Symmetry-breaking malachite green as a near-infrared light-activated fluorogenic photosensitizer for RNA proximity labeling.

Cellular RNA is asymmetrically distributed in cells and the regulation of RNA localization is crucial for proper cellular functions. However, limited chemical tools are available to capture dynamic RNA localization in complex biological systems with high spatiotemporal resolution. Here, we developed a new method for RNA proximity labeling activated by near-infrared (NIR) light, which holds the potential for deep penetration. Our method, termed FAP-seq, utilizes a genetically encoded fluorogen activating protein (FAP) that selectively binds to a set of substrates known as malachite green (MG). FAP binding restricts the rotation of MG and rapidly activates its fluorescence in a wash-free manner. By introducing a monoiodo modification to MG, we created a photosensitizer (MG-HI) with the highest singlet oxygen generation ability among various MG derivatives, enabling both protein and RNA proximity labeling in live cells. New insights are provided in the transcriptome analysis with FAP-seq, while a deeper understanding of the symmetry-breaking structural arrangement of FAP-MG-HI was obtained through molecular dynamics simulations. Overall, our wash-free and NIR light-inducible RNA proximity labeling method (FAP-seq) offers a powerful and versatile approach for investigating complex mechanisms underlying RNA-related biological processes.

Differential subcellular localization of ASPM RNA and protein.

RNAs encoding some centrosomal components are trafficked to the organelle during mitosis. Some RNAs, including ASPM , localize to the centrosome co-translationally. However, the relative position of these RNAs and their protein after trafficking to centrosomes remained unclear. We find that mislocalization of ASPM RNA from the centrosome does not affect the localization of ASPM protein. Further, ASPM RNA and ASPM protein reside in two physically close yet distinct subcellular spaces, with ASPM RNA on the astral side of the centrosome and ASPM protein on the spindle side. This suggests subtly distinct locations of ASPM RNA translation and ASPM protein function.

Arthroscopic decompression of calcific tendinitis without cuff repair.

Aims: The aim of this study was to investigate the outcomes of arthroscopic decompression of calcific tendinitis performed without repairing the rotator cuff defect. Methods: A total of 99 patients who underwent treatment between December 2013 and August 2019 were retrospectively reviewed. Visual analogue scale (VAS) and American Shoulder and Elbow Surgeons (ASES) scores were reviewed pre- and postoperatively according to the location, size, physical characteristics, and radiological features of the calcific deposits. Additionally, the influence of any residual calcific deposits shown on postoperative radiographs was explored. The healing rate of the unrepaired cuff defect was determined by reviewing the 29 patients who had follow-up MRIs. Results: Statistically significant improvement from pre- to postoperation was seen in all VAS and ASES scores for each group, but no statistical differences were seen between the postoperative scores according to the differences in the features of the calcific deposits. When residual calcification was observed postoperatively, the mean ASES and VAS (rest) scores improved significantly to 95.0 (SD 5.6) and 0.0 (SD 0.0), respectively (p = 0.006 and p < 0.001), and did not differ from those who had the complete removal. Of 29 patients who had follow-up MRIs, six (20.7%) showed signs of an interstitial tear. This group's mean postoperative ASES and VAS (rest) scores improved to excellent levels of 96.0 (SD 3.7) and 0.0 (SD 0.0), respectively, and were similar to those of the 23 patients with normal MRI appearances. Conclusion: Arthroscopic removal of calcific deposits without repairing the rotator cuff defect resulted in significant improvement in function and pain level, regardless of the deposit's location, size, type, and whether or not complete excision was achieved. Despite leaving the defects unrepaired, in the limited number of patients with follow-up MRIs, 23 of 29 patients (79.3%) showed good healing, and the rest, who had persistent signs of interstitial defects on the MRIs, still had excellent outcomes. The removal of calcific deposits without repairing the cuff defects provided excellent outcomes.

Human PRPF39 is an alternative splicing factor recruiting U1 snRNP to weak 5' splice sites.

Human PRPF39 is a homolog of the yeast Prp39 and Prp42 paralogs. We have previously shown that human PRPF39 forms a homodimer that interacts with the CTD of U1C, mirroring the yeast Prp39/Prp42 heterodimer. We demonstrate here that PRPF39 knockdown in HEK293 cells affects many alternative splicing events primarily by reducing the usage of weak 5'ss. Additionally, PRPF39 preferentially binds to a GC-rich RNA, likely at the interface between its NTD and CTD. These data indicate that PRPF39 potentially recruits U1 snRNP to a weak 5' ss, serving as a previously unrecognized alternative splicing factor. We further demonstrate that human TIA1 binds to U1C through its RRM1 and RRM3+Q domains but has no significant binding to PRPF39. Finally, all three human LUC7L isoforms directly interact with U1C. These results reveal significant parallels to the yeast U1 snRNP structure and support the use of yeast U1 snRNP as a model for understanding the mechanism of human alternative splicing.

