Genome-wide identification and expression analysis of the Dof gene family reveals their involvement in hormone response and abiotic stresses in sunflower (Helianthus annuus L.).

DNA binding with one finger (Dof), plant-specific zinc finger transcription factors, can participate in various physiological and biochemical processes during the life of plants. As one of the most important oil crops in the world, sunflower (Helianthus annuus L.) has significant economic and ornamental value. However, a systematic analysis of H. annuus Dof (HaDof) members and their functions has not been extensively conducted. In this study, we identified 50 HaDof genes that are unevenly distributed on 17 chromosomes of sunflower. We present a comprehensive overview of the HaDof genes, including their chromosome locations, phylogenetic analysis, and expression profile characterization. Phylogenetic analysis classified the 366 Dof members identified from 11 species into four groups (further subdivided into nine subfamilies). Segmental duplications are predominantly contributed to the expansion of sunflower Dof genes, and all segmental duplicate gene pairs are under purifying selection due to strong evolutionary constraints. Furthermore, we observed differential expression patterns for HaDof genes in normal tissues as well as under hormone treatment or abiotic stress conditions by analyzing RNA-seq data from previous studies and RT-qPCR data in our current study. The expression of HaDof04 and HaDof43 were not detected in any samples, which implied that they may be gradually undergoing pseudogenization process. Some HaDof genes, such as HaDof25 and HaDof30, showed responsiveness to exogenous plant hormones, such as kinetin, brassinosteroid, auxin or strigolactone, while others like HaDof15 and HaDof35 may participate in abiotic stress resistance of sunflower seedling. Our study represents the initial step towards understanding the phylogeny and expression characterization of sunflower Dof family genes, which may provide valuable reference information for functional studies on hormone response, abiotic stress resistance, and molecular breeding in sunflower and other species.

Traceless Protein-Selective Glycan Labeling and Chemical Modification.

Executing glycan editing at a molecular level not only is pivotal for the elucidation of complicated mechanisms involved in glycan-relevant biological processes but also provides a promising solution to potentiate disease therapy. However, the precision control of glycan modification or glyco-editing on a selected glycoprotein is by far a grand challenge. Of note is to preserve the intact cellular glycan landscape, which is preserved after editing events are completed. We report herein a versatile, traceless glycan modification methodology for customizing the glycoforms of targeted proteins (subtypes), by orchestrating chemical- and photoregulation in a protein-selective glycoenzymatic system. This method relies on a three-module, ligand-photocleavable linker-glycoenzyme (L-P-G) conjugate. We demonstrated that RGD- or synthetic carbohydrate ligand-containing conjugates (RPG and SPG) would not activate until after the ligand-receptor interaction is accomplished (chemical regulation). RPG and SPG can both release the glycoenzyme upon photoillumination (photoregulation). The adjustable glycoenzyme activity, combined with ligand recognition selectivity, minimizes unnecessary glycan editing perturbation, and photolytic cleavage enables precise temporal control of editing events. An altered target protein turnover and dimerization were observed in our system, emphasizing the significance of preserving the native physiological niche of a particular protein when precise modification on the carbohydrate epitope occurs.

Recent advances in small molecules for improving mitochondrial disorders.

Mitochondrial disorders are observed in various human diseases, including rare genetic disorders and complex acquired pathologies. Recent advances in molecular biological techniques have dramatically expanded the understanding of multiple pathomechanisms involving mitochondrial disorders. However, the therapeutic methods for mitochondrial disorders are limited. For this reason, there is increasing interest in identifying safe and effective strategies to mitigate mitochondrial impairments. Small-molecule therapies hold promise for improving mitochondrial performance. This review focuses on the latest advances in developing bioactive compounds for treating mitochondrial disease, aiming to provide a broader perspective of fundamental studies that have been carried out to evaluate the effects of small molecules in regulating mitochondrial function. Novel-designed small molecules ameliorating mitochondrial functions are urgent for further research.

Vitamin D supplementation improved physical growth and neurologic development of Preterm Infants receiving Nesting Care in the neonatal Intensive Care Unit.

