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2023 Volume 6 Issue 10  Published: 2023-10-20
    Research Article
  • Chao Zhang , Zedong Li , Jie Liu , Chang Liu , Haoqing Zhang , Won Gu Lee , Chunyan Yao , Hui Guo , Feng Xu
    doi: 10.34133/research.0217

    Circulating tumor DNA (ctDNA) detection has found widespread applications in tumor diagnostics and treatment, where the key is to obtain accurate quantification of ctDNA. However, this remains challenging due to the issue of background noise associated with existing assays. In this work, we developed a synthetic gene circuit-based assay with multilevel switch (termed CATCH) for background-free and absolute quantification of ctDNA. The multilevel switch combining a small transcription activating RNA and a toehold switch was designed to simultaneously regulate transcription and translation processes in gene circuit to eliminate background noise. Moreover, such a multilevel switch-based gene circuit was integrated with a Cas9 nickase H840A (Cas9n) recognizer and a molecular beacon reporter to form CATCH for ctDNA detection. The CATCH can be implemented in one-pot reaction at 35 °C with virtually no background noise, and achieve robust absolute quantification of ctDNA when integrated with a digital chip (i.e., digital CATCH). Finally, we validated the clinical capability of CATCH by detecting drug-resistant ctDNA mutations from the plasma of 76 non–small cell lung cancer (NSCLC) patients, showing satisfying clinical sensitivity and specificity. We envision that the simple and robust CATCH would be a powerful tool for next-generation ctDNA detection.

  • Review Article
  • Chenyu Zhang , Peixiang Ma , An Qin , Liao Wang , Kerong Dai , Yuanyuan Liu , Jie Zhao , Zuyan Lu
    doi: 10.34133/research.0220

    Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease accompanied by persistent multiarticular synovitis and cartilage degradation. The present clinical treatments are limited to disease-modifying anti-rheumatic drugs (DMARDs) and aims to relieve pain and control the inflammation of RA. Despite considerable advances in the research of RA, the employment of current clinical procedure is enormous, hindered by systemic side effect, frequent administration, tolerance from long-lasting administration, and high costs. Emerging immunoengineering-based strategies, such as multiple immune-active nanotechnologies via mechanism-based immunology approaches, have been developed to improve specific targeting and to reduce adverse reactions for RA treatments. Here, we review recent studies in immunoengineering for the treatment of RA. The prospect of future immunoengineering treatment for RA has also been discussed.

  • Research Article
  • Xiaorui Wang , Chang-Yu Hsieh , Xiaodan Yin , Jike Wang , Yuquan Li , Yafeng Deng , Dejun Jiang , Zhenxing Wu , Hongyan Du , Hongming Chen , Yun Li , Huanxiang Liu , Yuwei Wang , Pei Luo , Tingjun Hou , Xiaojun Yao
    doi: 10.34133/research.0231

    Effective synthesis planning powered by deep learning (DL) can significantly accelerate the discovery of new drugs and materials. However, most DL-assisted synthesis planning methods offer either none or very limited capability to recommend suitable reaction conditions (RCs) for their reaction predictions. Currently, the prediction of RCs with a DL framework is hindered by several factors, including: (a) lack of a standardized dataset for benchmarking, (b) lack of a general prediction model with powerful representation, and (c) lack of interpretability. To address these issues, we first created 2 standardized RC datasets covering a broad range of reaction classes and then proposed a powerful and interpretable Transformer-based RC predictor named Parrot. Through careful design of the model architecture, pretraining method, and training strategy, Parrot improved the overall top-3 prediction accuracy on catalysis, solvents, and other reagents by as much as 13.44%, compared to the best previous model on a newly curated dataset. Additionally, the mean absolute error of the predicted temperatures was reduced by about 4 °C. Furthermore, Parrot manifests strong generalization capacity with superior cross-chemical-space prediction accuracy. Attention analysis indicates that Parrot effectively captures crucial chemical information and exhibits a high level of interpretability in the prediction of RCs. The proposed model Parrot exemplifies how modern neural network architecture when appropriately pretrained can be versatile in making reliable, generalizable, and interpretable recommendation for RCs even when the underlying training dataset may still be limited in diversity.

