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LINE-1 as a Potential Therapeutic Target for High-Fat Diet-Induced Liver Pathology
No full textBackground: Transposable elements, particularly LINE-1 (L1), constitute a substantial portion of the genome and act as stress-responsive elements capable of modulating gene expression and innate immune signaling. While metabolic stress is known to alter chromatin states, it remains unclear whether high-fat diet (HFD) exposure can activate L1 in hepatocytes and what epigenetic mechanisms might mediate this effect. Histone succinylation, an alternative acylation linked to metabolic flux, has emerged as a potential regulator of chromatin accessibility, but its role in L1 regulation under lipid stress is unexplored. Objectives: This study aimed to (1) investigate whether saturated and unsaturated fatty acids influence L1 expression and inflammatory signaling in hepatocytes, (2) examine histone succinylation as a candidate epigenetic mechanism underlying L1 derepression in response to HFD-associated stress, (3) determine the role of L1 in IRF3-mediated immune activation, and (4) evaluate the therapeutic potential of L1 suppression in diet-induced metabolic disease. Methods: Hepatocytes were exposed to palmitic acid (PA) or oleic acid (OA), and transcriptomic changes were profiled using RNA-seq and validated by qRT-PCR. Chromatin-level alterations, including lysine succinylation and CBP/p300, were evaluated by chromatin immunoprecipitation. L1 knockdown was achieved with antisense oligonucleotides (ASOs) in vitro, and in vivo studies were performed in C57BL/6J mice fed a palmitate, fructose, and cholesterol (FPC) diet, followed by L1-targeting ASO administration. Results: PA, but not OA, induced dose-dependent upregulation of L1 transcripts and interferon-stimulated genes, accompanied by increased CBP/p300mediated H3K122 succinylation, enhanced p300 and lysine succinylation occupancy at L1 promoters. L1 knockdown mitigated PA-induced inflammatory responses in vitro. In vivo, L1 suppression improved insulin sensitivity, reduced expression of inflammation and fibrosis pathways, and alleviated hepatic lipid accumulation and fibrosis, demonstrating attenuation of key NAFLD/NASH phenotypes. Conclusions: These findings reveal that HFD-associated lipid stress can activate L1 in hepatocytes through p300-mediated H3K122 succinylation, identifying a previously unrecognized epigenetic mechanism linking metabolic state to chromatin remodeling. Therapeutically, L1 inhibition mitigates hepatic inflammation, fibrosis, and metabolic dysfunction, positioning L1 as a potential target in diet-induced liver disease
Electric Field-Driven Bacterial Membrane Disintegration with Real-Time Electrical Response in SWCNT Bioelectronic Platforms.
No full textWe report a bioelectronic platform that integrates hydrophilically functionalized single-walled carbon nanotubes (SWCNTs) with Escherichia coli and gold (Au) electrodes to investigate real-time charge transport at microbial-electrode interfaces. Acid-functionalized SWCNTs enhance aqueous dispersibility and facilitate electron transfer in a deionized water environment under applied bias. Upon bacterial introduction, the device exhibits a sharp transient current spike followed by a stabilization phase, indicative of dynamic bacterial attachment and interfacial electron exchange. Kelvin probe force microscopy (KPFM) mapping reveals changes in contact potential difference (CPD) among the SWCNTs, bacteria, and Au electrodes, confirming localized charge redistribution. Additionally, the formation of depletion regions near electrode edges─driven by bacterial repulsion and ionic interactions, generates capacitive effects that modulate device conductivity. Systematic variation of bacterial concentration demonstrates a direct influence on device response, providing mechanistic insight into microbial charge transfer behavior. These findings establish a foundational understanding of nanobioelectronic interactions and highlight the potential of SWCNT-based platforms in real-time microbial sensing, environmental biosurveillance, and next-generation bioelectronic applications.This work is partially supported by the Ministry of Electronics and Information Technology (MeitY) 5(1)/2017-NANO, 5(1)/2021-NANO, INUP-i2i, and the (DST) DST/NM/NNetRA/2018(G)-IIT-KGP, Government of India. We acknowledge financial support from the Council of Scientific and Industrial Research (CSIR) (File number −09/081(1397)/2020-EMR-I), Ministry of Science and Technology, Government of India
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025