NF-κB: A novel therapeutic pathway for gastroesophageal reflux disease?

Although gastroesophageal reflux disease (GERD), a common chronic disease in clinical practice, has been widely studied, its potential adverse impact on patients is still a significant clinical concern. It is necessary to understand the pathogenesis of the disease and choose appropriate treatment according to its mechanism. The pathogenesis of GERD is diverse and complex. As the traditional treatment methods are expensive and ineffective in alleviating symptoms in some patients, new treatment options need to be explored. Our previous study suggested that the activation of nuclear factor-kappa beta (NF-κB) in esophageal mucosa may be related to the injury of epithelial barrier function caused by reflux. Based on the literature and our previous study results, it is speculated that inhibition of NF-κB activation may block the insult of GERD on the esophageal mucosal barrier. NF-κB may play an important role in the development of GERD. This article reviews the pathogenesis of GERD and the relationship between NF-κB and GERD, in order to provide new strategies for the treatment of GERD.

Halo-seq: An RNA Proximity Labeling Method for the Isolation and Analysis of Subcellular RNA Populations.

The subcellular localization of specific RNA molecules promotes localized cellular activity across a variety of species and cell types. The misregulation of this RNA targeting can result in developmental defects, and mutations in proteins that regulate this process are associated with multiple diseases. For the vast majority of localized RNAs, however, the mechanisms that underlie their subcellular targeting are unknown, partly due to the difficulty associated with profiling and quantifying subcellular RNA populations. To address this challenge, we developed Halo-seq, a proximity labeling technique that can label and profile local RNA content at virtually any subcellular location. Halo-seq relies on a HaloTag fusion protein localized to a subcellular space of interest. Through the use of a radical-producing Halo ligand, RNAs that are near the HaloTag fusion are specifically labeled with spatial and temporal control. Labeled RNA is then specifically biotinylated in vitro via a click reaction, facilitating its purification from a bulk RNA sample using streptavidin beads. The content of the biotinylated RNA is then profiled using high-throughput sequencing. In this article, we describe the experimental and computational procedures for Halo-seq, including important benchmark and quality control steps. By allowing the flexible profiling of a variety of subcellular RNA populations, we envision Halo-seq facilitating the discovery and further study of RNA localization regulatory mechanisms. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Visualization of HaloTag fusion protein localization Basic Protocol 2: In situ copper-catalyzed cycloaddition of fluorophore via click reaction Basic Protocol 3: In vivo RNA alkynylation and extraction of total RNA Basic Protocol 4: In vitro copper-catalyzed cycloaddition of biotin via click reaction Basic Protocol 5: Assessment of RNA biotinylation by RNA dot blot Basic Protocol 6: Enrichment of biotinylated RNA using streptavidin beads and preparation of RNA-seq library Basic Protocol 7: Computational analysis of Halo-seq data.

Effect of Anesthetics on Functional Connectivity of Developing Brain.

The potential anesthetic neurotoxicity on the neonate is an important focus of research investigation in the field of pediatric anesthesiology. It is essential to understand how these anesthetics may affect the development and growth of neonatal immature and vulnerable brains. Functional magnetic resonance imaging (fMRI) has suggested that using anesthetics result in reduced functional connectivity may consider as core sequence for the neurotoxicity and neurodegenerative changes in the developed brain. Anesthetics either directly impact the primary structures and functions of the brain or indirectly alter the hemodynamic parameters that contribute to cerebral blood flow (CBF) in neonatal patients. We hypothesis that anesthetic agents may either decrease the brain functional connectivity in neonatal patients or animals, which was observed by fMRI. This review will summarize the effect and mechanism of anesthesia on the rapid growth and development infant and neonate brain with fMRI through functional connectivity. It is possible to provide the new mechanism of neuronal injury induced by anesthetics and objective imaging evidence in animal developing brain.

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.

CD36 maintains the gastric mucosa and associates with gastric disease.

