Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization.

The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA molecule known as 7S RNA is transcribed from a region immediately downstream of the light strand promoter in mammalian cells, and its levels change rapidly in response to physiological conditions. Here, we report that 7S RNA has a regulatory function, as it controls levels of mitochondrial transcription both in vitro and in cultured human cells. Using cryo-EM, we show that POLRMT dimerization is induced by interactions with 7S RNA. The resulting POLRMT dimer interface sequesters domains necessary for promoter recognition and unwinding, thereby preventing transcription initiation. We propose that the non-coding 7S RNA molecule is a component of a negative feedback loop that regulates mitochondrial transcription in mammalian cells.

The human mitochondrial genome contains a second light strand promoter.

The human mitochondrial genome must be replicated and expressed in a timely manner to maintain energy metabolism and supply cells with adequate levels of adenosine triphosphate. Central to this process is the idea that replication primers and gene products both arise via transcription from a single light strand promoter (LSP) such that primer formation can influence gene expression, with no consensus as to how this is regulated. Here, we report the discovery of a second light strand promoter (LSP2) in humans, with features characteristic of a bona fide mitochondrial promoter. We propose that the position of LSP2 on the mitochondrial genome allows replication and gene expression to be orchestrated from two distinct sites, which expands our long-held understanding of mitochondrial gene expression in humans.

Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion.

The in vivo role for RNase H1 in mammalian mitochondria has been much debated. Loss of RNase H1 is embryonic lethal and to further study its role in mtDNA expression we characterized a conditional knockout of Rnaseh1 in mouse heart. We report that RNase H1 is essential for processing of RNA primers to allow site-specific initiation of mtDNA replication. Without RNase H1, the RNA:DNA hybrids at the replication origins are not processed and mtDNA replication is initiated at non-canonical sites and becomes impaired. Importantly, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed accompanied by mtDNA depletion. The steady-state levels of mitochondrial transcripts follow the levels of mtDNA, and RNA processing is not altered in the absence of RNase H1. Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain of RNase H1 causing impaired mtDNA replication. In contrast to catalytically inactive variants of RNase H1, this mutant version has enhanced enzyme activity but shows impaired primer formation. This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.

Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing.

Deletions and duplications in mitochondrial DNA (mtDNA) cause mitochondrial disease and accumulate in conditions such as cancer and age-related disorders, but validated high-throughput methodology that can readily detect and discriminate between these two types of events is lacking. Here we establish a computational method, MitoSAlt, for accurate identification, quantification and visualization of mtDNA deletions and duplications from genomic sequencing data. Our method was tested on simulated sequencing reads and human patient samples with single deletions and duplications to verify its accuracy. Application to mouse models of mtDNA maintenance disease demonstrated the ability to detect deletions and duplications even at low levels of heteroplasmy.

[Pharmacokinetic behavior and brain tissue distribution of paeoniflorin combined with normal and toxic doses of strychnine in rats after percutaneous administration].

This study aims to establish a rapid and sensitive UPLC-MS/MS method for simultaneously determining the content of strychnine and paeoniflorin in plasma and brain tissue of rats, and compare the pharmacokinetic behavior and brain tissue distribution of paeoniflorin combined with normal and toxic doses of strychnine in rats after percutaneous administration. Compared with those in the toxic-dose strychnine group, the AUC_(0-t), AUC_(0-∞), and C_(max) of strychnine decreased by 51.51%, 45.68%, and 46.03%, respectively(P<0.01), and the corresponding values of paeoniflorin increased by 91.41%, 102.31%, and 169.32%, respectively(P<0.01), in the compatibility group. Compared with the normal-dose strychnine group, the compatibility group showed insignificantly decreased C_(max), AUC_(0-t), and AUC_(0-∞) of strychnine, increased C_(max) and T_(max) of paeoniflorin(P<0.01), 66.88% increase in AUC_(0-t), and 70.55% increase in AUC_(0-∞) of paeoniflorin. In addition, the brain tissue concentration of strychnine decreased and that of paeoniflorin increased after compatibility. The combination of paeoniflorin with normal dose and toxic dose of strychnine can inhibit the percutaneous absorption of strychnine, and greatly promote the percutaneous penetration of paeoniflorin, whereas the interaction mechanism remains to be explored. The UPLC-MS/MS method established in this study is easy to operate and has good precision. It is suitable for in vivo study of pharmacokinetic behavior and brain tissue distribution of paeoniflorin and strychnine after percutaneous administration in rats, which provides reference for the safe and rational clinical use of strychnine and the combined use of drugs, and lays a solid foundation for the development of external preparations containing Strychni Semen.

