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2023 Volume 6 Issue 1  Published: 2023-01-20
    Research Article
  • Nattanong Bupi , Vinoth Kumar Sangaraju , Le Thi Phan , Aamir Lal , Thuy Thi Bich Vo , Phuong Thi Ho , Muhammad Amir Qureshi , Marjia Tabassum , Sukchan Lee , Balachandran Manavalan
    doi: 10.34133/research.0016

    Tomato yellow leaf curl virus (TYLCV) dispersed across different countries, specifically to subtropical regions, associated with more severe symptoms. Since TYLCV was first isolated in 1931, it has been a menace to tomato industrial production worldwide over the past century. Three groups were newly isolated from TYLCV-resistant tomatoes in 2022; however, their functions are unknown. The development of machine learning (ML)-based models using characterized sequences and evaluating blind predictions is one of the major challenges in interdisciplinary research. The purpose of this study was to develop an integrated computational framework for the accurate identification of symptoms (mild or severe) based on TYLCV sequences (isolated in Korea). For the development of the framework, we first extracted 11 different feature encodings and hybrid features from the training data and then explored 8 different classifiers and developed their respective prediction models by using randomized 10-fold cross-validation. Subsequently, we carried out a systematic evaluation of these 96 developed models and selected the top 90 models, whose predicted class labels were combined and considered as reduced features. On the basis of these features, a multilayer perceptron was applied and developed the final prediction model (IML-TYLCVs). We conducted blind prediction on 3 groups using IML-TYLCVs, and the results indicated that 2 groups were severe and 1 group was mild. Furthermore, we confirmed the prediction with virus-challenging experiments of tomato plant phenotypes using infectious clones from 3 groups. Plant virologists and plant breeding professionals can access the user-friendly online IML-TYLCVs web server at https://balalab-skku.org/IML-TYLCVs, which can guide them in developing new protection strategies for newly emerging viruses.

  • Research Article
  • Jie Ren , Hao-Wen Li , Liang Chen , Min Zhang , Yan-Xiang Liu , Bo-Wen Zhang , Rui Xu , Yan-Yan Miao , Xue-Mei Xu , Xin Hua , Xiao-Gang Sun , Ru-Jia Yu , Yi-Tao Long , Sheng-Shou Hu
    doi: 10.34133/research.0019

    Heart failure (HF), leading as one of the main causes of mortality, has become a serious public health issue with high prevalence around the world. Single cardiomyocyte (CM) metabolomics promises to revolutionize the understanding of HF pathogenesis since the metabolic remodeling in the human hearts plays a vital role in the disease progression. Unfortunately, current metabolic analysis is often limited by the dynamic features of metabolites and the critical needs for high-quality isolated CMs. Here, high-quality CMs were directly isolated from transgenic HF mice biopsies and further employed in the cellular metabolic analysis. The lipids landscape in individual CMs was profiled with a delayed extraction mode in time-of-flight secondary ion mass spectrometry. Specific metabolic signatures were identified to distinguish HF CMs from the control subjects, presenting as possible single-cell biomarkers. The spatial distributions of these signatures were imaged in single cells, and those were further found to be strongly associated with lipoprotein metabolism, transmembrane transport, and signal transduction. Taken together, we systematically studied the lipid metabolism of single CMs with a mass spectrometry imaging method, which directly benefited the identification of HF-associated signatures and a deeper understanding of HF-related metabolic pathways.

  • Research Article
  • Fangfang Deng , Juntao Chen , Junxiang Xiang , Yong Li , Yan Qiao , Ze Liu , Tao Ding
    doi: 10.34133/research.0020

    Active particles have been regarded as the key models to mimic and understand the complex systems of nature. Although chemical and field-powered active particles have received wide attentions, light-programmed actuation with long-range interaction and high throughput remains elusive. Here, we utilize photothermal active plasmonic substrate made of porous anodic aluminum oxide filled with Au nanoparticles and poly(N-isopropylacrylamide) (PNIPAM) to optically oscillate silica beads with robust reversibility. The thermal gradient generated by the laser beam incurs the phase change of PNIPAM, producing gradient of surface forces and large volume changes within the complex system. The dynamic evolution of phase change and water diffusion in PNIPAM films result in bistate locomotion of silica beads, which can be programmed by modulating the laser beam. This light-programmed bistate colloidal actuation provides promising opportunity to control and mimic the natural complex systems.

