T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition.

MOTIVATION: Nanopore sequencing is a new macromolecular recognition and perception technology that enables high-throughput sequencing of DNA, RNA, even protein molecules. The sequences generated by nanopore sequencing span a large time frame, and the labor and time costs incurred by traditional analysis methods are substantial. Recently, research on nanopore data analysis using machine learning algorithms has gained unceasing momentum, but there is often a significant gap between traditional and deep learning methods in terms of classification results. To analyze nanopore data using deep learning technologies, measures such as sequence completion and sequence transformation can be employed. However, these technologies do not preserve the local features of the sequences. To address this issue, we propose a sequence-to-image (S2I) module that transforms sequences of unequal length into images. Additionally, we propose the Transformer-based T-S2Inet model to capture the important information and improve the classification accuracy. RESULTS: Quantitative and qualitative analysis shows that the experimental results have an improvement of around 2% in accuracy compared to previous methods. The proposed method is adaptable to other nanopore platforms, such as the Oxford nanopore. It is worth noting that the proposed method not only aims to achieve the most advanced performance, but also provides a general idea for the analysis of nanopore sequences of unequal length. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://github.com/guanxiaoyu11/S2Inet.

S2Snet: deep learning for low molecular weight RNA identification with nanopore.

Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacterium smegmatis porin A nanopore trap. Although it can achieve desirable classification results, compared with deep learning (DL) methods, this classic machine learning requires domain knowledge to manually extract features, which is sophisticated, labor-intensive and time-consuming. Meanwhile, the generated original RNA structural events are not strictly equal in length, which is incompatible with the input requirements of DL models. To alleviate this issue, we propose a sequence-to-sequence (S2S) module that transforms the unequal length sequence (UELS) to the equal length sequence. Furthermore, to automatically extract features from the RNA structural events, we propose a sequence-to-sequence neural network based on DL. In addition, we add an attention mechanism to capture vital information for classification, such as dwell time and blockage amplitude. Through quantitative and qualitative analysis, the experimental results have achieved about a 2% performance increase (accuracy) compared to the previous method. The proposed method can also be applied to other nanopore platforms, such as the famous Oxford nanopore. It is worth noting that the proposed method is not only aimed at pursuing state-of-the-art performance but also provides an overall idea to process nanopore data with UELS.

Active learning for efficient analysis of high-throughput nanopore data.

MOTIVATION: As the third-generation sequencing technology, nanopore sequencing has been used for high-throughput sequencing of DNA, RNA, and even proteins. Recently, many studies have begun to use machine learning technology to analyze the enormous data generated by nanopores. Unfortunately, the success of this technology is due to the extensive labeled data, which often suffer from enormous labor costs. Therefore, there is an urgent need for a novel technology that can not only rapidly analyze nanopore data with high-throughput, but also significantly reduce the cost of labeling. To achieve the above goals, we introduce active learning to alleviate the enormous labor costs by selecting the samples that need to be labeled. This work applies several advanced active learning technologies to the nanopore data, including the RNA classification dataset (RNA-CD) and the Oxford Nanopore Technologies barcode dataset (ONT-BD). Due to the complexity of the nanopore data (with noise sequence), the bias constraint is introduced to improve the sample selection strategy in active learning. Results: The experimental results show that for the same performance metric, 50% labeling amount can achieve the best baseline performance for ONT-BD, while only 15% labeling amount can achieve the best baseline performance for RNA-CD. Crucially, the experiments show that active learning technology can assist experts in labeling samples, and significantly reduce the labeling cost. Active learning can greatly reduce the dilemma of difficult labeling of high-capacity nanopore data. We hope active learning can be applied to other problems in nanopore sequence analysis. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://github.com/guanxiaoyu11/AL-for-nanopore. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Redox proteomics of PANC-1 cells reveals the significance of HIF-1 signaling protein oxidation in pancreatic ductal adenocarcinoma pathogenesis.

