A compact regulatory RNA element in mouse Hsp70 mRNA.

Hsp70 (70 kDa heat shock protein) performs molecular chaperone functions by assisting the folding of newly synthesized and misfolded proteins, thereby counteracting various cell stresses and preventing multiple diseases, including neurodegenerative disorders and cancers. It is well established that, immediately after heat shock, Hsp70 gene expression is mediated by a canonical mechanism of cap-dependent translation. However, the molecular mechanism of Hsp70 expression during heat shock remains elusive. Intriguingly, the 5' end of Hsp70 messenger RNA (mRNA) appears to form a compact structure with the potential to regulate protein expression in a cap-independent manner. Here, we determined the minimal length of the mHsp70 5'-terminal mRNA sequence that is required for RNA folding into a highly compact structure. This span of this RNA element was mapped and the secondary structure characterized by chemical probing, resulting in a secondary structural model that includes multiple stable stems, including one containing the canonical start codon. All of these components, including a short stretch of the 5' open reading frame (ORF), were shown to be vital for RNA folding. This work provides a structural basis for future investigations on the role of translational regulatory structures in the 5' untranslated region and ORF sequences of Hsp70 during heat shock.

The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization.

RIG-I is an essential innate immune receptor that responds to infection by RNA viruses. The RIG-I signaling cascade is mediated by a series of post-translational modifications, the most important of which is ubiquitination of the RIG-I Caspase Recruitment Domains (CARDs) by E3 ligase Riplet. This is required for interaction between RIG-I and its downstream adapter protein MAVS, but the mechanism of action remains unclear. Here we show that Riplet is required for RIG-I signaling in the presence of both short and long dsRNAs, establishing that Riplet activation does not depend upon RIG-I filament formation on long dsRNAs. Likewise, quantitative Riplet-RIG-I affinity measurements establish that Riplet interacts with RIG-I regardless of whether the receptor is bound to RNA. To understand this, we solved high-resolution cryo-EM structures of RIG-I/RNA/Riplet complexes, revealing molecular interfaces that control Riplet-mediated activation and enabling the formulation of a unified model for the role of Riplet in signaling.

Dense captioning and multidimensional evaluations for indoor robotic scenes.

The field of human-computer interaction is expanding, especially within the domain of intelligent technologies. Scene understanding, which entails the generation of advanced semantic descriptions from scene content, is crucial for effective interaction. Despite its importance, it remains a significant challenge. This study introduces RGBD2Cap, an innovative method that uses RGBD images for scene semantic description. We utilize a multimodal fusion module to integrate RGB and Depth information for extracting multi-level features. And the method also incorporates target detection and region proposal network and a top-down attention LSTM network to generate semantic descriptions. The experimental data are derived from the ScanRefer indoor scene dataset, with RGB and depth images rendered from ScanNet's 3D scene serving as the model's input. The method outperforms the DenseCap network in several metrics, including BLEU, CIDEr, and METEOR. Ablation studies have confirmed the essential role of the RGBD fusion module in the method's success. Furthermore, the practical applicability of our method was verified within the AI2-THOR embodied intelligence experimental environment, showcasing its reliability.

Polysaccharides from Oudemansiella radicata residues attenuate carbon tetrachloride-induced liver injury.

The present work aimed to investigate the potential hepatoprotective effects of Oudemansiella radicata residues polysaccharides (RPS). Our results demonstrated that RPS showed significantly protective effects against carbon tetrachloride (CCl4)-induced liver injury, and the possible mechanisms may be related with the predominant bioactivities of RPS containing anti-oxidation by activating the Nrf2 signal pathways, anti-inflammation by inhibiting NF-κB signal pathways and reducing the release of inflammatory cytokines, anti-apoptosis by regulating Bcl-2/Bax pathway, and anti-fibrosis by inhibiting the expressions of TGF-ß1, Hyp and α-SMA, respectively. These findings suggested that RPS, a typical ß-type glycosidic pyranose, could be used as a promising diet supplement or medication for the adjunctive treatment of hepatic diseases, and also contributed to promoting the recyclable utilization of mushroom residues.

A compact regulatory RNA element in mouse Hsp70 mRNA.