  • Research Article
  • Jiaying Li , Jinjin Ma , Qian Feng , En Xie , Qingchen Meng , Wenmiao Shu , Junxi Wu , Liming Bian , Fengxuan Han , Bin Li
    doi: 10.34133/research.0021

    The critical factor determining the in vivo effect of bone repair materials is the microenvironment, which greatly depends on their abilities to promote vascularization and bone formation. However, implant materials are far from ideal candidates for guiding bone regeneration due to their deficient angiogenic and osteogenic microenvironments. Herein, a double-network composite hydrogel combining vascular endothelial growth factor (VEGF)-mimetic peptide with hydroxyapatite (HA) precursor was developed to build an osteogenic microenvironment for bone repair. The hydrogel was prepared by mixing acrylated β-cyclodextrins and octacalcium phosphate (OCP), an HA precursor, with gelatin solution, followed by ultraviolet photo-crosslinking. To improve the angiogenic potential of the hydrogel, QK, a VEGF-mimicking peptide, was loaded in acrylated β-cyclodextrins. The QK-loaded hydrogel promoted tube formation of human umbilical vein endothelial cells and upregulated the expression of angiogenesis-related genes, such as Flt1, Kdr, and VEGF, in bone marrow mesenchymal stem cells. Moreover, QK could recruit bone marrow mesenchymal stem cells. Furthermore, OCP in the composite hydrogel could be transformed into HA and release calcium ions facilitating bone regeneration. The double-network composite hydrogel integrated QK and OCP showed obvious osteoinductive activity. The results of animal experiments showed that the composite hydrogel enhanced bone regeneration in skull defects of rats, due to perfect synergistic effects of QK and OCP on vascularized bone regeneration. In summary, improving the angiogenic and osteogenic microenvironments by our double-network composite hydrogel shows promising prospects for bone repair.

  • Research Article
  • Danqing Huang , Yi Cheng , Guopu Chen , Yuanjin Zhao
    doi: 10.34133/research.0022

    Management of infected wounds has raised worldwide concerns. Attempts in this field focus on the development of intelligent patches for improving the wound healing. Here, inspired by the cocktail treatment and combinational therapy stratagem, we present a novel Janus piezoelectric hydrogel patch via 3-dimensional printing for sonodynamic bacteria elimination and wound healing. The top layer of the printed patch was poly(ethylene glycol) diacrylate hydrogel with gold-nanoparticle-decorated tetragonal barium titanate encapsulation, which realizes the ultrasound-triggered release of reactive oxygen species without leaking nanomaterials. The bottom layer is fabricated with methacrylate gelatin and carries growth factors for the cell proliferation and tissue reconstruction. Based on these features, we have demonstrated in vivo that the Janus piezoelectric hydrogel patch can exert substantial infection elimination activity under the excitation of ultrasound, and its sustained release of growth factors can promote tissue regeneration during wound management. These results indicated that the proposed Janus piezoelectric hydrogel patch had practical significance in sonodynamic infection alleviation and programmable wound healing for treating different clinical diseases.

  • Research Article
  • Ran Tao , Wei Fang , Jun Wu , Binhong Dou , Wanghuai Xu , Zhanying Zheng , Bing Li , Zuankai Wang , Xiqiao Feng , Chonglei Hao
    doi: 10.34133/research.0023

    Achieving rapid shedding of droplets from solid surfaces has received substantial attention because of its diverse applications. Previous studies have focused on minimizing contact times of liquid droplets interacting with stationary surfaces, yet little consideration has been given to that of moving surfaces. Here, we report a different scenario: A water droplet rapidly detaches from micro/nanotextured rotating surfaces in an intriguing doughnut shape, contributing to about 40% contact time reduction compared with that on stationary surfaces. The doughnut-shaped bouncing droplet fragments into satellites and spontaneously scatters, thus avoiding further collision with the substrate. In particular, the contact time is highly dependent on impact velocities of droplets, beyond previous descriptions of classical inertial-capillary scaling law. Our results not only deepen the fundamental understanding of droplet dynamics on moving surfaces but also suggest a synergistic mechanism to actively regulate the contact time by coupling the kinematics of droplet impingement and surface rotation.

  • Research Article
  • Jia-Jin Wu , Senlin Zhu , Yi-Fan Tang , Fengfei Gu , Teresa G. Valencak , Jian-Xin Liu , Hui-Zeng Sun
    doi: 10.34133/research.0025

    Newborn ruminants are considered functionally monogastric animals. The poor understanding of cellular differences between newborn and mature ruminants prevents the improvement of health and performance of domestic ruminants. Here, we performed the single-cell RNA sequencing on the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, rectum, liver, salivary gland, and mammary gland from newborn and adult cattle. A comprehensive single-cell transcriptomic atlas covering 235,941 high-quality single cells and 78 cell types was deciphered. A Cattle Cell Landscape database (http://cattlecelllandscape.zju.edu.cn) was established to elaborately display the data and facilitate effective annotation of cattle cell types and subtypes for the broad research community. By measuring stemness states of epithelial cells in each tissue type, we revealed that the epithelial cells from newborn forestomach (rumen, reticulum, and omasum) were more transcriptionally indistinct and stochastic compared with the adult stage, which was in contrast to those of abomasum and intestinal tissues. The rapid forestomach development during the early life of calves was driven by epithelial progenitor-like cells with high DNA repair activities and methylation. Moreover, in the forestomach tissues of newborn calves, the Megasphaera genus was involved in regulating the transcriptional plasticity of the epithelial progenitor-like cells by DNA methylation regulation. A novel cell type, the STOML3+ cell, was found to be newborn-specific. It apparently plays a crucial role in stemness maintenance of its own and cholangiocytes in the hepatic microenvironment. Our results reveal that the age- and microbiota-dependent cell stemness plasticity drives the postnatal functional maturity of ruminants.

