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Abstract The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.

Background: Innate and adaptive immunity are two different parts of the immune system that have different characteristics and work together to provide immune protection. Inflammasomes are a major part of the innate immune system that are expressed widely in myeloid cells and are responsible for inflammatory responses. Recent studies have shown that inflammasomes are also expressed and activated in lymphocytes, especially in T and B cells, to regulate the adaptive immune response. Activation of inflammasomes is also under the control of lymphocytes. Therefore, we propose that inflammasomes act as a bridge and they provide crosstalk between the innate and adaptive immune systems to obtain a fine balance in immune responses. Aim of Review: This review systematially summarizes the interaction between inflammasomes and lymphocytes and describes the crosstalk between the innate and adaptive immune systems induced by inflammasomes, with the aim of providing new directions and important areas for further research. Key Scientific Concepts of Review: When considering the novel function of inflammasomes in various lymphocytes, attention should be given to the activity of specific inflammasomes in studies of lymphocyte function. Moreover, research on the function of various inflammasomes in lymphocytes will help advance knowledge on the mechanisms and treatment of various diseases, including autoimmune diseases and tumors. In addition, when studying inflammatory responses, inflammasomes in both lymphocytes and myeloid cells need to be considered.

Abstract A controlled growth of two‐dimensional (2D) π‐conjugated metal‐organic frameworks (MOFs) on solid substrates can open exciting opportunities for the application of 2D MOFs as optoelectronic devices. Some factors like solvent composition and type of substrates are known to influence the properties of solution‐processed 2D MOF crystals; however, a mechanistic understanding of how interactions between solvent, substrate, and precursors affect heterogeneous nucleation has been limited. Here, it is reported that the structure of Ni‐catecholate (Ni‐CAT‐1) MOFs at a solid–liquid interface is controlled by solvent–substrate and solvent–MOF precursor interactions. Specifically, the structure of the MOF film can be controlled by varying the affinity of the solvent to the substrate. As a fraction of N,N‐dimethylformamide (DMF) in a binary solvent mixture of water and DMF increases, the arrangement of Ni‐CAT‐1 crystals varies from vertically aligned nanorods to the graphite substrate to less ordered nanorods with the lower initial nucleation number density of Ni‐CAT‐1 crystals on the surface.

Abstract Stainless steels are used in a myriad of engineering applications, including construction, automobiles, and nuclear reactors. Developing accurate, predictive mechanistic models for corrosion and electrochemical corrosion kinetics of stainless steels has been a topic of research studies over many decades. Herein, we quantified the aqueous corrosion kinetics of a model austenitic Fe–18Cr–14Ni (wt%) alloy in the presence and absence of applied potential using systematic in situ electrochemical atomic force microscopy (EC-AFM) and transmission electron microscopy (TEM). Without an applied bias, vertical dissolution of corrosion pits is controlled by the surface kinetics/diffusion hybrid mechanism, whereas lateral dissolution is diffusion controlled. When an electric bias is applied, the increase in corrosion rate is dominated by the nucleation of new pits. These insights gained by the in situ EC-AFM will allow applications of this method for a quantitative understanding of corrosion of a wider class of materials.

Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). However, it is poorly understood how fundamental processes at the organic-inorganic interface, such as protein adsorption and/or incorporation into minerals, regulates nucleation and crystal growth due to technical challenges in observing and characterizing mineral-bound organics at high-resolution. Here, atom probe tomography techniques were developed and applied to characterize amelogenin-mineralized HAP particles in vitro, revealing distinct organic-inorganic interfacial structures and processes at the nanoscale. Specifically, visualization of amelogenin across the mineralized particulate demonstrates protein can become entrapped during HAP crystal aggregation and fusion. Identification of protein signatures and structural interpretations were further supported by standards analyses, i.e., defined HAP surfaces with and without amelogenin adsorbed. These findings represent a significant advance in the characterization of interfacial structures and, more so, interpretation of fundamental organic-inorganic processes and mechanisms influencing crystal growth. Ultimately, this approach can be broadly applied to inform how potentially unique and diverse organic-inorganic interactions at different stages regulates the growth and evolution of various biominerals.

