The characteristics of extrachromosomal circular DNA in patients with end-stage renal disease.

BACKGROUND: End-stage renal disease (ESRD) is the final stage of chronic kidney disease (CKD). In addition to the structurally intact chromosome genomic DNA, there is a double-stranded circular DNA called extrachromosomal circular DNA (eccDNA), which is thought to be involved in the epigenetic regulation of human disease. However, the features of eccDNA in ESRD patients are barely known. In this study, we identified eccDNA from ESRD patients and healthy people, as well as revealed the characteristics of eccDNA in patients with ESRD. METHODS: Using the high-throughput Circle-Sequencing technique, we examined the eccDNA in peripheral blood mononuclear cells (PBMCs) from healthy people (NC) (n = 12) and ESRD patients (n = 16). We analyzed the length distribution, genome elements, and motifs feature of eccDNA in ESRD patients. Then, after identifying the specific eccDNA in ESRD patients, we explored the potential functions of the target genes of the specific eccDNA. Finally, we investigated the probable hub eccDNA using algorithms. RESULTS: In total, 14,431 and 11,324 eccDNAs were found in the ESRD and NC groups, respectively, with sizes ranging from 0.01 kb to 60 kb at most. Additionally, the ESRD group had a greater distribution of eccDNA on chromosomes 4, 11, 13, and 20. In two groups, we also discovered several motifs of specific eccDNAs. Furthermore, we identified 13,715 specific eccDNAs in the ESRD group and 10,585 specific eccDNAs in the NC group, both of which were largely annotated as mRNA catalog. Pathway studies using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that the specific eccDNA in ESRD was markedly enriched in cell junction and communication pathways. Furthermore, we identified potentially 20 hub eccDNA-targeting genes from all ESRD-specific eccDNA-targeting genes. Also, we found that 39 eccDNA-targeting genes were associated with ESRD, and some of these eccDNAs may be related to the pathogenesis of ESRD. CONCLUSIONS: Our findings revealed the characteristics of eccDNA in ESRD patients and discovered potentially hub and ESRD-relevant eccDNA-targeting genes, suggesting a novel probable mechanism of ESRD.

Integrated proteome and acetylome analyses unveil protein features of gestational diabetes mellitus and preeclampsia.

Gestational diabetes mellitus (GDM) and preeclampsia (PE) are associated with maternal and infant health. Although the pathogenesis of PE and GDM remains controversial, oxidative stress is involved in the underlying pathology of GDM and PE. Protein lysine acetylation (Kac) plays an important regulatory role in biological processes. There is little data regarding the association of the maternal acetylome with GDM and PE. This study aimed to assess the potential value of the proteome and acetylome for GDM and PE. In our study, we included placental tissues from healthy individuals (n = 6), GDM patients (n = 6), and PE patients (n = 6) to perform 4D-label free quantification proteomics analysis and PRM analysis. We identified 22 significantly regulated proteins and 192 significantly regulated acetylated proteins between the GDM and PE groups. Furthermore, 192 significantly regulated acetylated proteins were mainly enriched in endoplasmic reticulum stress (ERS) and ferroptosis pathways. Seventeen acetylated sites in these two pathways were verified by PRM analysis. Our comprehensive analysis revealed key features of GDM/PE-significantly regulated acetylated proteins in the placentas from GDM and PE. The results of signaling pathway analysis focused on ERS and ferroptosis. These findings may help explore the underlying pathology, new biomarkers, and therapeutic targets of GDM and PE.

Integrating spatial transcriptomics with single-cell transcriptomics reveals a spatiotemporal gene landscape of the human developing kidney.

