Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction.

The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo.

Preliminary study on the active substances and cellular pathways of lactic acid bacteria for colorectal cancer treatment.

Colorectal cancer (CRC) is a common malignant tumor and is one of the three most common cancers worldwide. Traditional surgical treatment, supplemented by chemotherapy and radiotherapy, has obvious side effects on patients. Immunotherapy may lead to some unpredictable complications. Low introduction rate and high cost are some of the problems of gene therapy, so finding a safe, reliable and least toxic treatment method became the main research direction for this study. Lactic acid bacteria and their metabolites are widely used in functional foods or as adjuvant therapies for various diseases because they are safe to eat and have no adverse reactions. Research has shown that lactic acid bacteria and their metabolites play an auxiliary therapeutic role in colorectal cancer mainly by improving the intestinal flora composition, inhibiting the growth of pathogenic bacteria and inhibiting the proliferation of cancer cells. It is now widely believed that the substances that probiotics such as lactic acid bacteria exert anti-cancer effects are mainly secondary metabolites such as butyric acid. Lb. plantarum AY01 isolated from fermented food has good anti-cancer ability, and its main anti-cancer substance is 2'-deoxyinosine. Through flow cytometry detection, it was found that Lb. plantarum AY01 can block cell proliferation in the S phase. In addition, Lb. plantarum AY01 culture reduces the sensitivity of mice to colitis-associated CRC induced by azoxymethane (AOM)/dextran sulfate sodium salt (DSS) and exhibits the occurrence and promotion of tumors. According to transcriptome analysis, Lb. plantarum AY01 may induce apoptosis of colorectal cancer cells by activating the p38 MAPK pathway. This experiment provided possibilities for the treatment of CRC.

Swarming Magnetic Fe3O4@Polydopamine-Tannic Acid Nanorobots: Integrating Antibiotic-Free Superficial Photothermal and Deep Chemical Strategies for Targeted Bacterial Elimination.

Micro/nanorobots (MNRs) are envisioned to provide revolutionary changes to therapies for infectious diseases as they can deliver various antibacterial agents or energies to many hard-to-reach infection sites. However, existing MNRs face substantial challenges in addressing complex infections that progress from superficial to deep tissues. Here, we develop swarming magnetic Fe3O4@polydopamine-tannic acid nanorobots (Fe3O4@PDA-TA NRs) capable of performing targeted bacteria elimination in complicated bacterial infections by integrating superficial photothermal and deep chemical strategies. The Fe3O4@PDA-TA nanoparticles (NPs), serving as building blocks of the nanorobots, are fabricated by in situ polymerization of dopamine followed by TA adhesion. When driven by alternating magnetic fields, Fe3O4@PDA-TA NPs can assemble into large energetic microswarms continuously flowing forward with tunable velocity. Thus, the swarming Fe3O4@PDA-TA NRs can be navigated to achieve rapid broad coverage of a targeted superficial area from a distance and rapidly eradicate bacteria residing there upon exposure to near-infrared (NIR) light due to their efficient photothermal conversion. Additionally, they can concentrate at deep infection sites by traversing through confined, narrow, and tortuous passages, exerting sustained antibacterial action through their surface TA-induced easy cell adhesion and subsequent membrane destruction. Therefore, the swarming Fe3O4@PDA-TA NRs show great potential for addressing complex superficial-to-deep infections. This study may inspire the development of future therapeutic microsystems for various diseases with multifunction synergies, task flexibility, and high efficiency.

Topological Polymer Networks-Enabled Mechanically Strong Polyamide-Imide Aerogel Fibers for Thermal Insulation in Harsh Environments.

