State-selective modulation of heterotrimeric Gαs signaling with macrocyclic peptides.

The G protein-coupled receptor cascade leading to production of the second messenger cAMP is replete with pharmacologically targetable proteins, with the exception of the Gα subunit, Gαs. GTPases remain largely undruggable given the difficulty of displacing high-affinity guanine nucleotides and the lack of other drug binding sites. We explored a chemical library of 1012 cyclic peptides to expand the chemical search for inhibitors of this enzyme class. We identified two macrocyclic peptides, GN13 and GD20, that antagonize the active and inactive states of Gαs, respectively. Both macrocyclic peptides fine-tune Gαs activity with high nucleotide-binding-state selectivity and G protein class-specificity. Co-crystal structures reveal that GN13 and GD20 distinguish the conformational differences within the switch II/α3 pocket. Cell-permeable analogs of GN13 and GD20 modulate Gαs/Gßγ signaling in cells through binding to crystallographically defined pockets. The discovery of cyclic peptide inhibitors targeting Gαs provides a path for further development of state-dependent GTPase inhibitors.

Cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment.

Cerebrospinal fluid (CSF) contains a tightly regulated immune system. However, knowledge is lacking about how CSF immunity is altered with aging or neurodegenerative disease. Here, we performed single-cell RNA sequencing on CSF from 45 cognitively normal subjects ranging from 54 to 82 years old. We uncovered an upregulation of lipid transport genes in monocytes with age. We then compared this cohort with 14 cognitively impaired subjects. In cognitively impaired subjects, downregulation of lipid transport genes in monocytes occurred concomitantly with altered cytokine signaling to CD8 T cells. Clonal CD8 T effector memory cells upregulated C-X-C motif chemokine receptor 6 (CXCR6) in cognitively impaired subjects. The CXCR6 ligand, C-X-C motif chemokine ligand 16 (CXCL16), was elevated in the CSF of cognitively impaired subjects, suggesting CXCL16-CXCR6 signaling as a mechanism for antigen-specific T cell entry into the brain. Cumulatively, these results reveal cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment.

Brain-restricted mTOR inhibition with binary pharmacology.

On-target-off-tissue drug engagement is an important source of adverse effects that constrains the therapeutic window of drug candidates1,2. In diseases of the central nervous system, drugs with brain-restricted pharmacology are highly desirable. Here we report a strategy to achieve inhibition of mammalian target of rapamycin (mTOR) while sparing mTOR activity elsewhere through the use of the brain-permeable mTOR inhibitor RapaLink-1 and the brain-impermeable FKBP12 ligand RapaBlock. We show that this drug combination mitigates the systemic effects of mTOR inhibitors but retains the efficacy of RapaLink-1 in glioblastoma xenografts. We further present a general method to design cell-permeable, FKBP12-dependent kinase inhibitors from known drug scaffolds. These inhibitors are sensitive to deactivation by RapaBlock, enabling the brain-restricted inhibition of their respective kinase targets.

An atlas of gene regulatory elements in adult mouse cerebrum.

The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2-6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.

Strain-release alkylation of Asp12 enables mutant selective targeting of K-Ras-G12D.

K-Ras is the most commonly mutated oncogene in human cancer. The recently approved non-small cell lung cancer drugs sotorasib and adagrasib covalently capture an acquired cysteine in K-Ras-G12C mutation and lock it in a signaling-incompetent state. However, covalent inhibition of G12D, the most frequent K-Ras mutation particularly prevalent in pancreatic ductal adenocarcinoma, has remained elusive due to the lack of aspartate-targeting chemistry. Here we present a set of malolactone-based electrophiles that exploit ring strain to crosslink K-Ras-G12D at the mutant aspartate to form stable covalent complexes. Structural insights from X-ray crystallography and exploitation of the stereoelectronic requirements for attack of the electrophile allowed development of a substituted malolactone that resisted attack by aqueous buffer but rapidly crosslinked with the aspartate-12 of K-Ras in both GDP and GTP state. The GTP-state targeting allowed effective suppression of downstream signaling, and selective inhibition of K-Ras-G12D-driven cancer cell proliferation in vitro and xenograft growth in mice.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.

MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels.

Predicting protein localization and understanding its mechanisms are critical in biology and pathology. In this context, we propose a new web application of MULocDeep with improved performance, result interpretation, and visualization. By transferring the original model into species-specific models, MULocDeep achieved competitive prediction performance at the subcellular level against other state-of-the-art methods. It uniquely provides a comprehensive localization prediction at the suborganellar level. Besides prediction, our web service quantifies the contribution of single amino acids to localization for individual proteins; for a group of proteins, common motifs or potential targeting-related regions can be derived. Furthermore, the visualizations of targeting mechanism analyses can be downloaded for publication-ready figures. The MULocDeep web service is available at https://www.mu-loc.org/.