Abstract Two‐dimensional (2D) conductive metal‐organic frameworks (MOF) represent a unique class of electrode materials with high capacity and power density. Understanding molecular mechanisms and pathways for heterogeneous nucleation of 2D π‐conjugated MOFs is highly desirable for controlling the structure and properties of conductive MOFs on solid substrates. Herein, a systematic study of nucleation and growth of 2D π‐conjugated Ni‐catecholate (Ni‐CAT‐1) MOFs on highly oriented pyrolytic graphite (HOPG) and copper substrates is reported. It is discovered that the nucleation density and growth kinetics of the MOF film can be controlled by varying substrate interactions with the organic linker. Specifically, π–π interactions between the linker and the HOPG dictate lower nucleation density, whereas π–metal interactions between the linker and the copper substrate dictate faster nucleation and higher nucleation densities. These studies reveal the key mechanism for Ni‐CAT‐1 nucleation on different surfaces and provide insights into interfacial control over the growth of other 2D π‐conjugated MOF films on solid substrates to inform synthesis of functional materials.

Adsorption interactions between amelogenin and calcium phosphate minerals are believed to be important to amelogenin’s function in enamel formation, however, the role of specific amino acid residues and domains within the protein in controlling adsorption is not well known. We synthesized “mechanistic probes” by systematically removing charged regions of amelogenin in order to elucidate their roles. The probes included amelogenin without the charged residues in the N-terminus (SEKR), without two, three, or eight histidines (H) in the central protein region (H2, H3, H8), or without the C-terminal residues (Delta). In-situ atomic force microscopy (AFM) adsorption studies onto hydroxyapatite (HAP) single crystals confirmed that the C-terminus was the dominant domain in promoting adsorption. We propose that subtle changes in protein-protein interactions for proteins with histidines and N-terminal residues removed resulted in changes in the oligomer quaternary size and structure that also affected protein adsorption. HAP mineralization studies revealed that the oligomer-HAP binding energy and protein layer thickness were factors in controlling the amorphous calcium phosphate (ACP) to HAP induction time. Our studies with mechanistic probes reveal the importance of the oligomer quaternary structure in controlling amelogenin adsorption and HAP mineralization.

NLRP3 inflammasome activation is a central process in initiating gout flares. The unique conformational rearrangement of the P2X7 receptor (P2X7R) upon ATP binding is critical for the activation of the NLRP3 inflammasome. However, studies on allosteric modulation of P2X7R in gout treatment are limited. Here, we aimed to investigate the therapeutic implications of targeting P2X7R in gout by designing a P2X7R allosteric inhibitor and validating the inhibitory function on NLRP3 inflammasome activation. Through virtual screening, we identified Z1456467176 (N-{3-[(2-aminoethyl) sulfamoyl] phenyl}-2-methyl-3-[3-(trifluoromethyl) phenyl] propanamide hydrochloride) bound to the drug-binding pocket as a potential antagonist of P2X7R. In functional assays, ATP- or BzATP-induced P2X7R function was assessed in vitro in HEK-293T cells overexpressing hP2X7R (dye uptake assay) and macrophages (IL-1β release assay). Z1456467176 exhibited a stable and significant P2X7R inhibitory effect. Importantly, in MSU crystal-induced gout, the presence and involvement of ATP were confirmed. Z1456467176 blocked ATP-induced activation of the NLRP3-caspase-1-IL-1β pathway and exerted promising effects in reducing gouty joint inflammation in rats. In addition, molecular docking and molecular dynamics simulation studies showed that the P27XR protein conformation was remodeled by Z1456467176 binding. Collectively, our results provide a potent P2X7R allosteric inhibitor that facilitates the remission of MSU crystal-induced gout inflammation by inhibiting NLRP3 inflammasome activation, suggesting that allosteric inhibition of P2X7R represents a new direction in gout treatment.

