A Zero-Voltage-Writing Artificial Nervous System Based on Biosensor Integrated on Ferroelectric Tunnel Junction.

The artificial nervous system proves the great potential for the emulation of complex neural signal transduction. However, a more bionic system design for bio-signal transduction still lags behind that of physical signals, and relies on additional external sources. Here, we present a zero-voltage-writing artificial nervous system (ZANS) that integrates a bio-source-sensing device (BSSD) for ion-based sensing and power generation with a hafnium-zirconium oxide-ferroelectric tunnel junction (HZO-FTJ) for the continuously adjustable resistance state. The BSSD can use ion bio-source as both perception and energy source, and then output voltage signals varied with the change of ion concentrations to the HZO-FTJ, which completes the zero-voltage-writing neuromorphic bio-signal modulation. In view of in-/ex-vivo biocompatibility, we show the precise muscle control of a rabbit leg by integrating the ZANS with a flexible nerve stimulation electrode. The independence on external source enhances the application potential of ZANS in robotics and prosthetics. This article is protected by copyright. All rights reserved.

Interindividual- and blood-correlated sweat phenylalanine multimodal analytical biochips for tracking exercise metabolism.

In situ monitoring of endogenous amino acid loss through sweat can provide physiological insights into health and metabolism. However, existing amino acid biosensors are unable to quantitatively assess metabolic status during exercise and are rarely used to establish blood-sweat correlations because they only detect a single concentration indicator and disregard sweat rate. Here, we present a wearable multimodal biochip integrated with advanced electrochemical electrodes and multipurpose microfluidic channels that enables simultaneous quantification of multiple sweat indicators, including phenylalanine and chloride, as well as sweat rate. This combined measurement approach reveals a negative correlation between sweat phenylalanine levels and sweat rates among individuals, which further enables identification of individuals at high metabolic risk. By tracking phenylalanine fluctuations induced by protein intake during exercise and normalizing the concentration indicator by sweat rates to reduce interindividual variability, we demonstrate a reliable method to correlate and analyze sweat-blood phenylalanine levels for personal health monitoring.

Super enhancer-driven core transcriptional regulatory circuitry crosstalk with cancer plasticity and patient mortality in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer. Core transcriptional regulatory circuitry (CRC) consists of autoregulated transcription factors (TFs) and their enhancers, which dominate gene expression programs and control cell fate. However, there is limited knowledge of CRC in TNBC. Herein, we systemically characterized the activated super-enhancers (SEs) and interrogated 14 CRCs in breast cancer. We found that CRCs could be broadly involved in DNA conformation change, metabolism process, and signaling response affecting the gene expression reprogramming. Furthermore, these CRC TFs are capable of coordinating with partner TFs bridging the enhancer-promoter loops. Notably, the CRC TF and partner pairs show remarkable specificity for molecular subtypes of breast cancer, especially in TNBC. USF1, SOX4, and MYBL2 were identified as the TNBC-specific CRC TFs. We further demonstrated that USF1 was a TNBC immunophenotype-related TF. Our findings that the rewiring of enhancer-driven CRCs was related to cancer immune and mortality, will facilitate the development of epigenetic anti-cancer treatment strategies.

A dynamic parallel image acquisition method for slide scanning process.

Automated microscope systems have played an important role in the screening of numerous diseases. However, it is a very time-consuming process to continuously acquire images under the high magnification objective lens. This paper proposes a dynamic parallel image acquisition method, which can greatly improve image acquisition speed. Due to the relative motion between the x-y stage and the camera, some of the captured images have motion blur To this end, we also designed a motor variable speed motion curve to ensure the quality of the collected images. The experimental results show that the traditional image scanning mode needs 47.3 ms to obtain continuous microscopic images, while the dynamic parallel image acquisition method only needs 25.4 ms, which improves the acquisition speed without affecting the clarity of the acquired images.

A highly sensitive nanochannel device for the detection of SUMO1 peptides.