Customized treatment protocols for patients with closed fracture in hospitals at varying coronavirus disease 2019 (COVID-19) risk.

BACKGROUND: To determine an optimized treatment protocol during the COVID-19 epidemic for patients with closed fracture and delayed surgery. METHODS: The epidemic data of three hospitals, randomly selected from different administrative regions of Wuhan, were analyzed retrospectively from 23 January to 31 March 2020. Changes in the number of confirmed cases per day (cumulative and new) of each region were tracked as a reflection of changing epidemic risk levels. The risk level map was drawn. The epidemic status, treatment protocols, and treatment efficiencies for patients with closed fracture in the three hospitals were compared. RESULTS: Overall, 138 patients with closed fracture were admitted. Each hospital had established its own protocol, according to the initial perceived risk. Based on the risk level map, over the study period, the risk levels of the three regions changed independently and were not in sync. All patients recovered and were timely discharged. No staff member was detected with COVID-19. CONCLUSIONS: The COVID-19 risk level of each area is dynamic. To optimize medical resources, avoid cross-infection, and improve efficiency, changes in epidemic risk should be monitored. For patients with closed fracture, treatment protocols should be adjusted according to changes in epidemic risk.

Insight to the residue in P2 position prevents the peptide inhibitor from being hydrolyzed by serine proteases.

Peptidic inhibitors of proteases are attracting increasing interest not only as drug candidates but also for studying the function and regulation mechanisms of these enzymes. Previously, we screened out a cyclic peptide inhibitor of human uPA [Formula: see text] and found that Ala substitution of P2 residue turns upain-1 to a substrate. To further investigate the effect of P2 residue on the peptide behavior transformation, we constructed upain-1-W3F, which has Phe replacement in the P2 position. We determined KD and Ki of upain-1-W3F and found that upain-1-W3F might still exist as an inhibitor. Furthermore, the high-resolution crystal structure of upain-1-W3F·uPA reveals that upain-1-W3F indeed stays as an intact inhibitor bind to uPA. We thus propose that the P2 residue plays a nonnegligible role in the conversion of upain-1 to a substrate. These results also proposed a strategy to optimize the pharmacological properties of peptide-based drug candidates by hydrophobicity and steric hindrance.Abbreviations : uPA: urokinase-type plasminogen activator; SPD: serine protease domain; S1 pocket: specific substrate-binding pocket.

Identification of Key circRNAs/lncRNAs/miRNAs/mRNAs and Pathways in Preeclampsia Using Bioinformatics Analysis.

