Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair.

Transcription-coupled nucleotide excision repair (TC-NER) is initiated by the stalling of elongating RNA polymerase II (RNAPIIo) at DNA lesions. The ubiquitination of RNAPIIo in response to DNA damage is an evolutionarily conserved event, but its function in mammals is unknown. Here, we identified a single DNA damage-induced ubiquitination site in RNAPII at RPB1-K1268, which regulates transcription recovery and DNA damage resistance. Mechanistically, RPB1-K1268 ubiquitination stimulates the association of the core-TFIIH complex with stalled RNAPIIo through a transfer mechanism that also involves UVSSA-K414 ubiquitination. We developed a strand-specific ChIP-seq method, which revealed RPB1-K1268 ubiquitination is important for repair and the resolution of transcriptional bottlenecks at DNA lesions. Finally, RPB1-K1268R knockin mice displayed a short life-span, premature aging, and neurodegeneration. Our results reveal RNAPII ubiquitination provides a two-tier protection mechanism by activating TC-NER and, in parallel, the processing of DNA damage-stalled RNAPIIo, which together prevent prolonged transcription arrest and protect against neurodegeneration.

Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning.

This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes. The coexpression network of co-expression pairs (CP) genes was integrated with its protein-protein interaction (PPI) network, and machine learning was employed to identify essential disease-representing genes. Finally, immuno-penetration analysis was performed on the MASH and DN gene datasets using the CIBERSORT algorithm to evaluate the plausibility of these genes in diseases. We found 19 key CP genes. Fos proto-oncogene (FOS), belonging to the IL-17 signalling pathway, showed greater centrality PPI network; Hyaluronan Mediated Motility Receptor (HMMR), belonging to ECM-receptor interaction genes, showed most critical in the co-expression network map of 19 CP genes; Forkhead Box C1 (FOXC1), like FOS, showed a high ability to predict disease in XGBoost analysis. Further immune infiltration showed a clear positive correlation between FOS/FOXC1 and mast cells that secrete IL-17 during inflammation. Combining the results of previous studies, we suggest a FOS/FOXC1/HMMR regulatory axis in MASH and DN may be associated with mast cells in the acting IL-17 signalling pathway. Extracellular HMMR may regulate the IL-17 pathway represented by FOS through the Mitogen-Activated Protein Kinase 1 (ERK) or PI3K-Akt-mTOR pathway. HMMR may serve as a signalling carrier between MASH and DN and could be targeted for therapeutic development.

Risk factors for pterygium: Latest research progress on major pathogenesis.

A pterygium is a wedge-shaped fibrovascular growth of the conjunctiva membrane that extends onto the cornea, which is the outer layer of the eye. It is also known as surfer's eye. Growth of a pterygium can also occur on the either side of the eye, attaching firmly to the sclera. Pterygia are one of the world's most common ocular diseases. However, the pathogenesis remains unsolved to date. As the pathogenesis of pterygium is closely related to finding the ideal treatment, a clear understanding of the pathogenesis will lead to better treatment and lower the recurrence rate, which is notably high and more difficult to treat than a primary pterygium. Massive studies have recently been conducted to determine the exact causes and mechanism of pterygia. We evaluated the pathogenetic factors ultraviolet radiation, viral infection, tumor suppressor genes p53, growth factors, oxidative stress, apoptosis and neuropeptides in the progression of the disease. The heightened expression of TRPV1 suggests its potential contribution in the occurrence of pterygium, promoting its inflammation and modulating sensory responses in ocular tissues. Subsequently, the developmental mechanism of pterygium, along with its correlation with dry eye disease is proposed to facilitate the identification of pathogenetic factors for pterygia, contributing to the advancement of understanding in this area and may lead to improved surgical outcomes.

Research progress on measurement methods and clinical applications of corneal elastic modulus.