Aerogel fibers have sparked substantial interest as attractive candidates for thermal insulation materials. Developing aerogel fibers with the desired porous structure, good knittability, flame retardancy, and high- and low-temperature resistance is of great significance for practical applications; however, that is very challenging, especially by using an efficient method. Herein, mechanically strong and flexible aerogel fibers with remarkable thermal insulation performance are reported, which are achieved by constructing stiff-soft topological polymer networks and a multilevel hollow porous structure. The combination of polyamide-imide (PAI) with stiff chains and polyurethane (PU) with soft chains is first found to be able to form a topological entanglement architecture. More importantly, multilevel hollow pores can be constructed synchronously through just a one-step and green wet-spinning process. The resultant PAI/PU@340 aerogel fibers show an ultrahigh breaking strength of 94.5 MPa and superelastic property with a breaking strain of 20%. Furthermore, they can be knitted into fabrics with a low thermal conductivity of 25 mW/(m·K) and exhibit attractive thermal insulation property under extremely high (300 °C) and low temperatures (-191 °C), implying them as promising candidates for next-generation thermal insulation materials.

480†nm InGaN-based cyan laser diode grown on Si by interface engineering of active region.

InGaN-based long wavelength laser diodes (LDs) grown on Si are highly desirable for expanding the applications in laser display and lighting. Proper interface engineering of high In-content InGaN multi-quantum wells (MQWs) is urgently required for the epitaxial growth of InGaN-based long wavelength LD on Si, because the deteriorated interfaces and crystalline quality of InGaN MQWs can severely increase the photon scattering and further exacerbate the internal absorption loss of LDs, which prevents the lasing wavelength of InGaN-based LDs from extending. In this work, a significantly improved morphology and sharp interface of the InGaN active region are obtained by using a graded-compositional InGaN lower waveguide (LWG) capped with a 10-nm-thick Al0.1Ga0.9N layer. The V-pits density of the InGaN LWG was one order of magnitude reduction from 4.8 × 108 to 3.6 × 107 cm-2 along with the root-mean-square surface roughness decreasing from 0.3 to 0.1 nm. Therefore, a room-temperature electrically injected 480 nm InGaN-based cyan LD grown on Si under pulsed current operation was successfully achieved with a threshold current density of 18.3 kA/cm2.

Harnessing Disparities in Magnetic Microswarms: From Construction to Collaborative Tasks.

Individual differences in size, experience, and task specialization in natural swarms often result in heterogeneity and hierarchy, facilitating efficient and coordinated task accomplishment. Drawing inspiration from this phenomenon, a general strategy is proposed for organizing magnetic micro/nanorobots (MNRs) with apparent differences in size, shape, and properties into cohesive microswarms with tunable heterogeneity, controlled spatial hierarchy, and collaborative tasking capability. In this strategy, disparate magnetic MNRs can be manipulated to show reversible transitions between synchronization and desynchronization by elaborately regulating parameter sets of the rotating magnetic field. Utilizing these transitions, alongside local robust hydrodynamic interactions, diverse heterospecific pairings of disparate magnetic MNRs can be organized into heterogeneous microswarms, and their spatial organization can be dynamically adjusted from egalitarian to leader-follower-like hierarchies on the fly, both in open space and complex microchannels. Furthermore, when specializing the disparate MNRs with distinct functions ("division of labor") such as sensing and drug carrying, they can execute precise drug delivery targeting unknown sites in a collaborative sensing-navigating-cargo dropping sequence, demonstrating significant potential for precise tumor treatment. These findings highlight the critical roles of attribute differences and hierarchical organization in designing efficient swarming micro/nanorobots for biomedical applications.

Integration of Clinical Trial Spatial Multi-omics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery.