BACKGROUND: Protein cysteine oxidation is substantially involved in various biological and pathogenic processes, but its implications in pancreatic cancer development remains poorly understood. METHODS AND RESULTS: In this study, we performed a global characterization of protein oxidation targets in PDAC cells through iodoTMT-based quantitative proteomics, which identified over 4300 oxidized cysteine sites in more than 2100 proteins in HPDE6c7 and PANC-1 cells. Among them, 1715 cysteine residues were shown to be differentially oxidized between HPDE6c7 and PANC-1 cells. Also, charged amino acids including aspartate, glutamate and lysine were significantly overrepresented in flanking sequences of oxidized cysteines. Differentially oxidized proteins in PANC-1 cells were enriched in multiple cancer-related biological processes and signaling pathways. Specifically, the HIF-1 signaling proteins exhibited significant oxidation alterations in PANC-1 cells, and the reduced PHD2 oxidation in human PDAC tissues was correlated with lower survival time in pancreatic cancer patients. CONCLUSION: These investigations provided new insights into protein oxidation-regulated signaling and biological processes during PDAC pathogenesis, which might be further explored for pancreatic cancer diagnosis and treatment.

Super Enhancer-Associated Circular RNA-CircKrt4 Regulates Hypoxic Pulmonary Artery Endothelial Cell Dysfunction in Mice.

BACKGROUND: Circular RNAs (circRNAs) have been implicated in pulmonary hypertension progression through largely unknown mechanisms. Pulmonary artery endothelial cell (PAEC) dysfunction is a hallmark in the pathogenesis of pulmonary hypertension. However, the specific role of circular RNAs in PAEC injury caused by hypoxia remains unclear. METHODS: In this study, using the Western blotting, RNA pull down, Dual-luciferase reporter assay, immunohistochemistry, and immunofluorescence, we identified a novel circular RNA derived from alternative splicing of the keratin 4 gene (circKrt4). RESULTS: CircKrt4 was upregulated in lung tissues and plasma and specifically in PAECs under hypoxic conditions. In the nucleus, circKrt4 induces endothelial-to-mesenchymal transition by interacting with the Pura (transcriptional activator protein Pur-alpha) to promote N-cadherin gene activation. In the cytoplasm, increased circKrt4 leads to mitochondrial dysfunction by inhibiting cytoplasmic-mitochondrial shuttling of mitochondrial-bound Glpk (glycerol kinase). Intriguingly, circKrt4 was identified as a super enhancer-associated circular RNA that is transcriptionally activated by a transcription factor, CEBPA (CCAAT enhancer binding protein alpha). Furthermore, RBM25 (RNA-binding-motif protein 25) was found to regulate circKrt4 cyclization by increase the back-splicing of Krt4 gene. CONCLUSIONS: These findings demonstrate that a super enhancer-associated circular RNA-circKrt4 modulates PAEC injury to promote pulmonary hypertension by targeting Pura and Glpk.

The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis.

BACKGROUND: Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene that encodes histidine decarboxylase, is poorly understood. OBJECTIVE: We sought to investigate how enhancers regulate Hdc gene transcription and histamine synthesis in resting conditions and in a mouse model of anaphylaxis. METHODS: H3K27 acetylation histone modification and chromatin accessibility were used to identify candidate enhancers. The enhancer activity of candidate enhancers was measured in a reporter gene assay, and the function enhancers were validated by CRISPR deletion. RESULTS: Deletion of the GC box, which binds to zinc finger transcription factors, in the proximal Hdc enhancer reduced Hdc gene transcription and histamine synthesis in mouse and human mast cell lines. Mast cells, basophils, brain cells, and stomach cells from GC box-deficient mice transcribed the Hdc gene much less than similar cells from wild-type mice, and Hdc GC box-deficient mice failed to develop anaphylaxis. CONCLUSION: The HDC GC box within the proximal enhancer in the mouse and human HDC gene is essential for Hdc gene transcription, histamine synthesis, and histamine-mediated anaphylaxis in vitro and in vivo.

IL-33 priming and antigenic stimulation synergistically promote the transcription of proinflammatory cytokine and chemokine genes in human skin mast cells.

