtACS7 was phosphorylated at Ser216, Thr296, and Ser299 by AtCDPK16 in vitro. To investigate further the function of the ACS7 gene in Arabidopsis, an acs7-1 loss-of-function mutant was isolated. The acs7-1 mutant exhibited less sensitivity to the inhibition of root gravitropism by treatment with the calcium chelator ethylene glycol tetraacetic acid (EGTA). Seedlings were treated with gradient concentrations of ACC. The results showed that a certain concentration of ethylene enhanced the gravity response. Moreover, the acs7-1 mutant was less sensitive to inhibition of the gravity response by treatment with the auxin polar transport inhibitor 1-naphthylphthalamic acid, but exogenous ACC application recovered root gravitropism. Altogether, the results indicate that AtACS7 is involved in root gravitropism in a calcium-dependent manner in Arabidopsis.

Gold-nanorod contrast-enhanced photoacoustic micro-imaging of focused-ultrasound induced blood-brain-barrier opening in a rat model.

In this study, we develop a novel photoacoustic imaging technique based on gold nanorods (AuNRs) for quantitatively monitoring focused-ultrasound (FUS) induced blood-brain barrier (BBB) opening in a rat model in vivo. This study takes advantage of the strong near-infrared absorption (peak at ≈ 800 nm) of AuNRs and the extravasation tendency from BBB opening foci due to their nano-scale size to passively label the BBB disruption area. Experimental results show that AuNR contrast-enhanced photoacoustic microscopy (PAM) successfully reveals the spatial distribution and temporal response of BBB disruption area in the rat brains. The quantitative measurement of contrast enhancement has potential to estimate the local concentration of AuNRs and even the dosage of therapeutic molecules when AuNRs are further used as nano-carrier for drug delivery or photothermal therapy. The photoacoustic results also provide complementary information to MRI, being helpful to discover more details about FUS induced BBB opening in small animal models.

Transcranial imaging of functional cerebral hemodynamic changes in single blood vessels using in vivo photoacoustic microscopy.

Optical imaging of changes in total hemoglobin concentration (HbT), cerebral blood volume (CBV), and hemoglobin oxygen saturation (SO(2)) provides a means to investigate brain hemodynamic regulation. However, high-resolution transcranial imaging remains challenging. In this study, we applied a novel functional photoacoustic microscopy technique to probe the responses of single cortical vessels to left forepaw electrical stimulation in mice with intact skulls. Functional changes in HbT, CBV, and SO(2) in the superior sagittal sinus and different-sized arterioles from the anterior cerebral artery system were bilaterally imaged with unambiguous 36 × 65-µm(2) spatial resolution. In addition, an early decrease of SO(2) in single blood vessels during activation (i.e., 'the initial dip') was observed. Our results indicate that the initial dip occurred specifically in small arterioles of activated regions but not in large veins. This technique complements other existing imaging approaches for the investigation of the hemodynamic responses in single cerebral blood vessels.

In vivo photoacoustic micro-imaging of microvascular changes for Achilles tendon injury on a mouse model.

Since neovascularization has been reported that it is associated with tendinopathy, assessments of vascularity are important for both diagnosis and treatment estimation. Photoacoustic imaging, taking the advantages of good ultrasonic resolution and high optical absorption contrast, has been shown a promising tool for vascular imaging. In this study, we explore the feasibility of photoacoustic micro-imaging in noninvasive monitoring of microvascular changes in Achilles tendon injuries on a mouse model in vivo. During collagenase-induced tendinitis, a 25-MHz photoacoustic microscope was used to image microvascular changes in Achilles tendons of mice longitudinally up to 23 days. In addition, complementary tissue structural information was revealed by collateral 25-MHz ultrasound microscopy. Morphological changes and proliferation of new blood vessels in Achilles tendons were observed during and after the acute inflammation. Observed microvascular changes during tendinitis were similar to the findings in the literatures. This study demonstrates that photoacoustic imaging can potentially be a complementary tool for high sensitive diagnosis and assessment of treatment performance in tendinopathy.