Hsp70 performs molecular chaperone functions by assisting in folding newly synthesized or misfolded proteins, thereby counteracting various cell stresses and preventing multiple diseases including neurodegenerative disorders and cancer. It is well established that Hsp70 upregulation during post-heat shock stimulus is mediated by cap-dependent translation. However, the molecular mechanisms of Hsp70 expression during heat shock stimulus remains elusive, even though the 5' end of Hsp70 mRNA may form a compact structure to positively regulate protein expression in the mode of cap-independent translation. The minimal truncation which can fold to a compact structure was mapped and its secondary structure was characterized by chemical probing. The predicted model revealed a highly compact structure with multiple stems. Including the stem where the canonical start codon is located, several stems were identified to be vital for RNA folding, thereby providing solid structural basis for future investigations on the function of this RNA structure on Hsp70 translation during heat shock.

Ganoderma lucidum polysaccharides improve lipid metabolism against high-fat diet-induced dyslipidemia.

ETHNOPHARMACOLOGICAL RELEVANCE: As a kind of traditional medicinal fungi, Ganoderma lucidum has been employed as folk medicine in China against multiple metabolic diseases on account of its superior bioactivities. Recently, accumulated reports have investigated the protective effects of G. lucidum polysaccharides (GLP) on ameliorating dyslipidemia. However, the specific mechanism by which GLP improves dyslipidemia is not completely clear. AIMS OF THE STUDY: This study aimed to investigate the protective effects of GLP on high-fatdiet-induced hyperlipidemia and exploring its underlying mechanism. MATERIALS AND METHODS: The GLP was successfully obtained from G. lucidum mycelium. The mice were conducted with high-fatdiet to establish the hyperlipidemia model. Biochemical determination, histological analysis, immunofluorescence, western blot and real-time qPCR were used to assess the alterations in high-fatdiet-treated mice after the GLP intervention. RESULTS: It was found that GLP administration significantly decreased body weight gain and the excessive lipid levels, and partly alleviated tissue injury. Oxidative stress and inflammations were efficiently ameliorated after the treatment of GLP by activing Nrf2-Keap1 and inhibiting NF-κB signal pathways. GLP promoted cholesterol reverse transport by LXRα-ABCA1/ABCG1 signaling, increased the expressions of CYP7A1 and CYP27A1 responsible for bile acids production, accompanied by inhibition of intestinal FXR-FGF15 levels. Besides, multiple target proteins involved in lipid metabolism were also significantly modulated under the intervention of GLP. CONCLUSION: Taken together, our results suggested that GLP showed potential lipid-lowering effects and its possible mechanism was involved in improving oxidative stress and inflammation response, modulating bile acids synthesis and lipid regulatory factors, and promoting reverse cholesterol transport, thereby suggesting that GLP may possibly used as a dietary supplement or medication for the adjuvant therapy for hyperlipidemia.

A protocol for capturing RNA-sensing innate immune receptors in multiple conformations by single-particle cryo-EM.

Capturing different conformations of receptor proteins that are complexed with ligands by single-particle cryo-EM facilitates our understanding toward the mechanisms of ligand recognition and receptor activation cascades. Here, we present a protocol for capturing RNA-sensing innate immune receptors, such as RIG-I, in multiple conformations by single-particle cryo-EM. We describe steps for protein-ligand sample preparation, data acquisition, and image processing covering focused three-dimensional classification. This protocol can be adapted to capture the dynamic behavior of other receptors that can be stabilized. For complete details on the use and execution of this protocol, please refer to Wang and Pyle (2022).1.

A rapid RIG-I signaling relay mediates efficient antiviral response.

RIG-I is essential for host defense against viral pathogens, as it triggers the release of type I interferons upon encounter with viral RNA molecules. In this study, we show that RIG-I is rapidly and efficiently activated by small quantities of incoming viral RNA and that it relies exclusively on the constitutively expressed resident pool of RIG-I receptors for a strong antiviral response. Live-cell imaging of RIG-I following stimulation with viral or synthetic dsRNA reveals that RIG-I signaling occurs without mass aggregation at the mitochondrial membrane. By contrast, interferon-induced RIG-I protein becomes embedded in cytosolic aggregates that are functionally unrelated to signaling. These findings suggest that endogenous RIG-I efficiently recognizes viral RNA and rapidly relays an antiviral signal to MAVS via a transient signaling complex and that cellular aggregates of RIG-I have a function that is distinct from signaling.