BACKGROUND: Research on spatiotemporal gene landscape can provide insights into the spatial characteristics of human kidney development and facilitate kidney organoid cultivation. Here, we profiled the spatiotemporal gene programs of the human embryonic kidneys at 9 and 18 post-conception weeks (PCW) by integrating the application of microarray-based spatial transcriptomics and single-cell transcriptomics. RESULTS: We mapped transcriptomic signatures of scRNA-seq cell types upon the 9 and 18 PCW kidney sections based on cell-type deconvolution and multimodal intersection analyses, depicting a spatial landscape of developing cell subpopulations. We established the gene characteristics in the medullary regions and revealed a strong mitochondrial oxidative phosphorylation and glycolysis activity in the deeper medullary region. We also built a regulatory network centered on GDNF-ETV4 for nephrogenic niche development based on the weighted gene co-expression network analysis and highlighted the key roles of Wnt, FGF, and JAG1-Notch2 signaling in maintaining renal branching morphogenesis. CONCLUSIONS: Our findings obtained by this spatiotemporal gene program are expected to improve the current understanding of kidney development.

Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia.

Preeclampsia (PE) is a dangerous hypertensive disorder that occurs during pregnancy. The specific aetiology and pathogenesis of PE have yet to be clarified. To better reveal the specific pathogenesis of PE, we characterized the proteome and acetyl proteome (acetylome) profile of placental tissue from PE and normal-term pregnancy by label-free quantification proteomics technology and PRM analysis. In this research, 373 differentially expressed proteins (DEPs) were identified by proteome analysis. Functional enrichment analysis revealed significant enrichment of DEPs related to angiogenesis and the immune system. COL12A1, C4BPA and F13A1 may be potential biomarkers for PE diagnosis and new therapeutic targets. Additionally, 700 Kac sites were identified on 585 differentially acetylated proteins (DAPs) by acetylome analyses. These DAPs may participate in the occurrence and development of PE by affecting the complement and coagulation cascades pathway, which may have important implications for better understand the pathogenesis of PE. In conclusion, this study systematically analysed the reveals critical features of placental proteins in pregnant women with PE, providing a resource for exploring the contribution of lysine acetylation modification to PE.

Multiomics landscape of the autosomal dominant osteopetrosis type II disease-specific induced pluripotent stem cells.

BACKGROUND: Autosomal dominant osteopetrosis type II (ADO2) is a genetically and phenotypically metabolic bone disease, caused by osteoclast abnormalities. The pathways dysregulated in ADO2 could lead to the defects in osteoclast formation and function. However, the mechanism remains elusive. MATERIALS AND METHODS: To systematically explore the molecular characterization of ADO2, we performed a multi-omics profiling from the autosomal dominant osteopetrosis type II iPSCs (ADO2-iPSCs) and healthy normal control iPSCs (NC-iPSCs) using whole genome re-sequencing, DNA methylation and N6-methyladenosine (m6A) analysis in this study. RESULTS: Totally, we detected 7,095,817 single nucleotide polymorphisms (SNPs) and 1,179,573 insertion and deletions (InDels), 1,001,943 differentially methylated regions (DMRs) and 2984 differential m6A peaks, and the comprehensive multi-omics profile was generated from the two cells. Interestingly, the ISG15 m6A level in ADO2-iPSCs is higher than NC-iPSCs by IGV software, and the differentially expressed m6A-modified genes (DEMGs) were highly enriched in the osteoclast differentiation and p53 signaling pathway, which associated with the development of osteopetrosis. In addition, combining our previously published transcriptome and proteome datasets, we found that the change in DNA methylation levels correlates inversely with some gene expression levels. CONCLUSION: Our results indicate that the global multi-omics landscape not only provides a high-quality data resource but also reveals a dynamic pattern of gene expression, and found that the pathogenesis of ADO2 may begin early in life.

Histone succinylation and its function on the nucleosome.

Protein post-translational modifications (PTMs) of histones are ubiquitous regulatory mechanisms involved in many biological processes, including replication, transcription, DNA damage repair and ontogenesis. Recently, many short-chain acylation histone modifications have been identified by mass spectrometry (MS). Lysine succinylation (Ksuc or Ksucc) is a newly identified histone PTM that changes the chemical environment of histones and is similar to other acylation modifications; lysine succinylation appears to accumulate at transcriptional start sites and to correlate with gene expression. Although numerous studies are ongoing, there is a lack of reviews on the Ksuc of histones. Here, we review lysine succinylation sites on histones, including the chemical characteristics and the mechanism by which lysine succinylation influences nucleosomal structure, chromatin dynamics and several diseases and then discuss lysine succinylation regulation to identify theoretical and experimental proof of Ksuc on histones and in diseases to inspire further research into histone lysine succinylation as a target of disease treatment in the future.