Background: A large body of evidence has linked air pollution and temperature with chronic kidney disease (CKD) prevalence and hospitalizations. However, most studies have focused on the influence of heat stress on CKD prevalence, and the potential effect modification of temperature on the association between air pollution and CKD has not been well-investigated. In this study, we examined the associations of the whole temperature spectrum and air pollution with CKD-related hospital visits and explored whether temperature modifies the short-term association of air pollution with CKD-related hospital visits. Methods and findings: We collected 40 276 CKD-related hospital visits from the first Affiliated Hospital of Anhui Medical University and Anhui Provincial Hospital in Hefei, China, during 2015–2019. A two-stage time-series design was conducted to investigate the associations of air pollution and daily mean temperature with CKD-related hospital visits. First, we estimated the associations between air pollution and CKD-related hospital visits as well as temperature and CKD-related hospital visits. Second, we analyzed the associations of air pollution with CKD hospital visits at different temperatures. We found that NO2 exposure and low temperature were associated with an increased risk of CKD-related hospital visits. Low temperature enhanced the association between NO2 exposure and CKD-related hospital visits, with an increase of 4.30% (95% CI: 2.47–5.92%) per 10 μg/m3 increment in NO2 at low temperature. Effect modification of the association between NO2 and the risk of CKD-related hospital visits was stronger at low temperature across the whole population. Conclusions: Our findings indicate that low temperature–related chronic kidney damage should be of immediate public health concern. Impact of NO2 exposure on the risk of CKD–related hospital visits may increase under the low temperature, which suggests the need for NO2 exposure mitigation strategies in the context of climate change and an enhanced understanding of the mechanisms underlying the temperature variance of air pollution effect to help reduce the magnitude of the CKD burden on the healthcare systems.

Abstract Background Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease that involves a variety of cell types. However, how the epigenetic dysregulations of peripheral immune cells contribute to the pathogenesis of RA still remains largely unclear. Results Here, we analysed the genome-wide active DNA regulatory elements of four major immune cells, namely monocytes, B cells, CD4+ T cells and CD8+ T cells, in peripheral blood of RA patients, osteoarthritis (OA) patients and healthy donors using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq). We found a strong RA-associated chromatin dysregulation signature in monocytes, but no other examined cell types. Moreover, we found that serum C-reactive protein (CRP) can induce the RA-associated chromatin dysregulation in monocytes via in vitro experiments. And the extent of this dysregulation was regulated through the transcription factor FRA2. Conclusions Together, our study revealed a CRP-induced pathogenic chromatin dysregulation signature in monocytes from RA patients and predicted the responsible signalling pathway as potential therapeutic targets for the disease.

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multiple organ dysfunction resulting from the production of multiple autoantibodies and adaptive immune system abnormalities involving T and B lymphocytes. In recent years, inflammasomes have been recognized as an important component of innate immunity and have attracted increasing attention because of their pathogenic role in SLE. In short, inflammasomes regulate the abnormal differentiation of immune cells, modulate pathogenic autoantibodies, and participate in organ damage. However, due to the clinical heterogeneity of SLE, the pathogenic roles of inflammasomes are variable, and thus, the efficacy of inflammasome-targeting therapies is uncertain. To provide a foundation for the development of such therapeutic strategies, in this paper, we review the role of different inflammasomes in the pathogenesis of SLE and their correlation with clinical phenotypes and propose some corresponding treatment strategies.

Gout flares require monosodium urate (MSU) to activate the NLRP3 inflammasome and secrete sufficient IL-1β. However, MSU alone is not sufficient to cause a flare. This is supported by the evidence that most patients with hyperuricemia do not develop gout throughout their lives. Recent studies have shown that, besides MSU, various purine metabolites, including adenosine triphosphate, adenosine diphosphate, and adenosine bind to different purine receptors for regulating IL-1β secretion implicated in the pathogenesis of gout flares. Purine metabolites such as adenosine triphosphate mainly activate the NLRP3 inflammasome through P2X ion channel receptors, which stimulates IL-1β secretion and induces gout flares, while some purine metabolites such as adenosine diphosphate and adenosine mainly act on the G protein-coupled receptors exerting pro-inflammatory or anti-inflammatory effects to regulate the onset and resolution of a gout flare. Given that the purine signaling pathway exerts different regulatory effects on inflammation and that, during the inflammatory process of a gout flare, an altered expression of purine metabolites and their receptors was observed in response to the changes in the internal environment. Thus, the purine signaling pathway is involved in regulating gout flare and resolution. This study was conducted to review and elucidate the role of various purine metabolites and purinergic receptors during the process.

The COVID-19 pandemic, caused by SARS-CoV-2 infection, remains a dramatic threat to human life and economic well-being worldwide. Significant heterogeneity in the severity of disease was observed for patients infected with SARS-CoV-2 ranging from asymptomatic to severe cases. Moreover, male patients had a higher probability of suffering from high mortality and severe symptoms linked to cytokine storm and excessive inflammation. The NLRP3 inflammasome is presumably critical to this process. Sex differences may directly affect the activation of NLRP3 inflammasome, impacting the severity of observed COVID-19 symptoms. To elucidate the potential mechanisms underlying sex based differences in NLRP3 activation during SARS-CoV-2 infection, this review summarizes the reported mechanisms and identifies potential therapeutic targets.