Various corneal diseases are strongly associated with corneal biomechanical characteristics, and early measurement of patients' corneal biomechanics can be utilized in their diagnosis and treatment. Measurement methods for corneal biomechanical characteristics are classified into ex vivo and in vivo. Some of these methods can directly measure certain corneal biomechanical parameters, while others require indirect calculation through alternative methods. However, due to diversities in measurement techniques and environmental conditions, significant differences may exist in the corneal mechanical properties measured by these two methods. Therefore, comprehensive research on current measurement methods and the exploration of novel measurement techniques may have great clinical significance. The corneal elastic modulus, a critical indicator in corneal biomechanics, reflects the cornea's ability to return to its initial shape after undergoing stress. This review aims to provide a comprehensive summary of the corneal elastic modulus, which is a critical biomechanical parameter, and discuss its direct, indirect, and potential measurement methods and clinical applications.

Transcriptome and Metabolomic Analyses Reveal Tissue-Specific Glycosylation of Phenylpropanoids and Flavonoids in Toxicodendron vernicifluum.

Toxicodendron vernicifluum (Stokes) F. A. Barkley is a tree species used primarily for lacquer production. Our study utilized transcriptome and metabolomic analysis to investigate the biosynthesis of phenylpropanoids and flavonoids, specifically the glycosylated forms, in T. vernicifluum roots, stems, and leaves. HPLC-QTOF-MS/MS identified 186 compounds, with tissue-specific distributions revealed by PCA. Flavonoids and phenylpropanoids glycosides were significantly more abundant in leaves compared with roots and stems. Full-length sequencing uncovered 17,266 transcripts in T. vernicifluum. Gene expression analysis showed higher activity of phenylpropanoid and flavonoid biosynthesis pathways in leaves. Certain genes, such as CYP73A, 4CL, CRR, CYP84A/F5H, and CYP93C, displayed associations with compound content distributions. Root tissue exhibited a higher concentration of isoflavones. Notably, glycosyltransferase expression demonstrated significant correlations with glycosylated compounds' content. Biochemical validation confirmed the involvement of TvPB_c0_g2904, encoding a UDP-glucosyltransferase, in genistin biosynthesis in T. vernicifluum.

Functional characterization of GATA6 genetic variants associated with mild congenital heart defects.

Damaging GATA6 variants can cause moderate congenital heart defects. With the application of next-generation sequencing approaches, various novel GATA6 variants with unknown significance have been identified from a broad spectrum of congenital heart defects. However, functional assessment for distinct GATA6 variants from different severity of congenital heart defects, especially from mild defects, is lacking, which hinders our understanding of the genotype-phenotype correlations and underlying mechanisms. Here, we assessed the functional consequences of nine rare GATA6 variants, which had been implicated as the most significant variants associated with mild congenital heart defects using the largest case and control cohort. We examined the effects of these variants on subcellular localization, transcriptional activity, and protein interactions in 293T or AC16 cells and their ability to rescue heart malformation in gata6 zebrafish mutant. We found that two of these nine variants, Q120X and S424I, significantly decreased transcriptional activity. Additionally, Q120X altered subcellular localization. Consistent with the in vitro results, the in vivo results showed that Q120X and S424I lost their potency to rescue ventricular malformation in gata6 -/- embryos. The results indicated that Q120X and S424I are pathogenic in mild congenital heart defects. Further, the inconsistence of severely impaired Q120X function and mild CHDs phenotype suggested the complexity of the genotype-phenotype correlation between the GATA6 variant and heart phenotype, which may help to inform prenatal genetic counseling and pre-implantation genotyping for congenital heart defects.

BMP4 inhibits corneal neovascularization by interfering with tip cells in angiogenesis.

