State Key Laboratory of Digital Medical Engineering

MOTIVATION: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive QC tool to assess RNA-seq quality is sorely needed. RESULTS: We developed the RSeQC package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM/SAM files containing hundreds of millions of alignments. AVAILABILITY AND IMPLEMENTATION: RSeQC is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://code.google.com/p/rseqc/.

Droplet microfluidics generates and manipulates discrete droplets through immiscible multiphase flows inside microchannels. Due to its remarkable advantages, droplet microfluidics bears significant value in an extremely wide range of area. In this review, we provide a comprehensive and in-depth insight into droplet microfluidics, covering fundamental research from microfluidic chip fabrication and droplet generation to the applications of droplets in bio(chemical) analysis and materials generation. The purpose of this review is to convey the fundamentals of droplet microfluidics, a critical analysis on its current status and challenges, and opinions on its future development. We believe this review will promote communications among biology, chemistry, physics, and materials science.

Tissue engineering has become a promising strategy for repairing damaged cartilage and bone tissue. Among the scaffolds for tissue-engineering applications, injectable hydrogels have demonstrated great potential for use as three-dimensional cell culture scaffolds in cartilage and bone tissue engineering, owing to their high water content, similarity to the natural extracellular matrix (ECM), porous framework for cell transplantation and proliferation, minimal invasive properties, and ability to match irregular defects. In this review, we describe the selection of appropriate biomaterials and fabrication methods to prepare novel injectable hydrogels for cartilage and bone tissue engineering. In addition, the biology of cartilage and the bony ECM is also summarized. Finally, future perspectives for injectable hydrogels in cartilage and bone tissue engineering are discussed.

The generation of reactive oxygen species (ROS) is an important mechanism of nanomaterial toxicity. We found that Prussian blue nanoparticles (PBNPs) can effectively scavenge ROS via multienzyme-like activity including peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) activity. Instead of producing hydroxyl radicals (•OH) through the Fenton reaction, PBNPs were shown to be POD mimetics that can inhibit •OH generation. We theorized for the first time that the multienzyme-like activities of PBNPs were likely caused by the abundant redox potentials of their different forms, making them efficient electron transporters. To study the ROS scavenging ability of PBNPs, a series of in vitro ROS-generating models was established using chemicals, UV irradiation, oxidized low-density lipoprotein, high glucose contents, and oxygen glucose deprivation and reperfusion. To demonstrate the ROS scavenging ability of PBNPs, an in vivo inflammation model was established using lipoproteins in Institute for Cancer Research (ICR) mice. The results indicated that PBNPs hold great potential for inhibiting or relieving injury induced by ROS in these pathological processes.

Natural structural color materials, especially those that can undergo reversible changes, are attracting increasing interest in a wide variety of research fields. Inspired by the natural creatures, many elaborately nanostructured photonic materials with variable structural colors were developed. These materials have found important applications in switches, display devices, sensors, and so on. In this critical review, we will provide up-to-date research concerning the natural and bio-inspired photonic materials with variable structural colors. After introducing the variable structural colors in natural creatures, we will focus on the studies of artificial variable structural color photonic materials, including their bio-inspired designs, fabrications and applications. The prospects for the future development of these fantastic variable structural color materials will also be presented. We believe this review will promote the communications among biology, bionics, chemistry, optical physics, and material science (196 references).

Iron oxide nanoparticles (IONPs) are frequently used in biomedical applications, yet their toxic potential is still a major concern. While most studies of biosafety focus on cellular responses after exposure to nanomaterials, little is reported to analyze reactions on the surface of nanoparticles as a source of cytotoxicity. Here we report that different intracellular microenvironment in which IONPs are located leads to contradictive outcomes in their abilities to produce free radicals. We first verified pH-dependent peroxidase-like and catalase-like activities of IONPs and investigated how they interact with hydrogen peroxide (H(2)O(2)) within cells. Results showed that IONPs had a concentration-dependent cytotoxicity on human glioma U251 cells, and they could enhance H(2)O(2)-induced cell damage dramatically. By conducting electron spin resonance spectroscopy experiments, we showed that both Fe(3)O(4) and γ-Fe(2)O(3) nanoparticles could catalyze H(2)O(2) to produce hydroxyl radicals in acidic lysosome mimic conditions, with relative potency Fe(3)O(4) > γ-Fe(2)O(3), which was consistent with their peroxidase-like activities. However, no hydroxyl radicals were observed in neutral cytosol mimic conditions with both nanoparticles. Instead, they decomposed H(2)O(2) into H(2)O and O(2) directly in this condition through catalase-like activities. Transmission electron micrographs revealed that IONPs located in lysosomes in cells, the acidic environment of which may contribute to hydroxyl radical production. This is the first study regarding cytotoxicity based on their enzyme-like activities. Since H(2)O(2) is continuously produced in cells, our data indicate that lysosome-escaped strategy for IONP delivery would be an efficient way to diminish long-term toxic potential.

