HOXA-AS2 Epigenetically Inhibits HBV Transcription by Recruiting the MTA1-HDAC1/2 Deacetylase Complex to cccDNA Minichromosome

Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers. Further experiments demonstrate that HBV DNA polymerase (DNA pol) induces HOXA-AS2 after establishing persistent high-level HBV replication. Functional studies reveal that HOXA-AS2 physically binds to cccDNA and significantly inhibits its transcription. Mechanistically, HOXA-AS2 recruits the MTA1-HDAC1/2 deacetylase complex to cccDNA minichromosome by physically interacting with metastasis associated 1 (MTA1) subunit, resulting in reduced acetylation of histone H3 at lysine 9 (H3K9ac) and lysine 27 (H3K27ac) associated with cccDNA and subsequently suppressing cccDNA transcription. Altogether, the study reveals a mechanism to self-limit HBV replication, wherein the upregulation of lncRNA HOXA-AS2, induced by HBV DNA pol, can epigenetically suppress cccDNA transcription.

Scaling up of a Self-Confined Catalytic Hybridization Circuit for Robust microRNA Imaging

The precise regulation of cellular behaviors within a confined, crowded intracellular environment is highly amenable in diagnostics and therapeutics. While synthetic circuitry system through a concatenated chemical reaction network has rarely been reported to mimic dynamic self-assembly system. Herein, a catalytic self-defined circuit (CSC) for the hierarchically concatenated assembly of DNA domino nanostructures is engineered. By incorporating pre-sealed symmetrical fragments into the preying hairpin reactants, the CSC system allows the hierarchical DNA self-assembly via a microRNA (miRNA)-powered self-sorting catalytic hybridization reaction. With minimal strand complexity, this self-sustainable CSC system streamlined the circuit component and achieved localization-intensified cascaded signal amplification. Profiting from the self-adaptively concatenated hybridization reaction, a reliable and robust method has been achieved for discriminating carcinoma tissues from the corresponding para-carcinoma tissues. The CSC-sustained self-assembly strategy provides a comprehensive and smart toolbox for organizing various hierarchical DNA nanostructures, which may facilitate more insights for clinical diagnosis and therapeutic assessment.

Kinesin Family Member-18A (KIF18A) Promotes Cell Proliferation and Metastasis in Hepatocellular Carcinoma

BACKGROUND & AIMS

Kinesin family member 18A (KIF18A) is notable for its aberrant expression across various cancer types and its pivotal role is driving cancer progression. In this study, we aim to investigate the intricate molecular mechanisms underlying the impact of KIF18A on the progression of HCC.

METHODS

Western blotting assays, a quantitative real-time PCR and immunohistochemical analyses were performed to quantitatively assess KIF18A expression in HCC tissues. We then performed genetic manipulations within HCC cells by silencing endogenous KIF18A using short hairpin RNA (shRNA) and introducing exogenous plasmids to overexpress KIF18A. We monitored cell progression, analyzed cell cycle and cell apoptosis and assessed cell migration and invasion both in vitro and in vivo. Moreover, we conducted RNA-sequencing to explore KIF18A-related signaling pathways utilizing Reactome and KEGG enrichment methods and validated these critical mediators in these pathways.

RESULTS

Analysis of the TCGA-LIHC database revealed pronounced overexpression of KIF18A in HCC tissues, the finding was subsequently confirmed through the analysis of clinical samples obtained from HCC patients. Notably, silencing KIF18A in cells led to an obvious inhibition of cell proliferation, migration and invasion in vitro. Furthermore, in subcutaneous and orthotopic xenograft models, suppression of KIF18A sgnificantly redudce tumor weight and the number of lung metastatic nodules. Mechanistically, KIF18A appears to facilitate cell proliferation by upregulating MAD2 and CDK1/CyclinB1 expression levels, with the activation of SMAD2/3 signaling contributing to KIF18A-driven metastasis.

