Real-time imaging reveal anisotropic dissolution behaviors of silver nanorods.

The morphology and size control of anisotropic nanocrystals are critical for tuning shape-dependent physicochemical properties. Although the anisotropic dissolution process is considered to be an effective means to precisely control the size and morphology of nanocrystals, the anisotropic dissolution mechanism remains poorly understood. Here, usingin situliquid cell transmission electron microscopy, we investigate the anisotropic etching dissolution behaviors of polyvinylpyrrolidone (PVP)-stabilized Ag nanorods in NaCl solution. Results show that etching dissolution occurs only in the longitudinal direction of the nanorod at low chloride concentration (0.2 mM), whereas at high chloride concentration (1 M), the lateral and longitudinal directions of the nanorods are dissolved. First-principles calculations demonstrate that PVP is selectively adsorbed on the {100} crystal plane of silver nanorods, making the tips of nanorods the only reaction sites in the anisotropic etching process. When the chemical potential difference of the Cl-concentration is higher than the diffusion barrier (0.196 eV) of Cl-in the PVP molecule, Cl-penetrates the PVP molecular layer of {100} facets on the side of the Ag nanorods. These findings provide an in-depth insight into the anisotropic etching mechanisms and lay foundations for the controlled preparation and rational design of nanostructures.

3D printed protein-based robotic structures actuated by molecular motor assemblies.

Upscaling motor protein activity to perform work in man-made devices has long been an ambitious goal in bionanotechnology. The use of hierarchical motor assemblies, as realized in sarcomeres, has so far been complicated by the challenges of arranging sufficiently high numbers of motor proteins with nanoscopic precision. Here, we describe an alternative approach based on actomyosin cortex-like force production, allowing low complexity motor arrangements in a contractile meshwork that can be coated onto soft objects and locally activated by ATP. The design is reminiscent of a motorized exoskeleton actuating protein-based robotic structures from the outside. It readily supports the connection and assembly of micro-three-dimensional printed modules into larger structures, thereby scaling up mechanical work. We provide an analytical model of force production in these systems and demonstrate the design flexibility by three-dimensional printed units performing complex mechanical tasks, such as microhands and microarms that can grasp and wave following light activation.

Fine-Tuning Protein Self-Organization by Orthogonal Chemo-Optogenetic Tools.

A universal gain-of-function approach for the spatiotemporal control of protein activity is highly desirable when reconstituting biological modules in vitro. Here we used orthogonal translation with a photocaged amino acid to map and elucidate molecular mechanisms in the self-organization of the prokaryotic filamentous cell-division protein (FtsZ) that is highly relevant for the assembly of the division ring in bacteria. We masked a tyrosine residue of FtsZ by site-specific incorporation of a photocaged tyrosine analogue. While the mutant still shows self-assembly into filaments, dynamic self-organization into ring patterns can no longer be observed. UV-mediated uncaging revealed that tyrosine 222 is essential for the regulation of the protein's GTPase activity, self-organization, and treadmilling dynamics. Thus, the light-mediated assembly of functional protein modules appears to be a promising minimal-regulation strategy for building up molecular complexity towards a minimal cell.

Shaping Giant Membrane Vesicles in 3D-Printed Protein Hydrogel Cages.

Giant unilamellar phospholipid vesicles are attractive starting points for constructing minimal living cells from the bottom-up. Their membranes are compatible with many physiologically functional modules and act as selective barriers, while retaining a high morphological flexibility. However, their spherical shape renders them rather inappropriate to study phenomena that are based on distinct cell shape and polarity, such as cell division. Here, a microscale device based on 3D printed protein hydrogel is introduced to induce pH-stimulated reversible shape changes in trapped vesicles without compromising their free-standing membranes. Deformations of spheres to at least twice their aspect ratio, but also toward unusual quadratic or triangular shapes can be accomplished. Mechanical force induced by the cages to phase-separated membrane vesicles can lead to spontaneous shape deformations, from the recurrent formation of dumbbells with curved necks between domains to full budding of membrane domains as separate vesicles. Moreover, shape-tunable vesicles are particularly desirable when reconstituting geometry-sensitive protein networks, such as reaction-diffusion systems. In particular, vesicle shape changes allow to switch between different modes of self-organized protein oscillations within, and thus, to influence reaction networks directly by external mechanical cues.

