Transposable elements activation triggers necroptosis in mouse embryonic stem cells.

Deficiency of the histone H3K9 methyltransferase SETDB1 induces RIPK3-dependent necroptosis in mouse embryonic stem cells (mESCs). However, how necroptosis pathway is activated in this process remains elusive. Here we report that the reactivation of transposable elements (TEs) upon SETDB1 knockout is responsible for the RIPK3 regulation through both cis and trans mechanisms. IAPLTR2_Mm and MMERVK10c-int, both of which are suppressed by SETDB1-dependent H3K9me3, act as enhancer-like cis-regulatory elements and their RIPK3 nearby members enhance RIPK3 expression when SETDB1 is knockout. Moreover, reactivated endogenous retroviruses generate excessive viral mimicry, which promotes necroptosis mainly through Z-DNA-binding protein 1 (ZBP1). These results indicate TEs play an important role in regulating necroptosis.

Sedimentary and diagenetic characteristics of the Z21 field in the Huizhou depression, Pearl River Mouth basin, South China Sea.

The Huizhou Depression in the Pearl River Mouth basin has prospective hydrocarbon potential, with Miocene sandstones as its main oil and gas-bearing reservoir. The sandstones in Miocene formation of the Z21 offshore oil-gas field composed of medium-grained, moderately sorted subarkose and lithic arkose. In this study, a total of six depositional lithofacies, namely Massive fine- to medium-grained sandstone (Sm), ripple cross-laminated fine-grained sandstone (Sr), parallel-laminated siltstone and claystone (Fl), lenticular siltstone (Sl), parallel-bedded fine-grained sandstone (Sp), wavy laminated siltstone (Sw), and two depositional systems, namely nearshore sand bar (SB) and sand sheet (SS) were identified based on core observations and seismic study. Distributions of the porosity (13.9%) and permeability (35.8 mD) reveal that the Miocene sandstones have characteristics of low porosity and low permeability, with high heterogeneity. The sedimentary system, primary texture and diagenesis jointly control the reservoir quality. Sandstones with sand bars as well coarse-grained tend to exhibit a higher quality. Mechanical compaction and calcite (average 6.81%) cementation are the major determinants to reductions in porosity and permeability. The total clay minerals (average 5.27%) generally lead to reduction of porosity, whereas chlorite coatings and illite within a certain content range may enhance the preservation of porosity in eodiagenesis. Dissolution of feldspar and debris contribute significantly to improving the reservoir quality.

HIF-1α-regulated lncRNA-TUG1 promotes mitochondrial dysfunction and pyroptosis by directly binding to FUS in myocardial infarction.

Myocardial infarction (MI) is a fatal heart disease that affects millions of lives worldwide each year. This study investigated the roles of HIF-1α/lncRNA-TUG1 in mitochondrial dysfunction and pyroptosis in MI. CCK-8, DHE, lactate dehydrogenase (LDH) assays, and JC-1 staining were performed to measure proliferation, reactive oxygen species (ROS), LDH leakage, and mitochondrial damage in hypoxia/reoxygenation (H/R)-treated cardiomyocytes. Enzyme-linked immunoassay (ELISA) and flow cytometry were used to detect LDH, creatine kinase (CK), and its isoenzyme (CK-MB) levels and caspase-1 activity. Chromatin immunoprecipitation (ChIP), luciferase assay, and RNA-immunoprecipitation (RIP) were used to assess the interaction between HIF-1α, TUG1, and FUS. Quantitative real-time polymerase chain reaction (qRT-PCR), Western blotting, and immunohistochemistry were used to measure HIF-1α, TUG1 and pyroptosis-related molecules. Hematoxylin and eosin (HE), 2,3,5-triphenyltetrazolium chloride (TTC), and terminal deoxynucleotidyl transferase dUTP risk end labelling (TUNEL) staining were employed to examine the morphology, infarction area, and myocardial injury in the MI mouse model. Mitochondrial dysfunction and pyroptosis were induced in H/R-treated cardiomyocytes, accompanied by an increase in the expression of HIF-α and TUG1. HIF-1α promoted TUG1 expression by directly binding to the TUG1 promoter. TUG1 silencing inhibited H/R-induced ROS production, mitochondrial injury and the expression of the pyroptosis-related proteins NLRP3, caspase-1 and GSDMD. Additionally, H/R elevated FUS levels in cardiomyocytes, which were directly inhibited by TUG1 silencing. Fused in sarcoma (FUS) overexpression reversed the effect of TUG1 silencing on mitochondrial damage and caspase-1 activation. However, the ROS inhibitor N-acetylcysteine (NAC) promoted the protective effect of TUG1 knockdown on H/R-induced cardiomyocyte damage. The in vivo MI model showed increased infarction, myocardial injury, ROS levels and pyroptosis, which were inhibited by TUG1 silencing. HIF-1α targeting upregulated TUG1 promotes mitochondrial damage and cardiomyocyte pyroptosis by combining with FUS, thereby promoting the occurrence of MI. HIF-1α/TUG1/FUS may serve as a potential treatment target for MI.

