Comprehensive analysis of the complete mitochondrial genome of Lilium tsingtauense reveals a novel multichromosome structure.

KEY MESSAGE: Lilium tsingtauense mitogenome comprises 27 independent chromosome molecules, it undergoes frequent genomic recombination, and the rate of recombination and mutation between different repetitive sequences affects the formation of multichromosomal structures. Given the extremely large genome of Lily, which likely harbors additional genetic resources, it serves as an ideal material for studying the phylogenetic evolution of organisms. Although the Lilium chloroplast genome has been documented, the sequence of its mitochondrial genome (mitogenome) remains uncharted. Using BGI short reads and Nanopore long reads, we sequenced, assembled, and annotated the mitogenome of Lilium tsingtauense. This effort culminated in the characterization of Lilium's first complete mitogenome. Comparative analysis with other angiosperms revealed the unique multichromosomal structure of the L. tsingtauense mitogenome, spanning 1,125,108 bp and comprising 27 independent circular chromosomes. It contains 36 protein-coding genes, 12 tRNA genes, and 3 rRNA genes, with a GC content of 44.90%. Notably, three chromosomes in the L. tsingtauense mitogenome lack identifiable genes, hinting at the potential existence of novel genes and noncoding elements. The high degree of observed genome fragmentation implies frequent reorganization, with recombination and mutation rates among diverse repetitive sequences likely driving the formation of multichromosomal structures. Our comprehensive analysis, covering genome size, coding genes, structure, RNA editing, repetitive sequences, and sequence migration, sheds light on the evolutionary and molecular biology of multichromosomal mitochondria in Lilium. This high-quality mitogenome of L. tsingtauense not only enriches our understanding of multichromosomal mitogenomes but also establishes a solid foundation for future genome breeding and germplasm innovation in Lilium.

Comprehensive assembly and comparative examination of the full mitochondrial genome in Castanea mollissima Blume.

The Chinese chestnut, Castanea mollissima Blume, a nut-bearing tree native to China and North Korea, belongs to the Fagaceae family. As an important genetic resource, C. mollissima is vital in enhancing edible chestnut varieties and offers significant insights into the origin and evolution of chestnut species. While the chloroplast genome of C. mollissima has been sequenced, its mitochondrial genome (mitogenome) remains largely uncharted. In this study, we have characterized the C. mollissima mitogenome, assembling it utilizing reads from both BGI and Nanopore sequencing platforms, and conducted a comparative analysis with the mitochondrial genomes of closely related species. The mitogenome of C. mollissima manifests a polycyclic structure consisting of two circular molecules measuring 363,232 bp and 24,806 bp, respectively. This genome encompasses 35 unique protein-coding genes, 19 tRNA genes, and three rRNA genes. A total of 139 SSRs were identified throughout the entire C. mollissima mitogenome. Furthermore, the combined length of homologous fragments between the chloroplast and mitochondrial genomes was 5766 bp, constituting 1.49% of the mitogenome. We also predicted 484 RNA editing sites in C. mollissima, demonstrating C-to-U RNA editing. Phylogenetic analysis of related species' mitogenomes showed that C. mollissima was closely related to Lithocarpus litseifolius (Hance) Chun and Quercus acutissima Carruth. Interestingly, the mitogenome sequences of C. mollissima, L. litseifolius, Q. acutissima, Fagus sylvatica L., and Juglans mandshurica Maxim did not show conservation in their alignments, indicating frequent genome reorganization. This report marks the inaugural study of the C. mollissima mitogenome, serving as a benchmark genome for economically significant plants within the Castanea genus. Moreover, it supplies invaluable information that can guide future molecular breeding efforts and contribute to the broader understanding of chestnut genomics.

Analysis of clinical characteristics and automatic monitoring of drug-induced arrhythmias in 167,546 inpatients.

