Assembly of Dye Molecules in Covalent Organic Frameworks for Enhanced Colorimetric Biosensing.

Colorimetric assays have been extensively investigated for biosensing applications due to their advantages of visual recognizability, ease of use, and low cost. However, advancing their development is a great challenge due to the inherent limitations of colorimetric dyes. Herein, we report a strategy to assemble dyes in covalent organic frameworks (COFs) to effectively reinforce the applicability of pH-responsive dyes in colorimetric bioassays. Experimental results reveal that three-dimensional COFs can promote the assembly of dyes through hydrogen bonding, resulting in the formation of a dye-supermolecule@COF assembly. Consequently, when sensitized at increased pH levels (e.g., hydroxyl ions), disruption of hydrogen bonds may trigger a rapid transition from their insoluble fixed state within the COFs into soluble, visibly detectable dye anions. This process can also be facilitated by increased hydrophilicity and elevated electrostatic repulsion between the dye anions and COFs, leading to the substantial release of chromogenic dye anions from the COF pores into the solution, thereby amplifying the colorimetric signal output. Therefore, by employing various synthesized dye-supermolecule@COFs as signal tags, we developed a colorimetric bioassay capable of accurately identifying breast cancer cell subtypes. This study not only highlights the effectiveness of dye-supermolecule@COFs in enhancing colorimetric biosensing but also underscores the potential of employing the COF-mediated dye assembly strategy for colorimetric assays.

Synthesis of a COF-on-MOF hybrid nanomaterial for enhanced colorimetric biosensing.

The construction of hybrid materials is significant for the exploration of functionalities in colorimetric biosensing due to its structural designability and synergy effects. In this work, a COF-on-MOF hybrid nanomaterial has been newly synthesized for colorimetric biosensing. Experimental results reveal that on-surface synthesis of COF on MOF brings nanoscale proximity between COF and MOF, which exhibits more than two folds of peroxidase-like activity as compared to single Fe-MOF. Therefore, by using the MCA@Fe-MOF nanomaterial with the assist of a specific acetyl-peptide, MCA@Fe-MOF can serve as an efficient signal reporter for colorimetric assay of histone deacetylase (HDAC), and the limit of detection (LOD) can be as low as 0.261 nM. Looking forward, the demand for diverse and promising COF-on-MOF nanomaterials with varied functionalities is anticipated, propelling further exploration of their role in colorimetric biosensing.

An electrochemical biosensor designed with entropy-driven autocatalytic DNA circuits for sensitive detection of ovarian cancer-derived exosomes.

Intelligent artificial DNA circuits have emerged as a promising approach for modulating signaling pathways and signal transduction through rational design, which may contribute to comprehensively realizing biomolecular sensing of organisms. In this work, we have fabricated an electrochemical biosensor for the sensitive and accurate detection of ovarian cancer-derived exosomes by constructing an entropy-driven autocatalytic DNA circuit (EADC). Specifically, the robust EADC is prepared by the self-assembly of well-designed DNA probes, and upon stimulation of the presence of ovarian cancer cells-derived exosomes, numerous inputs can be produced to feedback and accelerate the reaction. The catalytic abilities of the generated input sequences play a pivotal role in EADC and dramatically enhance the signal amplification capability. Through the combination of the autocatalytic circuit and circular cleavage reactions, significantly changed electrochemical signals can be recorded for sensitive analysis of the exosomes with a remarkably low detection limit of 30 particles/µL. Moreover, the proposed enzyme-free biosensor shows exceptional performance in distinguishing patient samples from healthy samples, which exhibits promising prospects for the clinical diagnosis of ovarian cancer.

Enhanced performance of enzymes confined in biocatalytic hydrogen-bonded organic frameworks for sensing of glutamate in the central nervous system.