  • Research Article
  • June Li , Danielle Karakas , Feng Xue , Yingyu Chen , Guangheng Zhu , Yeni H. Yucel , Sonya A. MacParland , Haibo Zhang , John W. Semple , John Freedman , Qizhen Shi , Heyu Ni
    doi: 10.34133/research.0236

    Platelets are small, versatile blood cells that are critical for hemostasis/thrombosis. Local platelet accumulation is a known contributor to proinflammation in various disease states. However, the anti-inflammatory/immunosuppressive potential of platelets has been poorly explored. Here, we uncovered, unexpectedly, desialylated platelets (dPLTs) down-regulated immune responses against both platelet-associated and -independent antigen challenges. Utilizing multispectral photoacoustic tomography, we tracked dPLT trafficking to gut vasculature and an exclusive Kupffer cell-mediated dPLT clearance in the liver, a process that we identified to be synergistically dependent on platelet glycoprotein Ibα and hepatic Ashwell–Morell receptor. Mechanistically, Kupffer cell clearance of dPLT potentiated a systemic immunosuppressive state with increased anti-inflammatory cytokines and circulating CD4+ regulatory T cells, abolishable by Kupffer cell depletion. Last, in a clinically relevant model of hemophilia A, presensitization with dPLT attenuated anti-factor VIII antibody production after factor VIII ( infusion. As platelet desialylation commonly occurs in daily-aged and activated platelets, these findings open new avenues toward understanding immune homeostasis and potentiate the therapeutic potential of dPLT and engineered dPLT transfusions in controlling autoimmune and alloimmune diseases.

  • Research Article
  • Xin-Wei Yi , Zheng-Wei Liao , Jing-Yang You , Bo Gu , Gang Su
    doi: 10.34133/research.0238

    The recently discovered ATi3Bi5 (A=Cs, Rb) exhibit intriguing quantum phenomena including superconductivity, electronic nematicity, and abundant topological states. ATi3Bi5 present promising platforms for studying kagome superconductivity, band topology, and charge orders in parallel with AV3Sb5. In this work, we comprehensively analyze various properties of ATi3Bi5 covering superconductivity under pressure and doping, band topology under pressure, thermal conductivity, heat capacity, electrical resistance, and spin Hall conductivity (SHC) using first-principles calculations. Calculated superconducting transition temperature (Tc) of CsTi3Bi5 and RbTi3Bi5 at ambient pressure are about 1.85 and 1.92 K. When subject to pressure, Tc of CsTi3Bi5 exhibits a special valley and dome shape, which arises from quasi-two-dimensional compression to three-dimensional isotropic compression within the context of an overall decreasing trend. Furthermore, Tc of RbTi3Bi5 can be effectively enhanced up to 3.09 K by tuning the kagome van Hove singularities (VHSs) and flat band through doping. Pressures can also induce abundant topological surface states at the Fermi energy (EF) and tune VHSs across EF. Additionally, our transport calculations are in excellent agreement with recent experiments, confirming the absence of charge density wave. Notably, SHC of CsTi3Bi5 can reach up to 226ℏ ·(e· Ω ·cm)–1 at EF. Our work provides a timely and detailed analysis of the rich physical properties for ATi3Bi5, offering valuable insights for further experimental verifications and investigations in this field.

  • Review Article
  • Juncen Zhou , Carmine Wang See , Sai Sreenivasamurthy , Donghui Zhu
    doi: 10.34133/research.0239

    In the advancing landscape of technology and novel material development, additive manufacturing (AM) is steadily making strides within the biomedical sector. Moving away from traditional, one-size-fits-all implant solutions, the advent of AM technology allows for patient-specific scaffolds that could improve integration and enhance wound healing. These scaffolds, meticulously designed with a myriad of geometries, mechanical properties, and biological responses, are made possible through the vast selection of materials and fabrication methods at our disposal. Recognizing the importance of precision in the treatment of bone defects, which display variability from macroscopic to microscopic scales in each case, a tailored treatment strategy is required. A patient-specific AM bone scaffold perfectly addresses this necessity. This review elucidates the pivotal role that customized AM bone scaffolds play in bone defect treatment, while offering comprehensive guidelines for their customization. This includes aspects such as bone defect imaging, material selection, topography design, and fabrication methodology. Additionally, we propose a cooperative model involving the patient, clinician, and engineer, thereby underscoring the interdisciplinary approach necessary for the effective design and clinical application of these customized AM bone scaffolds. This collaboration promises to usher in a new era of bioactive medical materials, responsive to individualized needs and capable of pushing boundaries in personalized medicine beyond those set by traditional medical materials.

