Algorithm for optimized mRNA design improves stability and immunogenicity.

Messenger RNA (mRNA) vaccines are being used to combat the spread of COVID-19 (refs. 1-3), but they still exhibit critical limitations caused by mRNA instability and degradation, which are major obstacles for the storage, distribution and efficacy of the vaccine products4. Increasing secondary structure lengthens mRNA half-life, which, together with optimal codons, improves protein expression5. Therefore, a principled mRNA design algorithm must optimize both structural stability and codon usage. However, owing to synonymous codons, the mRNA design space is prohibitively large-for example, there are around 2.4 × 10632 candidate mRNA sequences for the SARS-CoV-2 spike protein. This poses insurmountable computational challenges. Here we provide a simple and unexpected solution using the classical concept of lattice parsing in computational linguistics, where finding the optimal mRNA sequence is analogous to identifying the most likely sentence among similar-sounding alternatives6. Our algorithm LinearDesign finds an optimal mRNA design for the spike protein in just 11 minutes, and can concurrently optimize stability and codon usage. LinearDesign substantially improves mRNA half-life and protein expression, and profoundly increases antibody titre by up to 128 times in mice compared to the codon-optimization benchmark on mRNA vaccines for COVID-19 and varicella-zoster virus. This result reveals the great potential of principled mRNA design and enables the exploration of previously unreachable but highly stable and efficient designs. Our work is a timely tool for vaccines and other mRNA-based medicines encoding therapeutic proteins such as monoclonal antibodies and anti-cancer drugs7,8.

Per- and polyfluoroalkyl substances inhibit human and rat 17ß-hydroxysteroid dehydrogenase 1: Quantitative structure-activity relationship and molecular docking analysis.

Per- and polyfluoroalkyl (PFAS) substances are enduring industrial materials. 17ß-Hydroxysteroid dehydrogenase isoform 1 (17ß-HSD1) is an estrogen metabolizing enzyme, which transforms estrone into estradiol in human placenta and rat ovary. Whether PFAS inhibit 17ß-HSD1 and what the structure-activity relationship (SAR) remains unexplored. We screened 18 PFAS for inhibiting human and rat 17ß-HSD1 in microsomes and studied their SAR and mode of action(MOA). Of the 11 perfluorocarboxylic acids (PFCAs), C8-C14 PFCAs at a concentration of 100 µM substantially inhibited human 17ß-HSD1, with order of C11 (half-maximal inhibition concentration, IC50, 8.94 µM) > C10 (10.52 µM) > C12 (14.90 µM) > C13 (30.97 µM) > C9 (43.20 µM) > C14 (44.83 µM) > C8 (73.38 µM) > others. Of the 7 per- and poly-fluorosulfonic acids (PFSAs), the potency was C8S (IC50, 14.93 µM) > C7S (80.70 µM) > C6S (177.80 µM) > others. Of the PFCAs, C8-C14 PFCAs at 100 µM markedly reduced rat 17ß-HSD1 activity, with order of C11 (IC50, 9.11 µM) > C12 (14.30 µM) > C10 (18.24 µM) > C13 (25.61 µM) > C9 (67.96 µM) > C8 (204.39 µM) > others. Of the PFSAs, the potency was C8S (IC50, 37.19 µM) > C7S (49.38 µM) > others. In contrast to PFOS (C6S), the partially fluorinated compound 6:2 FTS with an equivalent number of carbon atoms demonstrated no inhibition of human and rat 17ß-HSD1 activity at a concentration of 100 µM. The inhibition of human and rat enzymes by PFAS followed a V-shaped trend from C4 to C14, with a nadir at C11. Moreover, human 17ß-HSD1 was more sensitive than rat enzyme. PFAS inhibited human and rat 17ß-HSD1 in a mixed mode. Docking analysis revealed that they bind to the NADPH and steroid binding site of both 17ß-HSD1 enzymes. The 3D quantitative SAR (3D-QSAR) showed that hydrophobic region, hydrogen bond acceptor and donor are key factors in binding to 17ß-HSD1 active sites. In conclusion, PFAS exhibit inhibitory effects on human and rat 17ß-HSD1 depending on factors such as carbon chain length, degree of fluorination, and the presence of carboxylic acid or sulfonic acid groups, with a notable V-shaped shift observed at C11.