Corneal neovascularization (CNV) can lead to impaired corneal transparency, resulting in vision loss or blindness. The primary pathological mechanism underlying CNV is an imbalance between pro-angiogenic and anti-angiogenic factors, with inflammation playing a crucial role. Notably, a vascular endothelial growth factor（VEGF）-A gradient triggers the selection of single endothelial cells（ECs） into primary tip cells that guide sprouting, while a dynamic balance between tip and stalk cells maintains a specific ratio to promote CNV. Despite the central importance of tip-stalk cell selection and shuffling, the underlying mechanisms remain poorly understood. In this study, we examined the effects of bone morphogenetic protein 4 (BMP4) on VEGF-A-induced lumen formation in human umbilical vein endothelial cells (HUVECs) and CD34-stained tip cell formation. In vivo, BMP4 inhibited CNV caused by corneal sutures. This process was achieved by BMP4 decreasing the protein expression of VEGF-A and VEGFR2 in corneal tissue after corneal suture injury. By observing the ultrastructure of the cornea, BMP4 inhibited the sprouting of tip cells and brought forward the appearance of intussusception. Meanwhile, BMP4 attenuated the inflammatory response by inhibiting neutrophil extracellular traps （NETs）formation through the NADPH oxidase-2（NOX-2）pathway. Our results indicate that BMP4 inhibits the formation of tip cells by reducing the generation of NETs, disrupting the dynamic balance of tip and stalk cells and thereby inhibiting CNV, suggesting that BMP4 may be a potential therapeutic target for CNV.

CircRNA in ocular neovascular diseases: Fundamental mechanism and clinical potential.

Ocular neovascular disease (OND), characterized by the aberrant formation of immature blood vessels, is the leading cause of vision impairment and blindness. It is important to find effective ways to diagnose and treat these diseases. Circular RNA (circRNA) is a group of endogenous non-coding RNA that play a crucial role in regulating different biological processes. Due to their close association with ocular disease and angiogenesis, circRNAs have become a hotspot in OND research. In this review, we intensively investigate the possibility of using circRNAs in the management of ONDs. In general, angiogenesis is divided into five phases. On the basis of these five steps, we describe the potential of using circRNAs by introducing how they regulate angiogenesis. Subsequently, the interactions between circRNAs and ONDs, including pterygium, corneal neovascularization, age-related macular degeneration, diabetic retinopathy, and retinopathy of prematurity, are analyzed in detail. We also introduce the potential use of circRNAs as OND diagnostic biomarkers. Finally, we summarize the prospects of using circRNAs as a potential strategy in OND management. The gaps in recent research are also pointed out with the purpose of promoting the introduction of circRNAs into clinical applications.

Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case-control study.

OBJECTIVES: To compare clinical outcomes in patients with severe pneumonia according to the diagnostic strategy used. METHODS: In this retrospective, nested, case-control study, patients with severe pneumonia who had undergone endotracheal aspirate (ETA) metagenomic next-generation sequencing of (mNGS) testing (n = 53) were matched at a ratio of 1 to 2 (n = 106) by sex, age, underlying diseases, immune status, disease severity scores, and type of pneumonia with patients who had undergone bronchoalveolar lavage fluid (BALF) mNGS. The microbiological characteristics and patient's prognosis of the two groups were compared. RESULTS: An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections. However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%. There were more cases for whom targeted treatment was initiated (36.79% vs. 22.64%; P = 0.043) and fewer cases who received no clinical benefit after mNGS (5.66% vs. 15.09%; P = 0.048) in the BALF group. The pneumonia improvement rate in the BALF group was significantly higher than in the ETA group (73.58% vs. 87.74%, P = 0.024). However, there were no significant differences in ICU mortality or 28-day mortality. CONCLUSIONS: We do not recommend using ETA mNGS as the first-choice method for analyzing airway pathogenic specimens from severe pneumonia patients.

Research Progress on Morphological Changes and Surgery-Related Parameters of Corneal Cap in Small-Incision Lenticule Extraction.