  • Research Article
  • Zexuan Li , Zhenhua Wang , Chen Wang , Wenxi Li , Wenru Fan , Ruoqing Zhao , Haoyang Feng , Dengfeng Peng , Wei Huang
    doi: 10.34133/research.0243

    Organic mechanophores have been widely adopted for polymer mechanotransduction. However, most examples of polymer mechanotransduction inevitably experience macromolecular chain rupture, and few of them mimic mussel’s mechanochemical regeneration, a mechanically mediated process from functional units to functional materials in a controlled manner. In this paper, inorganic mechanoluminescent (ML) materials composed of CaZnOS-ZnS-SrZnOS: Mn2+ were used as a mechanotransducer since it features both piezoelectricity and mechanolunimescence. The utilization of ML materials in polymerization enables both mechanochemically controlled radical polymerization and the synthesis of ML polymer composites. This procedure features a mechanochemically controlled manner for the design and synthesis of diverse mechanoresponsive polymer composites.

  • Research Article
  • Qin Ren , Ye He , Hong Wang , Yanjuan Sun , Fan Dong
    doi: 10.34133/research.0244

    Photocatalytic reduction of CO2 into fuels provides a prospective tactic for regulating the global carbon balance utilizing renewable solar energy. However, CO2 molecules are difficult to activate and reduce due to the thermodynamic stability and chemical inertness. In this work, we develop a novel strategy to promote the adsorption and activation of CO2 molecules via the rapid energy exchange between the photoinduced Br vacancies and CO2 molecules. Combining in situ continuous wave-electron paramagnetic resonance (cw-EPR) and pulsed EPR technologies, we observe that the spin–spin relaxation time (T2) of BiOBr is decreased by 198 ns during the CO2 photoreduction reaction, which is further confirmed by the broadened EPR linewidth. This result reveals that there is an energy exchange interaction between in situ formed Br vacancies and CO2 molecules, which promotes the formation of high-energy CO2 molecules to facilitate the subsequent reduction reaction. In addition, theoretical calculations indicate that the bended CO2 adsorption configuration on the surface of BiOBr with Br vacancies caused the decrease of the lowest unoccupied molecular orbital of the CO2 molecule, which makes it easier for CO2 molecules to acquire electrons and get activated. In situ diffuse reflectance infrared Fourier transform spectroscopy further shows that the activated CO2 molecules are favorably converted to key intermediates of COOH*, resulting in a CO generation rate of 9.1 μmol g−1 h−1 and a selectivity of 100%. This study elucidates the underlying mechanism of CO2 activation at active sites and deepens the understanding of CO2 photoreduction reaction.

  • Research Article
  • Tianqi Xu , Dan Fang , Fulei Li , Zhiqiang Wang , Yuan Liu
    doi: 10.34133/research.0245

    The emergence of antibiotic tolerance, characterized by the prolonged survival of bacteria following antibiotic exposure, in natural bacterial populations, especially in pathogens carrying antibiotic resistance genes, has been an increasing threat to public health. However, the major causes contributing to the formation of antibiotic tolerance and underlying molecular mechanisms are yet poorly understood. Herein, we show that potassium sorbate (PS), a widely used food additive, triggers a high level of fluoroquinolone tolerance in bacteria carrying mobile colistin resistance gene mcr. Mechanistic studies demonstrate that PS treatment results in the accumulation of intracellular fumarate, which activates bacterial two-component system and decreases the expression level of outer membrane protein OmpF, thereby reducing the uptake of ciprofloxacin. In addition, the supplementation of PS inhibits aerobic respiration, reduces reactive oxygen species production and alleviates DNA damage caused by bactericidal antibiotics. Furthermore, we demonstrate that succinate, an intermediate product of the tricarboxylic acid cycle, overcomes PS-mediated ciprofloxacin tolerance. In multiple animal models, ciprofloxacin treatment displays failure outcomes in PS preadministrated animals, including comparable survival and bacterial loads with the vehicle group. Taken together, our works offer novel mechanistic insights into the development of antibiotic tolerance and uncover potential risks associated with PS use.