OBJECTIVE: To study the effects of vitamin D supplementation on physical growth and neurologic development of very preterm infants receiving nesting intervention in the neonatal intensive care unit (NICU). METHODS: A total of 196 preterm infants had been hospitalized in NICU with the gestational age (GA) between 28 and 32 weeks. Among them, 98 preterm infants received nesting intervention, and the other 98 cases received both nesting and vitamin D supplementation (400 IU). The interventions were continued until 36 weeks postmenstrual age (PMA). The 25(OH)D serum levels, anthropometric parameters, and Premie-Neuro (PN) scores were compared at 36 weeks PMA. RESULTS: Higher median serum level of 25(OH)D was found in the nesting + vitamin D [38.40 ng/mL (IQR: 17.20 ~ 70.88) ng/mL] as compared to the nesting group [15.95 ng/mL (IQR: 10.80 ~ 24.30) ng/mL] at 36 weeks PMA. Besides, infants receiving combined nesting intervention and vitamin D supplementation had less proportion of vitamin D deficiency [VDD, 25(OH)D levels < 20 ng/mL] than those receiving nesting intervention alone. After intervention, the anthropometric parameters of infants, including weight, length, BMI and head circumference were improved in the nesting + vitamin D group as compared to the nesting group at 36 weeks PMA, with higher scores of neurological, movement and responsiveness. CONCLUSIONS: Vitamin D supplementation effectively decreased the prevalence of VDD and led to higher concentrations of 25(OH)D at 36 weeks PMA. This was one more study that supported the necessity of vitamin D supplementation to improve physical growth and neurologic development of preterm-born newborns who received nesting intervention in the NICU.

Butyrate mitigates metabolic dysfunctions via the ERα-AMPK pathway in muscle in OVX mice with diet-induced obesity.

The higher prevalence of metabolic syndrome (MetS) in women after menopause is associated with a decrease in circulating 17ß-oestradiol. To explore novel treatments for MetS in women with oestrogen deficiency, we studied the effect of exogenous butyrate on diet-induced obesity and metabolic dysfunctions using ovariectomized (OVX) mice as a menopause model. Oral administration of sodium butyrate (NaB) reduced the body fat content and blood lipids, increased whole-body energy expenditure, and improved insulin sensitivity. Additionally, NaB induced oestrogen receptor alpha (ERα) expression, activated the phosphorylation of AMPK and PGC1α, and improved mitochondrial aerobic respiration in cultured skeletal muscle cells. In conclusion, oral NaB improves metabolic parameters in OVX mice with diet-induced obesity. Oral supplementation with NaB might provide a novel therapeutic approach to treating MetS in women with menopause. Video Abstract.

Recent Advances in Protein-Specific Glycan Imaging and Editing.

Glycosylation in live cell and animal modulate a constellation of biological functions. The advent of Chemical Biology has revolutionized the analysis and tailoring of glycans, by introducing myriads of glycan engineering methods. However, the ideal scenario to achieve glycan monitoring and structural manipulation at any hierarchical levels is unmet yet. Herein we review recent advances in the methodological innovation and the versatile applications of the protein-specific glycan visualization and editing in deciphering the biological functions of glycans. An outlook for future directions toward specific sugar-chain editing is also included.

Novel construction of multifunctional photo-responsive and nucleic acid-triggered doxorubicin-releasing liposomes for cancer therapy.

All-in-one nano theranostics integrating accurate diagnosis and combined therapy is promising for high-efficacy tumor treatment and receiving significant attention. In this study, we develop photo-controlled release liposomes with nucleic acid-triggered fluorescence and photoactivity for tumor imaging and synergistic antitumor therapy. Copper phthalocyanine as a photothermal agent is fused into lipid layers to prepare liposomes encapsulating cationic zinc phthalocyanine ZnPc(TAP)412+ and doxorubicin, followed by the modification of RGD peptide on the surface to obtain the final product RGD-CuPc:ZnPc(TAP)412+:DOX@LiPOs (RCZDL). RCZDL possesses favorable stability, significant photothermal effect, and photo-controlled release function through the characterization of physicochemical properties. It is shown that the fluorescence and ROS generation could be turned on by intracellular nucleic acid after illumination. RCZDL exhibits synergistic cytotoxicity, increased apoptosis, and significantly promoted cell uptake. Subcellular localization analysis indicates that ZnPc(TAP)412+ tends to be distributed in the mitochondria of HepG2 cells treated with RCZDL after exposure to light. The results of experiments in vivo on H22 tumor-bearing mice demonstrate that RCZDL had excellent tumor targeting, a prominent photothermal effect at the tumor sites, and synergistic antitumor efficiency. More importantly, little RCZDL has been found to be accumulated in the liver, and most were quickly metabolized by the liver. The results confirm that the proposed new intelligent liposomes provide a simple and cost-effective way for tumor imaging and combinatorial anticancer therapy.

Interbacterial Chemical Communication-Triggered Nascent Proteomics.

