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The E2 ubiquitin (Ub)-conjugating enzyme primarily determines Ub conjugation as Ub-isopeptide (lysine), Ub-oxyester (serine/threonine) or Ub-thioester (cysteine). However, E2-specific Ub conjugation profiles within cells remain elusive. Here we developed the fusion E2–Ub-R74G profiling (FUSEP) strategy to access E2-specific Ub conjugation profiles in cells with amino acid resolution. The probe-specific leucine-glycine-glycine-glycine-modified Ub remnant enables systematic studies of non-lysine Ub conjugation and provides site-specific information. Multiple E2 enzymes were found to be involved in non-lysine ubiquitination. Profiling with UBE2D3–Ub-R74G probes identified a post-translational modification, tyrosine ubiquitination, in human Cullin-1, a scaffold protein for Cullin-RING E3 Ub ligases. This modification is distinct from lysine ubiquitination. A single-pass membrane-bound E3 ligase, RNF149, was identified to pair with UBE2D3 to regulate pyroptosis by ubiquitinating apoptosis-associated speck-like protein ASC. The availability of this toolbox paves the way for uncovering E2-specific Ub conjugation profiles and identifying previously unknown E3 Ub ligases for potential therapeutic applications.

We introduce HiSC4D, a novel Human-centered interaction and 4D Scene Capture method, aimed at accurately and efficiently creating a dynamic digital world, containing large-scale indoor-outdoor scenes, diverse human motions, rich human-human interactions, and human-environment interactions. By utilizing body-mounted IMUs and a head-mounted LiDAR, HiSC4D can capture egocentric human motions in unconstrained space without the need for external devices and pre-built maps. This affords great flexibility and accessibility for human-centered interaction and 4D scene capturing in various environments. Taking into account that IMUs can capture human spatially unrestricted poses but are prone to drifting for long-period using, and while LiDAR is stable for global localization but rough for local positions and orientations, HiSC4D employs a joint optimization method, harmonizing all sensors and utilizing environment cues, yielding promising results for long-term capture in large scenes. To promote research of egocentric human interaction in large scenes and facilitate downstream tasks, we also present a dataset, containing 8 sequences in 4 large scenes (200 to 5,000 $\text{m}^{2}$m2), providing 36 k frames of accurate 4D human motions with SMPL annotations and dynamic scenes, 31k frames of cropped human point clouds, and scene mesh of the environment. A variety of scenarios, such as the basketball gym and commercial street, alongside challenging human motions, such as daily greeting, one-on-one basketball playing, and tour guiding, demonstrate the effectiveness and the generalization ability of HiSC4D. The dataset and code will be publicly available for research purposes.

Autonomous driving safety based on LiDAR perception is increasingly becoming a hot spot. Specifically, 3D adversarial examples always make the prediction results of deep neural network models unpredictable, which poses a major security risk to autonomous driving systems. However, the vulnerability of 3D neural network models to adversarial examples is less explored. At present, existing adversarial attack methods often obtain 3D adversarial examples by perturbing the entire point cloud, which requires a large number of perturbed points, i.e. requires a large perturbation budget. In this paper, we propose a Salient Region Adversarial attack method (SR-Adv) to generate adversarial point clouds, by perturbing fewer regions and fewer points. To our knowledge, we are the first to propose region-based attacks for 3D point clouds. First, the proposed SR-Adv employs game theory to extract salient regions of point clouds. This mechanism assigns a value to each region to measure its importance to the 3D neural network model prediction results and realizes the vulnerability analysis of the 3D model. Second, we propose a novel optimization-based gradient attack algorithm to achieve adversarial attacks on salient regions. We evaluate the proposed SR-Adv attack method on the synthetic datasets ModelNet40 and ShapeNetPart as well as the real-world dataset KITTI and NuScenes. Experimental results show that the proposed SR-Adv achieves a state-of-the-art attack success rate and better imperceptibility by perturbing fewer points on 3D point clouds.