CKBA suppresses mast cell activation via ERK signaling pathway in murine atopic dermatitis.

Atopic dermatitis (AD) is a common inflammatory skin disorder. Mast cells play an important role in AD because they regulate allergic reactions and inflammatory responses. However, whether and how the modulation of mast cell activity affects AD has not been determined. In this study, we aimed to determine the effects and mechanisms of 3-O-cyclohexanecarbonyl-11-keto-ß-boswellic acid (CKBA). This natural compound derivative alleviates skin inflammation by inhibiting mast cell activation and maintaining skin barrier homeostasis in AD. CKBA markedly reduced serum IgE levels and alleviated skin inflammation in calcipotriol (MC903)-induced AD mouse model. CKBA also restrained mast cell degranulation both in vitro and in vivo. RNA-seq analysis revealed that CKBA downregulated the extracellular signal-regulated kinase (ERK) signaling in BM-derived mast cells activated by anti-2,4-dinitrophenol/2,4-dinitrophenol-human serum albumin. We proved that CKBA suppressed mast cell activation via ERK signaling using the ERK activator (t-butyl hydroquinone) and inhibitor (selumetinib; AZD6244) in AD. Thus, CKBA suppressed mast cell activation in AD via the ERK signaling pathway and could be a therapeutic candidate drug for AD.

Enhancing X-Ray Sensitization with Multifunctional Nanoparticles.

In the progression of X-ray-based radiotherapy for the treatment of cancer, the incorporation of nanoparticles (NPs) has a transformative impact. This study investigates the potential of NPs, particularly those comprised of high atomic number elements, as radiosensitizers. This aims to optimize localized radiation doses within tumors, thereby maximizing therapeutic efficacy while preserving surrounding tissues. The multifaceted applications of NPs in radiotherapy encompass collaborative interactions with chemotherapeutic, immunotherapeutic, and targeted pharmaceuticals, along with contributions to photodynamic/photothermal therapy, imaging enhancement, and the integration of artificial intelligence technology. Despite promising preclinical outcomes, the paper acknowledges challenges in the clinical translation of these findings. The conclusion maintains an optimistic stance, emphasizing ongoing trials and technological advancements that bolster personalized treatment approaches. The paper advocates for continuous research and clinical validation, envisioning the integration of NPs as a revolutionary paradigm in cancer therapy, ultimately enhancing patient outcomes.

Ge-polymer bridge waveguide for mode-locked laser pulse generation.

A Ge-polymer hybrid waveguide is sandwiched between an indium phosphide (InP) reflective gain chip and a fiber Bragg grating (FBG) to construct a laser system. The hybrid waveguide serves as a bridge between the gain chip and the fiber with tailored mode-field matching at both facets. The 50-nm amorphous Ge (α-Ge) layer shows a nonlinear absorption effect at 1550 nm. The hybrid waveguide is further verified by a femtosecond laser transmission experiment to show the pulse width compression effect. Such waveguide is then integrated inside the laser cavity as a passive saturable absorber to modulate the longitudinal modes for a pulsed output. This polymer-bridged mode-locked laser adopts an InP gain chip for compact assembly and also a FBG with a flexible length to adjust the pulse repetition rate. The mode-locked laser output around the designed 50 MHz repetition rate is demonstrated. The pulse width is measured as 147 ps, and the signal-to-noise ratio is larger than 50 dB. This work introduces a "ternary" mode-locked laser system, taking advantage of discrete photonic components bridged by a polymer-based waveguide. It also proves the feasibility of applying α-Ge films as practical and low-cost saturable absorbers in photonic devices.

EO nonlinear function generator.

An electro-optical programmable nonlinear function generator (PNFG) is developed on a multimode waveguide with four parallel thermal electrodes. The current on one electrode is chosen as the input, while the rest serve as function-defining units to modulate the multimode interference. The electro-thermo-optical effects are analyzed step by step and the impact on the eigenmode properties is derived. It shows that the optical output power variation by altered interference, in response to the input current, manifests as a complex ensemble of functions in general. The PNFG aims to find the special setting under which such relation can be simplified into some basic functions. Through an optimization program, a variety of such functions are found, including Sigmoid, SiLU, and Gaussian. Furthermore, the shape of these functions can be adjusted by finetuning the defining units. This device may be integrated in a large-scale photonic computing network that can tackle complex problems with nonlinear function adaptability.