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands.

RIG-I is an essential innate immune receptor for detecting and responding to infection by RNA viruses. RIG-I specifically recognizes the unique molecular features of viral RNA molecules and selectively distinguishes them from closely related RNAs abundant in host cells. The physical basis for this exquisite selectivity is revealed through a series of high-resolution cryo-EM structures of RIG-I in complex with host and viral RNA ligands. These studies demonstrate that RIG-I actively samples double-stranded RNAs in the cytoplasm and distinguishes them by adopting two different types of protein folds. Upon binding viral RNA, RIG-I adopts a high-affinity conformation that is conducive to signaling, while host RNA induces an autoinhibited conformation that stimulates RNA release. By coupling protein folding with RNA binding selectivity, RIG-I distinguishes RNA molecules that differ by as little as one phosphate group, thereby explaining the molecular basis for selective antiviral sensing and the induction of autoimmunity upon RIG-I dysregulation.

Effect of Polymer Coatings on the Permeability and Chloride Ion Penetration Resistances of Nano-Particles and Fibers-Modified Cementitious Composites.

Nano-particles and fibers-modified cementitious composite (NFCC) can greatly overcome the shortcomings of traditional cementitious materials, such as high brittleness and low toughness, and improve the durability of the composite, which in turn increases the service life of the structures. Additionally, the polymer coatings covering the surface of the composite can exert a good physical shielding effect on the external water, ions, and gases, so as to improve the permeability and chloride ion penetration resistance of the composite. In this study, the effect of three types of polymer coatings on the water contact angle, permeability resistance, and chloride ion penetration resistance of the NFCC with varied water-binder ratios were investigated. Three kinds of polymers (chlorinated rubber coating, polyurethane coating, and silane coating) were applied in two types of coatings, including single-layer and double-layer coatings. Three water-binder ratios of 35 wt.%, 40 wt.%, and 45 wt.% were used for the NFCC. The research results revealed that the surface of the NFCC treated with polymer coatings exhibited excellent hydrophobicity. The permeability height and chloride diffusion coefficient of the NFCC coated with different types of polymer coatings were 31-48% and 36-47% lower, respectively, than those of the NFCC without polymer coatings. The durability of the NFCC was further improved when the polymer coatings were applied to the surface in two-layer. Furthermore, it was discovered that increasing the water-binder ratio of the NFCC would lessen the positive impact of polymer coatings on the durability of NFCC.

Mycelium polysaccharides of Macrolepiota procera alleviate reproductive impairments induced by nonylphenol.

Nonylphenol (NP) exposure has become a crucial inducement of male reproductive disorders in the world. Therefore, it is urgent to seek solutions to alleviate the toxicity of NP. This study was oriented toward studying the protective effects of Macrolepiota procera mycelium polysaccharides (MMP) on NP-induced reproductive impairments. After NP administration, declined sperm amounts and testis index, increased the deformity rate of sperms, aberrant hormone secretion and testicular pathological injury were observed, corporately leading to reproductive capacity attenuation. Importantly, MMP significantly reversed the foregoing changes in NP-treated mice. Notably, it has been observed that the MMP therapy remarkably improved oxidative stress, apoptosis, autophagy and inflammatory responses, and suppressed the Akt/mTOR signaling pathway in testicular tissues. These results manifested that MMP might be a promising treatment strategy for ameliorating the biotoxicity of NP.

Unique binding pattern for a lineage of human antibodies with broad reactivity against influenza A virus.