The gastric epithelium is often exposed to injurious elements and failure of appropriate healing predisposes to ulcers, hemorrhage, and ultimately cancer. We examined the gastric function of CD36, a protein linked to disease and homeostasis. We used the tamoxifen model of gastric injury in mice null for Cd36 (Cd36-/-), with Cd36 deletion in parietal cells (PC-Cd36-/-) or in endothelial cells (EC-Cd36-/-). CD36 expresses on corpus ECs, on PC basolateral membranes, and in gastrin and ghrelin cells. Stomachs of Cd36-/- mice have altered gland organization and secretion, more fibronectin, and inflammation. Tissue respiration and mitochondrial efficiency are reduced. Phospholipids increased and triglycerides decreased. Mucosal repair after injury is impaired in Cd36-/- and EC-Cd36-/-, not in PC-Cd36-/- mice, and is due to defect of progenitor differentiation to PCs, not of progenitor proliferation or mature PC dysfunction. Relevance to humans is explored in the Vanderbilt BioVu using PrediXcan that links genetically-determined gene expression to clinical phenotypes, which associates low CD36 mRNA with gastritis, gastric ulcer, and gastro-intestinal hemorrhage. A CD36 variant predicted to disrupt an enhancer site associates (p < 10-17) to death from gastro-intestinal hemorrhage in the UK Biobank. The findings support role of CD36 in gastric tissue repair, and its deletion associated with chronic diseases that can predispose to malignancy.

Mechanical Fractionation of Cultured Neuronal Cells into Cell Body and Neurite Fractions.

Many cells contain spatially defined subcellular regions that perform specialized tasks enabled by localized proteins. The subcellular distribution of these localized proteins is often facilitated by the subcellular localization of the RNA molecules that encode them. A key question in the study of this process of RNA localization is the characterization of the transcripts present at a given subcellular location. Historically, experiments aimed at answering this question have centered upon microscopy-based techniques that target one or a few transcripts at a time. However, more recently, the advent of high-throughput RNA sequencing has allowed the transcriptome-wide profiling of the RNA content of subcellular fractions. Here, we present a protocol for the isolation of cell body and neurite fractions from neuronal cells using mechanical fractionation and characterization of their RNA content. Graphic abstract: Fractionation of neuronal cells and analysis of subcellular RNA contents.

Association between dyslipidemia and risk of type 2 diabetes mellitus in middle-aged and older Chinese adults: a secondary analysis of a nationwide cohort.

AIMS: To evaluate the type 2 diabetes mellitus (T2DM) risk of individuals with different types of dyslipidaemia and compare the predictive value of distinct lipid parameters in predicting T2DM. METHODS: We conducted a secondary analysis of data from the China Health and Retirement Longitudinal Study (CHARLS). 17 708 individuals over 45 years old were interviewed, and 11 847 blood samples were collected at the baseline survey (2011-2012). Outcome of T2DM was confirmed during two follow-up surveys (2013-2014 and 2015-2016). The HRs and 95% CI of T2DM associated with dyslipidaemia were estimated by Cox proportional hazards regressions model. The discriminatory value of eight lipid parameters were compared by the area under the receiver operating characteristic (ROC) curve (AUC). RESULTS: A total of 7329 participants were enrolled in our analysis; during the mean follow-up time of 3.4 years, 387 (5.28%) participants developed new-onset diabetes. Compared with participants in normal lipid levels, the T2DM risk of those with hypercholesterolaemia, hypertriglyceridaemia and low high-density lipoprotein cholesterol (HDL-C) were significantly increased (HRs (95% CI) were 1.48 (1.11 to 1.96), 1.92 (1.49 to 2.46) and 1.67 (1.35 to 2.07), respectively). The AUCs of non-HDL-C (0.685, 95% CI 0.659 to 0.711), triglyceride (TG) (0.684, 95% CI 0.658 to 0.710), total cholesterol (TC)/HDL-C (0.685, 95% CI 0.659 to 0.712) and TG/HDL-C (0.680, 95% CI 0.654 to 0.706) were significantly (p<0.005) larger than that of other lipid parameters. CONCLUSION: Middle-aged and elderly adults with hypertriglyceridaemia, hypercholesterolaemia and low HDL-C were at higher risk for developing diabetes. Non-HDL-C, TG, TC/HDL and TG/HDL have greater performance than other lipid parameters in predicting T2DM incidence.

Activation and Monitoring of mtDNA Damage in Cancer Cells via the "Proton-Triggered" Decomposition of an Ultrathin Nanosheet.

Mitochondrial DNA (mtDNA) damage is a very important molecular event, which has significant effects on living organisms. Therefore, a particularly important challenge for biomaterials research is to develop functionalized nanoparticles that can activate and monitor mtDNA damage and instigate cancer cell apoptosis, and as such eliminate the negative effects on living organisms. Toward that goal, with this research, we have developed a hydroxyapatite ultrathin nanosheet (HAP-PDCns)-a high Ca2+ content biomaterial. HAP-PDCns undergoes proton-triggered decomposition after entering cancer cells via clathrin-mediated endocytosis, and then, it selectively concentrates in the charged mitochondrial membrane. This kind of proton-triggered decomposition phenomenon facilitates mtDNA damage by causing instantaneous local calcium overload in the mitochondria of cancer cells, and inhibits tumor growth. Importantly, at the same time, a real-time green-red-green fluorescence change occurs that correlates with the degree of mtDNA deterioration because of the changes in the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps during this process. Significantly, the decomposition and the fluorescence changes cannot be triggered in normal cells. Thus, HAP-PDCns can selectively induce apoptosis and the death of a cancer cell by facilitating mtDNA damage, but does not affect normal cells. In addition, HAP-PDCns can simultaneously monitor the degree of mtDNA damage. We anticipate that this design strategy can be generalized to develop other functionalized biomaterials that can be used to instigate the positive effects of mtDNA damage on living organisms while eliminating any negative effects.