BACKGROUND: Antigenic stimulation through cross-linking the IgE receptor and epithelial cell-derived cytokine IL-33 are potent stimuli of mast cell (MC) activation. Moreover, IL-33 primes a variety of cell types, including MCs to respond more vigorously to external stimuli. However, target genes induced by the combined IL-33 priming and antigenic stimulation have not been investigated in human skin mast cells (HSMCs) in a genome-wide manner. Furthermore, epigenetic changes induced by the combined IL-33 priming and antigenic stimulation have not been evaluated. RESULTS: We found that IL-33 priming of HSMCs enhanced their capacity to promote transcriptional synergy of the IL1B and CXCL8 genes by 16- and 3-fold, respectively, in response to combined IL-33 and antigen stimulation compared to without IL-33 priming. We identified the target genes in IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation using RNA sequencing (RNA-seq). We found that the majority of genes synergistically upregulated in the IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation were predominantly proinflammatory cytokine and chemokine genes. Moreover, the combined IL-33 priming and antigenic stimulation increase chromatin accessibility in the synergy target genes but not synergistically. Transcription factor binding motif analysis revealed more binding sites for NF-κB, AP-1, GABPA, and RAP1 in the induced or increased chromatin accessible regions of the synergy target genes. CONCLUSIONS: Our study demonstrates that IL-33 priming greatly potentiates MCs' ability to transcribe proinflammatory cytokine and chemokine genes in response to antigenic stimulation, shining light on how epithelial cell-derived cytokine IL-33 can cause exacerbation of skin MC-mediated allergic inflammation.

Tri-Layered Bicomponent Microfilament Composite Fabric for Highly Efficient Cold Protection.

Functional thin fabric with highly efficient cold protection properties are attracting the great attention of long-term dressing in a cold environment. Herein, a tri-layered bicomponent microfilament composite fabric comprised of a hydrophobic layer of PET/PA@C6 F13 bicomponent microfilament webs, an adhesive layer of LPET/PET fibrous web, and a fluffy-soft layer of PET/Cellulous fibrous web is designed and also successfully been fabricated through a facile process of dipping, combined with thermal belt bonding. The prepared samples exhibit a large resistance to wetting of alcohol, a high hydrostatic pressure of 5530 Pa, and brilliant water slipping properties, owing to the presence of dense micropores ranging from 25.1 to 70.3 µm, as well as to the smooth surface with an arithmetic mean deviation of surface roughness (Sa) ranging from 5.112 to 4.369 µm. Besides, the prepared samples exhibited good water vapor permeability, and a tunable CLO value ranging from 0.569 to 0.920, in addition to the fact that it exhibited a very suitable working temperature range of -5 °C to 15 °C. Additionally, it also showed excellent clothing tailorability including high mechanical strength with a remarkably soft texture and lightweight foldability that suitable for cold outdoor clothing applications.

Plasma transfusion in critically Ill patients with abnormal coagulation tests before invasive procedures: A propensity-adjusted cohort study.

OBJECTIVE: To evaluate the association between plasma transfusion and bleeding complications in critically ill patients with an elevated international normalized ratios undergoing invasive procedures. METHODS: A retrospective study was conducted to evaluate a consecutive sample of critically ill adult patients undergoing invasive procedures (N = 487) with an international normalized ratio ≥ 1.5 between January 1, 2019 and December 31, 2019. Among the followed patients, 125 were excluded due to incomplete case records and 362 were finally included in this investigation. The exposure was whether plasma had been transfused within 24 h before the invasive procedure. The primary outcome was the occurrence of postprocedural bleeding complications. Secondary outcomes included transfusion of red blood cells within 24 h of the invasive procedure, and additional patient-important outcomes such as mortality and length of stay. Tests were performed with univariate and propensity-matched analyses. RESULTS: Of the 362 study participants, 99 (27.3 %) received a preprocedural plasma transfusion. In the propensity score-matched analysis, the rate of the occurrence of postprocedural bleeding complications between two groups was not statistically different (OR, 0.605[95 % CI, 0.341-1.071]; P = .085). The rate of postoperative red blood cell transfusion in the plasma transfusion group was higher than that in the non-plasma transfusion group (35.5 % vs 21.5 %; P < .05). No statistically significant difference in mortality was observed between the two groups (29.0 % vs 31.6 %; P = .101). CONCLUSIONS: Prophylactic plasma transfusion failed to reduce postprocedural bleeding complications in ill critically patients with a coagulopathy. Meanwhile, it was associated with increased red blood cell transfusion after invasive procedures. Findings suggest that abnormal preprocedural international normalized ratios should be managed more conservatively.