Small-incision lenticule extraction (SMILE) is an "all-in-one" surgical method for refractive correction. An advantage of the SMILE over traditional surgery is that it depends on the corneal cap's design. This review discusses the morphological evaluation of the corneal cap, selection of the corneal cap with different thicknesses and diameters, influence of the corneal cap design on re-treatment, and management of corneal cap-related complications. The following points should be recognized to define the correct morphology and design of the operation-related parameters of the corneal cap during SMILE: (1) the thickness and diameter of the corneal cap are predictable and influence postoperative visual quality, (2) the change in the anterior surface curvature of the corneal cap should be considered in the design of the nomogram value, (3) for patients with moderate myopic correction, early visual quality is better with a 6.9-mm than with a 7.5-mm-diameter corneal cap, (4) there is no significant difference in visual quality or biomechanics among corneal caps with different thicknesses, (5) the primary corneal cap thickness plays an important role in the SMILE re-treatment, (6) a 7.78-mm diameter corneal cap has a greater risk of suction loss than a 7.60-mm diameter corneal cap, (7) if suction loss occurs when lenticular scanning exceeds 10%, then SMILE can be continued by changing the corneal cap thickness, (8) preventive collagen cross-linking with SMILE caps are 90-120 µm thick and 7-7.8 mm in diameter, and (9) properly treating SMILE-related complications ensures better postoperative results. The data presented herein shall deepen the understanding of the importance of the corneal cap during SMILE and provide diversified analysis for personalized operational design of corneal cap parameters.

The role of bone morphogenetic protein 4 in corneal injury repair.

PURPOSE: Corneal injury may cause neovascularization and lymphangiogenesis in cornea which have a detrimental effect to vision and even lead to blindness. Bone morphogenetic protein 4 (BMP4) regulates a variety of biological processes, which is closely relevant to the regulation of corneal epithelium and angiogenesis. Herein, we aimed to evaluate the effect of BMP4 on corneal neovascularization (CNV), corneal lymphangiogenesis (CL), corneal epithelial repair, and the role of BMP4/Smad pathway in these processes. METHODS: We used MTT assay to determine the optimal concentration of BMP4. The suture method was performed to induce rat CNV and CL. We used ink perfusion and HE staining to visualize the morphological change of CNV, and utilized RT-qPCR and ELISA to investigate the expression of angiogenic factors and lymphangiogenic factors. The effects of BMP4 and anti-VEGF antibody on migration, proliferation and adhesion of corneal epithelium were determined by scratch test, MTT assay and cell adhesion test. RESULTS: BMP4 significantly inhibited CNV and possibly CL. Topical BMP4 resulted in increased expression of endogenous BMP4, and decreased expression of angiogenic factors and lymphangiogenic factors. Compared with anti-VEGF antibody, BMP4 enhanced corneal epithelium migration, proliferation and adhesion, which facilitated corneal epithelial injury repair. Simultaneously, these processes could be regulated by BMP4/Smad pathway. CONCLUSIONS: Our results demonstrated unreported effects of BMP4 on CNV, CL, and corneal epithelial repair, suggesting that BMP4 may represent a potential therapeutic target in corneal injury repair.

Bone marrow mesenchymal stem cells enhance autophagy and help protect cells under hypoxic and retinal detachment conditions.

Our study aimed to evaluate the protective role and mechanisms of bone marrow mesenchymal stem cells (BMSCs) in hypoxic photoreceptors and experimental retinal detachment. The cellular morphology, viability, apoptosis and autophagy of hypoxic 661w cells and cells cocultured with BMSCs were analysed. In retinal detachment model, BMSCs were intraocularly transplanted, and then, the retinal morphology, outer nuclear layer (ONL) thickness and rhodopsin expression were studied as well as apoptosis and autophagy of the retinal cells. The hypoxia-induced apoptosis of 661w cells obviously increased together with autophagy levels increasing and peaking at 8 hours after hypoxia. Upon coculturing with BMSCs, hypoxic 661w cells had a better morphology and fewer apoptosis. After autophagy was inhibited, the apoptotic 661w cells under the hypoxia increased, and the cell viability was reduced, even in the presence of transplanted BMSCs. In retina-detached eyes transplanted with BMSCs, the retinal ONL thickness was closer to that of the normal retina. After transplantation, apoptosis decreased significantly and retinal autophagy was activated in the BMSC-treated retinas. Increased autophagy in the early stage could facilitate the survival of 661w cells under hypoxic stress. Coculturing with BMSCs protects 661w cells from hypoxic damage, possibly due to autophagy activation. In retinal detachment models, BMSC transplantation can significantly reduce photoreceptor cell death and preserve retinal structure. The capacity of BMSCs to reduce retinal cell apoptosis and to initiate autophagy shortly after transplantation may facilitate the survival of retinal cells in the low-oxygen and nutrition-restricted milieu after retinal detachment.

Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil.

Strain KUDC5002T was isolated from soil sampled on the Dokdo Islands, Republic of Korea. This bacterial strain was Gram stain-positive, non-motile, rod-shaped, capable of growing at 25-37°C and pH 5.0-12.0, and showed optimal growth at 30 °C and pH 7.0-8.0. Strain KUDC5002T could be grown in tryptic soy broth containing less than 7.0 % NaCl (w/v). The cell width ranged from 0.5 to 0.6 µm and length ranged from 0.8 to 1.0 µm. Strain KUDC5002T was catalase- and oxidase-positive. Its genomic G+C content was 72.2 mol%. Its major fatty acids were C18 : 1 ω9c (17.3 %), iso-C16 : 0 (16.0 %) and iso-C17 : 0 (11.4 %). Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain KUDC5002T belongs to the genus Nocardioides and is most closely related to strain Nocardioides humi DCY24T (97.0 %). Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, strain KUDC5002T should be considered a novel species in the genus Nocardioides, for which we have proposed the name Nocardioides sambongensis sp. nov. The type strain is KUDC5002T (=KCTC 39855T=DSM 106604T).

Flurbiprofen-chalcone hybrid Mannich base derivatives as balanced multifunctional agents against Alzheimer's disease: Design, synthesis and biological evaluation.

The complex pathogenesis of Alzheimer's disease (AD) calls for multitarget approach for disease management. Herein, a series of novel flurbiprofen-chalcone hybrid Mannich base derivatives were designed and synthesized. The biological screening results indicated that most of the derivatives exhibited potent multi-target effects involved in AD. In particular, compound 6c bearing a pyrrolidine group showed the highest activities against self- and Cu2+-induced Aß1-42 aggregation (70.65% and 54.89% at 25.0 µM, respectively), highly selective inhibition towards AChE and MAO-B (IC50 = 7.15 µM and 0.43 µM respectively), good antioxidant ability and metal-chelating property. Moreover, 6c displayed excellent anti-neuroinflammatory activity and appropriate BBB permeability in vitro. These outstanding results qualified compound 6c as a promising multifunctional agent for further development of disease-modifying treatment of AD.

Discovery of 4'-OH-flurbiprofen Mannich base derivatives as potential Alzheimer's disease treatment with multiple inhibitory activities.

A series of 4'-OH flurbiprofen Mannich base derivatives were designed, synthesized and evaluated as potential multifunctional agents for the treatment of Alzheimer's disease. The biological screening results indicated that most of these derivatives exhibited good multifunctional activities. Among them, compound 8n demonstrated the best inhibitory effects on self-induced Aß1-42 aggregation (65.03% at 25.0 µM). Moreover, this representative compound also exhibited good antioxidant activity, biometal chelating ability and anti-neuroinflammatory activity in vitro. Furthermore, compound 8n displayed appropriate blood-brain barrier permeability. These multifunctional properties highlight compound 8n as promising candidate for further development of multi-functional drugs against AD.

Proteins of the corneal stroma: importance in visual function.

The human cornea, consisting of five layers, is the transparent tissue that refracts and transmits light to the lens and retina, providing about two thirds of the refractive power of the eye. The stroma layer comprises nearly 90 % of the thickness of the cornea and thus plays a pivotal role in normal visual function. The bulk of this layer is constituted by proteins in the extracellular martrix secreted by the corneal epithelial, stroma, and endothelial cells. Clinical research has shown that corneal stroma diseases are common and involve conditions such as infections, injuries, and genetic defects, which cause severe visual disturbances or even blindness. To improve our understanding of the basic molecular mechanisms involved in the physiological and pathological activities of the corneal stroma, its proteins have been brought into the limelight to determine their crucial and irreplaceable roles. The data presented in a previous study have demonstrated the presence of 1679 proteins in the stroma, and this data set has subsequently been perfected by utilizing a highly sensitive isobaric peptide-labeling approach. According to their manifestations, these proteins can be classified as a gel-like organic material composed of proteoglycans, enzymes, and hemocyanin-binding proteins and a network of filaments composed of collagen, elastin, keratin, vimentin, and interconnected filaments comprising fibronectin and laminin. The aim of this review is to describe some corneal stroma proteins by highlighting their major functions and valuable applications in ophthalmologic research toward the better characterization and treatment of eye diseases.