Photoluminescence (PL), up-conversion PL (UCPL), and phosphorescence are three kinds of phenomena common to light-emitting materials, but it is very difficult to observe all of them simultaneously when they are derived from a single material at room temperature. For the first time, triple-mode emission (that is, PL, UCPL, and room temperature phosphorescence (RTP)) is reported, which relies on a composite of the luminescent carbon dots (CDs) prepared from m-phenylenediamine and poly(vinyl alcohol) (PVA). Moreover, the CDs-PVA aqueous dispersion is nearly colorless and demonstrates promise as a triple-mode emission ink in the field of advanced anti-counterfeiting.

Exosomes are nanoscale membrane vesicles secreted from many types of cells. Carrying functional molecules, exosomes transfer information between cells and mediate many physiological and pathological processes. In this report, utilizing selective inhibitors, molecular tools, and specific endocytosis markers, the cellular uptake of PC12 cell-derived exosomes was imaged by high-throughput microscopy and statistically analyzed. It was found that the uptake was through clathrin-mediated endocytosis and macropinocytosis. Furthermore, PC12 cell-derived exosomes can enter and deliver microRNAs (miRNAs) into bone marrow-derived mesenchymal stromal cells (BMSCs), and decrease the expression level of transforming growth factor β receptor II (TGFβRII) and tropomyosin-1 (TPM1) through miR-21. These results show the pathway of exosome internalization and demonstrate that tumor cell-derived exosomes regulate target gene expression in normal cells. Exosomes are nanoscale membrane vesicles secreted from many types of cells. Carrying functional molecules, exosomes transfer information between cells and mediate many physiological and pathological processes. In this report, utilizing selective inhibitors, molecular tools, and specific endocytosis markers, the cellular uptake of PC12 cell-derived exosomes was imaged by high-throughput microscopy and statistically analyzed. It was found that the uptake was through clathrin-mediated endocytosis and macropinocytosis. Furthermore, PC12 cell-derived exosomes can enter and deliver microRNAs (miRNAs) into bone marrow-derived mesenchymal stromal cells (BMSCs), and decrease the expression level of transforming growth factor β receptor II (TGFβRII) and tropomyosin-1 (TPM1) through miR-21. These results show the pathway of exosome internalization and demonstrate that tumor cell-derived exosomes regulate target gene expression in normal cells.

Abstract Background 5-Fluorouracil (5-FU) has been commonly prescribed for patients with colorectal cancer (CRC), but resistance to 5-FU is one of the main reasons for failure in CRC. Recently, microRNAs (miRNAs) have been established as a means of reversing the dilemma by regulating signaling pathways involved in initiation and progression of CRC. However, how to safely and effectively deliver miRNA to target cells becomes a main challenge. Results In this study, Engineered exosomes were exploited to simultaneously deliver an anticancer drug 5-FU and miR-21 inhibitor oligonucleotide (miR-21i) to Her2 expressing cancer cells. Purified engineered exosomes from the donor cells loaded with 5-FU and miR-21i via electroporation to introduce into 5-FU-resistant colorectal cancer cell line HCT-116 5FR . Furthermore, systematic administration of 5-FU and miR-21i loaded exosomes in tumor bearing mice indicated a significantly anti-tumor effect. The results showed that the engineered exosome-based 5-FU and miR-21i co-delivery system could efficiently facilitate cellular uptake and significantly down-regulate miR-21 expression in 5-FU resistant HCT-116 5FR cell lines. Consequently, the down-regulation of miR-21 induced cell cycle arrest, reduced tumor proliferation, increased apoptosis and rescued PTEN and hMSH2 expressions, regulatory targets of miR-21. Of particular importance was the significant reduction in tumor growth in a mouse model of colon cancer with systematic administration of the targeting miR-21i. More excitedly, the combinational delivery of miR-21i and 5-FU with the engineered exosomes effectively reverse drug resistance and significantly enhanced the cytotoxicity in 5-FU-resistant colon cancer cells, compared with the single treatment with either miR-21i or 5-FU. Conclusion The strategy for co-delivering the functional small RNA and anticancer drug by exosomes foreshadows a potential approach to reverse the drug resistance in CRC and thus to enhance the efficacy of the cancer treatment.