Most structurally characterized broadly neutralizing antibodies (bnAbs) against influenza A viruses (IAVs) target the conserved conformational epitopes of hemagglutinin (HA). Here, we report a lineage of naturally occurring human antibodies sharing the same germline gene, VH3-48/VK1-12. These antibodies broadly neutralize the major circulating strains of IAV in vitro and in vivo mainly by binding a contiguous epitope of H3N2 HA, but a conformational epitope of H1N1 HA, respectively. Our structural and functional studies of antibody 28-12 revealed that the continuous amino acids in helix A, particularly N49HA2 of H3 HA, are critical to determine the binding feature with 28-12. In contrast, the conformational epitope feature is dependent on the discontinuous segments involving helix A, the fusion peptide, and several HA1 residues within H1N1 HA. We report that this antibody was initially selected by H3 (group 2) viruses and evolved via somatic hypermutation to enhance the reactivity to H3 and acquire cross-neutralization to H1 (group 1) virus. These findings enrich our understanding of different antigenic determinants of heterosubtypic influenza viruses for the recognition of bnAbs and provide a reference for the design of influenza vaccines and more effective antiviral drugs.

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report.

SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 infection. Remdesivir therapy alleviated symptoms and produced a transient virologic response, but her course was complicated by recrudescence of high-grade viral shedding. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. In vitro experiments demonstrated that the mutation conferred a ~6-fold increase in remdesivir IC50 but resulted in a fitness cost in the absence of remdesivir. Sustained clinical and virologic response was achieved after treatment with casirivimab-imdevimab. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection.

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report.

SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 infection. Remdesivir therapy alleviated symptoms and produced a transient virologic response, but her course was complicated by recrudescence of high-grade viral shedding. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. In vitro experiments demonstrated that the mutation conferred a ∼6-fold increase in remdesivir IC50 but resulted in a fitness cost in the absence of remdesivir. Sustained clinical and virologic response was achieved after treatment with casirivimab-imdevimab. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection.

Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA.

Vertebrate organisms express a diversity of protein receptors that recognize and respond to the presence of pathogenic molecules, functioning as an early warning system for infection. As a result of mutation or dysregulated metabolism, these same innate immune receptors can be inappropriately activated, leading to inflammation and disease. One of the most important receptors for detection and response to RNA viruses is called RIG-I, and dysregulation of this protein is linked with a variety of disease states. Despite its central role in inflammatory responses, antagonists for RIG-I are underdeveloped. In this study, we use invitro selection from a pool of modified DNA aptamers to create a high affinity RIG-I antagonist. A high resolution crystal structure of the complex reveals molecular mimicry between the aptamer and the 5'-triphosphate terminus of viral ligands, which bind to the same amino acids within the CTD recognition platform of the RIG-I receptor. Our study suggests a powerful, generalizable strategy for generating immunomodulatory drugs and mechanistic tool compounds.

The molecular mechanism of RIG-I activation and signaling.

RIG-I is our first line of defense against RNA viruses, serving as a pattern recognition receptor that identifies molecular features common among dsRNA and ssRNA viral pathogens. RIG-I is maintained in an inactive conformation as it samples the cellular space for pathogenic RNAs. Upon encounter with the triphosphorylated terminus of blunt-ended viral RNA duplexes, the receptor changes conformation and releases a pair of signaling domains (CARDs) that are selectively modified and interact with an adapter protein (MAVS), thereby triggering a signaling cascade that stimulates transcription of interferons. Here, we describe the structural determinants for specific RIG-I activation by viral RNA, and we describe the strategies by which RIG-I remains inactivated in the presence of host RNAs. From the initial RNA triggering event to the final stages of interferon expression, we describe the experimental evidence underpinning our working knowledge of RIG-I signaling. We draw parallels with behavior of related proteins MDA5 and LGP2, describing evolutionary implications of their collective surveillance of the cell. We conclude by describing the cell biology and immunological investigations that will be needed to accurately describe the role of RIG-I in innate immunity and to provide the necessary foundation for pharmacological manipulation of this important receptor.

New exon and accelerated evolution of placental gene Nrk occurred in the ancestral lineage of placental mammals.

