Luciferase Reporter Systems in Investigating Interferon Antiviral Innate Immunity.

Luciferase reporter systems are commonly used in scientific research to investigate a variety of biological processes, including antiviral innate immunity. These systems employ the use of luciferase enzymes derived from organisms such as fireflies or renilla reniformis, which emit light upon reaction with a substrate. In the context of antiviral innate immunity, the luciferase reporter systems offer a noninvasive and highly sensitive approach for real-time monitoring of immune responses in vitro and in vivo, enabling researchers to delve into the intricate interactions and signaling pathways involved in host-virus dynamic interactions. Here, we describe the methods of the promoter-luciferase reporter and enhancer-luciferase reporter, which provide insights into the transcriptional and post-transcriptional regulation of antiviral innate immunity. Additionally, we outline the split-luciferase complementary reporter method, which was designed to explore protein-protein interactions associated with antiviral immunity. These methodologies offer invaluable knowledge regarding the molecular mechanisms underlying antiviral immune pathways and have the potential to support the development of effective antiviral therapies.

Roles of Long Noncoding RNA in Prostate Cancer Pathogenesis.

Prostate cancer stands as the most common cancer in men, and research into its genesis and spread is still vital. The idea that the human genome's transcriptional activity is more widespread than previously thought has received empirical validation through the application of deep sequencing-based transcriptome profiling techniques. An assortment of noncoding transcripts longer than 200 nucleotides is referred to as long noncoding RNAs (lncRNAs). Transposable elements comprise a substantial portion of the human genome, with projections indicating that their prospective proportion may reach 90%. Considering they can interact directly with proteins, alter the transcriptional activity of coding genes, and perhaps encode proteins, lncRNAs possess the capability to regulate a variety of biological processes. LncRNAs have been recognized to be key factors in the development of several types of human cancers, including lung, colorectal, and breast cancers, alongside other pathological processes that have a significant impact on the diagnosis and survival of cancer individuals. Furthermore, lncRNAs' discernible expression patterns throughout various cancer scenarios significantly raise their potential as biomarkers and therapeutic targets. We conducted an extensive analysis of the prevailing academic literature on the interaction between lncRNAs and prostate cancer in order to present a solid foundation for potential future studies on the prevention and intervention of prostate cancer. The discourse additionally expands on lncRNAs' prospective applications as targets and biomarkers for medical therapies.

Progress on deep learning in genomics.

With the rapid growth of data driven by high-throughput sequencing technologies, genomics has entered an era characterized by big data, which presents significant challenges for traditional bioinformatics methods in handling complex data patterns. At this critical juncture of technological progress, deep learning-an advanced artificial intelligence technology-offers powerful capabilities for data analysis and pattern recognition, revitalizing genomic research. In this review, we focus on four major deep learning models: Convolutional Neural Network(CNN), Recurrent Neural Network(RNN), Long Short-Term Memory(LSTM), and Generative Adversarial Network(GAN). We outline their core principles and provide a comprehensive review of their applications in DNA, RNA, and protein research over the past five years. Additionally, we also explore the use of deep learning in livestock genomics, highlighting its potential benefits and challenges in genetic trait analysis, disease prevention, and genetic enhancement. By delivering a thorough analysis, we aim to enhance precision and efficiency in genomic research through deep learning and offer a framework for developing and applying livestock genomic strategies, thereby advancing precision livestock farming and genetic breeding technologies.

Harnessing ZIKV NS2A RNA for alleviating acute hepatitis and cytokine release storm by targeting translation machinery.

BACKGROUND AND AIMS: Hyperactivated inflammatory responses induced by cytokine release syndrome (CRS) are the primary causes of tissue damage and even death. The translation process is precisely regulated to control the production of proinflammatory cytokines. However, it is largely unknown whether targeting translation can effectively limit the hyperactivated inflammatory responses during acute hepatitis and graft-versus-host disease (GVHD). APPROACH AND RESULTS: By using in vitro translation and cellular overexpression systems, we have found that the non-structural protein gene NS2A of Zika virus (ZIKV) functions as RNA molecules to suppress the translation of both ectopic genes and endogenous proinflammatory cytokines. Mechanistically, results from RNA pulldown and co-immunoprecipitation (Co-IP) assays have demonstrated that NS2A RNA interacts with the translation initiation factor eIF2α to disrupt the dynamic balance of the eIF2/eIF2B complex and translation initiation, which is the rate-limiting step during the translation process. In the acetaminophen (APAP)-, LPS/D-galactosamine (D-GalN)-, viral infection-induced acute hepatitis, and GVHD mouse models, mice with myeloid cell-specific knock-in of NS2A show decreased levels of serum proinflammatory cytokines and reduced tissue damage. CONCLUSIONS: ZIKV NS2A dampens the production of proinflammatory cytokines and alleviates inflammatory injuries by interfering translation process as RNA molecules, which suggests that NS2A RNA is potentially used to treat numerous acute inflammatory diseases characterized by CRS.