Metabolic labeling with clickable noncanonical amino acids has enabled nascent proteome profiling, which can be performed in a cell-type-specific manner. However, nascent proteomics in an intercellular communication-dependent manner remains challenging. Here we develop communication-activated profiling of protein expression (CAPPEX), which integrates the LuxI/LuxR quorum sensing circuit with the cell-type-specific nascent proteomics method to enable selective click-labeling of newly synthesized proteins in a specific bacterium upon receiving chemical signals from another reporter bacterium. CAPPEX reveals that E. coli competes with Salmonella for tryptophan as the precursor for indole, and the resulting indole suppressed the expression of virulence factors in Salmonella. This tryptophan-indole axis confers attenuation of Salmonella invasion in host cells and living mice. The CAPPEX strategy should be widely applicable for investigating various interbacterial communication processes.

Recent progress toward developing axial chirality bioactive compounds.

Atropisomers are stereoisomers with axial chirality arising from restricted rotation around a single bond. Lots of representatives of this class of axially chiral compounds exhibit remarkable biological properties for protein targets. This time-dependent chirality shows great potential for drug development. Herein, we comprehensively review axial chirality bioactive compounds, including C-C bonded atropisomers, C-N bonded atropisomers, and N-N bonded atropisomers. Examples of each are provided along with their biological activity. This review highlights the development of various examples of atropisomerism encountered in bioactive compounds, which is beneficial for medicinal chemists to advance atropisomeric drug molecules.

Indole-3-acetic acid improves the hepatic mitochondrial respiration defects by PGC1a up-regulation.

Recent evidences have linked indole-3-acetic acid (I3A), a gut microbiota-derived metabolite from dietary tryptophan, with the protection against non-alcoholic fatty liver disease (NAFLD). However, the values of I3A on mitochondrial homeostasis in NAFLD have yet to be analyzed. In this study, we verified that I3A alleviated dietary-induced metabolic impairments, particularly glucose dysmetabolism and liver steatosis. Importantly, we expanded the understanding of I3A further to enhance mitochondrial oxidative phosphorylation in the liver by RNA-seq. Consistently, I3A restored the deficiency of mitochondrial respiration complex (MRC) capacity in palmitic acid (PA)-induced HepG2 without initiating oxidative stress in vitro. These changes were dependent on peroxisome proliferator-activated receptor γ coactivator 1 (PGC1)-a, a key regulator of mitochondrial biogenesis. Silencing of PGC1a by siRNA and pharmacologic inhibitor SR-18292, blocked the restoration of I3A on mitochondrial oxidative phosphorylation. In addition, pre-treatment of I3A guarded against the deficiency of MRC capacity. In conclusion, our findings uncovered that I3A increased hepatic PGC1a expression, contributing to mitochondrial respiration improvement in NAFLD.

Systematic review and meta-analysis of the incidence rates of adverse events after digestive endoscopy in children.

Background: With the widespread use of digestive endoscopy in children, a variety of adverse events (AEs) have occurred after digestive endoscopy. However, there are notable differences in the incidence of adverse reactions in digestive endoscopy in children at present, which makes it difficult to assess the safety of digestive endoscopy in children. Methods: Studies related to digestive endoscopy in children were screened from January 2005 to October 2021 from PubMed, Web of Science, Spring, CNKI, and Science Direct databases. RevMan5.3 and Stata were employed to carry out meta-analysis on the incidence of adverse respiratory events, myoclonus, abdominal pain, fever, bleeding, chest pain, sore throat, vomiting, and delayed capsule discharge after digestive endoscopy in children. The article quality was evaluated by the Agency for Healthcare Research and Quality (AHRQ). The chi-square test and I2 were adopted to test literature heterogeneity, and the article publication bias was assessed by displaying an inverted funnel plot as a funnel plot. Results: In all, 15 articles were included, involving a total of 27,770 children. In all, 15 articles were included, involving a total of 27,770 children. The risk ratio (RR) value of adverse respiratory events after digestive endoscopy in children was 1.31 [95% confidence interval (CI): 1.17 to 1.47, P<0.00001]; the odds ratio (OR) value of the incidence of myoclonus was 1.21 (95% CI: 1.01 to 1.46, P=0.04); the incidence of abdominal pain was 1.18 (95% CI: 1.11 to 1.27, P<0.00001); the incidence of fever was 1.09 (95% CI: 1.06 to 1.12, P<0.00001); the incidence of bleeding was 1.24 (95% CI: 0.94 to 1.64, P=0.13); the incidence of chest pain was 1.06 (95% CI: 1.03 to 1.09, P<0.0001); incidence of sore throat was 1.11 (95% CI: 1.05 to 1.18, P=0.0004); incidence of vomiting was 1.13 (95% CI: 1.06 to 1.21, P=0.0001); and the incidence of delayed capsule expulsion was 1.18 (95% CI: 1.00 to 1.40, P=0.05). Discussion: The incidence of AEs after digestive endoscopy in children was low, which can be used in the diagnosis and therapy of digestive system diseases in children.