Network monitoring solutions need to cope with increasing network traffic volumes, as a result, sketch-based monitoring methods have been extensively studied to trade accuracy for memory scalability and storage reduction. However, sketches are sensitive to skewness in network flow distributions due to hash collisions, and need complicated performance optimization to adapt to line-rate packet streams. We provide Jellyfish, an efficient sketch method that performs one-pass clustering over the network stream. One-pass clustering is realized by adapting the monitoring granularity from the whole network flow to fragments called subflows, which not only reduces the ingestion rate but also provides an efficient intermediate representation for the input to the sketch. Jellyfish provides the network-flow level query interface by reconstructing the network-flow level counters by merging subflow records from the same network flow. We provide probabilistic analysis of the expected accuracy of both existing sketch methods and Jellyfish. Real-world trace-driven experiments show that Jellyfish reduces the average estimation errors by up to six orders of magnitude for per-flow queries, by six orders of magnitude for entropy queries, and up to ten times for heavy-hitter queries.

IEEE VAST Challenge 2021 provides fruitful data to test the visual analytics capability of participants. We summarize our work in this article. Trajectory data and consumption data contain a lot of information, such as consumption patterns, behavior characteristics, and so on. The information can provide favorable clues for law enforcement departments to crack a case about missing employees. We designed a visual analytics system called Sundial for spatio–temporal situation awareness with multidata fusion. It contains three views, that is, consumption view, temporal behavior view, and spatial–temporal map. With the system, analysts can effectively identify the consumption and behavior patterns of employees, and detect the suspicious activities and informal or formal relationships. Through case analysis, we illustrated how to use the system and obtain effective information.

The digital twin brain (DTB) computing model from brain-inspired computing research is an emerging artificial intelligence technique, which is realized by a computational modeling approach of hardware and software. It can achieve various cognitive abilities and their synergistic mechanisms in a manner similar to the human brain. Given that the task of the DTB is to simulate the functions of the human brain, comparing the similarities and differences between the two is crucial. However, the visualization study of the DTB is still under-researched. Moreover, the complexity of the datasets (multilevel spatiotemporal granularity and different types of comparison tasks) presents new challenges to the analysis and exploration of visualization. Therefore, in this study, we proposed DTBVis, a visual analytics system that supports comparison tasks for the DTB. DTBVis supports iterative explorations from different levels and at different granularities. Combined with automatic similarity recommendation, and high-dimensional exploration, DTBVis can assist experts in understanding the similarities and differences between the DTB and the human brain, thus helping them adjust their model and enhance its functionality. The highest level of DTBVis shows an overview of the datasets from the brain, which is used for comparison and exploration of the function and structure of the DTB and the human brain. The medium level is used for the comparison and exploration of a designated brain region. The low level can analyze a designated brain voxel. We worked closely with experts of brain science and held regular seminars with them. Feedback from the experts indicates that our approach helps them conduct comparative studies of the DTB and human brain and make modeling adjustments of the DTB through intuitive visual comparisons and interactive explorations.

MyD88 is a central player in innate immunity. The molecular mechanism of MyD88 mutation-related diseases largely remains elusive. Here, we report that MyD88 self-assembles into high-order supramolecular structures as a signal amplification machinery. We show that the combination of the death domain (MyD88DD) and the intermediate domain (MyD88ID) is the minimum unit for the filament formation, which is modulated by the TIR domain (MyD88TIR). The loss-of-function mutant L93P disrupts the filaments; the gain-of-function mutant L252P transforms the filaments into speckles. Atomic molecular dynamics simulations demonstrate that the L93P mutation induces conformational changes of MyD88DDby disrupting its hydrophobic core. The L252P mutation causes the unfolding of an α-helix between residues 246-252 and more exposure of the BB-loop. These pathologically relevant mutations alter the MyD88 assembly structure and function, which may contribute to a variety of disease development processes.