Directed crystallization of a poly(3,4-ethylenedioxythiophene) film by an iron(III) dodecyl sulfate lamellar superstructure.

Poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS), a successfully commercialized polymeric semiconductor material, has potential as a transparent electrode in flexible electronic devices, yet has insufficient conductivity. We present the synthesis, properties, and directed crystallization of the PEDOT:dodecyl sulfate (PEDOT:DS) film. Iron(III) dodecyl sulfate (Fe(DS)3) multi-lamellar vesicles (MLVs), a new growth template, are used to synthesize and direct the growth of the PEDOT:DS film via vapor-phase polymerization of 3,4-ethylenedioxythiophene to form huge PEDOT:DS co-crystal domains within the MLV superstructure. The polycrystalline film has metallic conductivity (avg. ~1.0 × 104 S cm-1), is highly transparent and mechanically durable yet flexible, and suitable for next-generation flexible electronics. These noteworthy properties are conferred by the MLV lamellar superstructure of Fe(DS)3, a selective oxidant and an efficient in situ dopant that enhances the film hydrophobicity and durability. Sophisticated MLV-type oxidants are foreseen to enable the synthesis of more conductive, transparent, robust, flexible, and water-stable polymer electrode materials in future.

Tuberculous peritonitis complicated by an intraperitoneal tuberculous abscess: A case report.

BACKGROUND: Tuberculous peritonitis (TBP) is a chronic, diffuse inflammation of the peritoneum caused by Mycobacterium tuberculosis. The route of infection can be by direct spread of intraperitoneal tuberculosis (TB) or by hematogenous dissemination. The former is more common, such as intestinal TB, mesenteric lymphatic TB, fallopian tube TB, etc., and can be the direct primary lesion of the disease. CASE SUMMARY: We present an older male patient with TBP complicated by an abdominal mass. The patient's preoperative symptoms, signs and imaging data suggested a possible abdominal tumor. After surgical treatment, the patient's primary diagnosis of TBP complicating an intraperitoneal tuberculous abscess was established by combining past medical history, postoperative pathology, and positive results of TB-related laboratory tests. The patient's symptoms were significantly reduced after surgical treatment, and he was discharged from the hospital with instructions to continue treatment at a TB specialist hospital and to undergo anti-TB treatment if necessary. CONCLUSION: This case report analyses the management of TBP complicated by intraperitoneal tuberculous abscess and highlights the importance of early definitive diagnosis in the hope of improving the clinical management of this type of disease.

The mediating and moderating role of nursing information competence between nurses' creative self-efficacy and innovation behavior in a specialized oncology hospital.

OBJECTIVE: This study aims to examine the impact of nurses' nursing information competence on their creative self-efficacy and innovation behavior, and to investigate its role as a mediating factor between these two elements. METHODS: A survey was conducted from July to September 2023 involving 1,200 nurses from two tertiary-level oncology specialty hospitals in Beijing, selected through convenience sampling. Instruments used included the Creative Self-Efficacy Scale, Nursing Information Competence Assessment Scale, and Nurses' Innovative Behavior Scale. Data analysis was conducted using SPSS 25.0 and R 4.1.2; AMOS26 was used to construct structural equation models and Bootstrap method was used to test the mediating hypotheses. RESULTS: Out of the distributed questionnaires, 1,166 were valid, yielding an effective response rate of 97.16%. Pearson correlation analysis revealed significant correlations between innovation self-efficacy, nursing information competence, and nurses' innovative behaviors (P < 0.001). The Bootstrap method indicated that nursing information competence serves as a mediating factor in the relationship between creative self-efficacy and innovative behaviors, contributing to 24.5% of the observed effect. Additionally, regression analysis suggested that nursing information competence moderates the relationship between creative self-efficacy and innovation behavior. CONCLUSION: The findings suggest that nursing information competence not only mediates but also moderates the relationship between creative self-efficacy and innovative behavior. Enhancing nurses' information competence could therefore foster creative self-efficacy, leading to an increase in innovative behavior and, subsequently, improvements in the quality of oncology nursing care.