Regulation of reversible conformational change, size switching, and immunomodulation of RNA nanocubes.

In biological systems, conformational changes and allosteric modulation play pivotal roles in regulating biological functions, such as the dynamic change of protein molecules, in response to binding or interacting with other factors such as pH, voltage, salt, light, or ligand. RNA can be manipulated and tuned with a level of simplicity that is characteristic of DNA or polymers, while displaying versatility in structure, diversity in function, and adaptability in a configuration similar to proteins. In the past, the work on the investigation of conformational change mainly focused on protein. The induced-fit and conformational capture in RNA have also been explored, such as in the study of riboswitches. Herein, we report the engineering of three-dimensional RNA nanocubes and demonstrated the operation and regulation for its configuration. We demonstrate the operation of reconfigurable RNA nanocubes whose shapes change precisely and reversibly in response to a specific trigger strand. The shape, size, and conformation can be regulated precisely and reversibly in response to the specific triggering signals. The shape and conformational conversion were observed by cryo-EM and gel electrophoresis, respectively. Harnessing the size, shape, conformation, and self-assembly capabilities of the RNA nanocube can provide a new potential use of this technology as nanocarriers for the treatment of various diseases.

Protectin conjugates in tissue regeneration 1 alleviates sepsis-induced acute lung injury by inhibiting ferroptosis.

BACKGROUND: Acute lung injury (ALI) is a common and serious complication of sepsis with high mortality. Ferroptosis, categorized as programmed cell death, contributes to the development of lung injury. Protectin conjugates in tissue regeneration 1 (PCTR1) is an endogenous lipid mediator that exerts protective effects against multiorgan injury. However, the role of PCTR1 in the ferroptosis of sepsis-related ALI remains unknown. METHODS: A pulmonary epithelial cell line and a mouse model of ALI stimulated with lipopolysaccharide (LPS) were established in vitro and in vivo. Ferroptosis biomarkers, including ferrous (Fe2+), glutathione (GSH), malondialdehyde (MDA) and 4-Hydroxynonenal (4-HNE), were assessed by relevant assay kits. Glutathione peroxidase 4 (GPX4) and prostaglandin-endoperoxide synthase 2 (PTGS2) protein levels were determined by western blotting. Lipid peroxides were examined by fluorescence microscopy and flow cytometry. Cell viability was determined by a CCK-8 assay kit. The ultrastructure of mitochondria was observed with transmission electron microscopy. Morphology and inflammatory cytokine levels predicted the severity of lung injury. Afterward, related inhibitors were used to explore the potential mechanism by which PCTR1 regulates ferroptosis. RESULTS: PCTR1 treatment protected mice from LPS-induced lung injury, which was consistent with the effect of the ferroptosis inhibitor ferrostatin-1. PCTR1 treatment decreased Fe2+, PTGS2 and lipid reactive oxygen species (ROS) contents, increased GSH and GPX4 levels and ameliorated mitochondrial ultrastructural injury. Administration of LPS or the ferroptosis agonist RSL3 resulted in reduced cell viability, which was rescued by PCTR1. Mechanistically, inhibition of the PCTR1 receptor lipoxin A4 (ALX), protein kinase A (PKA) and transcription factor cAMP-response element binding protein (CREB) partly decreased PCTR1 upregulated GPX4 expression and a CREB inhibitor blocked the effects ofPCTR1 on ferroptosis inhibition and lung protection. CONCLUSION: This study suggests that PCTR1 suppresses LPS-induced ferroptosis via the ALX/PKA/CREB signaling pathway, which may offer promising therapeutic prospects in sepsis-related ALI.

Deep Learning-based Trichoscopic Image Analysis and Quantitative Model for Predicting Basic and Specific Classification in Male Androgenetic Alopecia.