Light-Induced Printing of Protein Structures on Membranes in Vitro.

Reconstituting functional modules of biological systems in vitro is an important yet challenging goal of bottom-up synthetic biology, in particular with respect to their precise spatiotemporal regulation. One of the most desirable external control parameters for the engineering of biological systems is visible light, owing to its specificity and ease of defined application in space and time. Here we engineered the PhyB-PIF6 system to spatiotemporally target proteins by light onto model membranes and thus sequentially guide protein pattern formation and structural assembly in vitro from the bottom up. We show that complex micrometer-sized protein patterns can be printed on time scales of seconds, and the pattern density can be precisely controlled by protein concentration, laser power, and activation time. Moreover, when printing self-assembling proteins such as the bacterial cytoskeleton protein FtsZ, the targeted assembly into filaments and large-scale structures such as artificial rings can be accomplished. Thus, light mediated sequential protein assembly in cell-free systems represents a promising approach to hierarchically building up the next level of complexity toward a minimal cell.

miRNA editing landscape reveals miR-34c regulated spermatogenesis through structure and target change in pig and mouse.

Spermatogenesis has a close relationship with male infertility. MicroRNAs (miRNAs) play crucial roles in their regulation of target genes during spermatogenesis. A huge dataset of high-throughput sequencing all over the world provides the basis to dig the cryptic molecular mechanism. But how to take advantage of the big data and unearth the miRNA regulation is still a challenging problem. Here we integrated transcriptome of spermatogenesis and found miRNA regulate spermatogenesis through miRNA editing. We then compared different species and found that the distributions of miRNA editing site number and editing types among different cell types during spermatogenesis are conservative. Interesting, we further found that nearly half of the editing events occurred in the seed region in both mouse and pig. Finally, we foundmiR-34c, which is edited frequently at all stages during spermatogenesis, regulates its target genes through the RNA structure changing and shows dysfunction when it is edited. Summary, we depicted the overall profile of miRNA editing during spermatogenesis in mouse and pig and reveal miR-34c may play its roles through miRNA editing.

Solution-assisted ultrafast transfer of graphene-based thin films for solar cells and humidity sensors.

Vacuum filtration enables the fabrication of large-area graphene-based membranes (GBMs), possessing a smoother surface than that by spray, spin coating or drop casting. However, due to the strong interaction with substrates, the separation of thin GBMs from the filter is problematic. Conventional stamping separation/transfer of graphene oxide (GO) thin films requires another substrate and pressing for >10 h, which may damage the delicate structure of the transfer substrates. Other methods require GO to be reduced on filters before separation, thus limiting the reduction methods. Inspired by a coagulation bath that enables rapid formation of ultrastrong GO fibers, we present an ultrafast (<1 min) and solution-assisted strategy to fabricate smooth and freestanding GO films. The diverse interfacial energy of hydrogen bonds also demonstrates another reason for the successful separation. The film thickness ranges from 45 nm to several micrometers. When used as a composite of counter electrodes in dye sensitized solar cells, it showed higher (8.58%) power conversion efficiency than its spin-(7.71%) and spray-coated (8.07%) counterparts. It also showed promising performance in capacitive humidity sensors. The capacitance varied by three orders of magnitude in the range of the relative humidity of 15%-95%. Therefore the strategy realizes an ultrafast and high-quality film production which is suitable for various applications.

Normalization and noise reduction for single cell RNA-seq experiments.