Glutamate (Glu) is a key excitatory neurotransmitter associated with various neurological disorders in the central nervous system, so its measurement is vital to both basic research and biomedical application. In this work, we propose the first example of using biocatalytic hydrogen-bonded organic frameworks (HOFs) as the hosting matrix to encapsulate glutamate oxidase (GLOD) via a de novo approach, fabricating a cascaded-enzyme nanoreactor for Glu biosensing. In this design, the ferriporphyrin ligands can assemble to form Fe-HOFs with high catalase-like activity, while offering a scaffold for the in-situ immobilization of GLOD. Moreover, the formed GLOD@Fe-HOFs are favorable for the efficient diffusion of Glu into the active sites of GLOD via the porous channels, accelerating the cascade reaction with neighboring Fe-HOFs. Consequently, the constructed nanoreactor can offer superior activity and operational stability in the catalytic cascade for Glu biosensing. More importantly, rapid and selective detection can be achieved in the cerebrospinal fluid (CSF) collected from mice in a low sample consumption. Therefore, the successful fabrication of enzyme@HOFs may offer promise to develop high-performance biosensor for further biomedical applications.

Preparation of Well-Constructed and Metal-Modified Covalent Organic Framework Nanoparticles for Biosensing Design with Cascade Catalytic Capability.

Uniform covalent organic framework nanoparticles (COF NPs) with a well-defined pore structure may provide a robust platform for scaffolding enzymes. Herein, bipyridine-based spherical COF NPs have been successfully prepared in this work through the Schiff base condensation reaction. Moreover, they are functionalized by metal modification and are further used for biosensor fabrication. Experimental results reveal that the metal-modified COF NPs also display impressive peroxidase-like catalytic activities, while they can load enzymes, such as glucose oxidase (GOx) and sarcosine oxidase (SOx), to develop a cascade catalysis system for design of various kinds of biosensors with very well performance. For example, the optimized GOx@Fe-COFs can achieve a sensitive detection of glucose with a low limit of detection (LOD) of 12.8 µM. Meanwhile, the enzymes also exhibit a commendable preservation of 80% enzymatic activity over a span of 14 days under ambient conditions. This work may pave the way for advancing cascade catalysis and the analysis of different kinds of biological molecules based on COF NPs.

Operator growth from global out-of-time-order correlators.

In chaotic many-body systems, scrambling or the operator growth can be diagnosed by out-of-time-order correlators of local operators. We show that operator growth also has a sharp imprint in out-of-time-order correlators of global operators. In particular, the characteristic spacetime shape of growing local operators can be accessed using global measurements without any local control or readout. Building on an earlier conjectured phase diagram for operator growth in chaotic systems with power-law interactions, we show that existing nuclear spin data for out-of-time-order correlators of global operators are well fit by our theory. We also predict super-polynomial operator growth in dipolar systems in 3d and discuss the potential observation of this physics in future experiments with nuclear spins and ultra-cold polar molecules.

Dual DNA recycling amplifications coupled with Au NPs@ZIF-MOF accelerator for enhanced electrochemical ratiometric sensing of pathogenic bacteria.

Sensitive and accurate quantification of pathogenic bacteria is vastly significant to the related food safety. Herein, a sensitive ratiometric electrochemical biosensor was developed for the detection of Staphylococcus aureus (S. aureus) based on dual DNA recycling amplifications and Au NPs@ZIF-MOF accelerator. Gold nanoparticles-loaded Zeolitic imidazolate metal-organic framework (Au NPs@ZIF-MOF) as electrode substrate possessed a large specific surface area for nucleic acid adsorption, and as an accelerator promoted the transfer of electrons. The strong recognition of aptamer to target S. aureus could initiate the padlock probe-based exponential rolling circle amplification (P-ERCA, as the first DNA recycling amplification), generating large numbers of trigger DNA strands. The released trigger DNA further activated the catalytic hairpin assembly (CHA, as the second DNA recycling amplification) on electrode surface. Consequently, P-ERCA and CHA continuously brought about one target to many signal transduction, leading to an exponential amplification. To achieve the accuracy of detection, the signal ratio of methylene blue (MB) and ferrocene (Fc) (IMB/IFc) was applied for intrinsic self-calibrating. Taking advantages of dual DNA recycling amplifications and Au NPs@ZIF-MOF, the proposed sensing system displayed high sensitivity for S. aureus quantification with a linear range of 5-108 CFU/mL, and the limit of detection was 1 CFU/mL. Moreover, this system represented excellent reproducibility, selectivity, and practicability for S. aureus analysis in foods.