Since the results of basic and specific classification in male androgenetic alopecia are subjective, and trichoscopic data, such as hair density and diameter distribution, are potential quantitative indicators, the aim of this study was to develop a deep learning framework for automatic trichoscopic image analysis and a quantitative model for predicting basic and specific classification in male androgenetic alopecia. A total of 2,910 trichoscopic images were collected and a deep learning framework was created on convolutional neural networks. Based on the trichoscopic data provided by the framework, correlations with basic and specific classification were analysed and a quantitative model was developed for predicting basic and specific classification using multiple ordinal logistic regression. A deep learning framework that can accurately analyse hair density and diameter distribution on trichoscopic images and a quantitative model for predicting basic and specific classification in male androgenetic alopecia were established.

Neoadjuvant chemoradiotherapy, chemotherapy, and radiotherapy do not significantly increase the incidence of anastomotic leakage after esophageal cancer surgery: a meta-analysis.

This study investigated whether neoadjuvant therapies, such as neoadjuvant chemoradiotherapy (NCRT), neoadjuvant chemotherapy (NCT), and neoadjuvant radiotherapy (NRT), would affect the incidence of anastomotic leakage (AL) after esophageal cancer surgery. Published randomized controlled trials were reviewed, and the incidence of AL after esophageal cancer was statistically analyzed in each study. Meta-analysis was performed using Revman and Stata software. A total of 17 randomized controlled trials with 2874 patients were reviewed showing that, in general, preoperative neoadjuvant therapies were not significant risk factors for AL after esophageal cancer surgery (relative risk [RR] = 0.82, 95% CI = 0.64-1.04). NCRT and NRT did not significantly increase the risk of postoperative AL in patients with esophageal cancer (RR = 0.81, 95% CI = 0.63-1.05; RR = 0.64, 95% CI = 0.14-2.97, respectively). Moreover, NCT has no significant correlation with the occurrence of AL (RR = 1.01, 95% CI = 0.57-1.80). NCRT, NCT, and NRT do not significantly increase the incidence of gastroesophageal AL after esophageal cancer surgery.

Sparse-view CBCT reconstruction via weighted Schatten p-norm minimization.

A novel iterative algorithm is proposed for sparse-view cone beam computed tomography (CBCT) reconstruction based on the weighted Schatten p-norm minimization (WSNM). By using the half quadratic splitting, the sparse-view CBCT reconstruction task is decomposed into two sub-problems that can be solved through alternating iteration: simple reconstruction and image denoising. The WSNM that fits well with the low-rank hypothesis of CBCT data is introduced to improve the denoising sub-problem as a regularization term. The experimental results based on the digital brain phantom and clinical CT data indicated the advantages of the proposed algorithm in both structural information preservation and artifacts suppression, which performs better than the classical algorithms in quantitative and qualitative evaluations.

Optical properties of D and S defects induced by Si+/Ni+ ions co-implanting into Si films on insulator.

In the article, we report the photoluminescence (PL) properties of D and S defects induced by Si+/Ni+ ions co-implanting into the top Si film of the silicon-on-insulator (SOI) wafer. Variable-temperature PL spectra of these co-implanted SOI samples indicate that the light emitting from the D defects can be observed as high as 273 K. In comparison with the other ion-implantation, the Si+/Ni+ ion-co-implantation optimizes luminescent temperature stability of the both D and S defects and purifies the S defect type in silicon then effectively restrains the spectral broadening of the S-line in PL spectra. The depth distribution of the D and S defects along the normal direction of SOI surface at the corresponding ion-implantation energy has been well depicted by detecting the PL signals of the layer-by-layer etched SOI surface, respectively. These results provide valuable information to fabricate SOI-based infrared light sources for optical fiber communications.

Delivery of Anti-miRNA for Triple-Negative Breast Cancer Therapy Using RNA Nanoparticles Targeting Stem Cell Marker CD133.