UNLABELLED: A major roadblock towards accurate interpretation of single cell RNA-seq data is large technical noise resulted from small amount of input materials. The existing methods mainly aim to find differentially expressed genes rather than directly de-noise the single cell data. We present here a powerful but simple method to remove technical noise and explicitly compute the true gene expression levels based on spike-in ERCC molecules. AVAILABILITY AND IMPLEMENTATION: The software is implemented by R and the download version is available at http://wanglab.ucsd.edu/star/GRM. CONTACT: wei-wang@ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Eremophilane Sesquiterpenes from the Genus Ligularia.

Ligularia speices are widely used in Asian folk medicines for the treatment of various human diseases. Eremophilane-type sesquiterpenes are abundant and typical secondary metabolites found in this genus. Over 500 eremophilanes reported from members of Ligularia are reviewed in this article together with bioactivity data in an effort to highlight the development in this field.

STAR: an integrated solution to management and visualization of sequencing data.

MOTIVATION: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. RESULTS: STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. AVAILABILITY AND IMPLEMENTATION: STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.

Enhanced reduction of graphene oxide via laser-dispersion coupling: Towards large-scale, low-defect graphene for crease-free heat-dissipating membranes in advanced flexible electronics.

The advancement of flexible electronics demands improved components, necessitating heat dissipation membranes (HDMs) to exhibit high thermal conductivity while maintaining structural integrity and performance stability even after extensive deformation. Herein, we have devised a laser-modulated reduction technique for graphene oxide (GO), enabling the fabrication of high-quality, large-scale, low-defect graphene, which yields high-performance HDMs after orderly deposition. The work underscores the crucial role of the laser wavelength and dispersion liquid's coupling intensity in influencing the morphology and properties of graphene. Optimal coupling effect and energy conversion are realized when a laser of 1064 nm wavelength irradiates a triethylene glycol (TEG)/N,N-Dimethylformamide (DMF) dispersion. This unique synergy generates high transient energy, which facilitates the deprotonation process and ensures a swift, comprehensive GO reduction. In contrast to conventional water-based laser reduction methods, the accelerated reaction magnifies the size of the graphene sheets by mitigating the ablation effect. After membrane construction with an ordered structure, the corresponding membrane exhibits a high thermal conductivity of 1632 W m-1 K-1, requiring only ∼1/10 of the total preparation time required by other reported methods. Remarkably, the resulting HDM demonstrates superior resilience against creasing and folding, maintaining excellent smoothness and negligible reduction in thermal conductivity after violent rubbing. The combination of exceptional flexibility and thermal conductivity in HDMs paves the way for long-term practical use in the flexible electronics industry.

Halogenation of tyrosine perturbs large-scale protein self-organization.

Protein halogenation is a common non-enzymatic post-translational modification contributing to aging, oxidative stress-related diseases and cancer. Here, we report a genetically encodable halogenation of tyrosine residues in a reconstituted prokaryotic filamentous cell-division protein (FtsZ) as a platform to elucidate the implications of halogenation that can be extrapolated to living systems of much higher complexity. We show how single halogenations can fine-tune protein structures and dynamics of FtsZ with subtle perturbations collectively amplified by the process of FtsZ self-organization. Based on experiments and theories, we have gained valuable insights into the mechanism of halogen influence. The bending of FtsZ structures occurs by affecting surface charges and internal domain distances and is reflected in the decline of GTPase activities by reducing GTP binding energy during polymerization. Our results point to a better understanding of the physiological and pathological effects of protein halogenation and may contribute to the development of potential diagnostic tools.

Deep eutectic solvent electrolysis for preparing water-soluble magnetic iron oxide nanoparticles.

Magnetic iron oxide nanoparticles have been proven to have versatile applications in biomedicine. Although numerous strategies have been developed to synthesize hydrophilic magnetic nanoparticles, there is still a challenge in the quantity and controllability of preparation of highly dispersible, stably water-dispersive magnetic nanoparticles. The current work presents a deep-eutectic solvent electrolysis to synthesize magnetic nanoparticles. In the electrolysis process, iron atoms at the anode electrode are oxidized to ferric ions, and then the ferric ions are combined with reactive oxygen species that derived from the decomposition of deep-eutectic solvents to form iron oxide nanocrystals. Concomitantly, hydrophilic radicals of amine groups produced by electrolyte decomposition are grafted on the particles. The monodisperse nanoparticle size ranged from 6 to 9 nm. The hydrophilic group loaded nanoparticles can be highly dispersed in water with neither surface post-modification nor organic stabilizers. The hydrodynamic particle diameter is between 20 and 30 nm. The transparent aqueous dispersions can be maintained for more than 600 days without precipitation.