SUMOylation is an important and highly dynamic post-translational modification (PTM) process of protein, and its disequilibrium may cause various diseases, such as cancers and neurodegenerative disorders. SUMO proteins must be accurately detected to understand disease states and develop effective drugs. Reliable antibodies against SUMO2/3 are commercially available; however, efficient detectors are yet to be developed for SUMO1, which has only 50% homology with SUMO2 and SUMO3. Here, using phage display technology, we identified two cyclic peptide (CP) sequences that could specifically bind to the terminal dodecapeptide sequence of SUMO1. Then we combined the CPs and polyethylene terephthalate conical nanochannel films to fabricate a nanochannel device highly sensitive towards the SUMO1 terminal peptide and protein; sensitivity was achieved by ensuring marked variations in both transmembrane ionic current and Faraday current. The satisfactory SUMO1-sensing ability of this device makes it a promising tool for the time-point monitoring of the SENP1 enzyme-catalyzed de-SUMOylation reaction and cellular imaging. This study not only solves the challenge of SUMO1 precise recognition that could promote SUMO1 proteomics analysis, but also demonstrates the good potential of the nanochannel device in monitoring of enzymes and discovery of effective drugs.

Improved Cross-Linking Coverage for Protein Complexes Containing Low Levels of Lysine by Using an Enrichable Photo-Cross-Linker.

Chemical cross-linking coupled with mass spectrometry (XL-MS) is an important technique for the structural analysis of protein complexes where the coverage of amino acids and the identification of cross-linked sites are crucial. Photo-cross-linking has multisite reactivity and is valuable for the structural analysis of chemical cross-linking. However, a high degree of heterogeneity results from this multisite reactivity, which results in samples with higher complexity and lower abundance. Additionally, the applicability of photo-cross-linking is limited to purified protein complexes. In this work, we demonstrate a photo-cross-linker, alkynyl-succinimidyl-diazirine (ASD) with the reactive groups of N-hydroxysuccinimide ester and diazirine, as well as the click-enrichable alkyne group. Photo-cross-linkers can provide higher site reactivity for proteins that contain only a small number of lysine residues, thereby complementing the more commonly used lysine-targeting cross-linkers. By systematically analyzing proteins with differing lysine contents and differing flexibilities, we demonstrated clear enhancement in structure elucidation for proteins containing less lysine and with high flexibility. In addition, enrichment approaches of alkynyl-azide click chemistry conjugated with biotin-streptavidin purification (coinciding with parallel orthogonal digestion) improved the identification coverage of cross-links. We show that this photo-cross-linking approach can be used for membrane proteome-wide complex analysis. This method led to the identification of a total of 14066 lysine-X cross-linked site pairs from a total of 2784 proteins. Thus, this cross-linker is a valuable addition to a photo-cross-linking toolkit and improves the identification coverage of XL-MS in functional structure analysis.

Fast autofocus method for piezoelectric microscopy system for high interaction scenes.

Piezoelectric objective driver positioners are increasingly used in the field of microscopy. They have the advantages of high dynamic and fast response. This paper presents a fast autofocus algorithm for highly interactive microscope system. First, the Tenengrad gradient of the down-sampled image is used to calculate the image sharpness, and Brent search method is adopted to quickly converge to the correct focal length. At the same time, the input shaping method is used to eliminate the displacement vibration of the piezoelectric objective lens driver and further accelerate the image acquisition speed. Experimental results show that the proposed scheme can improve the speed of the automatic focusing task of the piezoelectric objective driver and improve the real-time focus of the automatic microscopic system. HIGHLIGHTS: A high real-time autofocus strategy. A vibration control method suitable for a piezoelectric objective driver.

In vivo cross-linking-based affinity purification and mass spectrometry for targeting intracellular protein-protein interactions.