Triple-negative breast cancer (TNBC) is an aggressive disease with a short median time from relapse to death. The increased aggressiveness, drug resistance, disease relapse, and metastasis are associated with the presence of stem cells within tumors. Several stem cell markers, such as CD24, CD44, CD133, ALDH1, and ABCG2, have been reported, but their roles in breast cancer tumorigenesis remain unclear. Herein, we apply RNA nanotechnology to deliver anti-microRNA (miRNA) for TNBC therapy. The thermodynamically and chemically stable three-way junction (3WJ) motif was utilized as the scaffold to carry an RNA aptamer binding to CD133 receptor and a locked nuclei acid (LNA) sequence for miRNA21 inhibition. Binding assays revealed the specific uptake of the nanoparticles to breast cancer stem cells (BCSCs) and TNBC cells. Functional assays showed that cancer cell migration was reduced, miR21 expression was inhibited, and downstream tumor suppressor PTEN and PDCD4 expressions were upregulated. In vitro and in vivo studies revealed that these therapeutic RNA nanoparticles did not induce cytokine secretion. Systemic injection of these RNA nanoparticles in animal trial demonstrated high specificity in TNBC tumor targeting and high efficacy for tumor growth inhibition. These results revealed the clinical translation potential of these RNA nanoparticles for TNBC therapy.

Osteoclastogenesis Modulatory Steroids from the South China Sea Gorgonian Coral Iciligorgia sp.

A new 9,11-secosteroid, (22R)-22-acetoxy-3ß,6α,11-trihydroxy-9,11-seco-5α-cholest-7-en-9-one, along with twelve known analogues were isolated from the South China Sea gorgonian coral Iciligorgia sp. Their structures were determined by the spectroscopic analysis and comparison with reported data. In an in vitro test of osteoclastic differentiation, three compounds exhibited significant down-regulating effect whereas two compounds showed significant up-regulating effect at 0.5 and 1.0 µm. This is the first report of the chemical investigation of the gorgonian Iciligorgia sp. The acetoxy substitution at C-22 seems to play an important role in the regulating activity.

Monocular Vision-Based Pose Determination in Close Proximity for Low Impact Docking.

Pose determination in close proximity is critical for space missions in which monocular vision is one of the most promising solutions. Although numerous approaches such as using artificial beacons or specific shapes on spacecrafts have proved to be effective, the high individuation and the large time delay limit their use in low impact docking. This paper proposes a unified framework to determinate the relative pose between two docking mechanisms by treating their guide petals as measurement objects. Fusing the pose information of one docking mechanism to simplify image processing and creating an intermediate coordinate system to solve the perspective-n-point problem greatly improve the real-time performance and the robustness of the method. Experimental results show that the position measurement error is within 3.7 mm, while the rotation error around docking direction is less than 0.16°, corresponding to a measurement time reduction of 85%.

Formulation and Characterization of Novel Dry Suspension and Dry Emulsion of 20(S)-Protopanaxadiol.

To improve the absorption of poorly water-soluble 20(S)-protopanaxadiol (20(S)-PPD), novel 20(S)-PPD-loaded redispersible dry suspension and dry emulsion were developed in this study. 20(S)-PPD dry suspension (PPD-DS) was prepared by enabling drug fully dispersed with suspending agent Avicel CL611 and solubilizer Poloxamer 188. 20(S)-PPD dry emulsion (PPD-DE) was prepared by employing oleic acid as oil phase, Cremophor RH-40 as surfactant, and n-butyl alcohol as co-surfactant. Both PPD-DS and PPD-DE were evaluated for their physicochemical characterization after being dispersed in distilled water. The in vivo pharmacokinetics was evaluated by UPLC-MS/MS. The droplet size of PPD-DS and PPD-DE was in the scope of 1446-1653 nm and 652.8-784.5 nm. The sedimentation volume ratios of PPD-DS and PPD-DE were both at value of 1. The zeta potential of PPD-DS and PPD-DE were from - 53.7 to - 70.4 mV and - 27.5 to - 34.5 mV, respectively, which indicated stable systems. PPD-DS and PPD-DE both achieved dramatically enhanced aqueous solubility and higher perfusion of 20(S)-PPD in rats' intestine. Although statistically, no oral bioavailability enhancements of 20(S)-PPD were achieved in PPD-DE and PPD-DS, there were some improvements in the pharmacokinetic behaviors. Especially, PPD-DS could be a promising drug delivery carrier for 20(S)-PPD with the advantages of long-term stability, dosing flexibility, and the convenience of administering to infants and to those who have difficulty swallowing tablets or capsules.