OBJECTIVE: The purpose of this study was to analyze the occurrence characteristics, clinical manifestations, medication distribution, and incidence of drug-induced arrhythmias in a real-world inpatient population. METHODS: According to the inclusion and exclusion criteria as well as the ADR evaluation criteria, we retrospectively evaluated hospitalized patients in 2019 using the arrhythmia module of the Adverse Drug Event Active Surveillance and Assessment System-II (ADE-ASAS-II). A detailed analysis was performed on the demographic data, ADR manifestations, and medication distribution of 2097 patients with drug-induced arrhythmias and QT interval prolongation. RESULTS: Of the 167,546 hospitalized patients, there were 1809 cases of drug-induced arrhythmias, with an incidence of 1.08%. The ADRs in 45.35% of positive patients occurred within 3 days after medication administration, and 46.73% of the patients were 65 years old or older. The predominant ADRs identified in this study were extrasystole, tachycardia, and QT interval prolongation, of which the incidence was 0.20%. Levofloxacin was the most involved drug, and levofloxacin-associated rates of incidence of arrhythmia and QT interval prolongation were 1.24% and 0.44%, respectively. The risk factors for drug-induced arrhythmias were male sex, advanced age, emaciation, obesity, and underlying illnesses such as cardiovascular diseases, diabetes mellitus, cerebrovascular diseases, and hepatic and renal inadequacy (P < 0.05). CONCLUSION: The incidence of drug-induced arrhythmias was in the range of common, while QTc interval prolongation was occasional. It is necessary to pay attention to patients with risk factors.

Impact of information diffusion on epidemic spreading in partially mapping two-layered time-varying networks.

We propose a new epidemic model considering the partial mapping relationship in a two-layered time-varying network, which aims to study the influence of information diffusion on epidemic spreading. In the model, one layer represents the epidemic-related information diffusion in the social networks, while the other layer denotes the epidemic spreading in physical networks. In addition, there just exist mapping relationships between partial pairs of nodes in the two-layered network, which characterizes the interaction between information diffusion and epidemic spreading. Meanwhile, the information and epidemics can only spread in their own layers. Afterwards, starting from the microscopic Markov chain (MMC) method, we can establish the dynamic equation of epidemic spreading and then analytically deduce its epidemic threshold, which demonstrates that the ratio of correspondence between two layers has a significant effect on the epidemic threshold of the proposed model. Finally, it is found that MMC method can well match with Monte Carlo (MC) simulations, and the relevant results can be helpful to understand the epidemic spreading properties in depth.

Fluorine-modified sialyl-Tn-CRM197 vaccine elicits a robust immune response.

Even though a vaccine that targets tumor-associated carbohydrate antigens on epithelial carcinoma cells presents an attractive therapeutic approach, relatively poor immunogenicity limits its development. In this study, we investigated the immunological activity of a fluoro-substituted Sialyl-Tn (F-STn) analogue coupled to the non-toxic cross-reactive material of diphtheria toxin197 (CRM197). Our results indicate that F-STn-CRM197 promotes a greater immunogenicity than non-fluorinated STn-CRM197. In the presence or absence of adjuvant, F-STn-CRM197 remarkably enhances both cellular and humoral immunity against STn by increasing antigen-specific lymphocyte proliferation and inducing a mixed Th1/Th2 response leading to production of IFN-γ and IL-4 cytokines, as well as STn-specific antibodies. Furthermore, antisera produced from F-STn-CRM197 immunization significantly recognizes STn-positive tumor cells and increases cancer cell lysis induced by antibody-dependent cell-mediated cytotoxicity (ADCC) or complement-dependent cytotoxicity (CDC) pathways. Our data suggest that this F-STn vaccine may be useful for cancer immunotherapy and possibly for prophylactic prevention of cancer.

EZH2 promotes invasion and metastasis of laryngeal squamous cells carcinoma via epithelial-mesenchymal transition through H3K27me3.

Enhancer of Zeste Homolog 2(EZH2), which can change chromatin structure by tri-methylation of the 27th lysine of H3 in nucleosome histone (H3K27me3), is involved in different types of cancers. However, the role and mechanism underlying aberrant EZH2 expression in laryngeal squamous cells carcinoma (LSCC) remain unclear. In the present study, we found that down-regulation of EZH2 and H3K27me3 in LSCC cells (Hep-2 and SCC10A) resulted in an mesenchymal-epithelial transition(MET) like cell morphology and lower invasion in vitro, weakened tumor growth, intrahepatic and pulmonary metastasis in vivo. Furthermore, EZH2 promoted the epithelial-mesenchymal transition(EMT) process through down-regulation of Ca2+ dependent cell adhesion molecule E (E-cadherin) and up-regulation of H3K27me3 in vitro and in vivo. Moreover, E-cadherin was transcriptionally induced upon stable knockdown of EZH2, and quantitative chromatin immunoprecipitation(qChIP) analysis confirmed the depletion of H3K27me3 enrichment on E-cadherin promoter upon EZH2 knockdown in Hep-2 and SCC10A cells. In addition, the expression of EZH2 was positively correlated with that of H3K27me3 and both of them were inversely correlated with E-cadherin expression in human LSCC tissues. In summary, this study indicated that EZH2 promoted invasion and metastasis of LSCC via EMT through H3K27me3.