Loss of Ufl1/Ufbp1 in hepatocytes promotes liver pathological damage and carcinogenesis through activating mTOR signaling.

BACKGROUND: Ufm1-specific ligase 1 (Ufl1) and Ufm1-binding protein 1 (Ufbp1), as putative targets of ubiquitin-fold modifier 1 (Ufm1), have been implicated in several pathogenesis-related signaling pathways. However, little is known about their functional roles in liver disease. METHODS: Hepatocyte-specific Ufl1Δ/Δhep and Ufbp1Δ/Δhep mice were used to study their role in liver injury. Fatty liver disease and liver cancer were induced by high-fat diet (HFD) and diethylnitrosamine (DEN) administration, respectively. iTRAQ analysis was employed to screen for downstream targets affected by Ufbp1 deletion. Co-immunoprecipitation was used to determine the interactions between the Ufl1/Ufbp1 complex and the mTOR/GßL complex. RESULTS: Ufl1Δ/Δhep or Ufbp1Δ/Δhep mice exhibited hepatocyte apoptosis and mild steatosis at 2 months of age and hepatocellular ballooning, extensive fibrosis, and steatohepatitis at 6-8 months of age. More than 50% of Ufl1Δ/Δhep and Ufbp1Δ/Δhep mice developed spontaneous hepatocellular carcinoma (HCC) by 14 months of age. Moreover, Ufl1Δ/Δhep and Ufbp1Δ/Δhep mice were more susceptible to HFD-induced fatty liver and DEN-induced HCC. Mechanistically, the Ufl1/Ufbp1 complex directly interacts with the mTOR/GßL complex and attenuates mTORC1 activity. Ablation of Ufl1 or Ufbp1 in hepatocytes dissociates them from the mTOR/GßL complex and activates oncogenic mTOR signaling to drive HCC development. CONCLUSIONS: These findings reveal the potential role of Ufl1 and Ufbp1 as gatekeepers to prevent liver fibrosis and subsequent steatohepatitis and HCC development by inhibiting the mTOR pathway.

UFL1, a UFMylation E3 ligase, plays a crucial role in multiple cellular stress responses.

The UFM1 conjugation system(UFMylation)is a novel type of ubiquitin-like system that plays an indispensable role in maintaining cell homeostasis under various cellular stress. Similar to ubiquitination, UFMylation consists of a three-step enzymatic reaction with E1-like enzymes ubiquitin-like modifier activating enzyme5 (UBA5), E2-like enzymes ubiquitin-fold modifier-conjugating enzyme 1(UFC1), and E3-like ligase UFM1-specific ligase 1 (UFL1). As the only identified E3 ligase, UFL1 is responsible for specific binding and modification of the substrates to mediate numerous hormone signaling pathways and endocrine regulation under different physiological or pathological stress, such as ER stress, genotoxic stress, oncogenic stress, and inflammation. Further elucidation of the UFL1 working mechanism in multiple cellular stress responses is essential for revealing the disease pathogenesis and providing novel potential therapeutic targets. In this short review, we summarize the recent advances in novel UFL1 functions and shed light on the potential challenges ahead, thus hopefully providing a better understanding of UFMylation-mediated cellular stress.

Dual-Gene-Controlled Rolling Circle Amplification Strategy for SARS-CoV-2 Analysis.

The development of sensitive, accurate, and conveniently operated methods for the simultaneous assay of two nucleic acids is promising while still challenging. In this work, by using two genes (the N gene and RdRp gene) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as examples, we have designed an ingenious dual-gene-controlled rolling circle amplification (RCA) strategy to propose an accurate and sensitive electrochemical method. Specifically, the coexistence of the two target genes can trigger the RCA reaction to generate a number of repeated G-quadruplex (G4)-forming sequences. These sequences then switch into G4/hemin complexes with redox activity after the incubation of hemin, which can catalyze the TMB/H2O2 substrates to produce significantly enhanced current responses. Experimental results reveal that the proposed method exhibits satisfying feasibility and analytical performance, enabling the sensitive detection of SARS-CoV-2 in the range of 0.1-5000 pM, with the detection limit of 57 fM. Meanwhile, because only the simultaneous existence of the two target genes can effectively trigger the downstream amplification reaction, this method can effectively avoid false-positives and ensure specificity as well as accuracy. Furthermore, our method can distinguish the COVID-19 samples from healthy people, and the outcomes show a satisfying agreement with the results of RT-PCR, manifesting that our label-free dual-gene-controlled RCA strategy exhibits great possibility in clinical application.