Green preparation of carbon dots from Momordica charantia L. for rapid and effective sensing of p-aminoazobenzene in environmental samples.

p-Aminoazobenzene (pAAB) is a hazardous azo dye that causes considerable harm to human health and the environment. The development of novel and sensitive sensors for the rapid detection of pAAB is in high demand. In this study, a simple fluorescent sensor for pAAB detection is designed based on carbon dots (CDs) which are prepared using green carbon source of Momordica charantia L. via a facile hydrothermal approach. The fluorescence spectra of CDs exhibit considerable overlap with the absorption band of pAAB, and the fluorescence is specifically suppressed in the presence of pAAB ascribed to the inner filter effect. Good and wide linearity is observed in the pAAB concentration range of 0.01-12.5 µg mL-1 with a lower detection limit of 3.9 ng mL-1. The established method achieves good results with a rapid analysis of pAAB in different practical water and soil samples. The as-constructed fluorescent sensor provides a simple, rapid, economical and eco-friendly platform and possesses prospective applications for the effective, selective and sensitive detection of pAAB in the environmental field.

Copper-Catalyzed Three-Component Carboboronation of Allenes Using Highly Strained Cyclic Ketimines as Electrophiles.

A diastereoselective copper and NHC-ligand-catalyzed three-component difunctionalization of allenes with bis(pinacolato)diboron and 2H-azirines to afford borylated allylaziridines is described. The reaction exhibits complete diastereoselectivity and good yields, and the further chlorination of the corresponding borylated products was also performed. It is believed that the high ring-strain force of 2H-azirines facilitates the reaction. More chemical transformations of borylated allylaziridines are also reported.

Application of single-cell RNA sequencing in embryonic development.

Embryonic development is a complex process that is regulated by a series of precise cellular behaviours. The limited number of cells in the early stages of embryonic development represents a challenge for studying early gene regulation and maintaining cell sternness. Single-cell sequencing is a new technology for high-throughput sequencing analysis at the single-cell level that not only reflects the heterogeneity between cells but also reveals gene expression characteristics in different cells from limited samples. Currently, the widespread application of single-cell RNA sequencing technology is gradually changing our understanding of disease pathogenesis. This article reviews the application of single-cell RNA sequencing in embryonic development in recent years and provides innovative ideas for research on embryonic development and the treatment of diseases related to embryonic development.

Cu-Catalysed synthesis of benzo[f]indole-2,4,9(3H)-triones by the reaction of 2-amino-1,4-napthoquinones with α-bromocarboxylates.

A copper-catalysed cascade ester amidation/radical cyclization of 2-amino-1,4-naphthoquinones with α-bromocarboxylates to afford benzo[f]indole-2,4,9(3H)-triones is described, and the reaction has a broad substrate scope and the desired products are obtained in mostly moderate to good yields. Mechanism-probing experiments indicate that the otherwise challenging radical coupling reaction of α-bromocarboxylates with 2-amino-1,4-naphthoquinones is facilitated by a 5-endo radical cyclization.

Rosmarinic acid alleviates ethanol-induced lipid accumulation by repressing fatty acid biosynthesis.