Comparative analysis of hepatitis B virus infections in blood donors born before and after the implementation of universal HBV vaccination in southern China.

BACKGROUND: In China, the vaccinated blood donors have rapidly increased by recent years, which may impact blood safety. The true prevalence of HBV between vaccinated blood donors and non-vaccinated blood donors should be explored. STUDY DESIGN AND METHODS: The samples of blood donors were collected and detected for serologic markers of HBV in the Shenzhen Blood Centre (SZBC). The discrepant results were tested with commercial electrochemiluminescence immunoassay (ELCI) for HBsAg, anti-HBs, HBeAg, Anti-HBe and Anti-HBc, alternative MPX ID NAT, nested PCR, and a quantitative real-time polymerase chain reaction (qPCR) assay for HBV DNA. The serological and molecular characteristics of HBV infected blood donors were analysed, and the effects on blood safety for donors born before and after the implementation of universal HBV vaccination were compared. RESULTS: Out of 242 presumed HBV infected donors from 26 318 donations, 131 (0.49%, [95% CI, 0.43-0.59]) chronic HBV infections (CHB, HBsAg detected with or without DNA), 58 (0.22%, [95% CI, 0.17-0.28]) occult hepatitis B infections (OBI, HBsAg not detected, assume anti-HBc positive and/or anti-HBs with HBV DNA) and 3 (0.011%, [95% CI, 0.0023-0.033]) window period (WP) infections were confirmed respectively. There were 28 CHBs (0.44%), 7 OBIs (0.11%) and 1 WP (0.016%) from vaccinated blood donor and 103 CHBs (0.52%), 51 OBIs (0.26%) and 2 WPs (0.01%) from non-vaccinated blood donor. The HBV+ (CHBs, OBIs and WPs) rate (0.56%) in vaccinated donors was lower than in non-vaccinated donors (0.78%, p < 0.05). The HBsAg titers of vaccinated infected blood donors (Median: 128.8 IU/ml) were much higher than non-vaccinated infected blood donors (58.4 IU/ml). The OBI yield rates in the vaccinated blood donors was significantly lower than the non-vaccinated blood donors (p < 0.05). There 102/124 (82.3%) samples were genotype B, 22/124 (17.7%) were genotype C respectively. There was no significant difference in the distribution of genotype between non-vaccinated blood donors (B/C, 86/17) and vaccinated blood donors (B/C, 23/6; p > 0.05). High frequency of vaccine escape mutations M133L (32.4%) and E164G in S region of genotype B strains and substitution L175S (40.9%) related to vaccine escape in S region of genotype C strains were identified. CONCLUSION: The universal HBV vaccination program markedly reduces the risk of HBV infection in blood donors, and provides a significant guarantee for the safety of blood transfusion. Several important mutations detected related vaccine escape and notable mutations needed further investigated.

Analgesic Efficacy of Pectoral Nerve Blocks in Implant-Based Mammoplasty: A Systematic Review and Meta-Analysis.

OBJECTIVE: To evaluate the analgesic effect of pectoral nerve block in implant-based mammoplasty. METHODS: EMbase, PubMed, Web of science, MEDLINE, CNKI, Wanfang Database, VIP and other databases were searched from establishment to February 2022 by computer to collect randomized controlled trials which applied pectoral nerve block in implant-based mammoplasty, and meta-analysis was conducted after data extraction and quality evaluation of the literature meeting the inclusion criteria. RESULTS: A total of 336 patients in seven RCT studies were included in this study. Pectoral nerve block has a significant effect on postoperative analgesia in patients with implant-based mammoplasty with 1h VAS score significantly reduced in the resting state (MD=-1.85, 95%CI: -2.64~-1.07, P<0.00001); VAS score was significantly decreased 4-6 hours after operation (MD=-1.51, 95%CI: -2.47~-0.55, P=0.002); postoperative opioid consumption was reduced (SMD=-1.37, 95%CI: -2.51~-0.24, P=0.02) in PECS block group; and the incidence of postoperative nausea and vomiting in the PECS block group was significantly lower (RR: 0.30, 95 %CI: 0.19-0.38, P<0.00001). CONCLUSIONS: The application of PECS block in submuscular implant-based mammoplasty can effectively reduce the degree of acute postoperative pain, opioid consumption and the incidence of postoperative nausea and vomiting, indicating its broad prospects in clinical application. LEVEL OF EVIDENCE III: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Association Between Body Weight and Removed Weight in Women Undergoing Reduction Mammaplasty-A 17-year Retrospective Study of 1777 Breasts.