Comprehensive interactome analysis of targeted proteins is important to understand how proteins work together in regulating functions. Commonly, affinity purification followed by mass spectrometry (AP-MS) has been recognized as the most often used technique for studying protein-protein interactions (PPIs). However, some proteins with weak interactions, which are responsible for key roles in regulation, are easily broken during cell lysis and purification through an AP approach. Herein, we have developed an approach termed in vivo cross-linking-based affinity purification and mass spectrometry (ICAP-MS). By this method, in vivo cross-linking was introduced to covalently fix intracellular PPIs in their functional states to assure all PPIs could be integrally maintained during cell disruption. In addition, the chemically cleavable crosslinkers which were employed enabled unbinding of PPIs for in-depth identification of components within the interactome and biological analysis, while allowing binding of PPIs for cross-linking-mass spectrometry (CXMS)-based direct interaction determination. Multi-level information on targeted PPIs network can be obtained by ICAP-MS, including composition of interacting proteins, as well as direct interacting partners and binding sites. As a proof of concept, the interactome of MAPK3 from 293A cells was profiled with 6.15-fold improvement in identification than by conventional AP-MS. Meanwhile, 184 cross-link site pairs of these PPIs were experimentally identified by CXMS. Furthermore, ICAP-MS was applied in the temporal profiling of MAPK3 interactions under activation by cAMP-mediated pathway. The regulatory manner of MAPK pathways was presented through the quantitative changes of MAPK3 and its interacting proteins at different time points after activation. Therefore, all reported results demonstrated that the ICAP-MS approach may provide comprehensive information on interactome of targeted protein for functional exploration.

Developing an Affinity-Based Chemical Proteomics Method to In Situ Capture Amorphous Aggregated Proteome and Profile Its Heterogeneity in Stressed Cells.

Stress induced amorphous proteome aggregation is a hallmark for diseased cells, with the proteomic composition intimately associated with disease pathogenicity. Due to its particularly dynamic, reversible, and dissociable nature, as well as lack of specific recognition anchor, it is difficult to capture aggregated proteins in situ. In this work, we develop a chemical proteomics method (AggLink) to capture amorphous aggregated proteins in live stressed cells and identify the proteomic contents using LC-MS/MS. Our method relies on an affinity-based chemical probe (AggLink 1.0) that is optimized to selectively bind to and covalently label amorphous aggregated proteins in live stressed cells. Especially, chaotrope-compatible ligation enables effective enrichment of labeled aggregated proteins under urea denaturation and dissociation conditions. Compared to conventional fractionation-based method to profile aggregated proteome, our method showed improved enrichment selectivity, detection sensitivity, and identification accuracy. In HeLa cells, the AggLink method reveals the constituent heterogeneity of aggregated proteome induced by inhibition of pro-folding (HSP90) or pro-degradation (proteasome) pathway, which uncovers a synergistic strategy to reduce cancer cell viability. In addition, the unique fluorogenicity of our probe upon labeling aggregated proteome detects its cellular location and morphology. Together, the AggLink method may help to expand our knowledge of the previously nontargetable amorphous aggregated proteome.

A Novel Feedforward Model of Piezoelectric Actuator for Precision Rapid Cutting.

The piezoelectric actuator has been widely used in modern precision cutting technology due to its fast response speed and high positioning accuracy. In recent years, with the development of precision technology, modern cutting requires higher and higher cutting accuracy and efficiency. Therefore, this paper proposes a feedforward control method based on the modified Bouc-Wen (MBW) model. Firstly, a novel asymmetrical modified Bouc-Wen model with an innovative form of shape control function is developed to model the hysteresis nonlinearity property of piezoelectric actuators. Then, a self-adaptive cooperative particle swarm optimization (PSO) algorithm is developed to identify the parameters of MBW model. The comparative evaluation reveals that the MBW model outperforms the classical Bouc-Wen (CBW) model by 66.4% in modeling accuracy. Compared with traditional PSO algorithm, the self-adaptive cooperative PSO algorithm can obtain minimum fitness in parameter identification. Furthermore, the feedforward control strategy is realized to improve the position tracking accuracy. A position tracking experiment verifies that the feedforward control strategy improves the tracking accuracy of piezoelectric actuators significantly compared with the open-loop control strategy.

Modeling of Rapid Response Characteristics of Piezoelectric Actuators for Ultra-Precision Machining.