Recent studies have demonstrated that rosmarinic acid is a valuable natural product for treatment of alcoholic liver disease. However, the mechanisms whereby rosmarinic acid improves alcoholic liver disease remain unclear. Here we performed experiments using a non-transformed mouse hepatocyte cell line (AML12). Oil-red O staining demonstrated that rosmarinic acid reduced ethanol-induced lipid accumulation. It was shown that rosmarinic acid prevented ethanol-induced elevation of the malondialdehyde level. We also found that rosmarinic acid inhibited ethanol-induced mRNA expression of tumor necrosis factor-α and interleukin 6. Metabolomics analysis revealed that rosmarinic acid ameliorated ethanol-induced fatty acid biosynthesis in the cytoplasm. In addition, palmitic acid was a candidate biomarker in cells exposed to ethanol or ethanol plus rosmarinic acid. Rosmarinic acid prevented the ethanol-induced increase in sorbitol that is a component of the polyol pathway. Moreover, we confirmed that rosmarinic acid attenuated ethanol-induced mRNA expression of fatty acid synthase, probably by modulating the AMPK/SREBP-1c pathway. Furthermore, rosmarinic acid prevented the ethanol-induced decrease in eight metabolites that are involved in mitochondrial metabolism, including glycine and succinic acid which are the components of carnitine synthesis. These results provide a crucial insight into the molecular mechanism of rosmarinic acid in alleviating ethanol-induced injury.

Copper-Catalyzed Three-Component Difunctionalization of Aromatic Alkenes with 2-Amino-1,4-naphthoquinones and α-Bromocarboxylates.

A copper-catalyzed three-component difunctionalization of aromatic alkenes to access 1,4-naphthoquinone derivatives with diverse structures is described. Experiments show that the difunctionalization reaction is accompanied by ester exchange reaction with the solvent. In this method, α-bromocarboxylates are used as radical precursors and 2-amino-1,4-naphthoquinones as radical trapping reagents. The substrate scope is broad because various aromatic alkenes, 2-amino-1,4-naphthoquinones, and α-bromocarboxylates are employed in the reaction, and corresponding products are obtained in moderate to good yields.

Silver-Catalyzed Three-Component Difunctionalization of Alkenes via Radical Pathways: Access to CF3-Functionalized Alkyl-Substituted 1,4-Naphthoquinone Derivatives.

A silver-catalyzed three-component difunctionalization of alkenes by using 2-amino- and 2-hydroxy-1,4-naphthoquinone derivatives as the radical-trapping reagents is reported. Various alkenes and 2-amino- or 2-hydroxy-1,4-naphthoquinones with diverse structures and electronic properties are applied to the reaction. The methodology provides an alternative method to access CF3-functionalized alkyl-substituted quinone derivatives which are prevalent structures in bioactive molecules. Furthermore, a plausible radical pathway for the reaction is proposed based on results from primary control experiments.

Maternal high-fat diet influences outcomes after neonatal hypoxic-ischemic brain injury in rodents.

The typical US diet has >30% calories from fat; yet, typical laboratory diets contain 17% calories from fat. This disparity could confound the clinical relevance of findings in cerebral ischemia models. We compared outcomes after neonatal brain injury in offspring of rat dams fed standard low-fat chow (17% fat calories) or a higher fat diet (34% fat calories) from day 7 of pregnancy. On postnatal day 7, hypoxic-ischemic injury was induced by right carotid ligation, followed by 60, 75 or 90 min 8% oxygen exposure. Sensorimotor function, brain damage, and serum and brain fatty acid content were compared 1 to 4 weeks later. All lesioned animals developed left forepaw placing deficits; scores were worse in the high-fat groups (p < 0.0001, ANOVA). Similarly, reductions in left forepaw grip strength were more pronounced in the high-fat groups. Severity of right hemisphere damage increased with hypoxia-ischemia duration but did not differ between diet groups. Serum and brain docosahexaenoic acid fatty acid fractions were lower in high-fat progeny (p < 0.05, ANOVA). We speculate that the high-fat diet disrupted docosahexaenoic acid-dependent recovery mechanisms. These findings have significant implications both for refinement of neonatal brain injury models and for understanding the impact of maternal diet on neonatal neuroplasticity.

Antimony release from contaminated mine soils and its migration in four typical soils using lysimeter experiments.