Computational methods that simulate tumors mathematically to describe cellular and molecular interactions are emerging as promising tools to simulate the impact of therapy entirely in silico, potentially greatly accelerating the delivery of new therapeutics to patients. To facilitate the design of dosing regimens and identification of potential biomarkers for immunotherapy, we developed a new computational model to track tumor progression at the organ scale while capturing the spatial heterogeneity of the tumor in HCC. This computational model of spatial quantitative systems pharmacology (spQSP) was designed to simulate the effects of combination immunotherapy. The model was initiated using literature-derived parameter values and fitted to the specifics of HCC. Model validation was done through comparison to spatial multi-omics data from a neoadjuvant HCC clinical trial combining anti-PD-1 immunotherapy and a multitargeted tyrosine kinase inhibitor (TKI) cabozantinib. Validation using spatial proteomics data from Imaging Mass Cytometry (IMC) demonstrated that closer proximity between CD8 T cells and macrophages correlated with non-response. We also compared the model output with Visium spatial transcriptomics (ST) profiling of samples from post-treatment tumor resections in the clinical trial and from another independent study of anti-PD1 monotherapy. ST data confirmed simulation results, suggesting the importance of spatial patterns of tumor vasculature and TGFß in tumor and immune cell interactions. Our findings demonstrate that incorporating mathematical modeling and computer simulations with high-throughput spatial multi-omics data provides a novel approach for patient outcome prediction and biomarker discovery.

Stimulus-Induced Dynamic Behavior Regulation of Flexible Crystals through the Tuning of Module Rigidity.

Introducing dynamic behavior into periodic frameworks has borne fruit in the form of flexible porous crystals. The detailed molecular design of frameworks in order to control their collective dynamics is of particular interest, for example, to achieve stimulus-induced behavior. Herein, by varying the degree of rigidity of ditopic pillar linkers, two isostructural flexible metal-organic frameworks (MOFs) with common rigid supermolecular building bilayers were constructed. The subtle substitution of single (in bibenzyl-4,4'-dicarboxylic acid; H2BBDC) with double (in 4,4'-stilbenedicarboxylic acid; H2SDC) C-C bonds in pillared linkers led to markedly different flexible behavior of these two MOFs. Upon the removal of guest molecules, both frameworks clearly show reversible single-crystal-to-single-crystal transformations involving the cis-trans conformation change and a resulting swing of the corresponding pillar linkers, which gives rise to Flex-Cd-MOF-1a and Flex-Cd-MOF-2a, respectively. Strikingly, a more favorable gas-induced dynamic behavior in Flex-Cd-MOF-2a was verified in detail by stepwise C3H6/C3H8 sorption isotherms and the corresponding in situ powder X-ray diffraction experiments. These insights are strongly supported by molecular modeling studies on the sorption mechanism that explores the sorption landscape. Furthermore, a consistency between the macroscopic elasticity and microscopic flexibility of Flex-Cd-MOF-2 was observed. This work fuels a growing interest in developing MOFs with desired chemomechanical functions and presents detailed insights into the origins of flexible MOFs.

Heterogeneous Sensor-Carrier Microswarms for Collaborative Precise Drug Delivery toward Unknown Targets with Localized Acidosis.

Micro/nanorobots hold the potential to revolutionize biomedicine by executing diverse tasks in hard-to-reach biological environments. Nevertheless, achieving precise drug delivery to unknown disease sites using swarming micro/nanorobots remains a significant challenge. Here we develop a heterogeneous swarm comprising sensing microrobots (sensor-bots) and drug-carrying microrobots (carrier-bots) with collaborative tasking capabilities for precise drug delivery toward unknown sites. Leveraging robust interspecific hydrodynamic interactions, the sensor-bots and carrier-bots spontaneously synchronize and self-organize into stable heterogeneous microswarms. Given that the sensor-bots can create real-time pH maps employing pH-responsive structural-color changes and the doxorubicin-loaded carrier-bots exhibit selective adhesion to acidic targets via pH-responsive charge reversal, the sensor-carrier microswarm, when exploring unknown environments, can detect and localize uncharted acidic targets, guide itself to cover the area, and finally deploy therapeutic carrier-bots precisely there. This versatile platform holds promise for treating diseases with localized acidosis and inspires future theranostic microsystems with expandability, task flexibility, and high efficiency.

The complete plastome and phylogenetic analysis of Commelina benghalensis L.1753 (Commelinaceae).