  • Research Article
  • Helmut Cölfen , Rose Rosenberg , Dirk Haffke , Simon Stemplinger , Thomas Zemb , Dominik Horinek
    doi: 10.34133/research.0026

    Water/ethyl acetate/ethanol is widely used as a “green” extractant system. We show that 2 different types of phase separation can be induced upon centrifugation in this ternary system using ethanol as a cosolvent of water and ethyl acetate: centrifuge-induced criticality and centrifuge-induced emulsification. The expected composition profiles of samples after centrifugation can be represented by bent lines in a ternary phase diagram when gravitational energy is added to the free energy of mixing. The experimental equilibrium composition profiles behave qualitatively as expected and can be predicted using a phenomenological theory of mixing. The concentration gradients are small except near the critical point, as expected for small molecules. Nevertheless, they are usable when accompanied by temperature cycles. These findings open new possibilities of centrifugal separation, even if control is delicate during temperature cycles. These schemes are accessible even at relatively low centrifugation speed for molecules that float and sediment with apparent molar masses several hundred times larger than the molecular mass.

  • Research Article
  • Dongqing Lin , Yang Li , He Zhang , Shuai Zhang , Yuezheng Gao , Tianrui Zhai , Shu Hu , Chuanxiang Sheng , Heng Guo , Chunxiang Xu , Ying Wei , Shifeng Li , Yelong Han , Quanyou Feng , Shasha Wang , Linghai Xie , Wei Huang
    doi: 10.34133/research.0027

    In situ self-assembly of semiconducting emitters into multilayer cracks is a significant solution-processing method to fabricate organic high-Q lasers. However, it is still difficult to realize from conventional conjugated polymers. Herein, we create the molecular super-hindrance-etching technology, based on the π-functional nanopolymer PG-Cz, to modulate multilayer cracks applied in organic single-component random lasers. Massive interface cracks are formed by promoting interchain disentanglement with the super-steric hindrance effect of π-interrupted main chains, and multilayer morphologies with photonic-crystal-like ordering are also generated simultaneously during the drop-casting method. Meanwhile, the enhancement of quantum yields on micrometer-thick films (Φ = 40% to 50%) ensures high-efficient and ultrastable deep-blue emission. Furthermore, a deep-blue random lasing is achieved with narrow linewidths ~0.08 nm and high-quality factors Q ≈ 5,500 to 6,200. These findings will offer promising pathways of organic π-nanopolymers for the simplification of solution processes applied in lasing devices and wearable photonics.

  • Research Article
  • Lan Xu , Geng Huangfu , Yiping Guo , Ya Yang
    doi: 10.34133/research.0028

    A traditional thermal conductivity vacuum gauge mainly detects low pressure (the degree of vacuum) by measuring the temperature change of a filament heated by the electric current. We propose a novel pyroelectric vacuum sensor that utilizes the effect of ambient thermal conductivity on the pyroelectric effect to detect vacuum through the charge density of ferroelectric materials under radiation. The functional relationship between the charge density and low pressure is derived, which is validated in a suspended (Pb,La)(Zr,Ti,Ni)O3 (PLZTN) ferroelectric ceramic-based device. The charge density of the indium tin oxide/PLZTN/Ag device under 405 nm of 60.5 mW cm−2 radiation at low pressure reaches 4.48 μC cm−2, which is increased by about 3.0 times compared with that at atmospheric pressure. The vacuum can improve the charge density without increasing the radiation energy, confirming the important role of ambient thermal conductivity on the pyroelectric effect. This research provides a demonstration for ambient thermal conductivity effectively tuning pyroelectric performance, a theoretical basis for pyroelectric vacuum sensors, and a feasible route for further optimizing the performance of pyroelectric photoelectric devices.

  • Research Article
  • Xin Zhang , Chunchun Yin , Jingxuan You , Ruiqiao Li , Jinming Zhang , Yaohui Cheng , Yirong Wang , Jun Zhang
    doi: 10.34133/research.0029

    How to achieve multicolor organic room-temperature phosphorescence (RTP) is still challenging and striking. Herein, we discovered a new principle to construct eco-friendly color-tunable RTP nanomaterials based on the nano-surface confining effect. Cellulose nanocrystal (CNC) immobilized cellulose derivatives (CX) containing aromatic substituents via hydrogen-bonding interactions, which effectively inhibit the motion of cellulose chains and luminescent groups to suppress the nonradiative transitions. Meanwhile, CNC with a strong hydrogen-bonding network can isolate oxygen. CX with different aromatic substituents regulate the phosphorescent emission. After mixing CNC and CX directly, a series of polychromatic ultralong RTP nanomaterials were obtained. The RTP emission of the resultant CX@CNC can be finely adjusted through the introduction of various CX and the regulation of the CX/CNC ratio. Such a universal, facile, and effective strategy can be used to fabricate various colorful RTP materials with wide color gamut. Because of the complete biodegradability of cellulose, the multicolor phosphorescent CX@CNC nanomaterials can be used as eco-friendly security inks to fabricate disposable anticounterfeiting labels and information-storage patterns via conventional printing and writing processes.