BACKGROUND This study aimed to identify significantly altered circRNAs/lncRNAs/miRNAs/mRNAs pathways in preeclampsia (PE), investigate their target relationships, and determine their biological functions. MATERIAL AND METHODS Base on RNA-seq technique and the GEO database, expression profiles of circRNAs/lncRNAs/miRNAs/mRNAs related to PE were obtained. Differentially expressed RNAs were determined using the Limma package in R. Gene set enrichment analysis (GSEA) was performed using GSEA software (v. 3.0) and illustrated by ClusterProfiler and ggplot2 package in R. DAVID database (v. 6.8) was implemented to analyze functional categories and the association between genes and the corresponding Gene Ontology (GO) classification. The R visualization package GOPlot was used to get a better visualization of the relationships between genes and the selected functional categories. CeRNA networks which visualized the correlations between circRNA/lncRNA-miRNA-mRNA were constructed using Cytoscape software (v. 3.6.0). Targetscan and miRanda database were used to predict target relationships between circRNA/lncRNA-miRNA-mRNA. QRT-PCR and luciferase reporter assay were used to verify the expression and target relationship of has_circ_0088196/LINC01492/miR-100-5p/LIF (leukemia inhibitory factor). RESULTS The jak-stat signaling pathway was activated and miR-100-5p was downregulated in PE compared with normal tissues both in collected placental tissue samples and GEO database. Upregulated LIF, LINC01492, and hsa_circ_0088196 were negatively correlated with miR-100-5p expression and had a targeted relationship with miR-100-5p. CONCLUSIONS miR-100-5p may suppress PE development, while LIF, LINC01492, and hsa_circ_0088196 may promote it though inhibiting miR-100-5p. The jak-stat signaling pathway was activated and involved in PE progression.

Ex Vivo Biomechanical Comparison of Titanium Locking Plate, Stainless Steel Nonlocking Plate, and Tie-in External Fixator Applied by a Dorsal Approach on Ostectomized Humeri of Pigeons (Columba livia).

To compare the bending strength of a locking plate (LP), nonlocking plate (NLP), and an external skeletal fixator intramedullary pin (ESF-IM) tie-in fixation applied by a dorsal approach in an avian humerus fracture model, 5 left humeri obtained from pigeon (Columba livia) cadavers were randomly assigned to each repair technique (n = 15). The ESF-IM group was repaired with a 0.062-inch intramedullary pin tied-in with two 0.035-inch positive profile transfixation pins using acrylic filled plastic tubing. The LP group was repaired with a dorsally applied titanium 1.6-mm screw 7-hole locking plate (1 bicortical and 2 monocortical screws in each segment). The NLP group was repaired with a dorsally applied 6-hole stainless steel 1.5-mm dynamic compression plate (all bicortical screws). All constructs were applied before complete ostectomy to allow perfect reconstruction. Constructs were cyclically tested nondestructively for 1000 cycles in four-point bending before being tested to failure. Outcome measures included stiffness, strength, and strain energy. All specimens cycled without failure. The ESF-IM specimens were significantly stiffer and stronger than the plated repair groups. Plated constructs had significantly higher strain energies than ESF-IM. LP and NLP were of equal stiffness, strength, and strain energies. This study demonstrated that bending biomechanical properties of the ESF-IM configuration were superior to those of the dorsal plate fixation. Exact properties of fixation required to facilitate avian fracture healing are largely unknown. Further study, including assessments of optimal plate position and configuration, and torsional and in vivo studies in avian species are warranted.

Metabonomics Approach To Comparing the Antistress Effects of Four Panax ginseng Components in Rats.

Different components of Panax ginseng have different properties and medicinal effects. Metabonomics was a prospective approach to analyze the global response of endogenous metabolites to physiological and pathological processes. In this study, an untargeted metabonomics method using GC/TOFMS combined with multivariate statistical techniques was applied to compare entire metabolite differences and the antistress variations among four components of P. ginseng, namely, total ginsenosides (TG), panaxadiol (PD), panaxatriol (PT), and ginseng polysaccharide (PS), in Wistar rats. The results of metabolite analysis showed that numerous urine metabolites involving neurotransmitters, amino acids, organic acids, and gut microbiota metabolites were changed after administration of the four components of P. ginseng, with TG having the least impact on urinary metabolites. The urinary metabolite profiling of these rats exposed to acute combined stress (forced swimming and behavior restriction) demonstrated that the four ginseng components attenuated urine metabolite changes involving gut microbiota metabolites, tricarboxylic acid (TCA) cycle and energy metabolites, and organic acids to different degrees, with TG improving most of the metabolites altered by stress.

Knockout of Drosophila RNase ZL impairs mitochondrial transcript processing, respiration and cell cycle progression.