Chemodynamic therapy (CDT), a novel cancer therapeutic strategy defined as the treatment using Fenton or Fenton-like reaction to produce •OH in the tumor region, was first proposed by Bu, Shi, and co-workers in 2016. Recently, with the rapid development of Fenton and Fenton-like nanomaterials, CDT has attracted tremendous attention because of its unique advantages: 1) It is tumor-selective with low side effects; 2) the CDT process does not depend on external field stimulation; 3) it can modulate the hypoxic and immunosuppressive tumor microenvironment; 4) the treatment cost of CDT is low. In addition to the Fe-involved CDT strategies, the Fenton-like reaction-mediated CDT strategies have also been proposed, which are based on many other metal elements including copper, manganese, cobalt, titanium, vanadium, palladium, silver, molybdenum, ruthenium, tungsten, cerium, and zinc. Moreover, CDT has been combined with other therapies like chemotherapy, radiotherapy, phototherapy, sonodynamic therapy, and immunotherapy for achieving enhanced anticancer effects. Besides, there have also been studies that extend the application of CDT to the antibacterial field. This review introduces the latest advancements in the nanomaterials-involved CDT from 2018 to the present and proposes the current limitations as well as future research directions in the related field.

The drug delivery system based on supramolecular vesicles that were self-assembled by a novel host-guest inclusion complex between a water-soluble pillar[6]arene (WP6) and hydrophobic ferrocene derivative in water has been developed. The inclusion complexation between WP6 and ferrocene derivative in water was studied by (1)H NMR, UV-vis, and fluorescence spectroscopy, which showed a high binding constant of (1.27 ± 0.42) × 10(5) M(-1) with 1:1 binding stoichiometry. This resulting inclusion complex could self-assemble into supramolecular vesicles that displayed a significant pH-responsive behavior in aqueous solution, which were investigated by fluorescent probe technique, dynamic laser scattering, and transmission electron microscopy. Furthermore, the drug loading and in vitro drug release studies demonstrated that these supramolecular vesicles were able to encapsulate mitoxantrone (MTZ) to achieve MTZ-loaded vesicles, which particularly showed rapid MTZ release at low-pH environment. More importantly, the cellular uptake of these pH-responsive MTZ-loaded vesicles by cancer cells was observed by living cell imaging techniques, and their cytotoxicity assay indicated that unloaded vesicles had low toxicity to normal cells, which could dramatically reduce the toxicity of MTZ upon loading of MTZ. Meanwhile, MTZ-loaded vesicles exhibited comparable anticancer activity in vitro as free MTZ to cancer cells under examined conditions. This study suggests that such supramolecular vesicles have great potential as controlled drug delivery systems.