CDK5RAP3, a key defender of udder, modulates NLRP3 inflammasome activation by regulating autophagolysosome degradation in S. agalactiae-infected mastitis.

Streptococcus agalactiae, as one of the main pathogens of clinical and subclinical mastitis, affects animal welfare and leads to huge economic losses to farms due to the sharp decline in milk yield. However, both the real pathogenic mechanisms of S. agalactiae-induced mastitis and the regulator which controls the inflammation and autophagy are largely unknown. Served as a substrate of ubiquitin-like proteins of E3 ligase, CDK5RAP3 is widely involved in the regulation of multiple signaling pathways. Our findings revealed that CDK5RAP3 was significantly down-regulated in mastitis infected by S. agalactiae. Surprisingly, inflammasome activation was triggered by CDK5RAP3 knockdown: up-regulated NLRP3, IL1ß and IL6, and cleaved caspase1 promoting by NF-κB, thereby resulting in pyroptosis. Additionally, the accumulation of autophagy markers (LC3B and p62) after CDK5RAP3 knockdown suggested that the autophagolysosome degradation pathway was inhibited, thereby activating the NF-κB pathway and NLRP3 inflammasome. Hence, our findings suggest that downregulation or ablation of CDK5RAP3 inhibits autophagolysosome degradation, causes inflammation by activating the NF-κB /NLRP3 inflammasome, and triggers cell death. In conclusion, CDK5RAP3 holds the key to understanding the interaction between autophagy and immune responses, its anti-inflammatory role in this study will throw new light on the clinical drug discovery to cure S. agalactiae mastitis.

Target-triggered cascade signal amplification for sensitive electrochemical detection of SARS-CoV-2 with clinical application.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the outbreak of the 2019 coronavirus (COVID-19) disease, which greatly challenges the global economy and health. Simple and sensitive diagnosis of COVID-19 at the early stage is important to prevent the spread of pandemics. Herein, we have proposed a target-triggered cascade signal amplification in this work for sensitive analysis of SARS-CoV-2 RNA. Specifically, the presence of SARS-CoV-2 RNA can trigger the catalytic hairpin assembly to generate plenty of DNA duplexes with free 3'-OH termini, which can be recognized and catalyzed by the terminal deoxynucleotidyl transferase (TdT) to generate long strand DNA. The prolonged DNA can absorb substantial Ru(NH3)63+ molecules via electrostatic interaction and produce an enhanced current response. The incorporation of catalytic hairpin assembly and TdT-mediated polymerization effectively lowers the detection limit to 45 fM, with a wide linear range from 0.1 pM to 3000 pM. Moreover, the proposed strategy possesses excellent selectivity to distinguish target RNA with single-base mismatched, three-base mismatched, and random sequences. Notably, the proposed electrochemical biosensor can be applied to analyze targets in complex circumstances containing 10% saliva, which implies its high stability and anti-interference. Moreover, the proposed strategy has been successfully applied to SARS CoV-2 RNA detection in clinical samples and may have the potential to be cultivated as an effective tool for COVID-19 diagnosis.

Operator Lévy Flight: Light Cones in Chaotic Long-Range Interacting Systems.

We argue that chaotic power-law interacting systems have emergent limits on information propagation, analogous to relativistic light cones, which depend on the spatial dimension d and the exponent α governing the decay of interactions. Using the dephasing nature of quantum chaos, we map the problem to a stochastic model with a known phase diagram. A linear light cone results for α≥d+1/2. We also provide a Lévy flight (long-range random walk) interpretation of the results and show consistent numerical data for 1D long-range spin models with 200 sites.