Techniques for the analysis of pentacyclic triterpenoids in medicinal plants.

Triterpenes are a major class of chemical compounds found in natural plants and can be categorized into acyclic triterpenoids, monocyclic triterpenoids, tricyclic triterpenoids, tetracyclic triterpenoids, and pentacyclic triterpenoids. Among them, pentacyclic triterpenoids have gained more extensive attention due to their biological activities, including anti-inflammation, antibacterial, antioxidation, antitumor, anti-HIV, hepatoprotection, and immunological adjuvant properties. In this review, we summarize the extraction and analytical methods for pentacyclic triterpenoids, where more than 56 triterpenes from 49 kinds of plants were involved. The analysis methods include gas chromatography, liquid chromatography, capillary electrophoresis, thin-layer chromatography, supercritical fluid chromatography, NMR spectroscopy, and X-ray spectroscopy. This review provides valuable reference for the determination of pentacyclic triterpenoids in medicinal plants.

Osteoclastogenesis Inhibitory Polyketides from the Sponge-Associated Fungus Xylaria feejeensis.

A new ten-membered macrolide (1) and a new α-pyrone derivative, (-)-annularin C (2), together with 14 known analogs (3-16) were isolated from the AcOEt extract of the fungus Xylaria feejeensis isolated from the South China Sea sponge Stylissa massa. The structures of the new compounds were elucidated by the spectroscopic analysis and by comparison with reported data. The absolute configuration was determined by the optical rotation and ECD experiments. In an in vitro test, compounds 1, 5 and 9 exhibited significant down-regulating activity of osteoclast cell differentiation at 0.5 and 1 µm. This is the first report of the fungus X. feejeensis from a marine sponge and of osteoclastogenesis inhibitory activity for the metabolites of these kinds.

Evaluating and correlating the mechanical, nutritional, and structural properties of carrots after multiple freezing/thawing processing.

This work evaluated and correlated the mechanical and nutritional properties of carrots after five freezing/thawing cycles (FTC). Results showed that after one FTC, the mechanical parameters (hardness, chewiness, springiness, cohesiveness, resilience, and storage modulus) and the glucose and fructose content sharply decreased and the tangent (Tanδ) dramatically increased in samples. The contents of lycopene and lutein reached the maximum level after two FTC. And there were no significant changes in the content of α- and ß-carotene (around 90 and 50 mg 100 g-1 dry matter, respectively) among all samples. Correlation analysis showed that the mechanical parameters were positively correlated with soluble sugars (fructose, glucose, and sucrose) and negatively with lycopene and lutein Tanδ were negatively related with soluble sugar. These results suggested that the first freezing/thawing condition could be the key factor for obtaining the products with acceptable quality. The changes in macroscopic mechanics could be used to predict the variations of potential nutritional components in tissues during FTC processing. The deteriorated structural changes (i.g. cell wall dissociation and turgidity loss) could be responsible for these results.

Three-dimensional N,B-doped graphene aerogel as a synergistically enhanced metal-free catalyst for the oxygen reduction reaction.

Here, a novel N,B-doped graphene aerogel, abbreviated as N,B-GA, was obtained via a two-step approach and served as a metal-free catalyst for the oxygen reduction reaction (ORR). This two-step method involved a hydrothermal reaction and a pyrolysis procedure, guaranteeing the efficient insertion of the heteroatoms. The resulting three-dimensional (3D) N,B-GA obtained at pyrolysis temperature of 1000 °C exhibited outstanding catalytic activity for the oxygen reduction reaction (ORR), comparable to that of Pt/C. In addition, the catalytic activity of this 3D N,B-GA was obviously better than that of the nitrogen-doped graphene aerogel (N-GA) and boron-doped graphene aerogel (B-GA) in terms of the onset potential, half-wave potential and diffusion limiting current density. The superior catalytic reactivity arises from the synergistic coupling of the B and N dopants within the graphene domains.

In-depth transcriptome profiling of Cherry Valley duck lungs exposed to chronic heat stress.