RNase Z(L) is a highly conserved tRNA 3'-end processing endoribonuclease. Similar to its mammalian counterpart, Drosophila RNase Z(L) (dRNaseZ) has a mitochondria targeting signal (MTS) flanked by two methionines at the N-terminus. Alternative translation initiation yields two protein forms: the long one is mitochondrial, and the short one may localize in the nucleus or cytosol. Here, we have generated a mitochondria specific knockout of the dRNaseZ gene. In this in vivo model, cells deprived of dRNaseZ activity display impaired mitochondrial polycistronic transcript processing, increased reactive oxygen species (ROS) and a switch to aerobic glycolysis compensating for cellular ATP. Damaged mitochondria impose a cell cycle delay at the G2 phase disrupting cell proliferation without affecting cell viability. Antioxidants attenuate genotoxic stress and rescue cell proliferation, implying a critical role for ROS. We suggest that under a low-stress condition, ROS activate tumor suppressor p53, which modulates cell cycle progression and promotes cell survival. Transcriptional profiling of p53 targets confirms upregulation of antioxidant and cycB-Cdk1 inhibitor genes without induction of apoptotic genes. This study implicates Drosophila RNase Z(L) in a novel retrograde signaling pathway initiated by the damage in mitochondria and manifested in a cell cycle delay before the mitotic entry.

Metabonomics Approach to Assessing the Metabolism Variation and Endoexogenous Metabolic Interaction of Ginsenosides in Cold Stress Rats.

Metabolic profiling technology, a massive information provider, has promoted the understanding of the metabolism of multicomponent medicines and its interactions with endogenous metabolites, which was previously a challenge in clarification. In this study, an untargeted GC/MS-based approach was employed to investigate the urinary metabolite profile in rats with oral administration of ginsenosides and the control group. Significant changes of urinary metabolites contents were observed in the total ginsenosides group, revealing the impact of ginsenosides as indicated by the up- or down-regulation of several pathways involving neurotransmitter-related metabolites, tricarboxylic acid (TCA) cycle, fatty acids ß-oxidation, and intestinal microflora metabolites. Meanwhile, a targeted UPLC-QQQ/MS-based metabonomic approach was developed to investigate the changes of urinary ginsenoside metabolites during the process of acute cold stress. Metabolic analysis indicated that upstream ginsenosides (rg1, re, and rf) increased significantly, whereas downstream ginsenosides (ck, ppd, and ppt) decreased correspondingly after cold exposure. Finally, the relationships between ginsenosides and significantly changed metabolites were investigated by correlation analysis.

A view through a chromatin loop: insights into the ecdysone activation of early genes in Drosophila.

The early genes are a key group of ecdysone targets that function at the top of the signaling hierarchy. In the presence of ecdysone, early genes exhibit a highly characteristic rapid and powerful induction that represents a primary response. Multiple isoforms encoded by early genes then coordinate the activation of a larger group of late genes. While the general mechanism of ecdysone-dependent transcription is well characterized, it is not known whether a distinct mechanism governs the hormonal response of early genes. We previously found that one of the Drosophila early genes, E75, harbors multiple functional ecdysone response elements (EcREs). In this study we extended the analysis to Broad and E74 and found that EcRE multiplicity is a general feature of the early genes. Since most of the EcREs within early gene loci are situated distantly from promoters, we employed the chromosome conformation capture method to determine whether higher order chromatin structure facilitates hormonal activation. For each early gene we detected chromatin loops that juxtapose their promoters and multiple distant EcREs prior to ecdysone activation. Our findings suggest that higher order chromatin structure may serve as an important mechanism underlying the distinct response of early genes to ecdysone.

Active site targeting of hedgehog precursor protein with phenylarsine oxide.

Hedgehog proteins, signaling molecules implicated in human embryo development and cancer, can be inhibited at the stage of autoprocessing by the trivalent arsenical phenyl arsine oxide (PhAs(III) ). The interaction (apparent Ki , 4 × 10(-7) M) is characterized by an optical binding assay and by NMR spectroscopy. PhAs(III) appears to be the first validated inhibitor of hedgehog autoprocessing, which is unique to hedgehog proteins and essential for biological activity.