  • Research Article
  • Jing Liu , Duyang Gao , Dehong Hu , Siyi Lan , Yu Liu , Hairong Zheng , Zhen Yuan , Zonghai Sheng
    doi: 10.34133/research.0030

    Targeted therapy of Parkinson’s disease is an important challenge because of the blood–brain barrier limitation. Here, we propose a natural killer cell membrane biomimetic nanocomplex (named BLIPO-CUR) delivered via the meningeal lymphatic vessel (MLV) route to further the therapeutic efficacy of Parkinson’s disease. The membrane incorporation enables BLIPO-CUR to target the damaged neurons, thus improving their therapeutic efficacy through clearing reactive oxygen species, suppressing the aggregation of α-synuclein, and inhibiting the spread of excess α-synuclein species. Compared with the conventional intravenous injection, this MLV administration can enhance the delivered efficiency of curcumin into the brain by ~20 folds. The MLV route administration of BLIPO-CUR enhances the treatment efficacy of Parkinson’s disease in mouse models by improving their movement disorders and reversing neuron death. Our findings highlight the great potential of MLV route administration used as targeted delivery of drugs to the brain, holding a great promise for neurodegenerative disease therapy.

  • Research Article
  • Jiaxiang Bai , Yonghai Feng , Wenming Li , Zerui Cheng , Jessica M. Rosenholm , Huilin Yang , Guoqing Pan , Hongbo Zhang , Dechun Geng
    doi: 10.34133/research.0031

    Nanozymes are considered to represent a new era of antibacterial agents, while their antibacterial efficiency is limited by the increasing tissue depth of infection. To address this issue, here, we report a copper and silk fibroin (Cu-SF) complex strategy to synthesize alternative copper single-atom nanozymes (SAzymes) with atomically dispersed copper sites anchored on ultrathin 2D porous N-doped carbon nanosheets (CuNx-CNS) and tunable N coordination numbers in the CuNx sites (x = 2 or 4). The CuNx-CNS SAzymes inherently possess triple peroxidase (POD)-, catalase (CAT)-, and oxidase (OXD)-like activities, facilitating the conversion of H2O2 and O2 into reactive oxygen species (ROS) through parallel POD- and OXD-like or cascaded CAT- and OXD-like reactions. Compared to CuN2-CNS, tailoring the N coordination number from 2 to 4 endows the SAzyme (CuN4-CNS) with higher multienzyme activities due to its superior electron structure and lower energy barrier. Meanwhile, CuNx-CNS display strong absorption in the second near-infrared (NIR-II) biowindow with deeper tissue penetration, offering NIR-II-responsive enhanced ROS generation and photothermal treatment in deep tissues. The in vitro and in vivo results demonstrate that the optimal CuN4-CNS can effectively inhibit multidrug-resistant bacteria and eliminate stubborn biofilms, thus exhibiting high therapeutic efficacy in both superficial skin wound and deep implant-related biofilm infections.

  • Research Article
  • Mingyu Chu , Xianpeng Wang , Xuchun Wang , Xiangxi Lou , Congyang Zhang , Muhan Cao , Lu Wang , Youyong Li , Sibao Liu , Tsun-Kong Sham , Qiao Zhang , Jinxing Chen
    doi: 10.34133/research.0032

    Catalytic hydrogenolysis of end-of-life polyolefins can produce value-added liquid fuels and therefore holds great promises in plastic waste reuse and environmental remediation. The major challenge limiting the recycling economic benefit is the severe methanation (usually >20%) induced by terminal C–C cleavage and fragmentation in polyolefin chains. Here, we overcome this challenge by demonstrating that Ru single-atom catalyst can effectively suppress methanation by inhibiting terminal C–C cleavage and preventing chain fragmentation that typically occurs on multi-Ru sites. The Ru single-atom catalyst supported on CeO2 shows an ultralow CH4 yield of 2.2% and a liquid fuel yield of over 94.5% with a production rate of 314.93 gfuels gRu−1 h−1 at 250 °C for 6 h. Such remarkable catalytic activity and selectivity of Ru single-atom catalyst in polyolefin hydrogenolysis offer immense opportunities for plastic upcycling.