  • Research Article
  • Abdulmottaleb E. Zetrini , HoYin Lip , Azhar Z. Abbasi , Ibrahim Alradwan , Taksim Ahmed , Chunsheng He , Jeffrey T. Henderson , Andrew M. Rauth , Xiao Yu Wu
    doi: 10.34133/research.0247

    Despite substantial progress in the treatment of castration-resistant prostate cancer (CRPC), including radiation therapy and immunotherapy alone or in combination, the response to treatment remains poor due to the hypoxic and immunosuppressive nature of the tumor microenvironment. Herein, we exploited the bioreactivity of novel polymer–lipid manganese dioxide nanoparticles (PLMDs) to remodel the tumor immune microenvironment (TIME) by increasing the local oxygen levels and extracellular pH and enhancing radiation-induced immunogenic cell death. This study demonstrated that PLMD treatment sensitized hypoxic human and murine CRPC cells to radiation, significantly increasing radiation-induced DNA double-strand breaks and ultimately cell death, which enhanced the secretion of damage-associated molecular patterns, attributable to the induction of autophagy and endoplasmic reticulum stress. Reoxygenation via PLMDs also polarized hypoxic murine RAW264.7 macrophages toward the M1 phenotype, enhancing tumor necrosis factor alpha release, and thus reducing the viability of murine CRPC TRAMP-C2 cells. In a syngeneic TRAMP-C2 tumor model, intravenous injection of PLMDs suppressed, while radiation alone enhanced recruitment of regulatory T cells and myeloid-derived suppressor cells. Pretreatment with PLMDs followed by radiation down-regulated programmed death-ligand 1 and promoted the infiltration of antitumor CD8+ T cells and M1 macrophages to tumor sites. Taken together, TIME modulation by PLMDs plus radiation profoundly delayed tumor growth and prolonged median survival compared with radiation alone. These results suggest that PLMDs plus radiation is a promising treatment modality for improving therapeutic efficacy in radioresistant and immunosuppressive solid tumors.

  • Research Article
  • Zhengjie Yang , Hongmiao Tian , Chunhui Wang , Xiangming Li , Xiaoliang Chen , Xiaoming Chen , Jinyou Shao
    doi: 10.34133/research.0248

    Improving droplet velocity as much as possible is considered as the key to improving both printing speed and printing distance of the piezoelectric drop-on-demand inkjet printing technology. There are 3 tough and contradictory issues that need to be addressed simultaneously, namely, the actuation pressure of the piezoelectric printhead, satellite droplets, and the air resistance, which seems almost impossible to achieve with classical methods. Herein, a novel solution is introduced. By modulating the positive crosstalk effect inside and outside the printhead, self-tuning can be achieved, including self-reinforcing of the actuation pressure, self-restraining of satellite droplets, and self-weakening of the air resistance, thereby greatly improving droplet velocity. Based on these mechanisms, waveform design methods for different inks and printheads are investigated. The results demonstrate that monodisperse droplet jetting with a maximum velocity of 27.53 m/s can be achieved, reaching 3 to 5 times that of the classical method (5 to 8 m/s). Correspondingly, the printing speed and distance can be simultaneously increased by almost 10 times, demonstrating an ability of direct printing on irregular surface. Meanwhile, the compatibility of ink materials is expanded, as the Ohnesorge number and the viscosity of printable inks for the printhead used are increased from 0.36–0.72 to 0.03–1.18 and from 10–12 cp to 1–40.3 cp, respectively, even breaking the traditional limitations of the piezoelectric printing technology (Ohnesorge number of 0.1 to 1; viscosity of 1 to 25 cp). All the above provide a new perspective for improving droplet velocity and may even offer a game-changing choice for expanding the boundaries of the piezoelectric drop-on-demand inkjet printing technology.

  • Research Article
  • Yun Xu , Kai Liu , Cong Li , Minghan Li , Fangqi Liu , Xiaoyan Zhou , Menghong Sun , Megha Ranganathan , Liying Zhang , Sheng Wang , Xin Hu , Ye Xu
    doi: 10.34133/research.0249