Shewanella mangrovi sp. nov., an acetaldehyde-degrading bacterium isolated from mangrove sediment.

A taxonomic study was carried out on strain YQH10T, which was isolated from mangrove sediment collected from Zhangzhou, China during the screening of acetaldehyde-degrading bacteria. Cells of strain YQH10T were Gram-stain-negative rods and pale brown-pigmented. Growth was observed at salinities from 0 to 11% and at temperatures from 4 to 42 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YQH10T is affiliated to the genus Shewanella, showing the highest similarity with Shewanella haliotis DW01T (95.7%) and other species of the genus Shewanella (91.4-95.6 %). The principal fatty acids were iso-C15 : 0 and C17 : 1ω8c. The major respiratory quinone was Q-8. The polar lipids comprised phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA had a G+C content of 48.3 mol%. Strain YQH10T can completely degrade 0.02% (w/v) acetaldehyde on 2216E at 28 °C within 48 h. Based on these phenotypic and genotypic data, strain YQH10T represents a novel species of the genus Shewanella, for which the name Shewanella mangrovi sp. nov. is proposed. The type strain is YQH10T ( = MCCC 1A00830T = JCM 30121T).

Developmental roles of Drosophila tRNA processing endonuclease RNase ZL as revealed with a conditional rescue system.

Drosophila RNase Z(L) (dRNaseZ) belongs to a family of endoribonucleases with a major role in tRNA 3'-end processing. The biochemical function of RNase Z(L) is conserved from yeast to human. Here we present a study of its biological function during Drosophila development. In flies, dRNaseZ provides a non-redundant function, as the RNZ(ED24) knockout (KO) mutation causes early larval lethality. Mosaic and conditional rescue techniques were employed to determine dRNaseZ requirements at later stages. We found that dRNaseZ activity is essential for all phases of fly development that involve cell division, including growth of adult tissue progenitors during larval and metamorphic stages, and gametogenesis in adults. At the cellular level, two major phenotypes were identified-cell growth deficiency in endoreplicating tissues and cell cycle arrest in mitotic tissues. While cell growth and proliferation are both dependant on protein synthesis, the two phenotypes displayed reliance on different dRNaseZ functions. We found that dRNaseZ KO completely blocks tRNA maturation without diminishing the abundance of mature tRNA molecules. Our data indicate that growth arrest of endoreplicating cells is primarily attributed to the relocation of the pool of mature tRNAs into the nuclei causing a decrease in translation efficiency. Mitotically dividing cells appear to be less dependent on translation machinery as they maintain their normal size when deprived of dRNaseZ activity, but rather display a cell cycle arrest at the G2-M transition.

[The anti-apoptotic effect of cytoplasmic alpha-fetoprotein in hepatoma cells induced by all-trans retinoic acid involves activation of the PI3K/AKT signaling pathway].

OBJECTIVE: To explore the effect of alpha-fetoprotein (AFP) on transduction of the PI3K/ AKT signal in hepatocellular carcinoma cells and the role played by AFP in resistance to cytotoxicity of all-trans retinoic acid (ATRA). METHODS: The effects of ATRA of human liver cancer cells was assessed using the BEL-7402 cell line with the MTT assay (to evaluate proliferation), microscopy (to evaluate morphology), flow cytometry (to evaluate apoptosis), laser confocal microscopy and coimmunoprecipitation (co-IP; to evaluate co-localization and interaction of AFP with PTEN), Western blotting (to evaluate expression of phosphorylated-protein kinase B (pAKT) and Src, and RNA interference (RNAi)-mediated knockdown of AFP. Finally, application of the PI3K-specific inhibitor Ly294002 was used to monitor the influence of AFP in transduction of the PI3K signal pathway. RESULTS: The human hepatoma cell line BEL-7402 were resistant to ATRA cytotoxicity. PTEN and AFP co-localized in the cytoplasm, and co-IP indicated that AFP interacts with PTEN in BEL-7402 cells.RNAi knockdown of AFP expression led to reduced growth of BEL-7402 cells.BEL-7402 cells transfected with AFP-short interfering (si)RNA vectors showed enhanced sensitivity to ATRA and reduced expression of pAKT(Ser473) and Src; Ly294002 reduced the role of AFP in stimulating expression of pAKT(Ser473) and Src. CONCLUSION: AFP can activate transduction of the PI3K/AKT signal, and expression of AFP in hepatoma cells is a pivotal event for resisting ATRA-induced apoptosis.