Clinical Characteristics of Moxifloxacin-Related Arrhythmias and Development of a Predictive Nomogram: A Case Control Study.

This study aimed to analyze the incidence, clinical characteristics, and risk factors of moxifloxacin-related arrhythmias and electrocardiographic alterations in hospitalized patients using real-world data. Concurrently, a nomogram was established and validated to provide a practical tool for prediction. Retrospective automatic monitoring of inpatients using moxifloxacin was performed in a Chinese hospital from January 1, 2017, to December 31, 2021, to obtain the incidence of drug-induced arrhythmias and electrocardiographic alterations. Propensity score matching was conducted to balance confounders and analyze clinical characteristics. Based on the risk and protective factors identified through logistic regression analysis, a prediction nomogram was developed and internally validated using the Bootstrap method. Arrhythmias and electrocardiographic alterations occurred in 265 of 21,711 cases taking moxifloxacin, with an incidence of 1.2%. Independent risk factors included medication duration (odds ratio [OR] 1.211, 95% confidence interval [CI] 1.156-1.270), concomitant use of meropenem (OR 4.977, 95% CI 2.568-9.644), aspartate aminotransferase >40 U/L (OR 3.728, 95% CI 1.800-7.721), glucose >6.1 mmol/L (OR 2.377, 95% CI 1.531-3.690), and abnormally elevated level of amino-terminal brain natriuretic peptide precursor (OR 2.908, 95% CI 1.640-5.156). Concomitant use of cardioprotective drugs (OR 0.430, 95% CI 0.220-0.841) was a protective factor. The nomogram showed good differentiation and calibration, with enhanced clinical benefit. The incidence of moxifloxacin-related arrhythmias and electrocardiographic alterations is in the range of common. The nomogram proves valuable in predicting the risk in the moxifloxacin-administered population, offering significant clinical applications.

A case-control study on the clinical characteristics of granisetron-related arrhythmias and the development of a predictive nomogram.

BACKGROUND: Automatic monitoring and assessment are increasingly employed in drug safety evaluations using hospital information system data. The increasing concern about granisetron-related arrhythmias requires real-world studies to improve our understanding of its safety. AIM: This study aimed to analyze the incidence, clinical characteristics, and risk factors of granisetron-related arrhythmias in hospitalized patients using real-world data obtained from the Adverse Drug Event Active Surveillance and Assessment System-II (ADE-ASAS-II) and concurrently aimed to develop and validate a nomogram to predict the occurrence of arrhythmias. METHOD: Retrospective automatic monitoring of inpatients using granisetron was conducted in a Chinese hospital from January 1, 2017, to December 31, 2021, to determine the incidence of arrhythmias using ADE-ASAS- II. Propensity score matching was used to balance confounders and analyze clinical characteristics. Based on risk factors identified through logistic regression analysis, a prediction nomogram was established and internally validated using the Bootstrap method. RESULTS: Arrhythmias occurred in 178 of 72,508 cases taking granisetron with an incidence of 0.3%. Independent risk factors for granisetron-related arrhythmias included medication duration, comorbid cardiovascular disease, concomitant use of other 5-hydroxytryptamine 3 receptor antagonists, alanine aminotransferase > 40 U/L, and blood urea nitrogen > 7.5 mmol/L. The nomogram demonstrated good differentiation and calibration, with enhanced clinical benefit observed when the risk threshold ranged from 0.10 to 0.82. CONCLUSION: The nomogram, based on the five identified independent risk factors, may be valuable in predicting the risk of granisetron-related arrhythmias in the administered population, offering significant clinical applications.

Development and internal validation of a model for predicting cefoperazone/sulbactam-associated coagulation disorders in Chinese inpatients.