  • Research Article
  • Jue Tang , Jing He , Huiqin Guo , Huiran Lin , Meng Li , Tianyou Yang , Hai-Yun Wang , Di Li , Jiabin Liu , Le Li , Huimin Xia , Zhenjian Zhuo , Lei Miao
    doi: 10.34133/research.0033

    The recurrence and metastasis of children with mediastinal neuroblastoma (NB) are also occurred after surgery, chemotherapy, or radiotherapy. Strategies targeting the tumor microenvironment have been reported to improve survival; however, thorough investigations of monocytes and tumor-associated macrophages (Mϕs) with specialized functions in NB are still lacking. Our data first demonstrated polypyrimidine tract binding protein 2 (PTBP2) as a possible identifier in patients with mediastinal NB screened by proteomic profiling and that PTBP2 predicted good outcomes. Functional studies revealed that PTBP2 in NB cells induced the chemotactic activity and repolarization of tumor-associated monocytes and Mϕs, which, in turn, inhibited NB growth and dissemination. Mechanistically, PTBP2 prevents interferon regulatory factor 9 alternative splicing and upregulates signal transducers and activators of transcription 1 to stimulate C-C motif chemokine ligand 5 (CCL5) and interferon-stimulated gene factor-dependent type I interferon secretion, to induce monocyte/Mϕs chemotaxis, and to sustain monocytes in a proinflammatory phenotype. Our study defined a critical event of PTBP2-induced monocytes/Mϕs in NB progression and revealed that RNA splicing occurred by PTBP2 benefits immune compartmentalization between NB cells and monocytes. This work revealed the pathological and biological role of PTBP2 in NB development and indicates that PTBP2-induced RNA splicing benefits immune compartmentalization and predicted a favorable prognosis in mediastinal NB.

  • Research Article
  • Chaoyu Yang , Yunru Yu , Yuanjin Zhao , Luoran Shang
    doi: 10.34133/research.0034

    Nonspherical particles have attracted increasing interest because of their shape anisotropy. However, the current methods to prepare anisotropic particles suffer from complex generation processes and limited shape diversity. Here, we develop a piezoelectric microfluidic system to generate complex flow configurations and fabricate jellyfish-like microparticles. In this delicate system, the piezoelectric vibration could evolve a jellyfish-like flow configuration in the microchannel and the in situ photopolymerization could instantly capture the flow architecture. The sizes and morphologies of the particles are precisely controlled by tuning the piezoelectric and microfluidic parameters. Furthermore, multi-compartmental microparticles with a dual-layer structure are achieved by modifying the injecting channel geometry. Moreover, such unique a shape endows the particles with flexible motion ability especially when stimuli-responsive materials are incorporated. On the basis of that, we demonstrate the capability of the jellyfish-like microparticles in highly efficient adsorption of organic pollutants under external control. Thus, it is believed that such jellyfish-like microparticles are highly versatile in potential applications and the piezoelectric-integrated microfluidic strategy could open an avenue for the creation of such anisotropic particles.

  • Research Article
  • Xinlei Gu , Chang Liu , Xinxin Gao , Kan Zhang , Weitao Zheng , Changfeng Chen
    doi: 10.34133/research.0035

    Solid solution strengthening enhances hardness of metals by introducing solute atoms to create local distortions in base crystal lattice, which impedes dislocation motion and plastic deformation, leading to increased strength but reduced ductility and toughness. In sharp contrast, superhard materials comprising covalent bonds exhibit high strength but low toughness via a distinct mechanism dictated by brittle bond deformation, showcasing another prominent scenario of classic strength–toughness tradeoff dilemma. Solving this less explored and understood problem presents a formidable challenge that requires a viable strategy of tuning main load-bearing bonds in these strong but brittle materials to achieve concurrent enhancement of the peak stress and related strain range. Here, we demonstrate a chemically tuned solid solution approach that simultaneously enhances hardness and toughness of superhard transition-metal diboride Ta1−xZrxB2. This striking phenomenon is achieved by introducing solute atom Zr that has lower electronegativity than solvent atom Ta to reduce the charge depletion on the main load-bearing B–B bonds during indentation, leading to prolonged deformation that gives rise to notably higher strain range and the corresponding peak stress. This finding highlights the crucial role of properly matched contrasting relative electronegativity of solute and solvent atoms in creating concurrent strengthening and toughening and opens a promising avenue for rational design of enhanced mechanical properties in a large class of transition-metal borides. This strategy of concurrent strength–toughness optimization via solute-atom-induced chemical tuning of the main load-bearing bonding charge is expected to work in broader classes of materials, such as nitrides and carbides.