Contamination characteristics, source analysis and health risk assessment of heavy metals in the soil in Shi River Basin in China based on high density sampling.

To explore the contamination of heavy metals in the Shi River Basin soil in China, a high density sampling of surface soil was conducted. In this study, an absolute principal component scores multiple linear regression model (APCS-MLR) was used to identify the sources of heavy metals in the soil and quantify their amounts. The methods to assess the heavy metals included a fuzzy synthetic evaluation, index and health risk assessment. The results show that heavy metals are relatively rich southwest of the study area. Their levels may be affected by natural sources, such as parent materials. The pollution caused by human factors cannot be ignored, and it is primarily influenced by traffic emissions and processing sources, which contribute 62.6%, followed by agricultural sources, such as pesticides and fertilizers, that contribute 21.1%. The risk assessment indicated that the study area was slightly to moderately polluted. All heavy metals pose higher carcinogenic and other health risks to children than adults, and ingestion is the main way that these pollutants enter the body. The carcinogenic risk of children owing to Cr from natural sources merits further study, while the carcinogenic risk to adults and the non-carcinogenic risk to both adults and children are at acceptable levels. Transportation and industrial processing sources are the main cause of the non-carcinogenic risk. The results could provide reference for reducing heavy metal pollution in the soil.

Geochemical Characteristics and Ecological Risk Assessment of Heavy Metals in Surface Soil of Gaomi City.

Gaomi City, the hinterland of Jiaolai Plain in Shandong Peninsula, was selected as the research object. A total of 8197 surface soil samples were collected to determine the contents of eight soil heavy metals (HMs)including Copper (Cu), Lead (Pb), Zinc (Zn), Nickel (Ni), Chromium (Cr), Cadmium (Cd), Arsenic (As), and Mercury (Hg). Statistical methods were used to find out the geochemical background (GCB) in the area, systematic clustering and factor analysis were used to study the homology between HMs, and single-factor evaluation method was used to evaluate the ecological risks in the study area. The results of the study show that the ecological risk of the surface soil in the study area is relatively low, dominated by a planar distribution, with only a few high-risk points. The uneven distribution of Hg in the surface soil is affected by human activities to a certain extent. The ratio of the GCB of the geological unit area to the GCB of the whole area shows that the Hg content of the Qingshan Group and Dasheng Group geological units is higher, and the Pb content in the subvolcanic rock area is slightly higher. The ecological pollution risk in the study area is generally low, and only exists individual high-risk areas, distributed radially in densely populated areas.

Source and Health Risk Assessment of Heavy Metals in Soil-Ginger System in the Jing River Basin of Shandong Province, North China.