    While genetic factors were associated with over 30% of colorectal cancer (CRC) patients, mutations in CRC-susceptibility genes were identified in only 5% to 10% of these patients. Besides, previous studies on hereditary CRC were largely designed to analyze germline mutations in patients with single genetic high-risk factor, which limited understanding of the association between genotype and phenotypes. From January 2015 to December 2018, we retrospectively enrolled 2,181 patients from 8,270 consecutive CRC cases, covering 5 categories of genetic high-risk factors. Leukocyte genomic DNA was analyzed for germline mutations in cancer predisposition genes. The germline mutations under each category were detected and analyzed in association with CRC susceptibility, clinical phenotypes, and prognoses. A total of 462 pathogenic variants were detected in 19.3% of enrolled CRC patients. Mismatch repair gene mutation was identified in 9.1% of patients, most prevalent across all high-risk groups. Homologous recombination (HR) gene mutations were detected in 6.5% of cases, penetrated in early-onset and extra-colonic cancer risk groups. Mutations in HR genes, including BARD1, RAD50, and ATM, were found to increase CRC risk with odds ratios of 2.8-, 3.1-, and 3.1-fold, respectively. CRC patients with distinct germline mutations manifested heterogeneous phenotypes in clinicopathology and long-term prognoses. Thus, germline mutation screenings should be performed for CRC patients with any of those genetic risk factors. This study also reveals that HR gene mutations may be another major driver for increased CRC risk.

  • Research Article
  • Shixu Yu , Yifang Zhou , Meixue Gan , Lu Chen , Yimin Xie , Yuning Zhong , Qinghua Feng , Chaoji Chen
    doi: 10.34133/research.0250

    Near-infrared (NIR) transparent optical filters show great promise in night vision and receiving windows. However, NIR optical filters are generally prepared by laborious, environmentally unfriendly processes that involve metal oxides or petroleum-based polymers. We propose a lignin capturing–fusing approach to manufacturing optical biofilters based on molecular collaboration between lignin and cellulose from waste agricultural biomass. In this process, lignin is captured via self-assembly in a cellulose network; then, the lignin is fused to fill gaps and hold the cellulose fibers tightly. The resulting optical biofilter featured a dense structure and smooth surface with NIR transmittance of ~90%, ultralow haze of close to 0%, strong ultraviolet-visible light blocking (~100% at 400 nm and 57.58% to 98.59% at 550 nm). Further, the optical biofilter has comprehensive stability, including water stability, solvent stability, thermal stability, and environmental stability. Because of its unique properties, the optical biofilter demonstrates potential applications in the NIR region, such as an NIR-transmitting window, NIR night vision, and privacy protection. These applications represent a promising route to produce NIR transparent optical filters starting from lignocellulose biomass waste.

  • Research Article
  • Hong Wang , Ji Liu , Xiaojun Zhu , Bin Yang , Zuping He , Xudong Yao
    doi: 10.34133/research.0252

    Prostate cancer (PCa) is a common malignant tumor with high morbidity and mortality worldwide. The prostate cancer stem cell (PCSC) model provides novel insights into the pathogenesis of PCa and its therapeutic response. However, the roles and molecular mechanisms of specific genes in mediating fate decisions of PCSCs and carcinogenesis of PCa remain to be elusive. In this study, we have explored the expression, function, and mechanism of AZGP1P2, a pseudogene of AZGP1, in regulating the stemness and apoptosis of PCSCs and treatment resistance of docetaxel in castration-resistant prostate cancer (CRPC). We revealed that AZGP1P2 was downregulated in CRPC cell lines and PCSCs, while it was positively associated with progression-free interval. Upregulation of the AZGP1P2 enhanced the sensitivity of docetaxel treatment in CRPCs via inhibiting their stemness. RNA pull-down associated with mass spectrometry analysis, co-immunoprecipitation assay, and RNA immunoprecipitation assay demonstrated that AZGP1P2 could bind to UBA1 and RBM15 as a “writer” of methyltransferase to form a compound. UBA1, an E1 ubiquitin-activating enzyme, contributed to RBM15 protein degradation via ubiquitination modification. Methylated RNA immunoprecipitation assay displayed that RBM15 controlled the mRNA decay of TPM1 in m6A methylation. Furthermore, a xenograft mouse model and patient-derived organoids showed that the therapeutic effect of docetaxel in CRPC was increased by AZGP1P2 in vivo. Collectively, these results imply that AZGP1P2 mediates the stemness and apoptosis of PCSCs and promotes docetaxel therapeutic effect by suppressing tumor growth and metastasis via UBA1/RBM15-mediated TPM1 mRNA decay in CRPC.