CONCLUSION

Our study elucidates the molecular mechanism by which KIF18A mediates proliferation and metastasis in HCC cells, offering new insights into potential therapeutic targets.

Study on large deformation of soil-rock mixed slope based on GPU accelerated material point method

This study assesses the effect of stone content on the stability of soil-rock mixture slopes and the dynamics of ensuing large displacement landslides using a material point strength reduction method. This method evaluates structural stability by incrementally decreasing material strength parameters. The author created four distinct soil-rock mixture slope models with varying stone contents yet consistent stone size distributions through digital image processing. The initial conditions were established by linearly ramping up the gravity in fixed proportionate steps until the full value was attained. Stability was monitored until a sudden shift in displacement marked the onset of instability. Upon destabilization, the author employed the material point method to reconstruct the landslide dynamics. Due to the substantial computational requirements, the author developed a high-performance GPU-based framework for the material point method, prioritizing the parallelization of the MPM algorithm and the optimization of data structures and memory allocation to exploit GPU parallel processing capabilities. Our results demonstrate a clear positive correlation between stone content and slope stability; increasing stone content from 10 to 20% improved the safety factor from 1.9 to 2.4, and further increments to 30% and 40% ensured comprehensive stability. This study not only sheds light on slope stability and the mechanics of landslides but also underscores the effectiveness of GPU-accelerated methods in handling complex geotechnical simulations.

Expressway traffic flow prediction based on MF-TAN and STSA

Highly accurate traffic flow prediction is essential for effectively managing traffic congestion, providing real-time travel advice, and reducing travel costs. However, traditional traffic flow prediction models often fail to fully consider the correlation and periodicity among traffic state data and rely on static network topology graphs. To solve this problem, this paper proposes a expressway traffic flow prediction model based on multi-feature spatial-temporal adaptive periodic fused graph convolutional network (MFSTAPFGCN). First, we make fine preprocessing of the raw data to construct a complete and accurate dataset. Second, by deeply investigating the correlation properties among section speed, traffic flow, and section saturation rate, we incorporate these features into a multi-feature temporal attention mechanism in order to dynamically model the correlation of traffic flow in different time periods. Next, we adopt a spatial-temporal adaptive fusion graph convolutional network to capture the daily cycle similarity and potential spatial-temporal dependence of traffic flow data. Finally, the superiority of the proposed MFSTAPFGCN model over the traditional baseline model is verified through comparative experiments on real Electronic Toll Collection (ETC) gantry transaction data, and the effectiveness of each module is demonstrated through ablation experiments.

A novel peptide PDHK1-241aa encoded by circPDHK1 promotes ccRCC progression via interacting with PPP1CA to inhibit AKT dephosphorylation and activate the AKT-mTOR signaling pathway

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) is the most prevalent kidney cancer with high aggressive phenotype and poor prognosis. Accumulating evidence suggests that circRNAs have been identified as pivotal mediators in cancers. However, the role of circRNAs in ccRCC progression remains elusive.

METHODS

The differentially expressed circRNAs in 4 paired human ccRCC and adjacent noncancerous tissues ccRCC were screened using circRNA microarrays and the candidate target was selected based on circRNA expression level using weighted gene correlation network analysis (WGCNA) and the gene expression omnibus (GEO) database. CircPDHK1 expression in ccRCC and adjacent noncancerous tissues (n = 148) were evaluated along with clinically relevant information. RT-qPCR, RNase R digestion, and actinomycin D (ActD) stability test were conducted to identify the characteristics of circPDHK1. The subcellular distribution of circPDHK1 was analyzed by subcellular fractionation assay and fluorescence in situ hybridization (FISH). Immunoprecipitation-mass spectrometry (IP-MS) and immunofluorescence (IF) were employed to evaluate the protein-coding ability of circPDHK1. ccRCC cells were transfected with siRNAs, plasmids or lentivirus approach, and cell proliferation, migration and invasion, as well as tumorigenesis and metastasis in nude mice were assessed to clarify the functional roles of circPDHK1 and its encoded peptide PDHK1-241aa. RNA-sequencing, western blot analysis, immunoprecipitation (IP) and chromatin immunoprecipitation (ChIP) assays were further employed to identify the underlying mechanisms regulated by PDHK1-241aa.