Commelina benghalensis L. 1753, a member of the Commelinaceae family, holds significant medicinal and culinary value. This study represents the first documentation of the sequencing and assembly of the entire plastome of C. benghalensis. The genome spans a total length of 160,663 bp, exhibiting a conventional quadripartite architecture that comprises a large single-copy (LSC) region (87,750 bp), a small single-copy (SSC) region (18,417 bp), and two inverted repeats (IR) regions (both 27,248 bp). In its entirety, the C. benghalensis plastome encompasses 129 genes (with 108 being unique), incorporating 77 individual protein-coding genes, 37 unique tRNA genes, and four unique rRNA genes. Phylogenetic analysis revealed a close resemblance between C. benghalensis and C. communis. The sequencing of this plastome stands to expedite the development of molecular markers and significantly contribute to genetic assays involving this distinctive plant.

Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology.

Understanding the intricate interactions of cancer cells with the tumor microenvironment (TME) is a pre-requisite for the optimization of immunotherapy. Mechanistic models such as quantitative systems pharmacology (QSP) provide insights into the TME dynamics and predict the efficacy of immunotherapy in virtual patient populations/digital twins but require vast amounts of multimodal data for parameterization. Large-scale datasets characterizing the TME are available due to recent advances in bioinformatics for multi-omics data. Here, we discuss the perspectives of leveraging omics-derived bioinformatics estimates to inform QSP models and circumvent the challenges of model calibration and validation in immuno-oncology.

A linker selective retention strategy to construct hierarchical porous metal-organic frameworks with high catalytic activity for oxidative desulfurization.

In order to improve the oxidative desulfurization (ODS) performance of MOF materials, an effective way is to convert a microporous MOF into a hierarchical porous MOF (HP-MOF) by utilizing the linker selective retention strategy. Herein, UiO-66 with the introduction of an unstable linker ligand (dihydro-1,2,4,5-tetrazine-3,6-dicarboxylate, dhtz) can selectively remove dhtz ligands to form HP-MOF (HP-UiO-66-dhtz) through heat treatment at high temperature. While maintaining the original structure of UiO-66, HP-UiO-66-dhtz features mesopores and abundant Lewis acid sites, showing excellent ODS performance for diphenylthiophene (DBT).

Regioselective Hydroxylation of Unsymmetrical Ketones Using Cu, H2O2, and Imine Directing Groups via Formation of an Electrophilic Cupric Hydroperoxide Core.

Herein, we describe the regioselective functionalization of unsymmetrical ketones using imine directing groups, Cu, and H2O2. The C-H hydroxylation of the substrate-ligands derived from 2-substituted benzophenones occurred exclusively at the γ-position of the unsubstituted ring due to the formation of only one imine stereoisomer. Conversely, the imines derived from 4-substituted benzophenones produced E/Z mixtures that upon reacting with Cu and H2O2 led to two γ-C-H hydroxylation products. Contrary to our initial hypothesis, the ratio of the hydroxylation products did not depend on the ratio of the E/Z isomers but on the electrophilicity of the reactive [LCuOOH]1+. A detailed mechanistic analysis suggests a fast isomerization of the imine substrate-ligand binding the CuOOH core before the rate-determining electrophilic aromatic hydroxylation. Varying the benzophenone substituents and/or introducing electron-donating and electron-withdrawing groups on the 4-position of pyridine of the directing group allowed for fine-tuning of the electrophilicity of the mononuclear [LCuOOH]1+ to reach remarkable regioselectivities (up to 91:9 favoring the hydroxylation of the electron-rich arene ring). Lastly, we performed the C-H hydroxylation of alkyl aryl ketones, and like in the unsymmetrical benzophenones, the regioselectivity of the transformations (sp3 vs sp2) could be controlled by varying the electronics of the substrate and/or the directing group.

A Dual Fluorescence Turn-On Sensor Array Formed by Poly(para-aryleneethynylene) and Aggregation-Induced Emission Fluorophores for Sensitive Multiplexed Bacterial Recognition.