Bone tissue is a complex organic-inorganic nanocomposite and strategies that replicate the characteristics of bone tissue are scarce. Here the authors demonstrate the deposition of nanoscale apatite in collagen embedded with mesenchymal, vascular and nerve cells, using a protein-guided biomineralization approach.

The aim of this study was to investigate the effects of two process-directing agents (polyaspartic acid and osteopontin) used in a polymer-induced liquid-precursor (PILP) process on the remineralization of bacteria-induced enamel demineralization. Enamel demineralization lesions (depths of about 180–200 µm) were created and exposed to Streptococcus mutans, cultured with a 10% sucrose solution for 21 days, and remineralized using a PILP process (pH = 7.4, 14 days) with a calcium phosphate solution containing either polyaspartic acid or osteopontin in the presence or absence of fluoride (0.5 ppm). The specimens were examined under scanning electron microscopy. The fluoride was successfully incorporated into the PILP remineralization process for both polyaspartic acid and osteopontin. When the fluoride was added to the PILP remineralization solution, there was more uniform remineralization throughout the lesion than with either polyaspartic acid or osteopontin alone. However, in the absence of these process-directing agents, fluoride alone showed less remineralization with the formation of a predominantly surface-only layer. The PILP remineralization process relies on the ability of process-directing agents to stabilize calcium phosphate ions and holds promise for enamel lesion remineralization, and these agents, in the presence of fluoride, seem to play an important role as a booster or supplement in the continuation of remineralization by reducing the mineral gains at the surface layer.

The aim of this study was to evaluate the effect of silver diamine fluoride and grape seed extract on the microstructure and mechanical properties of carious dentin following exposure to acidic challenge. Ninety-eight molars with occlusal caries were used. In the control group the specimens were kept in distilled water. In the GSE group, the specimens were immersed in 6.5% grape seed extract solution for 30 minutes. In the SDF group, the specimens were immersed in 30% SDF solution for 4 minutes. In the GSE+SDF group, the specimens were immersed in 6.5% grape seed extract solution for 30 minutes and then exposed to 30% SDF solution for 4 minutes. All the groups underwent pH cycling model for 8 days. Microhardness measurements were taken at the baseline before surface treatments and after pH cycling. Elastic modulus was measured, after pH cycling. In the control group, the final hardness was significantly lower than the initial hardness (P = 0.001). In the SDF group, the final hardness was significantly higher than the initial hardness (P < 0.001). There was no significant difference between the initial and final hardness values in the GSE and GSE + SDF groups (p = 0.92, p = 0.07). The H1-H0 in the SDF group was significantly higher than the other groups (P

Diffusible iodine-based contrast-enhanced computed tomography (diceCT) techniques allow visualization of soft tissues of fluid-preserved specimens in three dimensions without dissection or histology. Two popular diceCT stains, iodine-potassium iodide (I2KI) dissolved in water and elemental iodine (I2) dissolved in 100% ethanol (EtOH), yield striking results. Despite the widespread use of these stains in clinical and biological fields, the molecular mechanisms that result in color change and radiopacity attributed to iodine staining are poorly understood. Requests to apply these stains to anatomical specimens preserved in natural history museums are increasing, yet curators have little information about the potential for degradation of treated specimens. To assess the molecular effects of iodine staining on typical museum specimens, we compared the two popular stains and two relatively unexplored stains (I2KI in 70% EtOH, I2 in 70% EtOH). House sparrows (Passer domesticus) were collected and preserved under uniform conditions following standard museum protocols, and each was then subjected to one of the stains. Results show that the three ethanol-based stains worked equally well (producing fully stained, life-like, publication quality scans) but in different timeframes (five, six, or eight weeks). The specimen in I2KI in water became degraded in physical condition, including developing flexible, demineralized bones. The ethanol-based methods also resulted in some demineralization but less than the water-based stain. The pH of the water-based stain was notably acidic compared to the water used as solvent in the stain. Our molecular analyses indicate that whereas none of the stains resulted in unacceptable levels of protein degradation, the bones of a specimen stained with I2KI in water demineralized throughout the staining process. We conclude that staining with I2KI or elemental I2 in 70% EtOH can yield high-quality soft-tissue visualization in a timeframe that is similar to that of better-known iodine-based stains, with lower risk of negative impacts on specimen condition.