BACKGROUND AND AIM: The use of cefoperazone/sulbactam (CPZ/SAM) could commonly cause vitamin K-dependent coagulation disorders and even hemorrhage sometimes. However, there is a lack of prediction tools estimating the risk for this. This study aimed at developing and internally validating a model for predicting CPZ/SAM-associated coagulation disorders in Chinese inpatients. METHODS: A case-control study was conducted in 11,092 adult inpatients admitted to a Chinese general hospital between 2020 and 2021 and treated with CPZ/SAM. Patients with CPZ/SAM-associated coagulation disorders were identified through the Adverse Drug Events Active Surveillance and Assessment System-II and subsequent manual evaluation. Controls were selected from eligible patients who didn't develop coagulation disorders after CPZ/SAM therapy, with a 1:1 propensity score matching. The final predictors were obtained by univariable and multivariable logistic regression analyses. Internal validation and calibration for the model were performed using 1000 bootstrap resamplings. RESULTS: 258 patients were identified as CPZ/SAM-associated coagulation disorders in 2184 patients eligible for inclusions and exclusions and the incidence was 11.8%. A final population of 252 cases and 252 controls was included for model development and validation. Malnutrition (OR = 2.41 (1.56-3.77)), history of recent bleeding (OR = 1.95 (1.32-2.90)), treatment duration (OR = 1.10 (1.07-1.14)), combination with carbapenems (OR = 4.43 (1.85-11.88)), and serum creatinine (OR = 1.01 (1.00-1.01)) were identified as final predictors. The model showed good discrimination, calibration, and clinical practicality, with the validated area under the receiver operating characteristic curve being 0.723 (0.683-0.770). CONCLUSIONS: The model with good performance quantifies the risk for CPZ/SAM-associated coagulation disorders, and may support individual assessment and interventions to mitigate the risk after external validation.

[6]-gingerol: a novel AT1 antagonist for the treatment of cardiovascular disease.

Considering the prevalence of cardiovascular disease in public health and the limited validated therapeutic options, this study aimed to find novel compounds targeting the angiotensin II type 1 receptor, accepted as a therapeutic target in cardiovascular disease. A small library consisting of 89 compounds from 39 Chinese herbs was profiled using a cell-based calcium mobilization assay which was developed and characterized for high-throughput screening. [6]-Gingerol derived from Zingiber officinale Roscoe (ginger) was identified as a novel angiotensin II type 1 receptor antagonist, with an IC50 value of 8.173 µM. The hit was further tested by a specificity assay indicating that it had no antagonistic effects on other evaluated GPCRs, such as endothelin receptors. The major ingredient of ginger, [6]-gingerol, could inhibit angiotensin II type 1 receptor activation, which partially clarified the mechanism of ginger regulating blood pressure and strengthening heart in the cardiovascular system.

Deciphering the mitochondrial genome of Juglans mandshurica (Juglandaceae).

Juglans mandshurica Maxim., 1856 is a second-class, protected, rare tree species of high economic and ecological value. We elucidated the complete mitochondrial (mt) genome of J. mandshurica using the Illumina Novaseq 6000 and Nanopore platforms. The complete sequences of 558,032 and 161,386 bp had an overall GC content of 45.0% and 45.3%, respectively, and 61 genes could be annotated, including 38 protein-coding, 20 tRNA, and 3 rRNA genes. The high-quality J. mandshurica mt genomic sequences presented in this study will serve as a useful resource for a range of genetic, functional, evolutionary, and comparative genomic studies on this species of the Juglandaceae family.

A high-quality genome assembly and annotation of Quercus acutissima Carruth.

Introduction: Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation. Methods: Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. acutissima genome. Results: We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Ab initio, homology-based and RNA sequence-based gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. Phylogenetic analysis showed that Q. acutissima and Q. variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication. Conclusion: The assembled and annotated high-quality Q. acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.

Complete mitochondrial genome sequence of Acer miaotaiense (Aceraceae).

Acer miaotaiense P. C. Tsoong is a rare and endangered tree endemic to the Qinling Mountains of China and is listed as a national third-class protected plant. In this study, we sequenced the complete mitochondrial genome of Acer miaotaiense using the Illumina Novaseq 6000 and Nanopore platforms. The total mitochondrial genome length is 819,227 bp and has 69 genes, including 41 protein-coding, 25 tRNA, and 3 rRNA genes. The genome nucleotide composition was asymmetric, with an overall G + C content of 45.7%. Phylogenetic analysis indicated that Acer miaotaiense is closely related to the congeneric Acer yangbiense.

Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant.

Quercus acutissima Carruth. is a Chinese important energy plant with high ecological and economic values. While the species chloroplast genome has been reported, its mitochondrial genome (mitogenome) is still unexplored. Here, we assembled and annotated the Q. acutissima mitogenome, and we compared its characteristic differences with several closely related species. The Q. acutissima mitogenome's main structure is branched with three distinguished contigs (linear molecule 1, circular molecule 2, and circular molecule 3) with 448,982 bp total length and 45.72% GC content. The mitogenome contained 51 genes, including 32 protein-coding, 16 tRNA and 3 rRNA genes. We examined codon usage, repeated sequences, genome recombination, chloroplast to mitochondrion DNA transformation, RNA editing, and synteny in the Q. acutissima mitogenome. Phylogenetic trees based on 29 species mitogenomes clarified the species classification. Our results provided comprehensive information of Q. acutissima mitogenome, and they are expected to provide valuable information for Fagaceae evolutionary biology and to promote the species germplasm utilization.