Chemical acylation of an acquired serine suppresses oncogenic signaling of K-Ras(G12S).

Drugs that directly impede the function of driver oncogenes offer exceptional efficacy and a therapeutic window. The recently approved mutant selective small-molecule cysteine-reactive covalent inhibitor of the G12C mutant of K-Ras, sotorasib, provides a case in point. KRAS is the most frequently mutated proto-oncogene in human cancer, yet despite success targeting the G12C allele, targeted therapy for other hotspot mutants of KRAS has not been described. Here we report the discovery of small molecules that covalently target a G12S somatic mutation in K-Ras and suppress its oncogenic signaling. We show that these molecules are active in cells expressing K-Ras(G12S) but spare the wild-type protein. Our results provide a path to targeting a second somatic mutation in the oncogene KRAS by overcoming the weak nucleophilicity of an acquired serine residue. The chemistry we describe may serve as a basis for the selective targeting of other unactivated serines.

KRAS is vulnerable to reversible switch-II pocket engagement in cells.

Current small-molecule inhibitors of KRAS(G12C) bind irreversibly in the switch-II pocket (SII-P), exploiting the strong nucleophilicity of the acquired cysteine as well as the preponderance of the GDP-bound form of this mutant. Nevertheless, many oncogenic KRAS mutants lack these two features, and it remains unknown whether targeting the SII-P is a practical therapeutic approach for KRAS mutants beyond G12C. Here we use NMR spectroscopy and a cellular KRAS engagement assay to address this question by examining a collection of SII-P ligands from the literature and from our own laboratory. We show that the SII-Ps of many KRAS hotspot (G12, G13, Q61) mutants are accessible using noncovalent ligands, and that this accessibility is not necessarily coupled to the GDP state of KRAS. The results we describe here emphasize the SII-P as a privileged drug-binding site on KRAS and unveil new therapeutic opportunities in RAS-driven cancer.

Mid1 promotes synovitis in rheumatoid arthritis via ubiquitin-dependent post-translational modification.

INTRODUCTION: Current anti-rheumatic drugs are primarily modulating immune cell activation, yet their effectiveness remained suboptimal. Therefore, novel therapeutics targeting alternative mechanisms, such as synovial activation, is urgently needed. OBJECTIVES: To explore the role of Midline-1 (Mid1) in synovial activation. METHODS: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice were used to establish a subcutaneous xenograft model. Wild-type C57BL/6, Mid1-/-, Dpp4-/-, and Mid1-/-Dpp4-/- mice were used to establish a collagen-induced arthritis model. Cell viability, cell cycle, qPCR and western blotting analysis were used to detect MH7A proliferation, dipeptidyl peptidase-4 (DPP4) and Mid1 levels. Co-immunoprecipitation and proteomic analysis identified the candidate protein of Mid1 substrates. Ubiquitination assays were used to determine DPP4 ubiquitination status. RESULTS: An increase in Mid1, an E3 ubiquitin ligase, was observed in human RA synovial tissue by GEO dataset analysis, and this elevation was confirmed in a collagen-induced mouse arthritis model. Notably, deletion of Mid1 in a collagen-induced arthritis model completely protected mice from developing arthritis. Subsequent overexpression and knockdown experiments on MH7A, a human synoviocyte cell line, unveiled a previously unrecognized role of Mid1 in synoviocyte proliferation and migration, the key aspects of synovial activation. Co-immunoprecipitation and proteomic analysis identified DPP4 as the most significant candidate of Mid1 substrates. Mechanistically, Mid1 promoted synoviocyte proliferation and migration by inducing ubiquitin-mediated proteasomal degradation of DPP4. DPP4 deficiency led to increased proliferation, migration, and inflammatory cytokine production in MH7A, while reconstitution of DPP4 significantly abolished Mid1-induced augmentation of cell proliferation and activation. Additionally, double knockout model showed that DPP4 deficiency abolished the protective effect of Mid1 defect on arthritis. CONCLUSION: Overall, our findings suggest that the ubiquitination of DPP4 by Mid1 promotes synovial cell proliferation and invasion, exacerbating synovitis in RA. These results reveal a novel mechanism that controls synovial activation, positioning Mid1 as a promising target for therapeutic intervention in RA.

Identification of Two Novel QTL for Fusarium Head Blight Resistance in German Wheat Cultivar Centrum.