A Quadrature-Based Tunable Radio-Frequency Sensor for the Detection and Analysis of Aqueous Solutions.

A highly tunable and sensitive radio-frequency (RF) sensor is presented for the measurement of aqueous-solution dielectric properties. Two quadrature hybrids are utilized to achieve destructive interference that eliminates the probing signals at both measurement ports. As a result, weak signals of material-under-test (MUT) are elevated for high sensitivity detections at different frequencies. The sensor is demonstrated through measuring 2-propanol-water solution permittivity at 0.01 mole fraction concentration level from ~4 GHz to ~12 GHz. De-ionized water and methanol-water solution are used to calibrate the sensor for quantitative MUT analysis through our proposed model. Micro-meter coplanar waveguides (CPW) are fabricated as RF sensing electrodes. A polydimethylsiloxane (PDMS) microfluidic channel is employed to introduce 250 nL liquid, of which ~1 nL is effectively the MUT. The permittivity and the relaxation time of 2-propanol-water solution are obtained. Compared with our power divider based sensors, the differential reflection coefficients in this work provide additional information that complements the transmission coefficient methods.

Recent advances of stem cell therapy for retinitis pigmentosa.

Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by progressive loss of photoreceptors and eventually leads to retina degeneration and atrophy. Until now, the exact pathogenesis and etiology of this disease has not been clear, and many approaches for RP therapies have been carried out in animals and in clinical trials. In recent years, stem cell transplantation-based attempts made some progress, especially the transplantation of bone marrow-derived mesenchymal stem cells (BMSCs). This review will provide an overview of stem cell-based treatment of RP and its main problems, to provide evidence for the safety and feasibility for further clinical treatment.

Novel Drug Delivery Systems for the Management of Fungal Keratitis.

Fungal keratitis (FK) is a dangerous corneal infection that is common in tropical and subtropical areas. Its incidence is extremely high, and ocular trauma and contact lenses can lead to FK, but its common treatment such as using topical antifungal eye drop instillation is often less effective because of several drawbacks of the drugs typically used, including limited ocular penetration, high frequency of dosing, poor biocompatibility, and the potential for severe drug reactions. Therefore, the development of novel drug delivery devices for the treatment of FK is urgent. The urgent need for novel drug delivery devices to treat FK has led to the development of several techniques, including nanoparticles (NPs), in situ forming hydrogels, contact lenses, and microneedles (MNs). However, it is important to note that the main mechanisms differ between these techniques. NPs can transport large amounts of drugs and be taken up by cells owing to their large surface area and small size. In situ forming hydrogels can significantly extend the residence time of drugs because of their strong adhesive properties. Contact lenses, with their comfortable shape and drug-carrying capacity, can also act as drug delivery devices. MNs can create channels in the cornea, bypassing its barrier and enhancing drug bioavailability. This article will go over novel medication delivery techniques for treating FK and make a conclusion about their advantages and limitations in anticipation to serve the best option for the individual therapy of FK.

Corneal densitometry: A new evaluation indicator for corneal diseases.

Corneal densitometry (CD) uses the biological properties of the cornea to visualize the morphology of the cornea and determine the degree of corneal transparency. At present, it is an emerging metric that has shown promise in various clinical diagnosis and evaluation of eye diseases and surgeries. We introduce the different methodologies used to measure CD. Furthermore, we systematically categorize the diagnostic value of CD into high, medium, and low levels based on its clinical significance. By analyzing a wide range of conditions, including keratoconus, postrefractive surgery changes, and other corneal pathologies, we assess the utility of CD in each context. We also discuss the potential implications of these classifications for disease monitoring and prognosis evaluation. Our review underscores the importance of integrating CD assessments into routine clinical practice to enhance the accuracy and effectiveness of diagnostic processes for corneal disorders.