Variation in the internalization of differently sized nanoparticles induces different DNA-damaging effects on a macrophage cell line.

Although researchers have expended considerable effort on studying the cytotoxicity of nanomaterials, it is possible that there has been insufficient attention paid to their genotoxic potential. Here, we describe a test model that we have developed to evaluate the DNA-damaging effects of negatively charged nanoparticles of different sizes. We compared the DNA damaging effect induced by nanoparticles of various sizes and found that the effect is closely associated with the internalization pattern of the particles. Macrophage cell line RAW 264.7 cells were incubated with carboxylated polystyrene beads (COOH-PBs) ranging in size from 30 to 500 nm. Size-dependent DNA damage was detected, and the lesion induced by two carboxylated fullerene particles confirmed this observation. Confocal microscopy revealed that the entry pathways of these COOH-PBs shifted from direct penetration to endocytosis with increasing particle size, followed by changes in subcellular localization. Subsequent deposition of 30-nm COOH-PBs in the cytosol led to a reduction of Zn²âº and Mg²âº content in the nucleus and an increased p53 level in the whole cell rather than in nucleus, while localization of 50- and 100-nm COOH-PBs in acidic vesicles induced p53 accumulation in both types of extracts. Based on these results, we assume that the damage resulted from a disruption of the balance between DNA damage and repair.

Effects of different bronchoalveolar lavage methods on tracheobronchial foreign body patients.

OBJECTIVES/HYPOTHESIS: To compare the different effects of bronchoalveolar lavage (BAL) with diverse combinations of lidocaine, epinephrine, and dexamethasone on pediatric patients with an inhaled tracheobronchial foreign body (TFB). STUDY DESIGN: Randomized controlled study. METHODS: Two hundred forty cases of pediatric patients with inhaled TFB were included in this study, and were randomly divided into four groups using three kinds of drugs for BAL, namely 0.9% saline (S) group, 2% lidocaine with diluted epinephrine (LE) group, 2% lidocaine with diluted epinephrine and 0.5% dexamethasone (LED), control group (C) without BAL. The incidences of intraoperative or postoperative complications and recovery periods were compared. Meanwhile, the concentrations of interleukin (IL)-1ß, IL-6, and tumor necrosis factor (TNF)-α in BAL fluids and plasma were evaluated by enzyme-linked immunosorbent assay. RESULTS: The incidences of bronchospasm, hypoxemia, and postoperative fever were significantly lower in the LED group than other groups (P < .001). Fever after the TFB removal procedure appeared later in the LED group than the other groups. The improvement and healing periods in the LE and LED groups were significantly shorter than those in the C and S groups (P < .001). The concentrations of IL-1ß, IL-6, and TNF-α in BAL fluids were significantly higher in the LE and LED groups than those in the S group (P < .001), but those in the plasma of the C and S groups were lower compared with the LE and LED groups (P < .001). CONCLUSIONS: BAL with lidocaine, epinephrine, and dexamethasone could promote recovery for TFB patients and reduce incidences of complications, possibly by regulating release of proinflammatory cytokines. LEVEL OF EVIDENCE: 1b.

Adjusting the balance between effective loading and vector migration of macrophage vehicles to deliver nanoparticles.

The nature of macrophage allows the possibility that this cell type could be used as drug delivery system to track therapeutic drug nanoparticles (NPs) in cancer. However, there is no existing research on the regulation between effective loading of NPs and targeted delivery of macrophages. Here, we investigated the important parameters of intracellular NP quantity and the vector migration rate. Macrophage loading capacity was obtained by comparing the uptake quantity of varisized NPs, and the delivery ability of loaded cells was determined by measuring vector migration rates. We observed a positive correlation between the size of NPs and directed macrophage migration. Our findings suggest that the molecular mechanism of migration vector rate regulation involved increased expression levels of colony-stimulating factor-1 (CSF-1) receptor and integrin induced by 100-nm and 500-nm particles. The ability of macrophages uptake to varisized NPs showed the opposite trend, with the increased vector rate of cell migration influenced by NPs. We are able to demonstrate the important balance between effective macrophage loading and targeted delivery. By adjusting the balance parameters, it will be possible to utilize NPs in macrophage-mediated disease diagnosis and therapy.