Memory disorders are increasingly recognized as a widespread global concern, attracting significant attention and necessitating urgent intervention. In this study, the effects of fish scale collagen peptide-original flavor peptide (FSCP-OP) on memory-impaired mice were examined using behavioral experiments, histopathological staining, and assessments of choline function. The mechanisms by which FSCP-OP enhanced memory function were preliminary exploration through high-resolution mass spectrometry, in silicomethods, and molecular docking analyses. It was found that FSCP-OP enhanced learning and cognitive abilities, repaired the pathological state of the mouse hippocampus, increased the number of Nissl bodies in the CA1 and CA3 regions, reduced oxidative stress in the hippocampus, significantly elevated Acetylcholine (ACh) levels to (125.36 ± 10.95) μg/mg prot, and markedly decreased Acetylcholinesterase (AChE) activity to (199.91 ± 12.19) U/mg prot (P < 0.05). The molecular docking results for the digestion products GPF and GFD from the FSCP-OP group showed multiple interactions at the AChE binding site, with binding energies of −8.67 kcal/mol and −6.41 kcal/mol, indicating stable conformations. These findings suggest that FSCP-OP is effective in ameliorating memory impairment and that GPF and GFD are promising candidate peptides.

Photocaged cell-permeable ubiquitin probe holds promise in profiling the activity of cellular deubiquitinating enzymes (DUBs) with the much needed temporal control. Here we report a new photocaged cell-permeable ubiquitin probe that undergoes photoactivation upon 365 nm UV treatment and enables intracellular deubiquitinating enzyme profiling. We used a semisynthetic approach to generate modular ubiquitin-based probe containing a tetrazole-derived warhead at the C-terminus of ubiquitin and employed a cyclic polyarginine cell-penetrating peptide (cR10) conjugated to the N-terminus of ubiquitin via a disulfide linkage to deliver the probe into live cells. Upon 365 nm UV irradiation, the tetrazole group is converted to a nitrilimine intermediate in situ, which reacts with nearby nucleophilic cysteine residue from the DUB active site. The new photocaged cell-permeable probe showed good reactivity toward purified DUBs, including USP2, UCHL1, and UCHL3, upon photoirradiation. The Ub-tetrazole probe was also assessed in HeLa cell lysate and showed robust labeling only upon photoactivation. We further carried out protein profiling in intact HeLa cells using the new photocaged cell-permeable ubiquitin probe and identified DUBs captured by the probe using label-free quantitative (LFQ) mass spectrometry. Importantly, the photocaged cell-permeable ubiquitin probe captured DUBs specifically in respective G1/S and G2/M phases in synchronized HeLa cells. Moreover, using this probe DUBs were profiled at different time points following the release of HeLa cells from G1/S phase. Our results showed that photocaged cell-permeable probe represents a valuable new tool for achieving a better understanding of the cellular functions of DUBs.

Alcoholic gastric injury is a prevalent condition that can result in gastric ulcers. This research delves into the protective effects of sea cucumber gut peptides, Val-Thr-Pro-Tyr (VTPY) and Val-Leu-Leu-Tyr (VLLY), on ethanol-induced gastric injury. These peptides significantly alleviate the pathological symptoms of gastric tissue affected by ethanol, reducing ulcer area and index, epithelial cell loss, submucosal edema, and inflammatory infiltration. High doses of VTPY and VLLY resulted in a significant decrease in ulcer index, with reductions from 5.38 to 2.63 and 1.13, respectively (P < 0.05). Moreover, the levels of P-NF-κB/p65 expression decreased by 33.47% and 54.27%, while myeloperoxidase (MPO) activity decreased by 42.98% and 55.33%, respectively. These treatments also effectively suppressed inflammatory cytokine expression and inhibited macrophage infiltration, ultimately alleviating the inflammatory response in gastric mucosal tissue. They also enhance mitochondrial function by regulating factors associated with mitochondrial dynamics and increasing succinate dehydrogenase (SDH) activity. Furthermore, they alleviate endoplasmic reticulum stress by reducing the immunoglobulin heavy chain-binding protein (Bip), phosphorylated eukaryotic translation initiation factor 2 alpha (P-eIF2α), and activating transcription factor 4 (ATF4) expression levels. Ultimately, high doses of VTPY and VLLY increased the B-cell lymphoma-extra large to B-cell lymphoma-2 associated death promoter ratio (Bcl-XL/Bad ratio) by 138.68% and 247.99%, respectively, while the expression level of cleaved-caspase 3 decreased by 35.26% and 48.22%, thereby preventing the activation of the apoptotic pathway. Sea cucumber gut peptides VTPY and VLLY exhibit effective anti-inflammatory and anti-apoptotic properties, along with anti-endoplasmic reticulum stress effects, by inhibiting the ATF4/Bcl-2 signaling pathway, thus effectively shielding against ethanol-induced gastric damage. VLLY appears to be more potent in this aspect.