  • Research Article
  • Feng Qi , Jia Li , Zhuoran Qi , Jian Zhang , Bin Zhou , Biwei Yang , Wenxing Qin , Wenguo Cui , Jinglin Xia
    doi: 10.34133/research.0036

    Understanding the details of metabolic reprogramming in hepatocellular carcinoma (HCC) is critical to improve stratification for therapy. Both multiomics analysis and cross-cohort validation were performed to investigate the metabolic dysregulation of 562 HCC patients from 4 cohorts. On the basis of the identified dynamic network biomarkers, 227 substantial metabolic genes were identified and a total of 343 HCC patients were classified into 4 heterogeneous metabolic clusters with distinct metabolic characteristics: cluster 1, the pyruvate subtype, associated with upregulated pyruvate metabolism; cluster 2, the amino acid subtype, with dysregulated amino acid metabolism as the reference; cluster 3, the mixed subtype, in which lipid metabolism, amino acid metabolism, and glycan metabolism are dysregulated; and cluster 4, the glycolytic subtype, associated with the dysregulated carbohydrate metabolism. These 4 clusters showed distinct prognoses, clinical characteristics and immune cell infiltrations, which was further validated by genomic alterations, transcriptomics, metabolomics, and immune cell profiles in the other 3 independent cohorts. Besides, the sensitivity of different clusters to metabolic inhibitors varied depending on their metabolic features. Importantly, cluster 2 is rich in immune cells in tumor tissues, especially programmed cell death protein 1 (PD-1)-expressing cells, which may be due to the tryptophan metabolism disorders, and potentially benefiting more from PD-1 treatment. In conclusion, our results suggest the metabolic heterogeneity of HCC and make it possible to treat HCC patients precisely and effectively on specific metabolic characteristics.

  • Research Article
  • Yanjun Liu , Chunhua Jiao , Tao Zhang , Xue Li , Panpan Li , Meishan Lu , Zhan Ye , Yanpeng Du , Runfeng Du , Wenlong Zhang , Jie Xu , Zhaojun Zheng , Yongjiang Xu , Changhu Xue , Yi Zhang , Yuanfa Liu
    doi: 10.34133/research.0037

    Localized intestine inflammation could induce short-term increases in colonic oxygenation and leads to increases in the aerobic bacteria population and reduction in the anaerobic bacteria population by changing the intestinal environment. However, the mechanisms involved and the associated functions of intestinal anaerobes in gut health still remain unclear. Here, we found that early-life depletion of gut microbiota exacerbated later colitis, while mid-life microbiota depletion showed partially reduced colitis. Notably, we observed that early-life gut microbiota depletion confers susceptibility to ferroptosis in colitis. In contrast, restitution of early-life microbiota conferred protection against colitis and inhibited ferroptosis triggered by gut microbiota dysbiosis. Similarly, colonization with anaerobic microbiota from young mice suppressed colitis. These results may attribute to high abundance of plasmalogen-positive (plasmalogen synthase [PlsA/R]-positive) anaerobes and plasmalogens (one of the common ether lipids) in young mice but reduced abundance in the development of inflammatory bowel disease. Early-life anaerobic bacteria elimination also resulted in the aggravation of colitis, while this aggravation phenotype was reverted by plasmalogen administration. Interestingly, plasmalogens inhibited ferroptosis triggered by microbiota dysbiosis. We further find that the alkenyl-ether group of plasmalogens was critical to colitis prevention and ferroptosis inhibition. These data point to one of the mechanisms by which the gut microbiota controls susceptibility to colitis and ferroptosis early in life via microbial-derived ether lipids.

  • Review
  • Lijun Wang , Gui-e Xu , Michail Spanos , Guoping Li , Zhiyong Lei , Joost P. G. Sluijter , Junjie Xiao
    doi: 10.34133/research.0038

    Cardiovascular disease is one of the leading causes of mortality worldwide. Recent studies have shown that circular RNAs (circRNAs) have emerged as important players in the prevention and treatment of cardiovascular diseases. circRNAs are a class of endogenous noncoding RNAs that are generated by back-splicing and are involved in many pathophysiological processes. In this review, we outline the current research progress on the regulatory roles of circRNAs in cardiovascular diseases. Further, new technologies and methods available for identifying, validating, synthesizing, and analyzing circRNAs, as well as their applications in therapeutics, are highlighted here. Moreover, we summarize the increasing insights into the potential use of circRNAs as circulating diagnostic and prognostic biomarkers. Finally, we discuss the prospects and challenges of circRNA therapeutic applications for cardiovascular disease therapy, with a particular focus on developing circRNA synthesis and engineering delivery systems.