Inflammasomes play a crucial role in innate immunity by serving as signaling platforms which deal with a plethora of pathogenic products and cellular products associated with stress and damage. By far, the best studied and most characterized inflammasome is NLRP3 inflammasome, which consists of NLRP3 (nucleotide-binding domain leucine-rich repeat (NLR) and pyrin domain containing receptor 3), ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain), and procaspase-1. Activation of NLRP3 inflammasome is mediated by highly diverse stimuli. Upon activation, NLRP3 protein recruits the adapter ASC protein, which recruits the procaspase-1 resulting in its cleavage and activation, inducing the maturation, and secretion of inflammatory cytokines and pyroptosis. However, aberrant activation of the NLRP3 inflammasome is implicated in various diseases including diabetes, atherosclerosis, metabolic syndrome, cardiovascular, and neurodegenerative diseases; raising a tremendous clinical interest in exploring the potential inhibitors of NLRP3 inflammasome. Recent investigations have disclosed various inhibitors of the NLRP3 inflammasome pathway which were validated through in vitro studies and in vivo experiments in animal models of NLRP3-associated disorders. Some of these inhibitors directly target the NLRP3 protein whereas some are aimed at other components and products of the inflammasome. Direct targeting of NLRP3 protein can be a better choice because it can prevent off target immunosuppressive effects, thus restrain tissue destruction. This paper will review the various pharmacological inhibitors of the NLRP3 inflammasome and will also discuss their mechanism of action.

Abstract The dysregulation of NLRP3 inflammasome can cause uncontrolled inflammation and drive the development of a wide variety of human diseases, but the medications targeting NLRP3 inflammasome are not available in clinic. Here, we show that tranilast (TR), an old anti‐allergic clinical drug, is a direct NLRP3 inhibitor. TR inhibits NLRP3 inflammasome activation in macrophages, but has no effects on AIM2 or NLRC4 inflammasome activation. Mechanismly, TR directly binds to the NACHT domain of NLRP3 and suppresses the assembly of NLRP3 inflammasome by blocking NLRP3 oligomerization. In vivo experiments show that TR has remarkable preventive or therapeutic effects on the mouse models of NLRP3 inflammasome‐related human diseases, including gouty arthritis, cryopyrin‐associated autoinflammatory syndromes, and type 2 diabetes. Furthermore, TR is active ex vivo for synovial fluid mononuclear cells from patients with gout. Thus, our study identifies the old drug TR as a direct NLRP3 inhibitor and provides a potentially practical pharmacological approach for treating NLRP3‐driven diseases.

The extensive deposits of calcium carbonate (CaCO3) generated by marine organisms constitute the largest and oldest carbon dioxide (CO2) reservoir. These organisms utilize macromolecules like peptides and proteins to facilitate the nucleation and growth of carbonate minerals, serving as an effective method for CO2 sequestration. However, the precise mechanisms behind this process remain elusive. In this study, we report the use of sequence-defined peptoids, a class of peptidomimetics, to achieve the accelerated calcite step growth kinetics with the molecular level mechanistic understanding. By designing peptoids with hydrophilic and hydrophobic blocks, we systematically investigated the acceleration in step growth rate of calcite crystals using in situ atomic force microscopy (AFM), varying peptoid sequences and concentrations, CaCO3 supersaturations, and the ratio of Ca2+/HCO3-. Mechanistic studies using NMR, three-dimensional fast force mapping (3D FFM), and isothermal titration calorimetry (ITC) were conducted to reveal the interactions of peptoids with Ca2+ and HCO3- ions in solution, as well as the effect of peptoids on solvation and energetics of calcite crystal surface. Our results indicate the multiple roles of peptoid in facilitating HCO3- deprotonation, Ca2+ desolvation, and the disruption of interfacial hydration layers of the calcite surface, which collectively contribute to a peptoid-induced acceleration of calcite growth. These findings provide guidelines for future design of sequence-specific biomimetic polymers as crystallization promoters, offering potential applications in environmental remediation (such as CO2 sequestration), biomedical engineering, and energy storage where fast crystallization is preferred. [ABSTRACT FROM AUTHOR]