Bottom-up synthetic biology: reconstitution in space and time.

Bottom-up reconstituting well-characterized functional molecular entities, parts and modules towards a synthetic cell will give new insights into the mechanisms and origin of life. However, a remaining central challenge is how to organize cellular processes spatiotemporally from their component parts in vitro. Here, we review cutting edge tools and technologies that can facilitate such a bottom-up reconstitution towards a synthetic cell in space and time, particularly with regard to the following aspects: (1) reliable model membrane-environment and microenvironment; (2) dynamic genetic regulation and self-sustaining transcription and translation machinery; (3) spatially organized cytoskeleton that supports the biological architecture and cellular self-reproduction in 3D.

Temperature-sensitive protein expression in protocells.

We engineered a synthetic temperature regulation toolbox to enable protocells to sense and respond to heat, utilizing RNA thermometers. The thermo-sensitive protocells were generated by encapsulating temperature feedback transcription/translation machinery in droplets. Based on these temperature-sensing devices, the protocells can be operated with logic AND gates, differentially processing temperature stimuli into biological signals.

A Silica-Sol-Based Fortified Structure with Superhydrophobic Coating for Harsh Conditions.

Although numerous bio-inspired superhydrophobic coatings have been extensively studied in the last decades, most of them suffer from low chemical stability and mechanical weakness, which severely limit their extensive applications. Herein, a silica-based, superhydrophobic, highly stable and mechanically durable coating was prepared via a facile, energysaving strategy. Modified silica nanoparticles, were fortified with silane coupling agent and spray-deposited on substrates, forming a superhydrophobic, self-cleaning coating with high water contact angle (CA = 159.0°), as well as low rolling angle (RA ≈ 3°). The protective coating showed high chemical stability that endured various harsh conditions, such as wide temperature range (-18 to 250 °C), extreme pH (1 to 13), weeks of exposure under sunlight, etc. Moreover, the coating exhibited superior mechanical robustness that could resist the attack of shear force in vigorous ultrasonication for 7 hours. In addition, repetitive scratching with a steel blade could not undermine the protective coating (CA > 150°). It is believed that the present strategy is a potent candidate for facile fabrication of superhydrophobic surface coatings, which have promising applications on extreme conditions in both household and industry.

16-O-caffeoyl-16-hydroxylhexadecanoic acid, a medicinal plant-derived phenylpropanoid, induces apoptosis in human hepatocarcinoma cells through ROS-dependent endoplasmic reticulum stress.