Advancement in our knowledge of deubiquitinases (DUBs) and their biological functions requires biochemical tools permitting interrogation of DUB activities under physiologically relevant conditions. Activity-based DUB probes (DUB ABPs) have been widely used in investigating the function and activity of DUBs. However, most ubiquitin (Ub)-based DUB ABPs are not cell-permeable, limiting their utility to purified proteins and cell lysates. Lysis of cells usually leads to dilution of the cytoplasm and disruption of the normal cellular organization, which may alter the activity of many DUBs and DUB complexes. Here, we report a new class of cell-permeable DUB ABPs that enable intracellular DUB profiling. We used a semisynthetic approach to generate modular ubiquitin-based DUB probes containing a reactive warhead for covalent trapping of DUBs with a catalytic cysteine. We employed cell-penetrating peptides (CPPs), particualrly cyclic polyarginine (cR10), to deliver the DUB ABPs into cells, as confirmed using live-cell fluorescence microscopy and DUB ABPs containing a fluorophore at the C-terminus of Ub. In comparison to TAT, enhanced intacellular delivery was observed through conjugation of a cyclic polyarginine (cR10) to the N-terminus of ubiquitin via a disulfide linkage. Using the new cell-permeable DUB ABPs, we carried out DUB profiling in intact HeLa cells, and identified active DUBs using immunocapture and label-free quantitative mass spectrometry. Additionally, we demonstrated that the cell-permeable DUB ABPs can be used in assessing the inhibition of DUBs by small-molecule inhibitors in intact cells. Our results indicate that cell-permeable DUB ABPs hold great promise in providing a better understanding of the cellular functions of DUBs and advancing drug discovery efforts targeting human DUBs.

Heterozygous DDX41 germline mutations occur in familial myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML) and acute erythroid leukemia (AEL). DDX41 encodes an RNA helicase that regulates RNA splicing, cGAS-Sting signaling in innate immunity, and maintains genome stability in erythropoiesis. We described the innovation of a facile genetic rescue system to compare RNA-regulatory activities of wild type and disease-associated DDX41 variants in engineered HoxB8-immortalized (hi) murine myeloid progenitor cells (hi-Ddx41+/+ and Ddx41+/- cells) (Kim et al., Leukemia 2023). We identified DDX41-regulated transcripts and membrane proteins as quantitative metrics of DDX41 activity that discriminate benign from pathogenic DDX41 alleles. As these transcripts and the cognate proteins were not known to be components of GATA2 genetic networks that govern hematopoietic stem/progenitor cell (HSPC) transitions, we hypothesized that DDX41 mechanisms in progenitors operate in parallel with or independent of GATA2 mechanisms. Considering the biological and pathological importance of DDX41 and many unanswered questions on how clinical variants impact DDX41 activity, we instituted studies to discover DDX41-regulated transcript isoforms. The datasets are being used to unveil how DDX41 controls cellular functions, how clinical variants derail mechanisms, and to establish interconnections or independence with GATA factor mechanisms.