Interstitial lung disease presents with varying characteristics in patients with non-Hodgkin lymphoma undergoing rituximab-containing therapies.

Although the incidence and outcomes of rituximab-induced interstitial lung disease (RILD) have been partially reported, there are no systematic studies on the characteristics and types of RILD. This study aimed to investigate the clinical characteristics, bronchoalveolar lavage (BAL) findings, and treatment course of RILD in patients with non-Hodgkin lymphoma. We retrospectively analyzed the data from 321 patients with non-Hodgkin lymphoma who developed RILD between 2020 and 2022. The extent, distribution, and radiologic patterns of interstitial lung disease were determined using high-resolution computed tomography of the chest. BAL was performed in 299 (93.1%) patients to determine cellular distribution patterns and identify pathogenic microorganisms using metagenomic next-generation sequencing. All patients received combination therapy, with cyclophosphamide, doxorubicin, vincristine, and prednisone being the most commonly administered regimens. The median time from treatment to RILD development was 1.7 months. In the 217 patients who underwent metagenomic next-generation sequencing, 179 pathogenic microorganisms were detected, including 77 (43.0%) bacteria, 45 (25.1%) viruses, 28 (15.6%) Pneumocystis jirovecii strains, 17 (9.5%) fungi, 6 (3.5%) Mycobacterium tuberculosis, and 6 (3.5%) atypical pathogens. All RILD diagnoses were based on multidisciplinary team discussions and compliance with international standards. In conclusion, RILD exhibits a range of radiological and BAL patterns, reflecting different interstitial lung disease types. The most common patterns of RILD are infectious lung disease, organizing pneumonia, and nonspecific interstitial pneumonia. These findings enhance the understanding of RILD in patients with non-Hodgkin lymphoma and serve as a reference for best management guidelines in these patients.

Ultra-Fast Synthesis of Highly Dispersed Pt Nanoclusters Anchored on Sulfur-Doped Porous Carbon Carriers by Nanosecond Pulsed Laser for Hydrogen Evolution Reaction.

Nanosecond pulsed laser irradiation is employed for synthesis of highly active and stable Pt-based electrocatalysts by anchoring Pt nanoclusters on porous sulfur-doped carbon supports (L-Pt/SC). Strong metal-support interaction (SMSI) between Pt and S induces a local charge rearrangement and modulates the electronic structure of Pt surroundings, thus boosting the reaction kinetics and enhancing stability in long-term hydrogen evolution reaction (HER). The L-Pt/SC catalyst exhibits high activity toward HER, with an overpotential of 23 mV at current densities reaching 10 mA cm-2 and a Tafel slope of 24 mV dec-1. The unit mass activity of L-Pt/SC is calculated to be -10.8 A cm-2 mgPt -1 at an applied voltage of -0.3 V versus RHE. In situ Raman spectra reveals that L-Pt/SC catalyst exhibits fast hydrogen production efficiency and its electrocatalytic HER process is determined by the Tafel step. Density functional theory calculations suggest the strong bonding energy between SC and Pt induces the formation of smaller nanoclusters of L-Pt/SC during fast pulsed laser preparation, which increases the effective contact area during the HER process thereby increasing the activity per unit mass.

RBM25 is required to restrain inflammation via ACLY RNA splicing-dependent metabolism rewiring.