Antimony (Sb) can pose great risks to the environment in mining and smelting areas. The migration of Sb in contaminated mine soil was studied using lysimeter experiments. The exchangeable concentration of soil Sb decreased with artificial leaching. The concentrations of Sb retained in the subsoil layers (5-25cm deep) were the highest for Isohumosol and Ferrosol and the lowest for Sandy soil. The Sb concentrations in soil solutions decreased with soil depth, and were adequately simulated using a logarithmic function. The Sb migration pattern in Sandy soil was markedly different from the patterns in the other soils which suggested that Sb may be transported in soil colloids. Environmental factors such as water content, soil temperature, and oxidation-reduction potential of the soil had different effects on Sb migration in Sandy soil and Primosol. The high Fe and Mn contents in Ferrosol and Isohumosol significantly decreased the mobility of Sb in these soils. The Na and Sb concentrations in soils used in the experiments positively correlated with each other (P<0.01). The Sb concentrations in soil solutions, the Sb chemical fraction patterns, and the Sb/Na ratios decreased in the order Sandy soil>Primosol>Isohumosol>Ferrosol, and we concluded that the Sb mobility in the soils also decreased in that order.

Docosahexaenoic acid augments hypothermic neuroprotection in a neonatal rat asphyxia model.

BACKGROUND: In neonatal rats, early post-hypoxia-ischemia (HI) administration of the omega-3 fatty acid docosahexaenoic acid (DHA) improves sensorimotor function, but does not attenuate brain damage. OBJECTIVE: To determine if DHA administration in addition to hypothermia, now standard care for neonatal asphyxial brain injury, attenuates post-HI damage and sensorimotor deficits. METHODS: Seven-day-old (P7) rats underwent right carotid ligation followed by 90 min of 8% O2 exposure. Fifteen minutes later, pups received injections of DHA 2.5 mg/kg (complexed to 25% albumin) or equal volumes of albumin. After a 1-hour recovery, pups were cooled (3 h, 30°C). Sensorimotor and pathology outcomes were initially evaluated on P14. In subsequent experiments, sensorimotor function was evaluated on P14, P21, and P28; histopathology was assessed on P28. RESULTS: At P14, left forepaw function scores (normal: 20/20) were near normal in DHA + hypothermia-treated animals (mean ± SD 19.7 ± 0.7 DHA + hypothermia vs. 12.7 ± 3.5 albumin + hypothermia, p < 0.0001) and brain damage was reduced (mean ± SD right hemisphere damage 38 ± 17% with DHA + hypothermia vs. 56 ± 15% with albumin + hypothermia, p = 0.003). Substantial improvements on three sensorimotor function measures and reduced brain damage were evident up to P28. CONCLUSION: Unlike post-HI treatment with DHA alone, treatment with DHA + hypothermia produced both sustained functional improvement and reduced brain damage after neonatal HI.

[Factors influencing ammonia volatilization in a winter wheat field with plastic film mulched ridges and unmulched furrows].

The objective of this experiment was to quantify ammonia volatilization from a winter wheat field with plastic film mulched-ridges and unmulched-furrows (PMRF). The trial was conducted during the 2010-2011 winter wheat growing season at Yangling, Shaanxi Province. Ammonia volatilization from the soil was measured using the closed-chamber method. The results indicated that NH3 emission losses ranged between (1.66 +/- 0.3) and (3.28 +/- 0.51) kg x hm(-2) in the PMRF treatment. In comparison, the NH3 emission loss was (4.68 +/- 0.35) kg x ha(-1) in the conventional tillage treatment (i. e., smooth soil surface). The PMRF treatment reduced NH3 emissions by 29.8 to 63.8% compared with the conventional treatment. The NH3 emission losses were equivalent to 1.9% of the applied N in the conventional practice treatment. In contrast, the losses were equivalent to only 0.3% to 0.8% of the applied N in the PMRF treatment. Ammonia emissions were greatest during the first two weeks after sowing. Emissions before winter accounted for 82% of total NH3 emission in the conventional practice treatment, but only 49% to 61% of the total NH3 emission in the PMRF treatment. The soil NH4+ -N content and the soil moisture content had direct effects on NH3 emission before winter in the conventional treatment. In thePMRF treatment, the soil NH4+ -N content had a direct effect on NH3 emission before winter, whereas soil surface temperature and soil moisture had indirect effects. Ammonia emissions after the greening stage were mainly influenced by the soil NH4+ -N content. Simulation results indicated that logarithmic functions best described cumulative NH3 emission in the PMRF + high N rate treatment and the conventional treatment. A linear function best described cumulative NH3 emission in the PMRF + low N rate treatment and the unfertilized treatment. In conclusion, the PMRF treatment can significantly reduce N losses from winter wheat fields by changing the spatial-temporal dynamics of soil NH3 volatilization.