Successful Anesthesia Management in a Patient With Type A Aortic Dissection Complicated by Renal Failure and Suspected Coronavirus Disease.

Stanford type A acute aortic dissection (AAD) is a life-threatening illness that presents with chest pain and hemodynamic instability. AAD prompt and accurate evaluation and management are critical for survival as it is a cardiac surgical emergency. The initial treatment of AAD mandates strict blood pressure stabilization with intravenous antihypertensive medications. The progressive nature of the disease will increase the mortality as time elapses between diagnosis and surgical intervention. In addition, the patient's blood pressure control is challenged in the presence of renal failure requiring hemodialysis. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or named 2019-nCoV) pneumonia was a newly underrecognized illness (COVID-19 [coronavirus disease 2019]). COVID-19 can cause severe acute respiratory distress syndrome, acute kidney injury, heart injury, and liver dysfunction, which would aggravate the progress of aortic dissection. In this article, we report the successful anesthesia management in a pneumonia patient with AAD complicated with renal failure during the COVID-19 epidemic period, who underwent emergency surgery and deep hypothermic circulatory arrest repair.

Risk Stratification and Optimization to Prevent Right Heart Failure During Left Ventricular Assist Device Implantation.

Left ventricular assist device (LVAD) implantation results in superior survival rates compared with optimal medical therapy in patients with end-stage heart failure. However, a potential complication of LVAD implantation is right heart failure (RHF), which can be devastating. Therefore, identifying preoperative risk factors for RHF and optimal management for these patients are critical for ensuring favorable postoperative outcomes. This review focuses on methods of assessing the risk factors for RHF before surgery, including evaluation of biomarkers, echocardiography, hemodynamics, risk-scoring systems, and existing conditions of right heart dysfunction. In addition, the review also explores the perioperative strategic approaches to reducing the likelihood of RHF.

The Role of Alternative Polyadenylation in the Regulation of Subcellular RNA Localization.

Alternative polyadenylation (APA) is a widespread and conserved regulatory mechanism that generates diverse 3' ends on mRNA. APA patterns are often tissue specific and play an important role in cellular processes such as cell proliferation, differentiation, and response to stress. Many APA sites are found in 3' UTRs, generating mRNA isoforms with different 3' UTR contents. These alternate 3' UTR isoforms can change how the transcript is regulated, affecting its stability and translation. Since the subcellular localization of a transcript is often regulated by 3' UTR sequences, this implies that APA can also change transcript location. However, this connection between APA and RNA localization has only recently been explored. In this review, we discuss the role of APA in mRNA localization across distinct subcellular compartments. We also discuss current challenges and future advancements that will aid our understanding of how APA affects RNA localization and molecular mechanisms that drive these processes.

Coronary angiography or not after cardiac arrest without ST segment elevation: A systematic review and meta-analysis.

OBJECTIVE: This meta-analysis aimed to review the available evidence and evaluate the necessity of immediate coronary angiography (CAG) to obtain positive outcomes for out-of-hospital cardiac arrest (OHCA) patients without ST segment elevation. DATA SOURCES: Web of Science, PubMed, Embase, Chinese National Knowledge Infrastructure, Wanfang, and SinoMed databases. STUDY SELECTION: We included observational and case-control studies of outcomes among individuals without ST segment elevation experiencing OHCA who had immediate, delayed, or no CAG. DATA EXTRACTION: We extracted study details, as well as patient characteristics and outcomes. DATA SYNTHESIS: Six studies (n = 2665) investigating mortality until discharge demonstrated a significant increase in survival benefit with early CAG (odds ratio [OR] = 1.78; 95%CI = 1.51-2.11; I = 81%; P < .0001). Seven studies (n = 2909) showed a significant preservation of neurological functions with early CAG at discharge (OR = 1.66; 95%CI = 1.37-2.02; P < .00001). Four studies (n = 1357) investigating survival outcomes with middle-term follow-up revealed no significant benefit with early CAG (OR = 1.21; 95%CI = 0.93-1.57; I = 66%; P = .15). CONCLUSIONS: Our meta-analysis demonstrates that there may be significant benefits in performing immediate CAG on patients who experience OHCA without ST segment elevation.