Piezoelectric actuators are characterized by high positioning accuracy, high stiffness and a fast response and are widely used in ultra-precision machining technologies such as fast tool servo technology and ultrasonic machining. The rapid response characteristics of piezoelectric actuators often determine the overall quality of machining. However, there has been little research on the fast response characteristics of piezoelectric actuators, and this knowledge gap will lead to low precision and poor quality of the final machining. The fast response characteristics of a piezoelectric actuator were studied in this work. Firstly, the piezoelectric actuator was divided into a no-load state and a load state according to the working state. A fast response analysis and output characteristic analysis were carried out, the corresponding dynamic model was established, and then the model was simulated. Finally, an experimental system was established to verify the dynamic model of the piezoelectric actuator's fast response by conducting an experiment in which the piezoelectric actuator bounces a steel ball. The experimental results verify the correctness of the model and show that the greater the cross-sectional area and height of the piezoelectric actuator, the higher the bouncing height of the ball, and the better the dynamic performance of the piezoelectric actuator. It is believed that this study has guiding significance for the application of the dynamic characteristics of piezoelectric actuators in the machining field.

Wide Range Strain Distributions on the Electrode for Highly Sensitive Flexible Tactile Sensor with Low Hysteresis.

Flexible piezoresistive tactile sensors are widely used in wearable electronic devices because of their ability to detect mechanical stimuli. However, achieving high sensitivity and low hysteresis over a broad detection range remains a challenge with current piezoresistive tactile sensors. To address these obstacles, we designed elastomeric micropyramid arrays with different heights to redistribute the strain on the electrode. Furthermore, we mixed single-walled carbon nanotubes in the elastomeric micropyramids to compensate for the conductivity loss caused by random cracks in the gold film and increase the adhesion strength between the gold film (deposited on the pyramid surface) and the elastomer. Thus, the energy loss of the sensor during deformation and hysteresis (∼2.52%) was effectively reduced. Therefore, under the synactic effects of the percolation effect, tunnel effect, and multistage strain distribution, the as-prepared sensor exhibited a high sensitivity (1.28 × 106 kPa-1) and a broad detection range (4.51-54837.06 Pa). The sensitivity was considerably higher than those of most flexible pressure sensors with a microstructure design. As a proof of concept, the sensors were successfully applied in the fields of health monitoring and human-machine interaction.

Urinary protein biomarkers based on LC-MS/MS analysis to discriminate vascular dementia from Alzheimer's disease in Han Chinese population.

Objective: This study aimed to identify the potential urine biomarkers of vascular dementia (VD) and unravel the disease-associated mechanisms by applying Liquid chromatography tandem-mass spectrometry (LC-MS/MS). Methods: LC-MS/MS proteomic analysis was applied to urine samples from 3 groups, including 14 patients with VD, 9 patients with AD, and 21 normal controls (NC). By searching the MS data by Proteome Discoverer software, analyzing the protein abundances qualitatively and quantitatively, comparing between groups, combining bioinformatics analysis using Gene Ontology (GO) and pathway crosstalk analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG), and literature searching, the differentially expressed proteins (DEPs) of VD can be comprehensively determined at last and were further quantified by receiver operating characteristic (ROC) curve methods. Results: The proteomic findings showed quantitative changes in patients with VD compared to patients with NC and AD groups; among 4,699 identified urine proteins, 939 and 1,147 proteins displayed quantitative changes unique to VD vs. NC and AD, respectively, including 484 overlapped common DEPs. Then, 10 unique proteins named in KEGG database (including PLOD3, SDCBP, SRC, GPRC5B, TSG101/STP22/VPS23, THY1/CD90, PLCD, CDH16, NARS/asnS, AGRN) were confirmed by a ROC curve method. Conclusion: Our results suggested that urine proteins enable detection of VD from AD and VC, which may provide an opportunity for intervention.

Global profiling of AMG510 modified proteins identified tumor suppressor KEAP1 as an off-target.