Amidst rising global temperatures, chronic heat stress (CHS) is increasingly problematic for the poultry industry. While mammalian CHS responses are well-studied, avian-specific research is lacking. This study uses in-depth transcriptome sequencing to evaluate the pulmonary response of Cherry Valley ducks to CHS at ambient temperatures of 20°C and a heat-stressed 29°C. We detailed the CHS-induced gene expression changes, encompassing mRNAs, lncRNAs, and miRNAs. Through protein-protein interaction network analysis, we identified central genes involved in the heat stress response-TLR7, IGF1, MAP3K1, CIITA, LCP2, PRKCB, and PLCB2. Subsequent functional enrichment analysis of the differentially expressed genes and RNA targets revealed significant engagement in immune responses and regulatory processes. KEGG pathway analysis underscored crucial immune pathways, specifically those related to intestinal IgA production and Toll-like receptor signaling, as well as Salmonella infection and calcium signaling pathways. Importantly, we determined six miRNAs-miR-146, miR-217, miR-29a-3p, miR-10926, miR-146b-5p, and miR-17-1-3p-as potential key regulators within the ceRNA network. These findings enhance our comprehension of the physiological adaptation of ducks to CHS and may provide a foundation for developing strategies to improve duck production under thermal stress.

Deep learning-assisted multispectral imaging for early screening of skin diseases.

INTRODUCTION: Melanocytic nevi (MN), warts, seborrheic keratoses (SK), and psoriasis are four common types of skin surface lesions that typically require dermatoscopic examination for definitive diagnosis in clinical dermatology settings. This process is labor-intensive and resource-consuming. Traditional methods for diagnosing skin lesions rely heavily on the subjective judgment of dermatologists, leading to issues in diagnostic accuracy and prolonged detection times. OBJECTIVES: This study aims to introduce a multispectral imaging (MSI)-based method for the early screening and detection of skin surface lesions. By capturing image data at multiple wavelengths, MSI can detect subtle spectral variations in tissues, significantly enhancing the differentiation of various skin conditions. METHODS: The proposed method utilizes a pixel-level mosaic imaging spectrometer to capture multispectral images of lesions, followed by reflectance calibration and standardization. Regions of interest were manually extracted, and the spectral data were subsequently exported for analysis. An improved one-dimensional convolutional neural network is then employed to train and classify the data. RESULTS: The new method achieves an accuracy of 96.82 % on the test set, demonstrating its efficacy. CONCLUSION: This multispectral imaging approach provides a non-contact and non-invasive method for early screening, effectively addressing the subjective identification of lesions by dermatologists and the prolonged detection times associated with conventional methods. It offers enhanced diagnostic accuracy for a variety of skin lesions, suggesting new avenues for dermatological diagnostics.

Function of NEK2 in clear cell renal cell carcinoma and its effect on the tumor microenvironment.

BACKGROUND: Previous studies have revealed the critical functions of NEK2 in controlling the cell cycle which is linked to poor prognosis in multiple tumor types, but less research has been devoted to clear cell renal cell carcinoma (ccRCC). METHODS: We downloaded clinical data from the gene expression omnibus (GEO) and TCGA databases together with transcriptional and mutational datasets. Strongly coexpressed genes with NEK2 were extracted from TCGA-KIRC cohort, and were submitted to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional analyses. According to NEK2 levels, the survival status, mutational characteristics, response to immunotherapy and sensitivity to drugs of the patients were studied. The potential correlations between NEK2 levels and immune cell state as well as immune cell infiltration were examined using the GEPIA, TIMER and TISIDB databases. Double immunofluorescence (IF) was performed to identify the NEK2 overexpression and relationship with CD8 in ccRCC. RESULTS: The NEK2 gene was overexpressed and would enhance the nuclear division and cell cycle activities in ccRCC. ccRCC patients with high NEK2 expression had worse clinical outcomes, higher mutation burden and better therapeutic response. Moreover, NEK2 gene overexpression was positively related to various immune cell marker sets, which was also proved by validation cohort, and more infiltration of various immune cells. CONCLUSION: ccRCC patients with NEK2 high expression have a poorer prognosis than those with NEK2 low expression, resulting from its function of promoting proliferation, accompanied by increased infiltration of CD8 + T cells and Tregs and T-cell exhaustion and will respond better to proper treatments.