  • Research Article
  • Renjie Wu , Bangyan Zhou , Wei Wang , Feng Liu
    doi: 10.34133/research.0253

    Gene transcription often occurs in discrete bursts, and it can be difficult to deduce the underlying regulatory mechanisms for transcriptional bursting with limited experimental data. Here, we categorize numerous states of single eukaryotic genes and identify 6 essential transcriptional events, each comprising a series of state transitions; transcriptional bursting is characterized as a sequence of 4 events, capable of being organized in various configurations, in addition to the beginning and ending events. By associating transcriptional kinetics with mean durations and recurrence probabilities of the events, we unravel how transcriptional bursting is modulated by various regulators including transcription factors. Through analytical derivation and numerical simulation, this study reveals key state transitions contributing to transcriptional sensitivity and specificity, typical characteristics of burst profiles, global constraints on intrinsic transcriptional noise, major regulatory modes in individual genes and across the genome, and requirements for fast gene induction upon stimulation. It is illustrated how biochemical reactions on different time scales are modulated to separately shape the durations and ordering of the events. Our results suggest that transcriptional patterns are essentially controlled by a shared set of transcriptional events occurring under specific promoter architectures and regulatory modes, the number of which is actually limited.

  • Research Article
  • Yihang Zhang , Fupo He , Qiang Zhang , Haotian Lu , Shengtao Yan , Xuetao Shi
    doi: 10.34133/research.0255

    The limitations of autologous bone grafts necessitate the development of advanced biomimetic biomaterials for efficient cranial defect restoration. The cranial bones are typical flat bones with sandwich structures, consisting of a diploe in the middle region and 2 outer compact tables. In this study, we originally developed 2 types of flat-bone-mimetic β-tricalcium phosphate bioceramic scaffolds (Gyr-Comp and Gyr-Tub) by high-precision vat-photopolymerization-based 3-dimensional printing. Both scaffolds had 2 outer layers and an inner layer with gyroid pores mimicking the diploe structure. The outer layers of Gyr-Comp scaffolds simulated the low porosity of outer tables, while those of Gyr-Tub scaffolds mimicked the tubular pore structure in the tables of flat bones. The Gyr-Comp and Gyr-Tub scaffolds possessed higher compressive strength and noticeably promoted in vitro cell proliferation, osteogenic differentiation, and angiogenic activities compared with conventional scaffolds with cross-hatch structures. After implantation into rabbit cranial defects for 12 weeks, Gyr-Tub achieved the best repairing effects by accelerating the generation of bone tissues and blood vessels. This work provides an advanced strategy to prepare biomimetic biomaterials that fit the structural and functional needs of efficacious bone regeneration.

  • Research Article
  • Kang Xia , Tianyu Wang , Zhongbao Chen , Jiayu Guo , Bo Yu , Qi Chen , Tao Qiu , Jiangqiao Zhou , Shusen Zheng
    doi: 10.34133/research.0256

    Background: Hepatic ischemia-reperfusion injury (HIRI) stands as an unavoidable complication arising from liver surgery, profoundly intertwined with its prognosis. The role of lysine methyltransferase SET domain bifurcated 1 (SETDB1) in HIRI remains elusive, despite its confirmation as a potential therapeutic target for diverse diseases. Here, we investigated the mechanism by which SETDB1 regulated HIRI. Methods: RNA sequencing data were used to identify the expression and potential targets of SETDB1 through bioinformatics analysis. To elucidate the impact of SETDB1 on HIRI, both an in vivo model of HIRI in mice and an in vitro model of hepatocyte hypoxia/reoxygenation were established. Biochemical and histological analyses were used to investigate the influence of SETDB1 on liver damage mediated by HIRI. Chromatin immunoprecipitation and coimmunoprecipitation were implemented to explore the in-depth mechanism of SETDB1 regulating HIRI. Results: We confirmed that hepatocellular SETDB1 was up-regulated during HIRI and had a close correlation with HIRI-related inflammation and apoptosis. Moreover, inhibition of SETDB1 could mitigate HIRI-induced liver damage, inflammation, and apoptosis. Through our comprehensive mechanistic investigation, we revealed that SETDB1 interacts with apoptosis-signal-regulating kinase 1 (ASK1) and facilitates the methylation of its lysine residues. Inhibition of SETDB1 resulted in reduced phosphorylation of ASK1, leading to a marked suppression of downstream c-Jun N-terminal kinase (JNK)/p38 signaling pathway activation. The therapeutic effect on inflammation and apoptosis achieved through SETDB1 inhibition was nullified by the restoration of JNK/p38 signaling activation through ASK1 overexpression. Conclusions: The findings from our study indicate that SETDB1 mediates lysine methylation of ASK1 and modulates the activation of the ASK1–JNK/p38 pathway, thus involved in HIRI-induced inflammation and apoptosis. These results suggest that SETDB1 holds promise as a potential therapeutic target for mitigating HIRI.