Organic acid is prevalent in underground environments and, against the backdrop of biogeochemical cycles on Earth, holds significant importance in the degradation of contaminants by redox-active minerals. While earlier studies on the role of organic acid in the generation of reactive oxygen species (ROS) primarily concentrated on electron shuttle or ligand effects, this study delves into the combined impacts of organic acid decomposition and Mackinawite (FeS) oxidation in contaminant transformation under dark aerobic conditions. Using bisphenol A (BPA) as a model, our findings showed that oxalic acid (OA) notably outperforms other acids in enhancing BPA removal, attaining a rate constant of 0.69 h–1. Mass spectrometry characterizations, coupled with anaerobic treatments, advocate for molecule-O2activation as the principal mechanism behind pollutant transformation. Comprehensive results unveiled that carbon center radicals, initiated by hydroxyl radical (•OH) attack, serve as the primary agents in pollutant oxidation, accounting for at least 93.6% of the total •OH generation. This dynamic, driven by the decomposition of organic acids and the concurrent formation of carbon-centered radicals, ensures a steady supply of electrons for ROS generation. The obtained information highlights the importance of OA decomposition in the natural attenuation of pollutants and offers innovative strategies for FeS and organic acid-coupled decontamination.

Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable profiling of long-range genomic interactions. However, data from these technologies are prone to technical noise and biases that hinder downstream analysis. We develop a normalization approach, BandNorm, and a deep generative modeling framework, scVI-3D, to account for scHi-C specific biases. In benchmarking experiments, BandNorm yields leading performances in a time and memory efficient manner for cell-type separation, identification of interacting loci, and recovery of cell-type relationships, while scVI-3D exhibits advantages for rare cell types and under high sparsity scenarios. Application of BandNorm coupled with gene-associating domain analysis reveals scRNA-seq validated sub-cell type identification.

Cyclic GMP-AMP synthase (cGAS) binds to microbial and self-DNA in the cytosol and synthesizes cyclic GMP-AMP (cGAMP), which activates stimulator of interferon genes (STING) and downstream mediators to elicit an innate immune response. Regulation of cGAS activity is essential for immune homeostasis. Here, we identified the E3 ubiquitin ligase MARCH8 (also known as MARCHF8, c-MIR, and RNF178) as a negative regulator of cGAS-mediated signaling. The immune response to double-stranded DNA was attenuated by overexpression of MARCH8 and enhanced by knockdown or knockout of MARCH8. MARCH8 interacted with the enzymatically active core of cGAS through its conserved RING-CH domain and catalyzed the lysine-63 (K63)–linked polyubiquitylation of cGAS at Lys411. This polyubiquitylation event inhibited the DNA binding ability of cGAS, impaired cGAMP production, and attenuated the downstream innate immune response. Furthermore, March8-deficient mice were less susceptible than their wild-type counterparts to herpes simplex virus 1 (HSV-1) infection. Together, our findings reveal a mechanism underlying the functional regulation of cGAS and the fine-tuning of the innate immune response.

Stem and progenitor cell fate transitions constitute key decision points in organismal development that enable access to a developmental path or actively preclude others. Using the hematopoietic system, we analyzed the relative importance of cell fate–promoting mechanisms versus negating fate-suppressing mechanisms to engineer progenitor cells with multilineage differentiation potential. Deletion of the murine Gata2−77 enhancer, with a human equivalent that causes leukemia, downregulates the transcription factor GATA2 and blocks progenitor differentiation into erythrocytes, megakaryocytes, basophils, and granulocytes, but not macrophages. Using multiomics and single-cell analyses, we demonstrated that the enhancer orchestrates a balance between pro- and anti-fate circuitry in single cells. By increasing GATA2 expression, the enhancer instigates a fate-promoting mechanism while abrogating an innate immunity–linked, fate-suppressing mechanism. During embryogenesis, the suppressing mechanism dominated in enhancer mutant progenitors, thus yielding progenitors with a predominant monocytic differentiation potential. Coordinating fate-promoting and -suppressing circuits therefore averts deconstruction of a multifate system into a monopotent system and maintains critical progenitor heterogeneity and functionality.