Fusarium head blight (FHB) is a devastating disease that occurs in warm and humid environments. The German wheat 'Centrum' has displayed moderate to high levels of FHB resistance in the field for many years. In this study, an F6:8 recombinant inbred line (RIL) population derived from cross 'Centrum' × 'Xinong 979' was evaluated for FHB response following point inoculation in five environments. The population and parents were genotyped using the GenoBaits Wheat 16 K Panel. Stable quantitative trait loci (QTL) associated with FHB resistance in 'Centrum' were mapped on chromosome arms 2DS and 5BS. The most effective QTL, located in 2DS, was identified as a new chromosome region represented by a 1.4 Mb interval containing 17 candidate genes. Another novel QTL was mapped in chromosome arm 5BS of a 5BS to 7BS translocation chromosome. In addition, two environmentally sensitive QTL were mapped on chromosome arms 2BL from 'Centrum' and 5AS from 'Xinong 979'. Polymorphisms of flanking phenotypic variance explained (PVE) markers (allele-specific quantitative PCR [AQP]) AQP-6 for QFhb.nwafu-2DS and 16K-13073 for QFhb.nwafu-5BS were validated in a panel of 217 cultivars and breeding lines. These markers could be useful for marker-assisted selection (MAS) of FHB resistance and provide a starting point for fine mapping and marker-based cloning of the resistance genes.

Ship-Fire Net: An Improved YOLOv8 Algorithm for Ship Fire Detection.

Ship fire may result in significant damage to its structure and large economic loss. Hence, the prompt identification of fires is essential in order to provide prompt reactions and effective mitigation strategies. However, conventional detection systems exhibit limited efficacy and accuracy in detecting targets, which has been mostly attributed to limitations imposed by distance constraints and the motion of ships. Although the development of deep learning algorithms provides a potential solution, the computational complexity of ship fire detection algorithm pose significant challenges. To solve this, this paper proposes a lightweight ship fire detection algorithm based on YOLOv8n. Initially, a dataset, including more than 4000 unduplicated images and their labels, is established before training. In order to ensure the performance of algorithms, both fire inside ship rooms and also fire on board are considered. Then after tests, YOLOv8n is selected as the model with the best performance and fastest speed from among several advanced object detection algorithms. GhostnetV2-C2F is then inserted in the backbone of the algorithm for long-range attention with inexpensive operation. In addition, spatial and channel reconstruction convolution (SCConv) is used to reduce redundant features with significantly lower complexity and computational costs for real-time ship fire detection. For the neck part, omni-dimensional dynamic convolution is used for the multi-dimensional attention mechanism, which also lowers the parameters. After these improvements, a lighter and more accurate YOLOv8n algorithm, called Ship-Fire Net, was proposed. The proposed method exceeds 0.93, both in precision and recall for fire and smoke detection in ships. In addition, the mAP@0.5 reaches about 0.9. Despite the improvement in accuracy, Ship-Fire Net also has fewer parameters and lower FLOPs compared to the original, which accelerates its detection speed. The FPS of Ship-Fire Net also reaches 286, which is helpful for real-time ship fire monitoring.

Genome-Wide Identification, Molecular Characterization, and Expression Analysis of the HSP70 and HSP90 Gene Families in Thamnaconus septentrionalis.

Heat shock proteins (HSPs) are a class of highly conserved proteins that play an important role in biological responses to various environmental stresses. The mariculture of Thamnaconus septentrionalis, a burgeoning aquaculture species in China, frequently encounters stressors such as extreme temperatures, salinity variations, and elevated ammonia levels. However, systematic identification and analysis of the HSP70 and HSP90 gene families in T. septentrionalis remain unexplored. This study conducted the first genome-wide identification of 12 HSP70 and 4 HSP90 genes in T. septentrionalis, followed by a comprehensive analysis including phylogenetics, gene structure, conserved domains, chromosomal localization, and expression profiling. Expression analysis from RNA-seq data across various tissues and developmental stages revealed predominant expression in muscle, spleen, and liver, with the highest expression found during the tailbud stage, followed by the gastrula, neurula, and juvenile stages. Under abiotic stress, most HSP70 and HSP90 genes were upregulated in response to high temperature, high salinity, and low salinity, notably hspa5 during thermal stress, hspa14 in high salinity, and hsp90ab1 under low salinity conditions. Ammonia stress led to a predominance of downregulated HSP genes in the liver, particularly hspa2, while upregulation was observed in the gills, especially for hsp90b1. Quantitative real-time PCR analysis corroborated the expression levels under environmental stresses, validating their involvement in stress responses. This investigation provides insights into the molecular mechanisms of HSP70 and HSP90 in T. septentrionalis under stress, offering valuable information for future functional studies of HSPs in teleost evolution, optimizing aquaculture techniques, and developing stress-resistant strains.