Chemical Tagging of Protein Lipoylation.

Protein lipoylation is a post-translational modification of emerging importance in both prokaryotes and eukaryotes. However, labeling and large-scale profiling of protein lipoylation remain challenging. Here, we report the development of iLCL (iodoacetamide-assisted lipoate-cyclooctyne ligation), a chemoselective reaction that enables chemical tagging of protein lipoylation. We demonstrate that the cyclic disulfide of lipoamide but not linear disulfides can selectively react with iodoacetamide to produce sulfenic acid, which can be conjugated with cyclooctyne probes. iLCL enables tagging of lipoylated proteins for gel-based detection and cellular imaging. Furthermore, we apply iLCL for proteomic profiling of lipoylated proteins in both bacteria and mammalian cells. In addition to all of the eight known lipoylated proteins, we identified seven candidates for novel lipoylated proteins. The iLCL strategy should facilitate uncovering the biological function of protein lipoylation.

Metabolic RNA labeling for probing RNA dynamics in bacteria.

Metabolic labeling of RNAs with noncanonical nucleosides that are chemically active, followed by chemoselective conjugation with imaging probes or enrichment tags, has emerged as a powerful method for studying RNA transcription and degradation in eukaryotes. However, metabolic RNA labeling is not applicable for prokaryotes, in which the complexity and distinctness of gene regulation largely remain to be explored. Here, we report 2'-deoxy-2'-azidoguanosine (AzG) as a noncanonical nucleoside compatible with metabolic labeling of bacterial RNAs. With AzG, we develop AIR-seq (azidonucleoside-incorporated RNA sequencing), which enables genome-wide analysis of transcription upon heat stress in Escherichia coli. Furthermore, AIR-seq coupled with pulse-chase labeling allows for global analysis of bacterial RNA degradation. Finally, we demonstrate that RNAs of mouse gut microbiotas can be metabolically labeled with AzG in living animals. The AzG-enabled metabolic RNA labeling should find broad applications in studying RNA biology in various bacterial species.

[Application study on improving the methods of endotracheal cuff pressure measurement to prevent ventilator-associated pneumonia].

OBJECTIVE: To compare the intra cuff pressure changes during improved and the traditional method of cuff pressure measurement, then evaluate the effects of ventilator-associated pneumonia (VAP) prevention. The results highlighted practical recommendations in the process of ETT cuff pressure measurement. METHODS: (1) Experimental studies were carried out on the tracheal model with two groups: traditional pressure measurement group and improved pressure measurement group. The traditional pressure measurement group was connected to a handheld pressure gauge with the indicate cuff to get the intra-cuff pressure. The improved method was to insert a 3-way stopcock between the handheld pressure gauge and the indicate cuff. The 3-way stopcock to stabilize handheld pressure gauge reading at 32 cmH2O (1 cmH2O = 0.098 kPa) before measure the intra-cuff pressure. The pressure loss caused by two pressure measurement methods and the leakage of liquid on the balloon after 10 minutes was compared. (2) Clinical researches: a historic cohort study, patients with mechanical ventilation (MV) admitted to intensive care unit (ICU) of Guangxi Medical University Cancer Hospital from June 2014 to May 2018 were enrolled. The control group (249 cases) was treated with traditional method during June 2014 to May 2016, and the observation group (314 cases) was treated with improved method during June 2016 to May 2018. Clusters of strategies and actions of VAP prevention were applied in both groups. Incidence of VAP, duration of MV, and the length of ICU stay were compared between the two groups. RESULTS: (1) Experimental study: the pressure leakage of the traditional pressure measurement group was (10.18±0.47) cmH2O, and that of the improved pressure measurement group was (1.33±0.42) cmH2O, with statistically significant difference between the two groups (t = 32.535, P = 0.000). All fluid on the cuffs leak after 10 minutes of traditional ways of measurement, however, no visible fluid on the cuffs leaked with improved procedures. (2) Clinical research: the incidence of VAP in the observation group was slightly lower than that in the control group, however there was no significant difference [5.10% (16/314) vs. 8.43% (21/249), P > 0.05]. The duration of MV and the length of ICU stay in the observation group were significantly shorter than those in the control group (days: 9.93±3.14 vs. 16.77±5.45, 11.63 ±2.28 vs. 19.12±5.10, both P < 0.01). CONCLUSIONS: The improved procedures of intra-cuff pressure measurement is a practical method to avoid the pressure leakage and fluid leakage, and the clinical course of MV patients can be significantly improved by combining the clusters of nursing strategies and actions.

Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture (CARIC) Strategy.

A comprehensive identification of RNA-binding proteins (RBPs) is key to understanding the posttranscriptional regulatory network in cells. A widely used strategy for RBP capture exploits the polyadenylation [poly(A)] of target RNAs, which mostly occurs on eukaryotic mature mRNAs, leaving most binding proteins of non-poly(A) RNAs unidentified. Here we describe the detailed procedures of a recently reported method termed click chemistry-assisted RNA-interactome capture (CARIC), which enables the transcriptome-wide capture of both poly(A) and non-poly(A) RBPs by combining the metabolic labeling of RNAs, in vivo UV cross-linking, and bioorthogonal tagging.

Transcriptome-wide discovery of coding and noncoding RNA-binding proteins.

Transcriptome-wide identification of RNA-binding proteins (RBPs) is a prerequisite for understanding the posttranscriptional gene regulation networks. However, proteomic profiling of RBPs has been mostly limited to polyadenylated mRNA-binding proteins, leaving RBPs on nonpoly(A) RNAs, including most noncoding RNAs (ncRNAs) and pre-mRNAs, largely undiscovered. Here we present a click chemistry-assisted RNA interactome capture (CARIC) strategy, which enables unbiased identification of RBPs, independent of the polyadenylation state of RNAs. CARIC combines metabolic labeling of RNAs with an alkynyl uridine analog and in vivo RNA-protein photocross-linking, followed by click reaction with azide-biotin, affinity enrichment, and proteomic analysis. Applying CARIC, we identified 597 RBPs in HeLa cells, including 130 previously unknown RBPs. These newly discovered RBPs can likely bind ncRNAs, thus uncovering potential involvement of ncRNAs in processes previously unknown to be ncRNA-related, such as proteasome function and intermediary metabolism. The CARIC strategy should be broadly applicable across various organisms to complete the census of RBPs.

[Influence of intermittently monitoring on endotracheal tube cuff pressure using handheld pressure gauge].

OBJECTIVE: To discuss the influence of intermittently monitoring on endotracheal tube cuff pressure using handheld pressure gauge, and to provide some reference for the clinical work. METHODS: The experiment was carried out on the model of the glass tube, which was divided into three parts. Each part of the experiment was divided into normal pressure group and high pressure group according to the different inflation pressure target value. The endotracheal tube cuff pressure was determined intermittently by using the transparent tracheal models which had a static diameter of 2 cm. The target press value of normal pressure group was 32 cmH2O (1 cmH2O = 0.098 kPa) while that of high pressure group was 40 cmH2O. The handheld pressure gauge was connected with the indicated cuff through a tee joint, and the pressure in the cuff in both groups was determined. The pressure loss caused by intermittent measurement of the two groups was compared. By switching the tee joint, the pressure loss through the gauge self-structure and the pressure loss when connecting and disconnecting the indicated cuff were determined to analyze the causes of pressure loss caused by intermittent measurement of pressure gauge. RESULTS: The pressure loss caused by intermittent measurement of high pressure group was significantly higher than that of normal pressure group (cmH2O: 15.10±0.43 vs. 10.19±0.45) with statistical significance (t = -24.875, P = 0.000). The pressure loss through the gauge self-structure of high pressure group was also significantly higher than that of normal pressure group (cmH2O: 13.91±0.48 vs. 8.77±0.53), which showed a statistics significance (t = -22.854, P = 0.000). The pressure loss when connecting and disconnecting the indicated cuff of the normal pressure and high pressure groups were (1.33±0.49) cmH2O and (1.23±0.55) cmH2O, respectively, without statistics significance (t = 0.445, P = 0.662). It was figured that the total pressure loss caused by intermittent measurement of the endotracheal intubation cuff was approximately equal to the value of the pressure loss caused by the pressure gauge self-structure and the pressure loss when the indicated cuff was connected and disconnected [normal pressure group: (10.19±0.45) cmH2O ≍ (8.77±0.53) cmH2O + (1.33±0.49) cmH2O, high pressure group: (15.10±0.43) cmH2O ≍ (13.91±0.48) cmH2O + (1.23±0.55) cmH2O]. CONCLUSIONS: The intermittently monitoring on endotracheal tube cuff pressure is the main cause of the pressure loss. The total pressure loss consists of the pressure leak from the cuff to the gauge and the pressure leak when connecting and disconnecting the gauge and the indicated cuff during each test. When the pressure in the cuff is increased, it will cause more pressure loss.