No full textThe National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), offers a comprehensive suite of database resources to support the global scientific community. Amidst the unprecedented accumulation of multi-omics data, CNCB-NGDC is committed to continually evolving and updating its core database resources through big data archiving, integrative analysis and value-added curation. Over the past year, CNCB-NGDC has expanded its collaborations with international databases and established new subcenters focusing on biodiversity, traditional Chinese medicine and tumor genetics. Substantial efforts have been made toward encompassing a broad spectrum of multi-omics data, developing innovative resources and enhancing existing resources. Notably, new resources have been developed for single-cell omics (scTWAS Atlas), genome and variation (VDGE), health and disease (CVD Atlas, CPMKG, Immunosenescence Inventory, HemAtlas, Cyclicpepedia, IDeAS), biodiversity and biosynthesis (RefMetaPlant, MASH-Ocean) and research tools (CCLHunter). All resources and services are publicly accessible at https://ngdc.cncb.ac.cn.We thank our users for submitting data, sending suggestions,
reporting bugs and engaging in community curation. CNCBNGDC is indebted to its funders, including the Ministry of
Science and Technology and the Ministry of Finance of the
People’s Republic of China and the Chinese Academy of
Sciences.Chinese Academy of Sciences [XDB38030200, XDA0450100, XDA24040201, XDB38030100, XDB38030400, XDB38050300, XDA12030100, XDB38040300, XDB38030202, XDA16021403, XDB38000000, XDB38030000, XDB38010400, XDB38010401]; National Key Research and Development Program of China [2023YFC2605700, 2023YFC3041500, 2023YFF0725600, 2021YFF0703700, 2021YFF0703701, 2021YFF0703702, 2021YFF0703703, 2021YFF0703704, 2021YFF0704500, 2021YFC2301502, 2021YFC0863300, 2020YFA0907001, 2019YFA0801801, 2018YFA0801405, 2018YFC2000100, 2018YFC1406902, 2018YFC0910400, 2018YFC0310602, 2018YFA0903700, 2018YFA0900704, 2018YFA0900700]; National Natural Science Foundation of China [T2425005, 32170678, 31970565, 31871328, 31871294, 31970647, 31801104, 32000475, 1470330, 31961130380, 31822030, 31801113, 31801154, 91940303, 91940306, 31871281, 31930021, 32025009, 31970633, 32100520, 32170669, 32100506, 32100511, 62002388, 82161148009, 32270718, 32030021, 82270126, 82170542, 32200529, 82000536, 32300542, 32300468, 32470608]; Chinese Academy of Sciences [153D31KYSB20170121, 161GJHZ2022002MI];
Chinese Academy of Sciences [WX145XQ07-04]; Fundamental Research Funds for the Central Universities [2019kfyRCPY043]; UK Royal Society-Newton Advanced Fellowship [NAF\R1\191094]; Key Research Program of Frontier Sciences of the Chinese Academy of Sciences [QYZDJ-SSW-SYS009]; Chinese Academy of Sciences Key Technology Talent Program; Chinese Academy of Sciences; K.C. Wong Education Foundation; Chinese Academy of Sciences [Y2021038, Y2023027, 2022098, 2023110]; National Key R&D Program of China [SQ2017YFSF090210]; China Postdoctoral Science Foundation [2019M652623, 2018M632830, 2021M693109]; The Open Biodiversity and Health Big Data Program of IUBS; The Alliance of National and International Science Organizations for the Belt and Road Regions [ANSO-PA-2023-07, ANSO-CR-KP-2022- 09]; Funds for Basic Resources Investigation Research of the Ministry of Science and Technology [2018FY10080002]; Special Project on National Science and Technology Basic Resources Investigation [2019FY100102]; CAS Pioneer
100-Talent Program; Key Research Program of the Chinese Academy of Sciences [KFZD-SW-219-5]; Zhangjiang National Innovation Demonstration Zone [ZJ2018-ZD013]; Science and Technology Service Network Initiative of Chinese Academy of Sciences; Hunan Provincial Science and Technology Program [2018wk4001]; 111 Project [B18059], King Abdullah University of Science and Technology (KAUST) [FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, REI/1/0018-01- 01, REI/1/4216-01-01, REI/1/4437-01-01, REI/1/4473-01- 01, URF/1/4352-01-01, URF/1/4379-01-01, REI/1/4742- 01-01, URF/1/4098-01-01]; Biological Resources Programme, Chinese Academy of Sciences [KFJ-BRP-017-79, KFJ-BRP-009]; Specialized Research Assistant Program of the Chinese Academy of Sciences [202044]; National Natural Science Foundation of China [32061143024]; Shanghai Municipal Science and Technology Commission [2017SHZDZX01]; Guangdong Province ‘Pearl River Talent Plan’ Innovation and Entrepreneurship Team Project
[2019ZT08Y464], Guangdong Provincial Clinical Research Center for Digestive Diseases [2020B1111170004], National Key Clinical Discipline and the Informatization Plan of Chinese Academy of Sciences [CAS-WX2021SF-0307]; Technological Innovation 2030 [2022ZD0401701]; Beijing Nova Program [Z211100002121006]; Science and Technology Fundamental Resources Investigation Program
[2022FY101203]. Funding for open access charge: National Natural Science Foundation of China
Fluid Dynamic Characterization of Binary Droplet Collisions via the Pseudopotential Lattice-Boltzmann Method