  • Research Article
  • Chunchen Liu , Mengfei Li , Huilong Ma , Zhubin Hu , Xinyuan Wang , Rui Ma , Yingying Jiang , Haitao Sun , Shoujun Zhu , Yongye Liang
    doi: 10.34133/research.0039

    The second near-infrared (NIR-II, 1,000 to 1,700 nm) molecular fluorophores containing donor–acceptor–donor conjugated backbone have attracted substantial attention due to their outstanding advantages, such as stable emission and facilely tuned photophysical properties. However, it is still challenging for them to simultaneously achieve high brightness and red-shifted absorption and emission. Herein, furan is adopted as the D unit to construct NIR-II fluorophores, demonstrating red shift of absorption, enhanced absorption coefficient, and fluorescent quantum yield when compared with the generally used thiophene counterparts. The high brightness and desirable pharmacokinetics of the optimized fluorophore, IR-FFCHP, endows improved performance for angiography and tumor-targeting imaging. Furthermore, dual-NIR-II imaging of tumor and sentinel lymph nodes (LNs) has been achieved with IR-FFCHP and PbS/CdS quantum dots, enabling the in vivo imaging navigated LN surgery in tumor-bearing mice. This work demonstrates the potential of furan for constructing bright NIR-II fluorophores for biological imaging.

  • Review
  • Jing Peng , Zheng-jie Chen , Baofu Ding , Hui-Ming Cheng
    doi: 10.34133/research.0040

    Layered materials with unique structures and symmetries have attracted tremendous interest for constructing 2-dimensional (2D) structures. The weak interlayer interaction renders them to be readily isolated into various ultrathin nanosheets with exotic properties and diverse applications. In order to enrich the library of 2D materials, extensive progress has been made in the field of ternary layered materials. Consequently, many brand-new materials are derived, which greatly extend the members of 2D realm. In this review, we emphasize the recent progress made in synthesis and exploration of ternary layered materials. We first classify them in terms of stoichiometric ratio and summarize their difference in interlayer interaction, which is of great importance to produce corresponding 2D materials. The compositional and structural characteristics of resultant 2D ternary materials are then discussed so as to realize desired structures and properties. As a new family of 2D materials, we overview the layer-dependent properties and related applications in the fields of electronics, optoelectronics, and energy storage and conversion. The review finally provides a perspective for this rapidly developing field.

  • Research Article
  • Wei Guo , Yanling Cai , Xianming Liu , Yuge Ji , Cuiyu Zhang , Liyan Wang , Wenting Liao , Yuefei Liu , Nan Cui , Jinsheng Xiang , Zesong Li , Di Wu , Jingxin Li
    doi: 10.34133/research.0041

    Tumor metastasis is a hallmark of colorectal cancer (CRC), in which exosome plays a crucial role with its function in intercellular communication. Plasma exosomes were collected from healthy control (HC) donors, localized primary CRC and liver-metastatic CRC patients. We performed proximity barcoding assay (PBA) for single-exosome analysis, which enabled us to identify the alteration in exosome subpopulations associated with CRC progression. By in vitro and in vivo experiments, the biological impact of these subpopulations on cancer proliferation, migration, invasion, and metastasis was investigated. The potential application of exosomes as diagnostic biomarkers was evaluated in 2 independent validation cohorts by PBA. Twelve distinct exosome subpopulations were determined. We found 2 distinctly abundant subpopulations: one ITGB3-positive and the other ITGAM-positive. The ITGB3-positive cluster is rich in liver-metastatic CRC, compared to both HC group and primary CRC group. On the contrary, ITGAM-positive exosomes show a large-scale increase in plasma of HC group, compared to both primary CRC and metastatic CRC groups. Notably, both discovery cohort and validation cohort verified ITGB3+ exosomes as potential diagnostic biomarker. ITGB3+ exosomes promote proliferation, migration, and invasion capability of CRC. In contrast, ITGAM+ exosomes suppress CRC development. Moreover, we also provide evidence that one of the sources of ITGAM+ exosomes is macrophage. ITGB3+ exosomes and ITGAM+ exosomes are proven 2 potential diagnostic, prognostic, and therapeutic biomarkers for management of CRC.

  • Research Article
  • Lijun Cai , Dongyu Xu , Zeyou Zhang , Ning Li , Yuanjin Zhao
    doi: 10.34133/research.0044

    Micromotors are identified as a promising candidate in the field of sensing benefiting from their capacity of autonomous movement. Here, a review on the development of tailoring micromotors for sensing is presented, covering from their propulsion mechanisms and sensing strategies to applications. First, we concisely summarize the propulsion mechanism of micromotors involving fuel-based propulsion and fuel-free propulsion introducing their principles. Then, emphasis is laid to the sensing stratagems of the micromotors including speed-based sensing strategy, fluorescence-based sensing strategy, and other strategies. We listed typical examples of different sensing stratagems. After that, we introduce the applications of micromotors in sensing fields including environmental science, food safety, and biomedical fields. Finally, we discuss the challenges and prospects of the micromotors tailored for sensing. We believe that this comprehensive review can help readers to catch the research frontiers in the field of sensing and thus to burst out new ideas.