RESULTS

CircPDHK1 was upregulated in ccRCC tissues and closely related to WHO/ISUP stage, T stage, distant metastasis, VHL mutation and Ki-67 levels. CircPDHK1 had a functional internal ribosome entry site (IRES) and encoded a novel peptide PDHK1-241aa. Functionally, we confirmed that PDHK1-241aa and not the circPDHK1 promoted the proliferation, migration and invasion of ccRCC. Mechanistically, circPDHK1 was activated by HIF-2A at the transcriptional level. PDHK1-241aa was upregulated and interacted with PPP1CA, causing the relocation of PPP1CA to the nucleus. This thereby inhibited AKT dephosphorylation and activated the AKT-mTOR signaling pathway.

CONCLUSIONS

Our data indicated that circPDHK1-encoded PDHK1-241aa promotes ccRCC progression by interacting with PPP1CA to inhibit AKT dephosphorylation. This study provides novel insights into the multiplicity of circRNAs and highlights the potential use of circPDHK1 or PDHK1-241aa as a therapeutic target for ccRCC.

RNA Binding Protein PTBP1 Promotes the Metastasis of Gastric Cancer by Stabilizing PGK1 mRNA

Gastric cancer (GC) is the most common type of malignant tumor within the gastrointestinal tract, and GC metastasis is associated with poor prognosis. Polypyrimidine tract binding protein 1 (PTBP1) is an RNA-binding protein implicated in various types of tumor development and metastasis. However, the role of PTBP1 in GC metastasis remains elusive. In this study, we verified that PTBP1 was upregulated in GC tissues and cell lines, and higher PTBP1 level was associated with poorer prognosis. It was shown that PTBP1 knockdown in vitro inhibited GC cell migration, whereas PTBP1 overexpression promoted the migration of GC cells. In vivo, the knockdown of PTBP1 notably reduced both the size and occurrence of metastatic nodules in a nude mice liver metastasis model. We identified phosphoglycerate kinase 1 (PGK1) as a downstream target of PTBP1 and found that PTBP1 increased the stability of PGK1 by directly binding to its mRNA. Furthermore, the PGK1/SNAIL axis could be required for PTBP1's function in the promotion of GC cell migration. These discoveries suggest that PTBP1 could be a promising therapeutic target for GC.

Improved Dynamic Event-Triggered Robust Control for Flexible Robotic Arm Systems with Semi-Markov Jump Process

In this paper, we investigate the problem of a dynamic event-triggered robust controller design for flexible robotic arm systems with continuous-time phase-type semi-Markov jump process. In particular, the change in moment of inertia is first considered in the flexible robotic arm system, which is necessary for ensuring the security and stability control of special robots employed under special circumstances, such as surgical robots and assisted-living robots which have strict lightweight requirements. To handle this problem, a semi-Markov chain is conducted to model this process. Furthermore, the dynamic event-triggered scheme is used to solve the problem of limited bandwidth in the network transmission environment, while considering the impact of DoS attacks. With regard to the challenging circumstances and negative elements previously mentioned, the adequate criteria for the existence of the resilient H∞ controller are obtained using the Lyapunov function approach, and the controller gains, Lyapunov parameters and event-triggered parameters are co-designed. Finally, the effectiveness of the designed controller is demonstrated via numerical simulation using the LMI toolbox in MATLAB.