No full textA thermodynamically consistent modified pseudopotential lattice Boltzmann (LB) model was implemented to investigate the hydrodynamic behavior of picoliter droplets undergoing binary collisions for a wide range of realistic conditions and at large liquid-gas density ratios. The model was thoroughly validated for two benchmark cases, namely a stationary droplet for thermodynamic consistency assessment (equilibrium density and surface tension evaluation), and an ellipsoidal oscillating droplet for fidelity of capturing the transient behavior. For the latter, the deviations of the predicted oscillation period with respect to the analytical solution were below 1%. Regarding the binary collisions of equal-size picoliter droplets at different impact velocities and collision angles, the predicted hydrodynamic behavior was compared with the recent experimental results McCarthy et al. (2022), showing good agreement. The detailed simulation results were further analyzed to provide insights into the distinct physical characteristics in binary droplet collisions by examining the transient evolution of local momentum and energy budget in terms of kinetic energy, surface tension energy, and viscous dissipation, while also identifying the collision sub-regimes associated with each primary collision case. In the coalescence regime, a single main peak in the momentum profile, corresponding to droplet impact, is followed by a decaying oscillation pattern. The reflexive separation regime exhibits three distinct momentum peaks, associated with droplet impact, liquid head recombination, and stretching separation. In contrast, the stretching separation regime lacks the liquid head recombination phase, resulting in only two momentum peaks. Overall, reflexive separation involves seven sub-regimes: free droplet movement, droplet impact, initial elongation, liquid filament retraction, liquid head recombination, secondary stretching, and liquid filament breakup. However, in the stretching separation regime, both liquid head recombination and secondary stretching are absent. The present LB model faithfully captured the detailed physical characteristics for a wide range of parametric conditions. Lastly, extensive parametric simulations were undertaken to reproduce the Weber number-impact factor collision regime map and predict satellite droplet formation, showing good agreement with previous studies, further demonstrating the fidelity and robustness of the LB model for real droplet collision problems.This work was sponsored by King Abdullah University of Science and Technology (KAUST) under the Competitive Research Grant, URF/1/1677-01-01. Computational resources were provided by the KAUST Supercomputing Laboratory (KSL)
Interseismic Deformation of the Húsavík-Flatey Fault (North Iceland) from two Decades of GNSS Data
No full textThe Tjörnes Fracture Zone in North Iceland is one of two transform zones in Iceland capable of generating earthquakes of magnitude ∼7. More than 150 years have passed since the last two major earthquakes occurred on the Húsavík-Flatey fault, one of the two main transform structures within the Tjörnes Fracture Zone. Given the seismic hazard posed to Húsavík and adjacent coastal communities, accurately determining the slip rate and locking depth of this fault is crucial for a robust earthquake hazard and risk assessment. In this study, we significantly expand the existing GNSS dataset for the Tjörnes Fracture Zone by incorporating more than a decade of additional data and doubling the number of stations. This expansion not only improves the spatial coverage of the network, but also refines the station velocities. We present an updated interseismic velocity field for North Iceland and implement a backslip model with nine dislocation segments to describe the plate boundary deformation. Additionally, we include a point pressure source for the ongoing broad uplift signal in the study area. Our findings indicate a locking depth of km and an average slip rate of 6.9 ± 0.2 mm/yr for the Húsavík-Flatey fault. With our updated approach, we can narrow down model parameter constraints from previous studies and thereby provide an enhanced understanding of the earthquake potential of this region.We thank Ulas Avsar, Teng Wang, Rishabh Dutta, Wenbin Xu, Jon Harrington, Ayrat Abdullin
and Max Mai for taking part in the 2013 measurement campaign, Joel Ruch, Hannes VasyuraBathke, Tim Sonnemann and James Scott Berdahl for taking part in the 2016 campaign, Laura
Parisi, Daniele Trippanera, Xing Li, Sturla Thengilsson, Laila Mai, Kári Daníel Alexandersson
and Margrét Hrafnsdóttir for taking part in the 2019 campaign, and Jochen Woessner, Matthieu
Ribot, Adriano Nobile, Adrien Moulin, Sturla Thengilsson, Paul Mai, Margrét María Hallgrímsdóttir, and Margrét Hrafnsdóttir for taking part in the 2022 campaign. We thank Guðmundur Valsson (National Land Survey of Iceland) for providing the ISNET GNSS data. This research was supported by the King Abdullah University of Science and Technology (KAUST), under Award
Number BAS/1/1353-01-01
Computational Design of Heterogeneous Catalysts: Bridging Density Functional Theory and Artificial Intelligence for Sustainable CO₂ Conversion and Ammonia Synthesis
No full textThis dissertation tackles two pressing challenges in sustainable catalysis: the conversion of carbon dioxide (CO₂) into value-added products and the development of energy-efficient alternatives to the Haber–Bosch ammonia synthesis. The research combines density functional theory (DFT) with advanced machine learning (ML), particularly graph neural networks (GNNs), to connect atomic-scale mechanistic insight with accelerated catalyst discovery.