KRAS inhibitor AMG510 covalently modifies the G12C residue and inactivates the KRAS/G12C function. Because there are many reactive cysteines in the proteome, it is important to characterize AMG510 on-target modification and off-targets. Here, we presented a streamlined workflow to measure abundant AMG510 modified peptides including that of KRAS/G12C by direct profiling, and a pan-AMG510 antibody peptide IP workflow to profile less abundant AMG510 off-targets. We identified over 300 off-target sites with three distinct kinetic patterns, expanding the AMG510 modified proteome involved in the nucleocytoplasmic transport, response to oxidative stress, adaptive immune system, and glycolysis. We found that AMG510 covalently modified cys339 of ALDOA and inhibited its enzyme activity. Moreover, AMG510 modified KEAP1 cys288 and induced NRF2 accumulation in the nuclear of NSCLC cells independent of KRAS/G12C mutation. Our study provides a comprehensive resource of protein off-targets of AMG510 and elucidates potential toxicological sideeffects for this covalent KRASG12C inhibitor.

Enhanced protein-protein interaction network construction promoted by in vivo cross-linking with acid-cleavable click-chemistry enrichment.

Chemical cross-linking coupled with mass spectrometry has emerged as a powerful strategy which enables global profiling of protein interactome with direct interaction interfaces in complex biological systems. The alkyne-tagged enrichable cross-linkers are preferred to improve the coverage of low-abundance cross-linked peptides, combined with click chemistry for biotin conjugation to allow the cross-linked peptide enrichment. However, a systematic evaluation on the efficiency of click approaches (protein-based or peptide-based) and diverse cleavable click-chemistry ligands (acid, reduction, and photo) for cross-linked peptide enrichment and release is lacking. Herein, together with in vivo chemical cross-linking by alkyne-tagged cross-linkers, we explored the click-chemistry-based enrichment approaches on protein and peptide levels with three cleavable click-chemistry ligands, respectively. By comparison, the approach of protein-based click-chemistry conjugation with acid-cleavable tags was demonstrated to permit the most cross-linked peptide identification. The advancement of this strategy enhanced the proteome-wide cross-linking analysis, constructing a 5,518-protein-protein-interaction network among 1,871 proteins with widely abundant distribution in cells. Therefore, all these results demonstrated the guideline value of our work for efficient cross-linked peptide enrichment, thus facilitating the in-depth profiling of protein interactome for functional analysis.

Dual sensing signal decoupling based on tellurium anisotropy for VR interaction and neuro-reflex system application.

Anisotropy control of the electronic structure in inorganic semiconductors is an important step in developing devices endowed with multi-function. Here, we demonstrate that the intrinsic anisotropy of tellurium nanowires can be used to modulate the electronic structure and piezoelectric polarization and decouple pressure and temperature difference signals, and realize VR interaction and neuro-reflex applications. The architecture design of the device combined with self-locking effect can eliminate dependence on displacement, enabling a single device to determine the hardness and thermal conductivity of materials through a simple touch. We used a bimodal Te-based sensor to develop a wearable glove for endowing real objects to the virtual world, which greatly improves VR somatosensory feedback. In addition, we successfully achieved stimulus recognition and neural-reflex in a rabbit sciatic nerve model by integrating the sensor signals using a deep learning technique. In view of in-/ex-vivo feasibility, the bimodal Te-based sensor would be considered a novel sensing platform for a wide range application of metaverse, AI robot, and electronic medicine.

Alkynyl-Enrichable Carboxyl-Selective Crosslinkers to Increase the Crosslinking Coverage for Deciphering Protein Structures.