Operator dynamics in a Brownian quantum circuit.

We view the operator spreading in chaotic evolution as a stochastic process of height growth. The height of an operator represents the size of its support and chaotic evolution increases the height. We consider N-spin models with all two-body interactions and embody the height picture in a random model. The exact solution shows that the mean height, being proportional to the squared commutator, grows exponentially within logN scrambling time and saturates in a manner of logistic function. We propose that the temperature dependence of the chaos bound could be due to initial height biased toward high operators, which has a smaller Lyapunov exponent.

Development of a blocking ELISA for Caprine parainfluenza virus type 3.

Caprine parainfluenza virus type 3 (CPIV3) is a novel pathogen mainly causing respiratory diseases in goats. At present, there are no high throughput and rapid testing methods available for epidemiological investigation. In this study, we designed a modified method for selection of hybridomas that secrete monoclonal antibodies (mAb) specific for CPIV3. The monoclonal antibodies were obtained by combination of indirect enzyme-linked immunosorbent assay (iELISA) and blocking ELISA (bELISA). The technique was efficient to determine each mAb with specificity and sensitivity. One bELISA was validated for the serological diagnosis of CPIV3. After optimization conditions were established, a total of 205 reference goat sera were tested in parallel by bELISA and by virus neutralization (VN) for their relative performances. The cut-off point was ultimately defined as 33.6% by ROC curve analysis. The bELISA specificity and sensitivity were 99.2% and 98.7%, respectively, and agreement with the VN test was >99.0%. Furthermore, testing another 2919 goat sera by bELISA demonstrated 39.3% prevalence in the goat population, more sensitive than HI detection. This new bELISA would offer higher throughput, sensitivity, and specific detection for CPIV3, and will be of great value not only for surveillance, but also for monitoring the efficiency of vaccination programs in the future.

Pathogenicity and horizontal transmission studies of caprine parainfluenza virus type 3 JS2013 strain in goats.

Parainfluenza virus type 3 (PIV3) is one of the most important viral respiratory pathogens for humans and for many animals, but goat infection has been rarely reported. In 2014, one novel PIV3 strain was first isolated from goats suffered respiratory diseases in Jiangsu and Anhui provinces of eastern China and named as caprine PIV3 (CPIV3) JS2013. In order to systematically evaluate the pathogenicity and horizontal transmission ability of this new virus, experimental infection of goats with the CPIV3 strain was done. The virus-inoculated goats (challenge control (CC) group) displayed coughing and nasal discharges from 3days post infection (dpi) and lasted for about 2 weeks. Two goats in group CC showed fever between 7 and 12dpi. As detected by a TaqMan real time quantitative RT-PCR (qRT-PCR), viremia was detected during 3-11dpi, peaked at 6dpi; and virus shedding from nasal discharge and faeces were confirmed during 3-21dpi and 4-21dpi, respectively. Virus-specific HI antibodies and neutralizing antibodies (NAs) became positive since 7dpi and 14dpi; peaked at 14dpi and 28dpi, respectively; and lasted at least 70days. Pathological lesions were mainly found on the lungs and tracheas. In addition, viruses were also detected in part of the tracheal secretion and lung samples, and the viral load in tracheal secretion was higher than that in lungs. Goats in horizontal infected group (hCC, kept in different cages in the same house with CC group) showed to be horizontally infected, with slightly milder clinical signs and pathological changes; and slightly shorter period of viremia and virus shedding. This was the first report of the detailed pathogenicity characterization of the novel CPIV3 and demonstrated its horizontal transmission ability. The results would be helpful for further studies on the preventive and control strategies for CPIV3 infections.

Wigner translations and the observer dependence of the position of massless spinning particles.

The Wigner little group for massless particles is isomorphic to the Euclidean group SE(2). Applied to momentum eigenstates, or to infinite plane waves, the Euclidean "Wigner translations" act as the identity. We show that when applied to finite wave packets, the translation generators move the packet trajectory parallel to itself through a distance proportional to the particle's helicity. We relate this effect to the spin Hall effect of light and to the Lorentz-frame dependence of the position of a massless spinning particle.