Four catalytic systems were studied in detail. DFT modelling of Ca₃CrN₃ and its hydride derivative Ca₃CrN₃H showed that associative nitrogen activation can occur under milder conditions than Haber–Bosch, aided by hydrogen vacancy engineering and the unique role of lattice hydrides. In alkali-modified In₂O₃, promoter-induced changes to oxygen vacancies selectively stabilised *COOH intermediates, improving reverse water–gas shift (RWGS) selectivity toward CO. Fe–Co bimetallic catalysts displayed cooperative behaviour, where cobalt enhanced H₂ dissociation and iron maintained CO₂ activation, while potassium carbonate promotion reduced *CO poisoning and improved turnover.
To expand these findings into large-scale screening, CHGNet, M3GNet, and ORB GNN models were benchmarked against spin-polarised, dispersion-corrected DFT data for CO, N₂, and H adsorption on oxide and perovskite surfaces. ORB provided the highest accuracy in both adsorption energy and site prediction, demonstrating that high-fidelity GNNs can serve as computational pre-filters, greatly reducing the cost of surface mapping.
The integration of DFT and ML revealed general design strategies, including targeted defect engineering, promoter-driven electronic tuning, bifunctional site synergy, and predictive structure–activity mapping. These approaches form a transferable framework for moving from fundamental theory to practical catalyst design, accelerating the discovery of heterogeneous catalysts for a low-carbon, resource-efficient future
Imaging Gas-Involved Structural Dynamics by Environmental Electron Microscopy.
No full textUnderstanding gas-involved physicochemical reactions is undoubtedly one of the most significant challenges in the modern chemical industry. To clarify how those reactions precede requires deep insights into the real-time visualization of reaction dynamics within a gas environment. The emergence and rapid development of in situ environmental electron microscopy (EEM) including scanning electron microscopy (ESEM) and transmission electron microscopy (ETEM) have enabled multiscale observation of dynamic gas-involved physicochemical reactions. This review examines the state-of-art EEM technologies, categorizing those gas reactions into various physical and chemical processes and detailing the corresponding dynamic behaviors. It begins by reviewing the state-of-the-art EEM techniques and is followed by detailing their application in typical physical processes. It clarifies physical vapor condensation, deposition, and geometric reshaping with gaseous involving. More importantly, all the gas-involved chemical reactions into electrochemical reactions, thermochemical reactions, chemical crystal growth, and catalytic reactions are thoroughly explored and categorized. Finally, the review highlights the technical challenges and valuable perspectives provided by in situ EEM for addressing critical gas-involved issues. Overall, this article offers a multiscale and comprehensive understanding of the physicochemical origins associated with gas-involved reactions, envisioning fundamental strategies for designing high-performance gas-involved functional materials
Fourier-based proper orthogonal decomposition of a turbulent round jet
No full textWe use scanning-tomographic particle image velocimetry introduced by Casey, Sakakibara & Thoroddsen (Phys. Fluids, vol. 25 (2), 2013, p. 025102) to measure the volumetric velocity field in a fully turbulent round jet. The experiments are performed for Re=2640, 5280 and 10700. Using Fourier-based proper orthogonal decomposition (POD), the dominant modes that describe the velocity and vorticity fields are extracted. We employ a new method of averaging POD modes from different experimental runs using a phase-synchronisation with respect to a common basis. For the dominant azimuthal wavenumber m =1, the first and second POD modes of the axial velocity have opposite signs and appear as embracing helical structures, with opposite twist, while, for the same parameters, POD modes of the radial velocity extend to the axis of symmetry and, interestingly, also show a helical shape. The (m = 1)-POD modes for the azimuthal vorticity appear as two separate structures, consisting of C-shaped loops in the region away from the axis and helically twisted axial tubes close to the axis. The corresponding axial vorticity modes are cone-like and appear as inclined streaks of alternate sign in the r–z-plane, similar to velocity streaks seen in wall-bounded shear flows. Temporal analysis of the dynamics shows that a (m =1) two-mode velocity POD representation precesses with a Strouhal number of approximately St =0.05, while the same reconstruction based on vorticity POD modes has a slightly higher Strouhal number of St =0.06.This study was supported by King Abdullah University of Science and Technology (KAUST) under BAS/1/1352-01-01
Genome sequences of four novel <i>Endozoicomonas</i> strains associated with a tropical octocoral in a long-term aquarium facility.