  • Research Article
  • Cheng Ma , Xiaodan Gou , Zejing Xing , Min-Xuan Wang , Wenlei Zhu , Qin Xu , Dechen Jiang , Jun-Jie Zhu
    doi: 10.34133/research.0257

    Electrochemiluminescence (ECL) has established itself as an excellent transduction technique in biosensing and light-emitting device, while conventional ECL mechanism depending on spontaneous emission of luminophores lacks reversibility and tunable emission characters, limiting the universality of ECL technique in the fields of fundamental research and clinical applications. Here, we report the first observation of stimulated emission route in ECL and thus establish a reversible tuning ECL microscopy for single-cell imaging. This microscopy uses a focused red-shifted beam to transfer spontaneous ECL into stimulated ECL, which enables selective and reversible tuning of ECL emission from homogeneous solution, single particles, and single cells. After excluding other possible competitive routes, the stimulated ECL emission route is confirmed by a dual-objective system in which the suppressed spontaneous ECL is accompanied by the enhanced stimulated ECL. By incorporating a commercial donut-shaped beam, the sharpness of single-cell matrix adhesion is improved 2 to 3 times compared with the counterpart in confocal ECL mode. The successful establishment of this stimulated emission ECL will greatly advance the development of light-emitting device and super-resolution ECL microscopy.

  • Research Article
  • Yumeng Zhang , Jiahao Guan , Chen Li , Zhikang Wang , Zixin Deng , Robin B. Gasser , Jiangning Song , Hong-Yu Ou
    doi: 10.34133/research.0258

    Proteins secreted by Gram-negative bacteria are tightly linked to the virulence and adaptability of these microbes to environmental changes. Accurate identification of such secreted proteins can facilitate the investigations of infections and diseases caused by these bacterial pathogens. However, current bioinformatic methods for predicting bacterial secreted substrate proteins have limited computational efficiency and application scope on a genome-wide scale. Here, we propose a novel deep-learning-based framework—DeepSecE—for the simultaneous inference of multiple distinct groups of secreted proteins produced by Gram-negative bacteria. DeepSecE remarkably improves their classification from nonsecreted proteins using a pretrained protein language model and transformer, achieving a macro-average accuracy of 0.883 on 5-fold cross-validation. Performance benchmarking suggests that DeepSecE achieves competitive performance with the state-of-the-art binary predictors specialized for individual types of secreted substrates. The attention mechanism corroborates salient patterns and motifs at the N or C termini of the protein sequences. Using this pipeline, we further investigate the genome-wide prediction of novel secreted proteins and their taxonomic distribution across ~1,000 Gram-negative bacterial genomes. The present analysis demonstrates that DeepSecE has major potential for the discovery of disease-associated secreted proteins in a diverse range of Gram-negative bacteria. An online web server of DeepSecE is also publicly available to predict and explore various secreted substrate proteins via the input of bacterial genome sequences.

  • Research Article
  • Yuhang Lin , Shuya Liu , Dongpeng Yan
    doi: 10.34133/research.0259

    Molecular luminescent materials with optical waveguide have wide application prospects in light-emitting diodes, sensors, and logic gates. However, the majority of traditional optical waveguide systems are based on brittle molecular crystals, which limited the fabrication, transportation, storage, and adaptation of flexible devices under diverse application situations. To date, the design and synthesis of photofunctional materials with high flexibility, novel optical waveguide, and multi-port color-tunable emission in the same solid-state system remain an open challenge. Here, we have constructed new types of zero-dimensional organic metal halides (Au-4-dimethylaminopyridine [DMAP] and In-DMAP) with a rarely high elasticity and rather low loss coefficients for optical waveguide. Theoretical calculations on the intermolecular interactions showed that the high elasticity of 2 molecular crystalline materials was original from their herringbone structure and slip plane. Based on one-dimensional flexible microrods of 2 crystals and the 2-dimensional microplate of the Mn-DMAP, heterojunctions with multi-color and space-resolved optical waveguides have been fabricated. The formation mechanism of heterojunctions is based on the surface selective growth on account of the low lattice mismatch ratio between contacting crystal planes. Therefore, this work describes the first attempt to the design of metal-halide-based crystal heterojunctions with high flexibility and optical waveguide, expanding the prospects of traditional luminescent materials for smart optical devices, such as logic gates and multiplexers.