Spliceosome dysfunction and aberrant RNA splicing underline unresolved inflammation and immunopathogenesis. Here, we revealed the misregulation of mRNA splicing via the spliceosome in the pathogenesis of rheumatoid arthritis (RA). Among them, decreased expression of RNA binding motif protein 25 (RBM25) was identified as a major pathogenic factor in RA patients and experimental arthritis mice through increased proinflammatory mediator production and increased hyperinflammation in macrophages. Multiomics analyses of macrophages from RBM25-deficient mice revealed that the transcriptional enhancement of proinflammatory genes (including Il1b, Il6, and Cxcl10) was coupled with histone 3 lysine 9 acetylation (H3K9ac) and H3K27ac modifications as well as hypoxia inducible factor-1α (HIF-1α) activity. Furthermore, RBM25 directly bound to and mediated the 14th exon skipping of ATP citrate lyase (Acly) pre-mRNA, resulting in two distinct Acly isoforms, Acly Long (Acly L) and Acly Short (Acly S). In proinflammatory macrophages, Acly L was subjected to protein lactylation on lysine 918/995, whereas Acly S did not, which influenced its affinity for metabolic substrates and subsequent metabolic activity. RBM25 deficiency overwhelmingly increased the expression of the Acly S isoform, enhancing glycolysis and acetyl-CoA production for epigenetic remodeling, macrophage overactivation and tissue inflammatory injury. Finally, macrophage-specific deletion of RBM25 led to inflammaging, including spontaneous arthritis in various joints of mice and inflammation in multiple organs, which could be relieved by pharmacological inhibition of Acly. Overall, targeting the RBM25-Acly splicing axis represents a potential strategy for modulating macrophage responses in autoimmune arthritis and aging-associated inflammation.

Preparation of ultra-light, highly compressible, and biodegradable chitosan porous materials for heavy metal adsorption, dye adsorption and oil-water separation.

Chitosan materials are much important in adsorption, separation and water treatment due to their hydrophilicity, biodegradability and easy functionalization. However, they were difficult to form structural materials, which limited its application in engineering. In this paper, a new type of chitosan porous materials was prepared with two-step strategy involving the freezing crosslinking of chitosan with glutaraldehyde to form cryogels, and their subsequent reduction with NaBH4 to transform CN bonds into CN bonds, resulting in remarkable improvement of mechanical property. That is, the strength remained almost unchanged after 80 % deformation. The abundant -NH2 and -OH on the surface of materials, as well as the unique pore structure from cryogels, gave relatively high adsorption capacity for metals and dyes (88.73 ± 4.25 mg·g-1 for Cu(II) and 3261.05 ± 36.10 mg·g-1 for Congo red). The surface hydrophilicity of materials made it possible for selective water permeation with over 95 % separation efficiency for oil-water mixtures. In addition, simple hydrophobic modification using bromotetradecane achieved selective oil permeation with over 96 % separation efficiency for oil-water mixtures. This study not only provides a new strategy to endow chitosan materials with excellent mechanical property, large adsorption capacity and good oil-water separation performance, but also offers environmentally friendly materials for sewage treatment applications.

Long Non-Coding RNA AGAP2-AS1: A Comprehensive Overview on Its Biological Functions and Clinical Significances in Human Cancers.

Long non-coding RNAs (lncRNAs) are well known for their oncogenic or anti-oncogenic roles in cancer development. AGAP2-AS1, a new lncRNA, has been extensively demonstrated as an oncogenic lncRNA in various cancers. Abundant experimental results have proved the aberrantly high level of AGAP2-AS1 in a great number of malignancies, such as glioma, colorectal, lung, ovarian, prostate, breast, cholangiocarcinoma, bladder, colon and pancreatic cancers. Importantly, the biological functions of AGAP2-AS1 have been extensively demonstrated. It could promote the proliferation, migration and invasion of cancer cells. Simultaneously, the clinical significances of AGAP2-AS1 were also illustrated. AGAP2-AS1 was exceptionally overexpressed in various cancer tissues. Clinical studies disclosed that the abnormal overexpression of AGAP2-AS1 was tightly connected with overall survival (OS), lymph nodes metastasis (LNM), clinical stage, tumor infiltration, high histological grade (HG), serous subtype and PFI times. However, to date, the biological actions and clinical significances of AGAP2-AS1 have not been systematically reviewed in human cancers. In the present review, the authors overviewed the biological actions, potential mechanisms and clinical features of AGAP2-AS1 according to the previous studies. In summary, AGAP2-AS1, as a vital oncogenic gene, is a promising biomarker and potential target for carcinoma prognosis and therapy.

Adsorption mechanism and remediation of heavy metals from soil amended with hyperthermophilic composting products: Exploration of waste utilization.