Bacterial infections have emerged as the leading causes of mortality and morbidity worldwide. Herein, we developed a dual-channel fluorescence "turn-on" sensor array, comprising six electrostatic complexes formed from one negatively charged poly(para-aryleneethynylene) (PPE) and six positively charged aggregation-induced emission (AIE) fluorophores. The 6-element array enabled the simultaneous identification of 20 bacteria (OD600=0.005) within 30s (99.0 % accuracy), demonstrating significant advantages over the array constituted by the 7 separate elements that constitute the complexes. Meanwhile, the array realized different mixing ratios and quantitative detection of prevalent bacteria associated with urinary tract infection (UTI). It also excelled in distinguishing six simulated bacteria samples in artificial urine. Remarkably, the limit of detection for E. coli and E. faecalis was notably low, at 0.000295 and 0.000329 (OD600), respectively. Finally, optimized by diverse machine learning algorithms, the designed array achieved 96.7 % accuracy in differentiating UTI clinical samples from healthy individuals using a random forest model, demonstrating the great potential for medical diagnostic applications.

Mechanism of p-Type Heteroatom Doping of Lithium Stannate for the Photodegradation of 2,4-Dichlorophenol: Enhanced Hole Oxidative Capability and Concentrations.

A systematic evaluation of enhancing photocatalysis via aliovalent cation doping is conducted. Cation In3+, being p-type-doped, was chosen to substitute the Sn site (Sn4+) in Li2SnO3, and the photodegradation of 2,4-dichlorophenol was applied as a model reaction. Specifically, Li2Sn0.90In0.10O3 exhibited superior catalytic performance; the photodegradation efficiency reached about 100% within only 12 min. This efficiency is far greater than that of pure Li2SnO3 under identical conditions. Density functional theory calculations reveal that introducing In3+ increased the electron mobility, yet decreased the hole mobility, leading to photogenerated carrier separation. However, photoluminescence and time-resolved photoluminescence suggest that In3+ induced nonradiative coupling in the matrix, reducing the photogenerated carrier separation ratio compared with that of Li2SnO3. The optical band gap of Li2Sn0.90In0.10O3 was almost unchanged compared with that of Li2SnO3 via ultraviolet-visible absorption. The increased photocatalytic efficiency was ascribed to the lower valence band position and enhanced hole concentrations by valence band X-ray photoelectron spectroscopy and electrochemical measurements. Finally, a 2,4-dichlorophenol degradation pathway, an intermediate toxicity assessment, and a photocatalytic mechanism were proposed. This work offers insights into designing and optimizing semiconductor photocatalysts with high performance.

Unpaired low-dose computed tomography image denoising using a progressive cyclical convolutional neural network.

BACKGROUND: Reducing the radiation dose from computed tomography (CT) can significantly reduce the radiation risk to patients. However, low-dose CT (LDCT) suffers from severe and complex noise interference that affects subsequent diagnosis and analysis. Recently, deep learning-based methods have shown superior performance in LDCT image-denoising tasks. However, most methods require many normal-dose and low-dose CT image pairs, which are difficult to obtain in clinical applications. Unsupervised methods, on the other hand, are more general. PURPOSE: Deep learning methods based on GAN networks have been widely used for unsupervised LDCT denoising, but the additional memory requirements of the model also hinder its further clinical application. To this end, we propose a simpler multi-stage denoising framework trained using unpaired data, the progressive cyclical convolutional neural network (PCCNN), which can remove the noise from CT images in latent space. METHODS: Our proposed PCCNN introduces a noise transfer model that transfers noise from LDCT to normal-dose CT (NDCT), denoised CT images generated from unpaired CT images, and noisy CT images. The denoising framework also contains a progressive module that effectively removes noise through multi-stage wavelet transforms without sacrificing high-frequency components such as edges and details. RESULTS: Compared with seven LDCT denoising algorithms, we perform a quantitative and qualitative evaluation of the experimental results and perform ablation experiments on each network module and loss function. On the AAPM dataset, compared with the contrasted unsupervised methods, our denoising framework has excellent denoising performance increasing the peak signal-to-noise ratio (PSNR) from 29.622 to 30.671, and the structural similarity index (SSIM) was increased from 0.8544 to 0.9199. The PCCNN denoising results were relatively optimal and statistically significant. In the qualitative result comparison, PCCNN without introducing additional blurring and artifacts, the resulting image has higher resolution and complete detail preservation, and the overall structural texture of the image is closer to NDCT. In visual assessments, PCCNN achieves a relatively balanced result in noise suppression, contrast retention, and lesion discrimination. CONCLUSIONS: Extensive experimental validation shows that our scheme achieves reconstruction results comparable to supervised learning methods and has performed well in image quality and medical diagnostic acceptability.