INTRODUCTION: The chorioallantoic placenta is a specific organ for placental mammals. However, the adaptive events during its emergence are still poorly investigated. METHODS: We scanned the chromosome X to detect the accelerated evolution in the ancestral lineage of placental mammals, and constructed 3D protein structure models of a candidate by homology modeling. RESULTS: Eight branch-specific accelerated regions were identified. Five of these regions (P=5.61×10-11 ~ 9.03×10-8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Nrk belongs to the germinal center kinase-IV subfamily with the overall similar protein structure; however, a new exon emerged in ancestors of placental mammals and its sequence has been conserved since then. Structure modelling of NRK suggests that the accelerated exons and the placental-mammal-specific exon (as a new loop) could change the enzymatic activity and the structure of placental mammal NRK. DISCUSSION: Since the new loop is surrounded by the accelerated protein regions, it is likely that the new loop occurred and shifted the function of NRK, and then the accelerated evolution of Nrk occurred to adapt the structure change caused by the new loop in the ancestral lineage of placental mammals. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection.

Characterization and Hepatoprotections of Ganoderma lucidum Polysaccharides against Multiple Organ Dysfunction Syndrome in Mice.

BACKGROUND: The liver is one of the most commonly affected organs in multiple organ dysfunction syndrome (MODS). In recent years, there have been many studies on Ganoderma lucidum polysaccharides (GLP), but the role of GLP in MODS is still unclear. The purpose of this work was to explore the antioxidant, anti-inflammatory, and protective effects of GLP on the liver in MODS model mice. METHODS: The characteristic properties of GLP were processed by physicochemical analysis. The MODS models were successfully established with intraperitoneal injection of zymosan in Kunming strain mice. The antioxidant, anti-inflammatory, and hepatoprotective effects of GLP were processed both in vitro and in vivo by evaluating the oxidative parameters, inflammatory factors, and liver pathological observations. RESULTS: The characterization analysis revealed that GLP was a pyranose mainly composed of glucose with the molecular weights (Mw) of 8309 Da. The experimental results proved that GLP had potential hepatoprotection possibly by improving the antioxidant status (scavenging excessive oxygen radicals, increasing the antioxidant enzyme activities, and reducing the lipid peroxide), alleviating the inflammatory response (reducing the inflammatory factor levels), and guaranteeing the liver functions. CONCLUSIONS: This research suggested that GLP had the potential to be developed as a natural medicine for the treatment of multiple organ failure.

Wettability of semispherical droplets on layered elastic gradient soft substrates.

Research on the wettability of soft matter is one of the most urgently needed studies in the frontier domains, of which the wetting phenomenon of droplets on soft substrates is a hot subject. Scholars have done considerable studies on the wetting phenomenon of single-layer structure, but it is noted that the wetting phenomenon of stratified structure is ubiquitous in nature, such as oil exploitation from geological structural layers and shale gas recovery from shale formations. Therefore, the wettability of droplets on layered elastic gradient soft substrate is studied in this paper. Firstly, considering capillary force, elastic force and surface tension, the constitutive equation of the substrate in the vector function system is derived by using the vector function system in cylindrical coordinates, and the transfer relation of layered structure is obtained. Further, the integral expressions of displacement and stress of double Bessel function are given. Secondly, the numerical results of displacement and stress are obtained by using the numerical formula of double Bessel function integral. The results show that the deformation of the substrate weakens with the increase of the elastic modulus, also the displacement and stress change dramatically near the contact line, while the variation is flat when the contact radius is far away from the droplet radius.

Antioxidation, anti-hyperlipidaemia and hepatoprotection of polysaccharides from Auricularia auricular residue.

As hyperlipidemia was a pathological progress by lipid dysfunctions, the present object was to investigate the hypolipidemic and hepatoprotective effects of Auricularia auricular residue polysaccharides (RPS) against HFE (high-fat emulsion) toxicities in mice. The structure analysis showed that the RPS was pyranose-polysaccharides mainly composed of glucose with the weight-average molecular weight of 2.00 × 105 Da. The in vivo experiments demonstrated that the RPS had potential hepatoprotections by enhancing the antioxidant and anti-hyperlipidaemia status, and could inhibit the increasing body weights. Besides, the RPS could improve the glucose utilization with the oral glucose tolerance test (120 min) of 5.04 ± 0.12 mmol/L at the dose of 400 mg/kg bw. The results in present study demonstrated that RPS could be used as a functional foods and natural medicines against the HFE-induced hyperlipidemia and its complications.