Due to high humification, hyperthermophilic composting products (HP) show potential for remediating heavy metal pollution. However, the interaction between HP and heavy metals remains unclear. This study investigated the adsorption mechanism and soil remediation effect of HP on heavy metals. The results showed that the maximum adsorption capacity of HP increased by an average of 30.74 % compared to conventional composting products. HP transformed 34.87 % of copper, 42.55 % of zinc, and 35.63 % of lead from exchangeable and reducible forms into residual and oxidizable forms, thus reducing the soil risk level. In conclusion, HP significantly enhanced the adsorption of heavy metals and their transformation from unstable to stable forms, primarily due to the higher content of hydroxyl and carboxyl groups. This study aims to demonstrate the effectiveness of HP for remediating heavy metal pollution and to enhance the understanding of the underlying mechanism, which lays a foundation for waste utilization.

Ubiquitination of NS1 Confers Differential Adaptation of Zika Virus in Mammalian Hosts and Mosquito Vectors.

Arboviruses, transmitted by medical arthropods, pose a serious health threat worldwide. During viral infection, Post Translational Modifications (PTMs) are present on both host and viral proteins, regulating multiple processes of the viral lifecycle. In this study, a mammalian E3 ubiquitin ligase WWP2 (WW domain containing E3 ubiquitin ligase 2) is identified, which interacts with the NS1 protein of Zika virus (ZIKV) and mediates K63 and K48 ubiquitination of Lys 265 and Lys 284, respectively. WWP2-mediated NS1 ubiquitination leads to NS1 degradation via the ubiquitin-proteasome pathway, thereby inhibiting ZIKV infection in mammalian hosts. Simultaneously, it is found Su(dx), a protein highly homologous to host WWP2 in mosquitoes, is capable of ubiquitinating NS1 in mosquito cells. Unexpectedly, ubiquitination of NS1 in mosquitoes does not lead to NS1 degradation; instead, it promotes viral infection in mosquitoes. Correspondingly, the NS1 K265R mutant virus is less infectious to mosquitoes than the wild-type (WT) virus. The above results suggest that the ubiquitination of the NS1 protein confers different adaptations of ZIKV to hosts and vectors, and more importantly, this explains why NS1 K265-type strains have become predominantly endemic in nature. This study highlights the potential application in antiviral drug and vaccine development by targeting viral proteins' PTMs.

Integrating untargeted and targeted LC-MS-based metabolomics to identify the serum metabolite biomarkers for tuberculosis.

Given the limitations of untargeted metabolomics in precise metabolite quantification, our current research employed a novel approach by integrating untargeted and targeted metabolomics utilizing ultra-high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS/MS) to analyze the metabolic profile and potential biomarkers for tuberculosis (TB). A cohort of 36 TB patients and 36 healthy controls (HC) was enlisted to obtain serum samples. Multivariate pattern recognition and univariate statistical analysis were employed to screen and elucidate the differential metabolites, whereas dot plots and receiver operating characteristic (ROC) curves were established for the identification of potential biomarkers of TB. The results indicated a distinct differentiation between the two groups, identifying 99 metabolites associated with five primary metabolic pathways in relation to TB. Of these, 19 metabolites exhibited high levels of sensitivity and specificity, as evidenced by the area under curve values approaching 1. Following targeted quantitative analysis, three potential metabolites, namely, L-asparagine, L-glutamic acid, and arachidonic acid, were demonstrated excellent discriminatory ability as evidenced by the results of the ROC curve, dot plots, and random forest model. Particularly noteworthy was the enhanced diagnostic efficacy of the combination of these three metabolites compared to singular biomarkers, suggesting their potential utility as serum biomarkers for TB diagnosis.

Protocol for siRNA-mediated U1 snRNA knockdown using fluorinated α-helical polypeptide in vitro and in vivo.

Here, we present a protocol for small interfering RNA (siRNA)-mediated U1 small nuclear RNA (snRNA) knockdown using fluorinated α-helical polypeptide in macrophages and mouse lungs, providing a dependable approach to silence U1 snRNA in vitro and in vivo. We describe steps for preparing P7F7/siRNA polyplexes and silencing U1 snRNA with P7F7/siRNA polyplexes in macrophages and mouse lungs. Knockdown efficiency is validated through reverse-transcription quantitative real-time PCR analysis. This protocol is applicable for studying the physiological or pathophysiological function of U1 snRNA. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.