Research Note: Xylooligosaccharide directly attenuates Salmonella Typhimurium colonization and its induction of impairments in intestinal barrier and growth performance of broilers.

Xylooligosaccharide (XOS) is known as a prebiotic, however, it is unknown whether XOS can directly protect against bacterial infection. This study aimed to investigate the direct inhibitory effects of XOS on Salmonella Typhimurium colonization and the inductive impairments in gut health and growth performance in broilers. We first probed the inhibitory effects of XOS on S. Typhimurium adhesion and its induction of intestinal epithelial cell (IPEC-J2) injuries. Afterward, 168 one-day-old yellow-feathered broilers were randomly divided into 3 groups (7 replicates/group): negative control (NC, received a basal diet), positive control (PC, received a basal diet with S. Typhimurium challenge) and XOS group (PC birds + 1,500 mg/kg XOS). All birds except those in NC were orally challenged with S. Typhimurium from 8 to 10 d of age. Parameters were analyzed on d 11. The results showed that XOS inhibited S. Typhimurium adhesion and the inductive injuries of IPEC-J2 cells by lowering (P < 0.05) certain adhesion-related genes expression of this bacterium. It also alleviated S. Typhimurium-induced increase (P < 0.05) in the expression of certain inflammatory cytokines and tight junction (TJ) proteins of IPEC-J2 cells. Supplementing XOS to S. Typhimurium-challenged broilers attenuated the elevations (P < 0.05) in S. Typhimurium colonization of ileal mucosa and its translocation to the liver and spleen, as well as increased (P < 0.05) certain TJ proteins expression of ileum. Besides, XOS addition normalized S. Typhimurium-induced impairments (P < 0.05) in ileal morphology, final body weight and average daily gain in broilers. Collectively, supplemental XOS directly suppressed intestinal colonization of S. Typhimurium by diminishing its adhesiveness and subsequently mitigated destructions in intestinal barriers, thus contributing to weaken growth retardation in challenged broilers. Our findings provide a new insight into the mechanisms of XOS limiting Salmonella infection in chickens.

Ligand-based pharmacophore modelling, structure optimisation, and biological evaluation for the identification of 2-heteroarylthio-N-arylacetamides as novel HSP90 C-terminal inhibitors.

Targeting Heat shock protein 90 (HSP90) C-terminus is an important strategy to develop HSP90 inhibitors without inducing heat shock response. The development of C-terminal inhibitors, however, is hampered by a lack of understanding regarding the interaction between the HSP90 C-terminus and the present inhibitors. We collected seven classical and structurally diverse HSP90 C-terminal inhibitors and constructed a ligand-based pharmacophore model. The subsequent virtual screening and structural optimisation led to the identification of 2-heteroarylthio-N-arylacetamides as novel HSP90 C-terminal inhibitors. 9 and 27 exhibited strong antitumour activity in vitro by inhibiting proliferation and inducing apoptosis in multiple cancer cell lines. These compounds disrupted the interaction between HSP90 C-terminus and peptidylprolyl isomerase D, exerting a stronger inhibitory effect than novobiocin. 27 significantly induced the degradation of HSP90 clients without triggering heat shock response. In an in vivo study using 4T1 mice breast cancer models, 9 showed a potent antitumour effect without obvious toxicity.