This study investigated the characteristics and sources of heavy metals in a soil-ginger system and assessed their health risks. To this end, 321 topsoil samples and eight soil samples from a soil profile, and 18 ginger samples with root-soil were collected from a ginger-planting area in the Jing River Basin. The average concentration of heavy metals in the topsoil followed the order: Cr > Zn > Pb > Ni > Cu > As > Cd > Hg. In the soil profile, at depths greater than 80 cm, the contents of Cr, Ni, and Zn tended to increase with depth, which may be related to the parent materials, whereas As and Cu contents showed little change. In contrast, Pb content decreased sharply from top to bottom, which may be attributable to external environmental and anthropogenic factors. Multivariate statistical analysis showed that Cr, Ni, Cu, Zn, and Cd contents in soil are affected by natural sources, Pb and As contents are significantly affected by human activities, and Hg content is affected by farmland irrigation. Combined results of the single pollution index (Pi), geo-accumulation index (Igeo), and potential ecological risk assessment (Ei and RI) suggest that soil in the study area is generally not polluted by heavy metals. In ginger, Zn content was the highest (2.36 mg/kg) and Hg content was the lowest (0.0015 mg/kg). Based on the bioconcentration factor, Cd and Zn have high potential for enrichment in ginger. With reference to the limit of heavy metals in tubers, Cr content in ginger exceeds the standard in the study area. Although Cr does not accumulate in ginger, Cr enrichment in soil significantly increases the risk of excessive Cr content in ginger.

Analysis of very important pharmacogene variants in the Tibetan population from China.

Personalized medicine, the treatment best suited for an individual, is a hot field of clinical research in the world. Many recent studies have shown that genetic variations have a great influence on the treatment. This study aimed to identify the distribution differences of very important pharmacogene (VIP) variants between the Tibetan population and the other 26 populations from the 1000 Genomes project. Based on the PharmGKB database, we successfully genotyped 50 VIP variants located in 27 genes in the Tibetan population. We also compared the genotype frequencies of VIP variants between Tibetan population and the other 26 populations. Without adjustment, the Chi-square test showed that the only significant variant between Tibetans and every other group was rs1801159 in dihydropyrimidine dehydrogenase (DPYD), followed by rs1800566 in NAD(P)H quinone dehydrogenase 1 (NQO1) and rs1051296 in solute carrier family 19 member 1 (SLC19A1). After Bonferroni's multiple adjustments, the genotype frequencies distribution of DPYD rs1801159 was found to be different in Tibetans compared to the other 26 groups, apart from ACB and ASW. Moreover, genetic structure/F-statistics (Fst) analysis and the phylogenetic tree illustrated that Tibetans had a closer affinity with CDX, CHB, CHS, JPT and KHV. Our data will complement pharmacogenomics information of the Tibetan population and provide theoretical support for the realization of individualized medical treatment for Tibetans in the future.

Study on the interaction mechanism of phospholipid imbalance and endoplasmic reticulum protein secretion imbalance in Aspergillus niger.

As the largest membrane organelle, the endoplasmic reticulum (ER) is the main location for protein preliminary processing and phospholipid synthesis. Phospholipid bilayer is the main component of the ER, so it plays an intuitively important role in the steady state of protein synthesis in the ER. Despite of their importance, relationship between phospholipid homeostasis and protein processing in Aspergillus niger remains poorly understood. In this study, phosphatidyl ethanolamine (PE)/phosphatidyl choline (PC) and phosphatidyl acid (PA) metabolic mutants and ER protein processing mutants were established by knockout the key genes in phospholipid synthesis or UPR effector hacA. Based on global transcriptome and lipidome analysis, the relationship between the phospholipids imbalance and ER protein secretory imbalance was revealed as followed: The cells compensate for the damage caused by ER protein secretory deficiency or phospholipid deficiency from enhancing the protein processing and the synthesis of phospholipids at the transcription level, therefore phospholipid deficiency (Δopi3) and continuous activation of UPR (hacAi) have a synergistic effect in promoting protein secretion and phospholipid biosynthesis. At the same time, the metabolic deficiencies of phospholipid homeostasis and the processing deficiencies of ER protein will also cause cells sensitive to oxidative stress, cell wall inhibition and DNA damage.

Correlations between lipoprotein(a) gene polymorphisms and calcific aortic valve disease and coronary heart disease in Han Chinese.