  • Research Article
  • Xuan Mao , Guo-Qing Qin , Hao Zhang , Bo-Yang Wang , Dan Long , Gui-Qin Li , Gui-Lu Long
    doi: 10.34133/research.0260

    Non-Hermitian systems associated with exceptional points (EPs) are expected to demonstrate a giant response enhancement for various sensors. The widely investigated enhancement mechanism based on diverging from an EP should destroy the EP and further limits its applications for multiple sensing scenarios in a time sequence. To break the above limit, here, we proposed a new enhanced sensing mechanism based on shifting an EP. Different from the mechanism of diverging from an EP, our scheme is an EP nondemolition and the giant enhancement of response is acquired by a slight shift of the EP along the parameter axis induced by perturbation. The new sensing mechanism can promise the most effective response enhancement for all sensors in the case of multiple sensing in a time sequence. To verify our sensing mechanism, we construct a mass sensor and a gyroscope with concrete physical implementations. Our work will deepen the understanding of EP-based sensing and inspire designing various high-sensitivity sensors in different physical systems.

  • Research Article
  • Shi-Chao Qi , Zhen Sun , Zhi-Hui Yang , Yun-Jie Zhao , Jia-Xin Li , Xiao-Qin Liu , Lin-Bing Sun
    doi: 10.34133/research.0261

    Great efforts have been devoted to the study of photo-responsive adsorption, but its current methodology largely depends on the well-defined photochromic units and their photo-driven molecular deformation. Here, a methodology to fabricate nondeforming photo-responsive sorbents is successfully exploited. With C60-fullerene doping in metalloporphyrin metal-organic frameworks (PCN-M, M = Fe, Co, or Ni) and intensively interacting with the metalloporphyrin sites, effective charge-transfer can be achieved over the metalloporphyrin-C60 architectures once excited by the light at 350 to 780 nm. The electron density distribution and the resultant adsorption activity are thus changed by excited states, which are also stable enough to meet the timescale of microscopic adsorption equilibrium. The charge-transfer over Co(II)-porphyrin-C60 is proved to be more efficient than the Fe(II)- and Ni(II)-porphyrin-C60 sites, as well as than all the metalloporphyrin sites, so the CO2 adsorption capacity (CAC; at 0 °C and 1 bar) over the C60-doped PCN-Co can be largely improved from 2.05 mmol g−1 in the darkness to 2.69 mmol g−1 with light, increased by 31%, in contrast to photo-irresponsive CAC over all C60-undoped PCN-M sorbents and only the photo-loss CAC over C60.

  • Research Article
  • Jiesi Wang , Wei Zhang , Hang Xu , Bart Ellenbroek , Jiajie Dai , Li Wang , Chaogan Yan , Weiwen Wang
    doi: 10.34133/research.0264

    Early-life stress can lead to sustained alterations in regional resting-state brain functions, but the underlying molecular mechanism remains unclear. Stress can also induce sustained changes in epigenetic modifications across brain regions, which are not limited to a few genes; rather, they often tend to produce global levels of change. The functional implication of these changes also remains to be elucidated. We hypothesize that global epigenetic changes may partly modulate the resting-state functions of brain regions to influence behavior. To test this hypothesis, we used an adolescent social stress (ASS) model in mice and examined the relationship between epigenetic modifications and regional resting-state brain activity using resting-state functional magnetic resonance imaging (rs-fMRI). The results showed that, compared to the control mice, the stressed mice showed increased anxiety and social avoidance behaviors and greater levels of dimethylation of histone H3 at lysine 9 (H3K9me2) in the medial prefrontal cortex (mPFC). In addition, the resting-state activity represented by the amplitude of low-frequency fluctuation (ALFF) was significantly lower in the mPFC of stressed mice. To verify the relationship of H3K9me2 and ALFF, the specific inhibition of H3Kme2 was performed by using the drug UNC0642, which reversed the anxiety behavior induced by ASS and significantly increase the ALFF value of mPFC in both normal and ASS animals. Our study is the first to report an association between histone modifications and rs-fMRI findings, providing a new perspective for understanding of the significance of regional brain epigenetic changes and a possible molecular explanation for rs-fMRI findings.