BACKGROUND: Breast hypertrophy causes physical and psychological symptoms. Reduction mammaplasty is a surgical procedure to lessen discomfort. However, there is a dispute about whether the weight of breast resection is related to body weight. This study aims to provide Chinese data and assess the association between body weight and removed weight in women undergoing reduction mammaplasty. METHODS: Retrospective data were collected from 1777 breasts in a single center in 17 years. Simple linear regression analysis was performed to establish whether removed weight and removed weight ratio (removed weight/body weight) correlated with the body weight. The correlations were then analyzed again after grouping according to the removed weight. RESULTS: For all breasts included, removed weight or ratio positively correlates with body weight. When the removed weight is more than 1000g, there is no statistically significant correlation between body weight and removed breast weight. When removed per breast weight is more than 600g, there is no correlation between body weight and removed breast weight ratio. CONCLUSIONS: The correlation between body weight and removed weight or ratio decreased with increasing removed weight. When removed weight >600g, the degree of breast hypertrophy is not related to body shape. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these evidence-based medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 . Therapeutic study.

Genome-Wide Identification and Characterization of Aldo-Keto Reductase (AKR) Gene Family in Response to Abiotic Stresses in Solanum lycopersicum.

Tomato is one of the most popular and nutritious vegetables worldwide, but their production and quality are threatened by various stresses in the environment in which they are grown. Thus, the resistance and tolerance of tomatoes to various biotic and abiotic stresses should be improved. Aldo-keto reductases (AKR) are a superfamily of NAD(P)(H)-dependent oxidoreductases that play multiple roles in abiotic and biotic stress defenses by detoxification and reactive oxygen species (ROS) clearance pathways. Here, 28 identified AKR family genes of tomatoes were identified genome-wide, and their characteristics, including chromosomal location, gene structures, protein motifs, and system evolution, were analyzed. Furthermore, the phylogenetic and syntenic relationships in Arabidopsis thaliana, rice, and tomatoes were compared. Expression patterns at different tissues and in response to abiotic stresses, such as drought and salt, were monitored to further explore the function of SlAKRs. Finally, three SlAKRs candidate genes were silenced by Virus induced gene silencing (VIGS) systems in Solanum lycopersicum, showing sensitivity to drought and salt stresses with low contents of proline (Pro) and peroxidase (POD) and high content of malonaldehyde (MDA). This study provides the characteristics and potential functions of SlAKRs in response to abiotic stresses that will be helpful for further studies in S. lycopersicum.

High-value utilization of Cr-containing sludge: Eco-friendly and ultra-low-cost electrocatalyst for efficient OER in alkaline media from Cr-containing sludge.

Economically sustainable development requires more viable waste recycling solutions. In this context, we address the problem of utilizing chromium-containing sludge, a prevalent and environmentally hazardous waste. Meanwhile, sustainable energy development must develop ecology-friendly and low-cost electrocatalysts for the oxygen evolution reaction (OER) in alkaline media. Herein, we report an ultra-low-cost electrocatalyst from chromium-containing sludge. The optimum preparation conditions are determined by optimizing the calcination temperature and the loading of nickel acetylacetonate. The optimized catalyst delivers excellent stability and outstanding OER activity with overpotentials of 320 mV at 10 mA cm-2 in alkaline media. Density functional theory calculations reveal that the energy barrier of OER is decreased because of the catalyst's heterogeneous structure arrangement and confirm the influence of chromium on performance improvement. The concept of "turning waste into treasure" stimulates the search for methods to process Cr-containing waste and produce low-cost, high-performance electrocatalysts.