[Comparative study of main components of ginseng on immune function of rats].

Ginseng and its effective components are famous for their influence to enhance human immunity, regulate endocrine and antioxidant action. However, the different effects of different components are not clear. In this study, Wistar rats were used to study the effects of main components of ginseng, including total ginsenoside, panaxadiol saponins, panaxtrol saponin and ginseng polysaccharide. The results showed that the effects of panaxadiol saponins and ginseng polysaccharide on improving animal immune organ weight, plasma interleukin 2 (IL-2), interleukin 6 (IL-6), plasma gamma-interferon (IFN-γ), tumor necrosis factor alpha (TNF-α) were better than that of the other groups. Total ginsenoside and panaxtrol saponin can effectively increase the concentration of spleen NK cells (NKC) while panaxadiol saponins and ginseng polysaccharide can significantly increase the concentrations of rat plasma adrenocorticotrophic hormone (ACTH), corticosterone (CORT) and thyroid stimulating hormone (TSH). As for the effect of increasing organization nitric oxide (NO) and superoxide dismutase (SOD), glutathione (GSH) and malondialdehyde (MDA), total ginsenoside is better than that of other groups. In brief, different components in ginseng possess different effects on enhancing immunity, regulating endocrine and resisting oxidation. Panaxadiol saponins and ginseng polysaccharide are better in enhancing immune, and total ginsenoside shows advantages in resisting oxidation and stress.

[Urine metabonomic study on long-term use of total ginsenosides in rats].

Due to its effect of systems regulation and promotion on body, Ginseng is always referred to be long-term used as a dietary supplement. But it was still unclear about its target of the tonic effects and also the side-effects long-term use may bring. Urine metabolomic method is suitable for long-term studies of pharmaco-dynamics, pharmacology and toxicology of traditional Chinese medicine because of its characteristics of non-invasive and monitoring the whole-body metabolism. This study was designed to detect the dynamic variation of rat urine metabolome along with a long-term administration of total ginsenosides using GC-TOF based metabolomic technology. Our result showed that either short-term or chronic administration of ginsenosides did not impact the rat urine metabolome significantly (as the PCA subgroup was not successful). By comparison, the short-term (1-3 w) dose of ginsenosides had the biggest metabolic influence including TCA cycle, catecholamines and neurotransmitter amino acids. Medium-term (6-10 w) dose had a gradually lower effect and long-term (27 w) dose almost had no effect. Our study indicates that both short and long-term administration of ginsenosides showed almost no obvious side-effect on the experimental animals.

Visualization of mtDNA Using FISH.

Proper mitochondrial DNA (mtDNA) levels are critical for many cellular biological functions and are associated with aging and many mitochondria disorders. Defects in core subunits of the mtDNA replication machinery lead to decreased mtDNA levels. Other indirect mitochondrial contexts including ATP concentration, lipid composition, and nucleotide composition also contribute to mtDNA maintenance. Furthermore, mtDNA molecules are distributed evenly throughout the mitochondrial network. This uniform distribution pattern is required for oxidative phosphorylation and ATP production and has been linked to many diseases when perturbed. Thus, it is important to visualize mtDNA in the cellular context. Here we provide detailed protocols for cellular visualization of mtDNA using fluorescence in situ hybridization (FISH). The fluorescent signals are targeted to the mtDNA sequence directly, ensuring both sensitivity and specificity. This mtDNA FISH method can be combined with immunostaining and used for visualizing mtDNA-protein interactions and dynamics.