Polyphenols, the phenolic hydroxyl group-containing organic molecules, are widely found in natural plants and have shown beneficial effects on human health. Recently, polyphenol-containing nanoparticles have attracted extensive research attention due to their antioxidation property, anticancer activity, and universal adherent affinity, and thus have shown great promise in the preparation, stabilization, and modification of multifunctional nanoassemblies for bioimaging, therapeutic delivery, and other biomedical applications. Additionally, the metal-polyphenol networks, formed by the coordination interactions between polyphenols and metal ions, have been used to prepare an important class of polyphenol-containing nanoparticles for surface modification, bioimaging, drug delivery, and disease treatments. By focusing on the interactions between polyphenols and different materials (e.g., metal ions, inorganic materials, polymers, proteins, and nucleic acids), a comprehensive review on the synthesis and properties of the polyphenol-containing nanoparticles is provided. Moreover, the remarkable versatility of polyphenol-containing nanoparticles in different biomedical applications, including biodetection, multimodal bioimaging, protein and gene delivery, bone repair, antibiosis, and cancer theranostics is also demonstrated. Finally, the challenges faced by future research regarding the polyphenol-containing nanoparticles are discussed.

butterflies. These examples indicated that the stratagem could provide an intrinsic color-sensing feedback to modify the system behavior/action for future biohybrid robots. In addition, by integrating the biohybrid structural color hydrogels into microfluidics, we developed a "heart-on-a-chip" platform featuring microphysiological visuality for biological research and drug screening. This biohybrid, living, structural color hydrogel may be widely used in the design of a variety of intelligent actuators and soft robotic devices.

All-solid-state, flexible, symmetric, and asymmetric microsupercapacitors are fabricated by a simple method in a scalable fashion from laser-induced graphene on commercial polyimide films, followed by electrodeposition of pseudocapacitive materials on the interdigitated in-plane architectures. These microsupercapacitors demonstrate comparable energy density to commercial lithium thin-film batteries, yet exhibit more than two orders of magnitude higher power density with good mechanical flexibility. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

To distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (pseudo pre-miRNAs), a hybrid feature which consists of local contiguous structure-sequence composition, minimum of free energy (MFE) of the secondary structure and P-value of randomization test is used. Besides, a novel machine-learning algorithm, random forest (RF), is introduced. The results suggest that our method predicts at 98.21% specificity and 95.09% sensitivity. When compared with the previous study, Triplet-SVM-classifier, our RF method was nearly 10% greater in total accuracy. Further analysis indicated that the improvement was due to both the combined features and the RF algorithm. The MiPred web server is available at http://www.bioinf.seu.edu.cn/miRNA/. Given a sequence, MiPred decides whether it is a pre-miRNA-like hairpin sequence or not. If the sequence is a pre-miRNA-like hairpin, the RF classifier will predict whether it is a real pre-miRNA or a pseudo one.

Abstract Photoluminescence (PL), up‐conversion PL (UCPL), and phosphorescence are three kinds of phenomena common to light‐emitting materials, but it is very difficult to observe all of them simultaneously when they are derived from a single material at room temperature. For the first time, triple‐mode emission (that is, PL, UCPL, and room temperature phosphorescence (RTP)) is reported, which relies on a composite of the luminescent carbon dots (CDs) prepared from m ‐phenylenediamine and poly(vinyl alcohol) (PVA). Moreover, the CDs‐PVA aqueous dispersion is nearly colorless and demonstrates promise as a triple‐mode emission ink in the field of advanced anti‐counterfeiting.

Cells release exosomes to transfer various molecules to other cells. Exosomes are involved in a number of physiological and pathological processes. They are emerging great potential utility for diseases diagnosis and treatment recently. However, the internalization and intracellular trafficking of exosomes have not been described clearly. In this work, exosomes were isolated from the culture medium of PC12 cells, labeled by lipophilic dye and amino-reactive fluorophore, incubated with resting PC12 cells. The results of live-cell microscopy indicated that exosomes were internalized through endocytosis pathway, trapped in vesicles, and transported to perinuclear region. Particle tracking fluorescent vesicles suggested that the active transport of exosomes may be mediated by cytoskeleton. The proteins on exosome membrane were found to be released from exosomes and trapped in lysosome. The inverted transport of lipophilic dye from perinuclear region to cell peripheries was revealed, possibly caused by recycling of the exosome lipids. This study provides new sight into the mechanisms of exosome uptake and intracellular fate.