Optimization of culture medium and scale-up production of astaxanthin using corn steep liquor as substrate by response surface methodology.

Astaxanthin is a natural carotenoid with strong antioxidant activity. In this paper, the effects of carbon source, corn steep liquor, distiller grains, and initial pH on the growth and astaxanthin production of Phaffia rhodozyma D3 were evaluated. The optimal medium composition was 32 g/L glucose, 12 g/L corn steep liquor as nitrogen source, and the initial pH was 6.7. Phaffia rhodozyma D3 was cultured in a shake flask under these optimized conditions, the biomass was 6.47 g/L, the astaxanthin/OD475 was 15.16, and the astaxanthin content was 1.41 mg/g. The astaxanthin content was further increased to 4.70 mg/g by the combination of TiO2 stimulation and the expanding cultivation of P. rhodozyma D3 in a 5 L fermenter, which was 2.81 times that of the control group. Expanding fermentation implies the possibility of large-scale production in the astaxanthin industry. Corn steep liquor was used as an alternative nitrogen source to culture P. rhodozyma D3, which could both reduce the production cost of astaxanthin and increased the by-products utilization rate.

Metabolite analysis of soybean oil on promoting astaxanthin production of Phaffia rhodozyma.

BACKGROUND: Astaxanthin is a carotenoid with strong antioxidant property. In addition, it has anti-cancer, anti-tumor, anti-inflammatory and many other functions. The micro-organisms that mainly produce astaxanthin are Haematococcus pluvialis and Phaffia rhodozyma. Compared with H. pluvialis, P. rhodozyma has shorter fermentation cycle and easier to control culture conditions, but the yield of astaxanthin in P. rhodozyma is low. This article studied how to improve the astaxanthin production of P. rhodozyma. RESULTS: The results showed that when 10 mL L-1 soybean oil was added to the culture medium, astaxanthin production increased significantly, reaching 7.35 mg L-1 , which was 1.4 times that of the control group, and lycopene and ß-carotene contents also increased significantly. Through targeted metabolite analysis, the fatty acids in P. rhodozyma significantly increased under the soybean oil stimulation, especially the fatty acids closely related to the formation of astaxanthin esters, included palmitic acid (C16:0), stearic acid (C18:0), oleic acid (C18:1n9), linoleic acid (C18:2n6), α-linolenic acid (C18:3n3) and γ-linolenic acid (C18:3n6), thereby increasing the astaxanthin esters content. CONCLUSION: It showed that the addition of soybean oil can promote the accumulation of astaxanthin by promoting the increase of astaxanthin ester content. © 2022 Society of Chemical Industry.

LncRNA FENDRR with m6A RNA methylation regulates hypoxia-induced pulmonary artery endothelial cell pyroptosis by mediating DRP1 DNA methylation.

BACKGROUND: Pyroptosis is a form of programmed cell death involved in the pathophysiological progression of hypoxic pulmonary hypertension (HPH). Emerging evidence suggests that N6-methyladenosine (m6A)-modified transcripts of long noncoding RNAs (lncRNAs) are important regulators that participate in many diseases. However, whether m6A modified transcripts of lncRNAs can regulate pyroptosis in HPH progression remains unexplored. METHODS: The expression levels of FENDRR in hypoxic pulmonary artery endothelial cells (HPAECs) were detected by using quantitative real-time polymerase chain reaction (qRT-PCR) and fluorescence in situ hybridization (FISH). Western blot, Lactate dehydrogenase (LDH) release assay, Annexin V-FITC/PI double staining, Hoechst 33342/PI fluorescence staining and Caspase-1 activity assay were used to detect the role of FENDRR in HPAEC pyroptosis. The relationship between FENDRR and dynamin-related protein 1 (DRP1) was explored using bioinformatics analysis, Chromatin Isolation by RNA Purification (CHIRP), Electrophoretic mobility shift assay (EMSA) and Methylation-Specific PCR (MSP) assays. RNA immunoprecipitation (RIP) and m6A dot blot were used to detect the m6A modification levels of FENDRR. A hypoxia-induced mouse model of pulmonary hypertension (PH) was used to test preventive effect of conserved fragment TFO2 of FENDRR. RESULTS: We found that FENDRR was significantly downregulated in the nucleus of hypoxic HPAECs. FENDRR overexpression inhibited hypoxia-induced HPAEC pyroptosis. Additionally, DRP1 is a downstream target gene of FENDRR, and FENDRR formed an RNA-DNA triplex with the promoter of DRP1, which led to an increase in DRP1 promoter methylation that decreased the transcriptional level of DRP1. Notably, we illustrated that the m6A reader YTHDC1 plays an important role in m6A-modified FENDRR degradation. Additionally, conserved fragment TFO2 of FENDEE overexpression prevented HPH in vivo. CONCLUSION: In summary, our results demonstrated that m6A-induced decay of FENDRR promotes HPAEC pyroptosis by regulating DRP1 promoter methylation and thereby provides a novel potential target for HPH therapy.