BACKGROUND: Hepatocellular carcinoma (HCC) is the leading cause of cancer death, and novel chemotherapeutic drugs for treating HCC are urgently needed. 16-O-caffeoyl-16-hydroxylhexadecanoic acid (CHHA) is a new phenylpropanoid isolated by our group from Euphorbia nematocypha which is commonly used to treat solid tumors. However, the underlying mechanisms responsible for the CHHA-induced apoptosis in cancer cells, particularly in HCC, remain unknown. PURPOSE: In the present work, we evaluated the growth inhibitory effect of CHHA on HCC cells and explored the underlying molecular mechanisms. METHODS/STUDY DESIGNS: The anti-proliferative activity of CHHA was evaluated by MTT assay. Cell cycle, apoptosis, reactive oxygen species and mitochondrial membrane potential were determined by flow cytometry. ER localization was performed by ER-tracker red staining. The effect of CHHA on the expression of mRNA in HCC cells was detected by RT-PCR. The potential mechanisms for proteins level in ER pathway and apoptosis were analyzed by Western blot. RESULTS: Our results showed that CHHA exerted strong anti-proliferative activity against both HepG2 and Bel-7402 cells in a concentration- and time-dependent manner. Mechanistic studies demonstrated that CHHA induced apoptosis through mitochondrial apoptotic pathway, and arrested the cell cycle at G1 phase. CHHA was also found to induce endoplasmic reticulum (ER) stress, accompanied by ROS production, increase of intracellular calcium and up-regulation of GRP78, CHOP, caspase-12 and p-PERK. Inhibition of endoplasmic reticulum stress by salubrinal pretreatment could suppress both apoptosis and ER stress, indicating that ER stress induction contributes to apoptosis and is required for the latter. Besides, the ROS scavenger N-acetyl cysteine (NAC) significantly attenuated apoptosis induced by CHHA and reversed CHHA-stimulated the expression of ER markers. CONCLUSION: In conclusion, CHHA inhibited HCC cell growth and induced apoptosis through mitochondria-mediated pathway and ROS-mediated endoplasmic reticulum stress. This provides molecular bases for developing CHHA into a drug candidate for the treatment of HCC.

Genetic variants regulate NR1H3 expression and contribute to multiple sclerosis risk.

A recent study analyzed 2053 multiple sclerosis (MS) cases and 799 healthy controls to investigate whether five genetic variants (rs11039149, rs12221497, rs2279238, rs7120118 and rs7114704) in NR1H3 are associated with MS risk. However this study reported negative results. It is very important that the appropriate samples and approach should be used in replication studies, which may provide the correct interpretation of the results. Here, we evaluated the above findings using large-scale MS genome-wide association studies with a total of 27,148 samples including 9772 MS cases and 17,376 controls, and multiple expression quantitative trait loci datasets. The results suggest that rs7120118 and rs2279238 variants are significantly associated with MS risk, and could significantly regulate NR1H3 expression in kinds of human tissues and cells. In summary, these findings provide important supplementary information about the association between NR1H3 variants and MS risk.

ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases.

Autophagy is the natural, regulated, destructive mechanism of the eukaryotes cell that disassembles unnecessary or dysfunctional components. In recent years, the association between autophagy and diseases has attracted more and more attention, but our understanding of the molecular mechanism about the association in the system perspective is limited and ambiguous. Hence, we developed the comprehensive bioinformatics resource Autophagy To Disease (ATD, http://auto2disease.nwsuaflmz.com) to archive autophagy-associated diseases. This resource provides bioinformatics annotation system about genes and chemicals about autophagy and human diseases by extracting results from previous studies with text mining technology. Based on the big data from ATD, we found that some classes of disease tend to be related with autophagy, including respiratory disease, cancer, urogenital disease and digestive system disease. We also found that some classes of autophagy-related diseases have a strong association among each other and constitute modules. Furthermore, we extracted the autophagy-disease-related genes (ADGs) from ATD and provided a novel algorithm Optimized Random Forest with Label model to predict potential ADGs. This bioinformatics annotation system about autophagy and human diseases may provide a basic resource for the further detection of the molecular mechanisms of autophagy pathway to disease.

Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks.

The construction of a minimal cell that exhibits the essential characteristics of life is a great challenge in the field of synthetic biology. Assembling a minimal cell requires multidisciplinary expertise from physics, chemistry and biology. Scientists from different backgrounds tend to define the essence of 'life' differently and have thus proposed different artificial cell models possessing one or several essential features of living cells. Using the tools and methods of molecular biology, the bottom-up engineering of a minimal cell appears in reach. However, several challenges still remain. In particular, the integration of individual sub-systems that is required to achieve a self-reproducing cell model presents a complex optimization challenge. For example, multiple self-organisation and self-assembly processes have to be carefully tuned. We review advances and developments of new methods and techniques, for cell-free protein synthesis as well as micro-fabrication, for their potential to resolve challenges and to accelerate the development of minimal cells.