Overview and Evolution of Insect Fibroin Heavy Chain (FibH).

The FibH gene, crucial for silk spinning in insects, encodes a protein that significantly influences silk fiber mechanics. Due to its large size and repetitive sequences, limited known sequences of insect FibH impede comprehensive understanding. Here, we analyzed 114 complete FibH gene sequences from Lepidoptera (71 moths, 24 butterflies) and 13 Trichoptera, revealing single-copy FibH in most species, with 2-3 copies in Hesperinae and Heteropterinae (subfamily of skippers). All FibH genes are structured with two exons and one intron (39-45 bp), with the second exon being notably longer. Moths exhibit higher GC content in FibH compared to butterflies and Trichoptera. The FibH composition varies among species, with moths and butterflies favoring Ala, Gly, Ser, Pro, Gln, and Asn, while Trichoptera FibH is enriched in Gly, Ser, and Arg, and has less Ala. Unique to Trichoptera FibH are Tyr, Val, Arg, and Trp, whereas Lepidoptera FibH is marked by polyAla (polyalanine), polySer (polyserine), and the hexapeptide GAGSGA. A phylogenetic analysis suggests that Lepidoptera FibH evolved from Trichoptera, with skipper FibH evolving from Papilionoidea. This study substantially expands the FibH repertoire, providing a foundation for the development of artificial silk.

The investigation of the binding ability between sodium dodecyl sulfate and Cu (II) in urban stormwater runoff.

The simultaneous presence of heavy metals and surfactants in runoff induces complexation and ecological harm during migration. However, interactions between these pollutants are often overlooked in past studies. Thus, investigating heavy metal-surfactant complexes in runoff is imperative. In this work, Cu (II) and sodium dodecyl sulfate (SDS) were selected to investigate the interaction between heavy metals and surfactants due to the higher detected frequency in runoff. Through 1H NMR and FTIR observation of hydrogen atom nuclear displacement and functional group displacement of SDS, the change of SDS and Cu (II) complexation was obtained, and then the complexation form of Cu (II) and SDS was verified. The results showed that solution pH values and ionic strength had significant effects on the complexation of Cu (II). When the pH values increase from 3.0 to 6.0, the complexation efficiency of SDS with Cu (II) increased by 12.12% at low concentration of SDS, which may be attributed to the excessive protonation in the aqueous solution at acidic condition. The increase of ionic strength would inhibit the complexation reaction efficiency by 19.57% and finally reached the platform with concentration of NaNO3 was 0.10 mmol/L, which was mainly due to the competitive relationship between Na (I) and Cu (II). As a general filtering material in stormwater treatment measures, natural zeolite could affect the interaction between SDS and Cu (II) greatly. After the addition of SDS, the content of free Cu (II) in the zeolite-SDS-Cu (II) three-phase mixed system was significantly reduced, indicating that SDS had a positive effect on the removal of Cu (II) from runoff. This study is of great significance for investigating the migration and transformation mechanism of SDS and Cu (II) in the future and studying the control technology of storm runoff pollution.

Occurrence and ecological risk of PAHs in urban road runoff in Beijing.

The occurrence and ecological risks of 16 polycyclic aromatic hydrocarbons (PAHs) in different types of urban road runoff in Beijing during two typical rainfall events were studied. The average concentration of PAHs in road runoff particulate was in the order of Guanyuanqiao Road (ring road, 15,175 ng/L) > Huayuanqiao Road (primary road, 4,792 ng/L) > Dongcheng Alley (alley, 4,774 ng/L) > Nansihuan Viaduct (viaduct, 770 ng/L), much higher than dissolved PAHs. The total concentration of ∑16PAHs decreased with runoff scouring. Rainfall conditions and the accumulation of PAHs in the early rainfall period show a significant impact on PAHs pollution. The event mean concentration range of PAHs is 674-21,596 ng/L, following in the order of ring road > primary road > alley > viaduct. The proportion of four-ring PAHs was the highest. The first flush effect of PAHs is found in both rainfall events, and the effect of different ring PAHs is relatively similar. The content of PAHs is positively correlated with the amount of total organic carbon and suspended substance in runoff (r2> 0.72). The ecological risk assessment indicated that PAHs in road runoff except viaduct road corresponded to high risk.