No full textWe report the genome sequences of four Endozoicomonas sp. strains isolated from the octocoral Litophyton maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type II, III, IV, and VI secretion systems; and the biosynthesis of novel ribosomally synthesized and post-translationally modified peptides.This study was financed by the “Blue Bioeconomy Pact” (Project N°.C644915664-00000026), co-funded by Next Generation EU European Fund, under the incentive line “Agendas for Business Innovation” within Funding Scheme 5-Capitalization
and Business Innovation of the Portuguese Recovery and Resilience Plan (RRP). Further support was provided by the Portuguese Foundation for Science and Technology (FCT) through the projects UIDB/04565/2020 and UIDP/04565/2020 of iBB and the project
LA/P/0140/2020 of i4HB. Sequencing, assembly, and annotation of the four Endozoicomonas sp. genomes were performed at the Joint Genome Institute (JGI) as part of the Genomic Encyclopedia of Type Strains, Phase V (KMG-V): Genome sequencing to
study the core and pangenomes of soil and plant-associated prokaryotes. The work (proposal: 10.46936/10.25585/60001079) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility,
is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. M.M. is the recipient of a PhD scholarship conceded by FCT through the MIT Portugal program (10.54499/SFRH/BD/151376/2021). D.M.G.D.S.
is the recipient of a MSc grant conceded by the “Blue Bioeconomy Pact” project. T.K.-C. is the recipient of a Research Scientist contract conceded by FCT (CEECIND/00788/2017)
Paradox in Sintering of Nascent Ultrahigh Molecular Weight Polymers in the Solid State
No full textThe sintering of ceramics, metals, and polymers has been a subject of intense interest, especially when the materials can be sintered without melting in the solid state. In contrast to inorganic materials, crystallizable polymers have segments of the same chain residing in crystalline and noncrystalline regions. The topological constraints between the chain segments residing in the noncrystalline region are strongly influenced by the crystallization and/or polymerization history. Here, we address the influence of topological constraints on the deformation of crystalline domains to the extent that lattice diffusion and grain boundary diffusion in semicrystalline polymers can be achieved without melting. This allows ease in translation of the macroscopic forces to the molecular length scale in the sintered polymer, facilitating uniaxial and biaxial deformation below the melting temperature. Since solid-state processing circumvents the challenges of melt processing, entropic relaxation of the oriented chains, and thermal degradation of the polymers at high temperatures, unprecedented mechanical properties in the uniaxial and biaxial drawn intractable ultrahigh molar mass polymers have been achieved. Thus, solvent-free sustainable solutions are provided for the processing of the intractable engineering polymers needed for demanding applications. The ease of sintering allows the fabrication of grain-boundary-free products, with advantages in prostheses.The authors wish to acknowledge Mrudul Thaliyil Puthiyaveettil for his valuable help in SEM measurements in ultrahigh molecular weight alternating polyketones; Joris van der Eem and Amr El-Sakran for their valuable help in providing images of tape made by solid-state processing; Dr. Dario Romano, Dr. Ravindra P. Gote, Dr. Sanjay Lolage, Dr. Ameur Louhichi, and Abdulaziz Alsubhi for their valuable help in polymerization and discussions. The authors extend their thanks to the KAUST Imaging and Characterization Core lab facilities. This project was funded by KAUST BAS/1/1407-01-01 and KAUST URF/1/5131-01-01