  • Research Article
  • Shuaiwei Ren , Mei Huang , Raoxian Bai , Lijiao Chen , Jiao Yang , Junyu Zhang , Wenting Guo , Weizhi Ji , Yongchang Chen
    doi: 10.34133/research.0045

    Splice-switching antisense oligonucleotides (ASOs) and engineered U7 small nuclear ribonucleoprotein (U7 Sm OPT) are the most commonly used methods for exon skipping. However, challenges remain, such as limited organ delivery and repeated dosing for ASOs and unknown risks of by-products produced by U7 Sm OPT. Here, we showed that antisense circular RNAs (AS-circRNAs) can effectively mediate exon skipping in both minigene and endogenous transcripts. We also showed a relatively higher exon skipping efficiency at the tested Dmd minigene than U7 Sm OPT. AS-circRNA specifically targets the precursor mRNA splicing without off-target effects. Moreover, AS-circRNAs with adeno-associated virus (AAV) delivery corrected the open reading frame and restored the dystrophin expression in a mouse model of Duchenne muscular dystrophy. In conclusion, we develop an alternative method for regulating RNA splicing, which might be served as a novel tool for genetic disease treatment.

  • Research Article
  • Weiju Han , Qi Chu , Junliang Li , Zixuan Dong , Xuetao Shi , Xiaoling Fu
    doi: 10.34133/research.0049

    Myofibroblasts, the primary effector cells for implant-induced fibrosis, contribute to this process by secreting excessive collagen-rich matrix and contracting. Thus, approaches that suppress myofibroblasts may achieve desirable suppression effects in the fibrotic process. As one of the important physical properties of materials, material topographical structures have been proven to affect various aspects of cell behaviors, so is it possible to manipulate the formation of myofibroblasts by tailoring the topographical properties of medical devices? In this study, polycaprolactone (PCL) surfaces with typical micropatterns (micro column and micro pit) were fabricated. The regulatory effects of surface micropatterns on the myofibroblastic differentiation of fibroblasts were investigated. Compared to the flat surfaces and surfaces with micro pit, surfaces with micro columns triggered the F- to G-actin transition, inhibiting the nuclear transfer of myocardin-related transcription factor-A. Subsequently, the downstream gene α-smooth muscle actin, which is a marker of myofibroblasts, was suppressed. Further in vivo investigation showed that PCL implants with micro-column-patterned surfaces inhibited the formation of peri-implant fibrotic capsules. Our results demonstrate that surface topographical properties are a potent regulator of fibroblast differentiation into myofibroblasts and highlight the antifibrotic potential of modifying surfaces with micro-column patterns.

  • Research Article
  • Jiwen Geng , Zhefeng Kang , Qian Sun , Man Zhang , Peng Wang , Yupei Li , Jiameng Li , Baihai Su , Qiang Wei
    doi: 10.34133/research.0054

    Cellular behaviors and functions can be regulated by mechanical cues from microenvironments, which are transmitted to nucleus through the physical connections of cytoskeletons in the cells. How these physical connections determine transcriptional activity were not clearly known. The actomyosin, which generates intracellular traction force, has been recognized to control the nuclear morphology. Here, we have revealed that microtubule, the stiffest cytoskeleton, is also involved in the process of nuclear morphology alteration. The microtubule negatively regulates the actomyosin-induced nuclear invaginations but not the nuclear wrinkles. Moreover, these nuclear shape changes are proven to mediate the chromatin remodeling, which essentially mediates cell gene expression and phenotype determination. The actomyosin disruption leads to the loss of chromatin accessibility, which can be partly recovered by microtubule interference through nuclear shape control. This finding answers the question of how mechanical cues regulate chromatin accessibility and cell behaviors. It also provides new insights into cell mechanotransduction and nuclear mechanics.

  • Research Article
  • Jieyuan Li , Ruimin Chen , Kaiwen Wang , Yan Yang , Jielin Wang , Weiping Yang , Shengyao Wang , Guidong Yang , Fan Dong
    doi: 10.34133/research.0055

    As 2 indispensable counterparts in one catalysis system, the independent reduction and oxidation reactions require synergetic regulation for cooperatively promoting redox efficiency. Despite the current success in promoting the catalytic efficiency of half reduction or oxidation reactions, the lack of redox integration leads to low energy efficiency and unsatisfied catalytic performance. Here, we exploit an emerging photoredox catalysis system by combining the reactions of nitrate reduction for ammonia synthesis and formaldehyde oxidation for formic acid production, in which superior photoredox efficiency is achieved on the spatially separated dual active sites of Ba single atoms and Ti3+. High catalytic redox rates are accomplished for respective ammonia synthesis (31.99 ± 0.79 mmol gcat−1 h−1) and formic acid production (54.11 ± 1.12 mmol gcat−1 h−1), reaching a photoredox apparent quantum efficiency of 10.3%. Then, the critical roles of the spatially separated dual active sites are revealed, where Ba single atoms as the oxidation site using h+ and Ti3+ as the reduction site using e− are identified, respectively. The efficient photoredox conversion of contaminants is accomplished with environmental importance and competitive economic value. This study also represents a new opportunity to upgrade the conventional half photocatalysis into the complete paradigm for sustainable solar energy utilization.