The coverage of chemical crosslinking coupled with mass spectrometry (CXMS) is of great importance to determine its ability for deciphering protein structures. At present, N-hydroxysuccinimidyl (NHS) ester-based crosslinkers targeting lysines have been predominantly used in CXMS. However, they are not always effective for some proteins with few lysines. Other amino acid residues such as carboxyl could be crosslinked to complement lysines and improve the crosslinking coverage of CXMS, but the low intrinsic chemical reactivity of carboxyl compromises the application of carboxyl-selective crosslinkers for complex samples. To enhance the crosslinking efficiency targeting acidic residues and realize in-depth crosslinking analysis of complex samples, we developed three new alkynyl-enrichable carboxyl-selective crosslinkers with different reactive groups such as hydrazide, amino, and aminooxy. The crosslinking efficiencies of the three crosslinkers were systematically evaluated, giving the best reactivity of the amino-functionalized crosslinker BAP. Furthermore, BAP was extended to the crosslinking analysis of Escherichia coli lysate in combination with efficient crosslink enrichment. A total of 1291 D/E-D/E crosslinks involved in 392 proteins were identified under a false discovery rate (FDR) of ≤1%. Obvious structural complementarity of BAP was exhibited to the lysine-targeting crosslinker, facilitating the capability of CXMS for protein structure elucidation. To the best of our knowledge, this was the first time for the carboxyl-selective crosslinker to achieve proteome-wide crosslinking analysis of the whole cell lysate. Collectively, we believe that this work not only expands on a promising toolkit of CXMS targeting acidic residues but also provides a valuable guideline to advance the performance of carboxyl-selective crosslinkers.

Surface-Charged Hybrid Monolithic Column for MS-Compatible Peptide Separation with High Peak Capacity and Its Application in Proteomic Analysis.

For bottom-up proteomics, peptide separation with high peak capacity under MS-compatible conditions is of vital significance to increase proteome coverage. Herein, a surface-charged ethane-bridged hybrid monolithic column was prepared based on the efficient ring-opening reaction of N-methyl-aza-2,2,4-trimethyl-silacyclopentane after C18-functionalization. The existence of secondary amino groups on the surface was beneficial to reduce the secondary interactions of silanol groups and increase peak capacity for peptide separation with MS-compatible mobile phases (e.g., using 0.1% FA as the mobile phase modifier). Such columns offered a 4-fold increase in peak capacity compared with ethane-bridged hybrid monolithic columns without surface charge modification. By a 100 cm length surface-charged ethane-bridged hybrid capillary column, high peak capacity of 700 was achieved within a 240 min gradient for the separation of Hela tryptic peptides with 0.1% FA-containing mobile phases, under the low backpressure of ∼200 bar. On average, 44493 ± 459 peptides corresponding to 5148 ± 47 proteins were identified from 750 ng Hela tryptic digests. Finally, the surface-charged ethane-bridged hybrid monolithic column was successfully applied in the quantitative proteomic analysis of dopaminergic neuron death model of N-methyl-4-phenylpyridinium iodide induced SH-SY5Y cells. These results demonstrated great promise of such surface-charged ethane-bridged hybrid monolithic columns for bottom-up proteomic analysis in complex samples.

In-Depth In Vivo Crosslinking in Minutes by a Compact, Membrane-Permeable, and Alkynyl-Enrichable Crosslinker.

Chemical crosslinking coupled with mass spectrometry (CXMS) has emerged as a powerful technique to obtain the dynamic conformations and interaction interfaces of protein complexes. Limited by the poor cell membrane permeability, chemical reactivity, and biocompatibility of crosslinkers, in vivo crosslinking to capture the dynamics of protein complexes with finer temporal resolution and higher coverage is attractive but challenging. In this work, a trifunctional crosslinker bis(succinimidyl) with propargyl tag (BSP), involving compact size, proper amphipathy, and enrichment capacity, was developed to enable better cell membrane permeability and efficient crosslinking in 5 min without obvious cellular interference. Followed by a two-step enrichment method based on click chemistry at the peptide level, 13,098 crosslinked peptides (5068 inter-crosslinked peptides and 8030 intra-crosslinked peptides) were identified under the data threshold of peptide-spectrum matches (PSMs) ≥2 on the basic of the FDR control of 1%, which was the most comprehensive dataset for homo species cells by a non-cleavable crosslinker. Besides, the interactome network comprising 1519 proteins connected by 2913 interaction edges in various intracellular compartments, as well as 80S ribosome structural dynamics, were characterized, showing the great potential of our in vivo crosslinking approach in minutes. All these results demonstrated that our developed BSP could provide a valuable toolkit for the in-depth in vivo analysis of protein-protein interactions (PPIs) and protein architectures with finer temporal resolution.