Acid-Free Copper-Catalyzed Electrophilic Nitration of Electron-Rich Arenes with Guanidine Nitrate.

A practical copper-catalyzed nitration of electron-rich arenes with trimethylsilyl chloride and guanidine nitrate is reported. A variety of nitrated products were generated in moderate to excellent yields (32-99%) at ambient temperature under acid-free, open-flask, and operationally simple conditions.

The crystal structure of Cpf1 in complex with CRISPR RNA.

The CRISPR-Cas systems, as exemplified by CRISPR-Cas9, are RNA-guided adaptive immune systems used by bacteria and archaea to defend against viral infection. The CRISPR-Cpf1 system, a new class 2 CRISPR-Cas system, mediates robust DNA interference in human cells. Although functionally conserved, Cpf1 and Cas9 differ in many aspects including their guide RNAs and substrate specificity. Here we report the 2.38 Å crystal structure of the CRISPR RNA (crRNA)-bound Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1). LbCpf1 has a triangle-shaped architecture with a large positively charged channel at the centre. Recognized by the oligonucleotide-binding domain of LbCpf1, the crRNA adopts a highly distorted conformation stabilized by extensive intramolecular interactions and the (Mg(H2O)6)(2+) ion. The oligonucleotide-binding domain also harbours a looped-out helical domain that is important for LbCpf1 substrate binding. Binding of crRNA or crRNA lacking the guide sequence induces marked conformational changes but no oligomerization of LbCpf1. Our study reveals the crRNA recognition mechanism and provides insight into crRNA-guided substrate binding of LbCpf1, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.

A possible dose-response equation: Viral load after plasma infusion in COVID-19 patients and anti-SARS-CoV-2 antibody titers in convalescent plasma.

BACKGROUND: Clinical trials of convalescent plasma therapy for coronavirus disease 2019 (COVID-19) are extensive, but the relationship between antibody titers, infused volume of plasma and virus clearance in patients remains unknown. This study proposed a possible estimating equation for clinical use of high antibody titer convalescent plasma. METHODS: A total of 38 patients were recruited in the Guanggu District Maternal and Child Health Hospital of Hubei Province from March 1 to 30, 2020. COVID-19 convalescent plasma was collected and high-titer (≥1:640) anti-S-RBD units used. The SARS-CoV-2 nucleic acid viral load was measured 24 h before and 72 h after convalescent plasma infusion. RESULTS: Convalescent plasma therapy was associated with reduced viral load in patients with moderate and severe severity. The viral negative rate at 72 h was 65.8%. The disappearance of viral nucleic acid in study patients was positively correlated with infuscate antibody titer and volume (r = 0.3375, p = 0.04). A possible estimation equation was as follows: Log10 (Reduction in viral load) = 0.18 + 0.001 × (Log2 S-RBD antibody titer × Plasma infusion volume) (r = 0.424, p = 0.009). In a single case, the viral nucleic acid persisted 14 days after the fourth plasma infusion. CONCLUSIONS: This study proposes a potential dose-response equation that adds a convenient way to estimate the dose of convalescent plasma product. It is beneficial to facilitate the rational allocation of plasma with high antibody titers and provide an individualised use strategy for convalescent plasma therapy.