Co3O4 nanoparticles (Co3O4 NPs), synthesized by the coprecipitation method, showed intrinsic catalase-like, peroxidase-like, and SOD-like activity. The catalytic activity of Co3O4 NPs was much higher than analogous Fe3O4 NPs. Co3O4's mechanisms of catalytic activity were analyzed in detail using the electron spin resonance (ESR) method, which confirmed that Co3O4 NPs don't follow the classical Fenton reactions with hydrogen peroxide the way Fe3O4 NPs do. The high redox potential of Co(3+)/Co(2+) was supposed to be the leading cause of the differences in both activity and mechanism with Fe3O4. Based on the high, peroxidase-like activity, a new immunohistochemical assay was designed in which the avastin antibody was conjugated onto the surface of Co3O4 NPs. The conjugates obtained were used to detect vascular endothelial growth factor (VEGF) that was overexpressed in tumor tissue. When the experimental and control groups were stained, there were clear distinctions between them. This study showed that there are many opportunities to improve the enzyme-like activities of nanomaterials and also to improve their potential applications for biocatalysis and bioassays, especially in relatively harsh conditions.

A patch with the capability of avoiding wound infection and promoting tissue remolding is of great value for wound healing. In this paper, we develop a biomass chitosan microneedle array (CSMNA) patch integrated with smart responsive drug delivery for promoting wound healing. Chitosan possesses many outstanding features such as the natural antibacterial property and has been widely utilized for wound healing. Besides, the microstructure of microneedles enables the effective delivery of loaded drugs into the target area and avoids the excessive adhesion between the skin and the patch. Also, vascular endothelial growth factor (VEGF) is encapsulated in the micropores of CSMNA by temperature sensitive hydrogel. Therefore, the smart release of the drugs can be controllably realized via the temperature rising induced by the inflammation response at the site of wounds. It is demonstrated that the biomass CSMNA patch can promote inflammatory inhibition, collagen deposition, angiogenesis, and tissue regeneration during the wound closure. Thus, this versatile CSMNA patch is potentially valuable for wound healing in clinical applications.

CONSPECTUS: Colloidal photonic crystals (PhCs), periodically arranged monodisperse nanoparticles, have emerged as one of the most promising materials for light manipulation because of their photonic band gaps (PBGs), which affect photons in a manner similar to the effect of semiconductor energy band gaps on electrons. The PBGs arise due to the periodic modulation of the refractive index between the building nanoparticles and the surrounding medium in space with subwavelength period. This leads to light with certain wavelengths or frequencies located in the PBG being prohibited from propagating. Because of this special property, the fabrication and application of colloidal PhCs have attracted increasing interest from researchers. The most simple and economical method for fabrication of colloidal PhCs is the bottom-up approach of nanoparticle self-assembly. Common colloidal PhCs from this approach in nature are gem opals, which are made from the ordered assembly and deposition of spherical silica nanoparticles after years of siliceous sedimentation and compression. Besides naturally occurring opals, a variety of manmade colloidal PhCs with thin film or bulk morphology have also been developed. In principle, because of the effect of Bragg diffraction, these PhC materials show different structural colors when observed from different angles, resulting in brilliant colors and important applications. However, this angle dependence is disadvantageous for the construction of some optical materials and devices in which wide viewing angles are desired. Recently, a series of colloidal PhC materials with spherical macroscopic morphology have been created. Because of their spherical symmetry, the PBGs of spherical colloidal PhCs are independent of rotation under illumination of the surface at a fixed incident angle of the light, broadening the perspective of their applications. Based on droplet templates containing colloidal nanoparticles, these spherical colloidal PhCs can be generated by evaporation-induced nanoparticle crystallization or polymerization of ordered nanoparticle crystallization arrays. In particular, because microfluidics was used for the generation of the droplet templates, the development of spherical colloidal PhCs has progressed significantly. These new strategies not only ensure monodispersity, but also increase the structural and functional diversity of the PhC beads, paving the way for the development of advanced optoelectronic devices. In this Account, we present the research progress on spherical colloidal PhCs, including their design, preparation, and potential applications. We outline various types of spherical colloidal PhCs, such as close-packed, non-close-packed, inverse opal, biphasic or multiphasic Janus structured, and core-shell structured geometries. Based on their unique optical properties, applications of the spherical colloidal PhCs for displays, sensors, barcodes, and cell culture microcarriers are presented. Future developments of the spherical colloidal PhC materials are also envisioned.