Longitudinal and Lateral Control Strategies for Automatic Lane Change to Avoid Collision in Vehicle High-Speed Driving

The vehicle particle model was built to compare and analyze the effectiveness of three different collision avoidance methods. The results show that during vehicle high-speed emergency collision avoidance, lane change collision avoidance requires a smaller longitudinal distance than braking collision avoidance and is closer to that with a combination of lane change and braking collision avoidance. Based on the above, a double-layer control strategy is proposed to avoid collision when vehicles change lanes at high speed. The quintic polynomial is chosen as the reference path after comparing and analyzing three polynomial reference trajectories. The multiobjective optimized model predictive control is used to track the lateral displacement, and the optimization objective is to minimize the lateral position deviation, yaw rate tracking deviation, and control increment. The lower longitudinal speed tracking control strategy is to control the vehicle drive system and brake system to track the expected speed. Finally, the lane changing conditions and other speed conditions of the vehicle at 120 km/h are verified. The results show that the control strategy can track the longitudinal and lateral trajectories well and achieve effective lane change and collision avoidance.

The effects of voluntary running exercise on the astrocytes of the medial prefrontal cortex in APP/PS1 mice

Pathological changes in the medial prefrontal cortex (mPFC) and astrocytes are closely associated with Alzheimer's disease (AD). Voluntary running has been found to effectively delay AD. However, the effects of voluntary running on mPFC astrocytes in AD are unclear. A total of 40 10-month-old male amyloid precursor protein/presenilin 1 (APP/PS1) mice and 40 wild-type (WT) mice were randomly divided into control and running groups, and the running groups underwent voluntary running for 3 months. Mouse cognition was assessed by the novel object recognition (NOR), Morris water maze (MWM), and Y maze tests. The effects of voluntary running on mPFC astrocytes were investigated using immunohistochemistry, immunofluorescence, western blotting, and stereology. APP/PS1 mice performed significantly worse than WT mice in the NOR, MWM, and Y maze tests, and voluntary running improved the performance of APP/PS1 mice in these tests. The total number of mPFC astrocytes was increased, cell bodies were enlarged, and protrusion number and length were increased in AD mice compared with WT mice, but there was no difference in component 3 (C3) levels in the mPFC (total mPFC level); however, C3 and S100B levels in astrocytes were increased in AD mice. Voluntary running reduced the total number of astrocytes and S100B levels in astrocytes and increased the density of PSD95⁺ puncta in direct contact with astrocyte protrusions in the APP/PS1 mouse mPFC. Three months of voluntary running inhibited astrocyte hyperplasia and S100B expression in astrocytes, increased the density of synapses in contact with astrocytes, and improved cognitive function in APP/PS1 mice.

Research on brownfield redevelopment based on Wuli-Shili-Renli system theory and catastrophe progression method

Brownfields are an important part of urban land resources. Strengthening the governance and redevelopment of brownfields is significant to environmental protection, high-quality urban development and sustainable development. However, due to the complexity and harmfulness of brownfield pollution, the hasty, untimely, and blind development can cause serious consequences. It is infeasible to pay more attention to development than governance or vice versa. In this paper, aiming at brownfield redevelopment evaluation, we introduced the Wuli-Shili-Renli (WSR) system methodology, an oriental system thought combining qualitative and quantitative analyses, comprehensively analyzed the influencing factors of brownfields from three dimensions of Wuli, Shili and Renli, and constructed the evaluation index system of brownfield redevelopment. To avoid much subjectivity in the evaluation process, we established the evaluation model of brownfield redevelopment using the catastrophe progression method. Taking the renovation project of Shanghai Xintiandi in 1999-2001 as a reference, the evaluation index system and evaluation model were applied to the renovation project of Wenjia Street in Qingyang District, Chengdu, Sichuan Province, China in 2022, and the results provided a good basis for the decision-making process.