[Effects of seeding rate and nitrogen fertilization rate on physiological traits of winter wheat after anthesis in a field with plastic mulched rides and unmulched furrows].

Taking winter wheat cultivar Xiaoyan 22 as test material, a field experiment with central composite rotatable design was conducted to investigate the effects of seeding rate and nitrogen (N) fertilization rate on the physiological traits of the cultivar after anthesis under ridge-furrow cultivation with plastic film mulching, aimed to harmonize the relationships between winter wheat population and its individuals and to fully use the advantages of ridge-furrow cultivation in dry land areas. With increasing N fertilization rate, the leaf area index and the flag leaf chlorophyll content and net photosynthesis rate after anthesis increased; with increasing seeding rate, the leaf area index increased first and was stable then at early and middle milking stages but decreased at later milking stage, the flag leaf chlorophyll content and net photosynthesis rate decreased, and the grain yield per plant increased after an initial decrease. Appropriate seeding rate could optimize the relationships between winter wheat population and its individuals, and optimal N fertilization rate benefited the improvement of winter wheat physiological traits after anthesis and the enhancement of winter wheat yield. Under our experimental condition, seeding rate 112.5 kg x hm(-2) plus N fertilization rate 180-222 kg N x hm(-2) is a scheme beneficial to optimize the relationships between winter wheat population and its individuals and to establish a good winter wheat community structure with a reasonable leaf area index after anthesis, higher flag leaf chlorophyll content and net photosynthesis rate, higher grain yield per plant, and high yield per unit area.

Bumetanide augments the neuroprotective efficacy of phenobarbital plus hypothermia in a neonatal hypoxia-ischemia model.

INTRODUCTION: The NaKCl cotransporter NKCC1 facilitates intraneuronal chloride accumulation in the developing brain. Bumetanide (BUM), a clinically available diuretic, inhibits this chloride transporter and augments the antiepileptic effects of phenobarbital (PB) in neonatal rodents. In a neonatal cerebral hypoxia-ischemia (HI) model, elicited by right carotid ligation, followed by 90 min 8% O(2) exposure in 7-d-old (P7) rats, PB increases the neuroprotective efficacy of hypothermia (HT). We evaluated whether BUM influenced the neuroprotective efficacy of combination treatment with PB and HT. METHODS: P7 rats underwent HI lesioning; 15 min later, all received PB (30 mg/kg), and 10 min later, half received BUM (10 mg/kg, PB-HT+BUM) and half received saline (PB-HT+SAL). One hour after HI, all were cooled (30 °C, 3 h). Contralateral forepaw sensorimotor function and brain damage were evaluated 1-4 wk later. RESULTS: Forepaw functional measures were close to normal in the PB-HT+BUM group, whereas deficits persisted in PB-HT+SAL controls; there were corresponding reductions in right cerebral hemisphere damage (at P35, % damage: PB-HT+BUM, 21 ± 16 vs. 38 ± 20 in controls). DISCUSSION: These results provide evidence that NKCC1 inhibition amplifies PB bioactivity in the immature brain and suggest that coadministration of PB and BUM may represent a clinically feasible therapy to augment the neuroprotective efficacy of therapeutic HT in asphyxiated neonates.