Selective biosorption of thorium (IV) from aqueous solutions by ginkgo leaf

Low-cost biosorbents (ginkgo leaf, osmanthus leaf, banyan leaf, magnolia leaf, holly leaf, walnut shell, and grapefruit peel) were evaluated in the simultaneous removal of La3+, Ce3+, Pr3+, Nd3+, Sm3+, Eu3+, Gd3+, Yb3+, Lu3+, UO22+, Th4+, Y3+, Co2+, Zn2+, Ni2+, and Sr2+ from aqueous solutions. In single metal systems, all adsorbents exhibited good to excellent adsorption capacities toward lanthanides and actinides. In a simulated multicomponent mixed solution study, higher selectivity and efficiency were observed for Th4+ over other metal cations, with ginkgo leaves providing the highest adsorptivity (81.2%) among the seven biosorbents. Through optimization studies, the selectivity of Th4+ biosorption on ginkgo leaf was found to be highly pH-dependent, with optimum Th4+ removal observed at pH 4. Th4+ adsorption was found to proceed rapidly with an equilibrium time of 120 min and conform to pseudo-second-order kinetics. The Langmuir isotherm model best described Th4+ biosorption, with a maximum monolayer adsorption capacity of 103.8 mg g-1. Thermodynamic calculations indicated that Th4+ biosorption was spontaneous and endothermic. Furthermore, the physical and chemical properties of the adsorbent were determined by scanning electron microscopy, Brunauer-Emmett-Teller, X-ray powder diffraction, and Fourier transform infrared analysis. The biosorption of Th from a real sample (monazite mineral) was studied and an efficiency of 90.4% was achieved from nitric acid at pH 4 using ginkgo leaves.

Comparative genomics of chemosensory protein genes (CSPs) in twenty-two mosquito species (Diptera: Culicidae): Identification, characterization, and evolution

Chemosensory proteins (CSP) are soluble carrier proteins that may function in odorant reception in insects. CSPs have not been thoroughly studied at whole-genome level, despite the availability of insect genomes. Here, we identified/reidentified 283 CSP genes in the genomes of 22 mosquitoes. All 283 CSP genes possess a highly conserved OS-D domain. We comprehensively analyzed these CSP genes and determined their conserved domains, structure, genomic distribution, phylogeny, and evolutionary patterns. We found an average of seven CSP genes in each of 19 Anopheles genomes, 27 CSP genes in Cx. quinquefasciatus, 43 in Ae. aegypti, and 83 in Ae. albopictus. The Anopheles CSP genes had a simple genomic organization with a relatively consistent gene distribution, while most of the Culicinae CSP genes were distributed in clusters on the scaffolds. Our phylogenetic analysis clustered the CSPs into two major groups: CSP1-8 and CSE1-3. The CSP1-8 groups were all monophyletic with good bootstrap support. The CSE1-3 groups were an expansion of the CSP family of genes specific to the three Culicinae species. The Ka/Ks ratios indicated that the CSP genes had been subject to purifying selection with relatively slow evolution. Our results provide a comprehensive framework for the study of the CSP gene family in these 22 mosquito species, laying a foundation for future work on CSP function in the detection of chemical cues in the surrounding environment.

Comparative transcriptome analyses reveal the genetic basis underlying the immune function of three amphibians' skin

Skin as the first barrier against external invasions plays an essential role for the survival of amphibians on land. Understanding the genetic basis of skin function is significant in revealing the mechanisms underlying immunity of amphibians. In this study, we de novo sequenced and comparatively analyzed skin transcriptomes from three different amphibian species, Andrias davidianus, Bufo gargarizans, and Rana nigromaculata Hallowell. Functional classification of unigenes in each amphibian showed high accordance, with the most represented GO terms and KEGG pathways related to basic biological processes, such as binding and metabolism and immune system. As for the unigenes, GO and KEGG distributions of conserved orthologs in each species were similar, with the predominantly enriched pathways including RNA polymerase, nucleotide metabolism, and defense. The positively selected orthologs in each amphibian were also similar, which were primarily involved in stimulus response, cell metabolic, membrane, and catalytic activity. Furthermore, a total of 50 antimicrobial peptides from 26 different categories were identified in the three amphibians, and one of these showed high efficiency in inhibiting the growth of different bacteria. Our understanding of innate immune function of amphibian skin has increased basis on the immune-related unigenes, pathways, and antimicrobial peptides in amphibians.