OBJECTIVE: To investigate the relationship between lipoprotein(a) gene (LPA) polymorphisms and calcific aortic valve disease (CAVD) and coronary heart disease (CHD) in Han Chinese. METHODS: A total of 148 patients were recruited (n = 71 with CAVD and n = 77 with CHD) based on a diagnosis achieved using color Doppler echocardiography, coronary angiography, or computed tomography angiography. Seventy-one control individuals without CAVD or CHD were also recruited. Biomarkers including levels of lipoprotein(a) [Lp(a)], low-density lipoprotein and high-density lipoprotein cholesterol, apolipoprotein A1, and apolipoprotein B were tested. LPA polymorphisms rs10455872, rs6415084, rs3798221, and rs7770628 were analyzed using SNaPshot SNP. RESULTS: Lp(a) levels were significantly higher in CAVD and CHD groups compared with controls. There was no significant difference in the allelic frequency distribution of rs3798221, rs7770628, or rs6415084 between CHD, CAVD, and control groups. Linear regression showed that rs3798221, rs7770628, and rs6415084 were associated with increased Lp(a) concentrations. Two CAVD patients among the 219 participants carried AG minor alleles at rs10455872, while the remainder carried AA minor alleles. CONCLUSION: rs3798221, rs6415084, and rs7770628 polymorphisms within LPA are associated with higher Lp(a) plasma levels, which correlate with increased CAVD and CHD risks.

miR-9-3p inhibits glioma cell proliferation and apoptosis by directly targeting FOXG1.

There is accumulating evidence indicating that microRNA (miR)-9-3p expression is abnormal in patients with glioma; however, the role of miR-9-3p in glioma remains unclear. In the present study, reverse transcription-quantitative PCR and immunohistochemical assays were conducted to assess miR-9-3p and forkhead box G1 (FOXG1) expression, respectively. A luciferase reporter assay was performed to confirm the target of miR-9-3p. Moreover, cell counting kit-8 and flow cytometry assays were used to assess proliferation and apoptosis, respectively. The present study demonstrated that miR-9-3p is significantly downregulated, and FOXG1 is significantly upregulated, in patients with glioma. miR-9-3p overexpression inhibited proliferation and increased the apoptosis of both U87MG and TG-905 cells. In addition, FOXG1 was identified as a direct target of miR-9-3p, and FOXG1 silencing enhanced the inhibitory effect of miR-9-3p on proliferation and apoptosis in U87 MG and TG-905 cells. In conclusion, the present results suggest that miR-9-3p may suppress malignant biological properties by targeting FOXG1. Thus, miR-9-3p may serve as a diagnostic target and novel prognostic marker in patients with glioma.

Highly efficient single base editing in Aspergillus niger with CRISPR/Cas9 cytidine deaminase fusion.

Classic genome editing tools including ZFN, TALEN, and CRISPR/Cas9 rely on DNA double-strand breaks for genome editing. To prevent the potential hazard caused by double-strand breaks (DSBs), a series of single base editing tools that convert cytidine (C) to thymine (T) without DSBs have been developed extensively in multiple species. Herein, we report for the first time that C was converted to T with a high frequency in the filamentous fungi Aspergillus niger by fusing cytidine deaminase and Cas9 nickase. Using the CRISPR/Cas9-dependent base editor and inducing nonsense mutations via single base editing, we inactivated the uridine auxotroph gene pyrG and the pigment gene fwnA with an efficiency of 47.36%-100% in A.niger. At the same time, the single-base editing results of the non-phenotypic gene prtT showed an efficiency of 60%. The editable window reached 8 bases (from C2 to C9 in the protospacer) in A. niger. Overall, we successfully constructed a single base editing system in A. niger. This system provides a more convenient tool for investigating gene function in A. niger, and provides a new tool for genetic modification in filamentous fungi.

Efficient genome editing in Aspergillus niger with an improved recyclable CRISPR-HDR toolbox and its application in introducing multiple copies of heterologous genes.

Aspergillus niger is an important industrial producer of enzymes due to its high capacity for producing exocellular secretory proteins. The CRISPR/Cas9 system has been developed as a genetic manipulation tool in A. niger. However, only the basic functions of the CRISPR/Cas9 system, such as codon optimization of Cas9 nucleases and promoter screening of guide RNA (gRNA) expression, have been developed in A. niger. The CRISPR/Cas9 system for manipulating large genomic fragments and multiple gene knock-ins still needs to be established. Here, we improved the CRISPR/Cas9 homologous direct repair (CRISPR-HDR) tool box based on donor DNAs (dDNAs) and plasmid harboring AMA1 and the pyrG marker, allowing recycling of pyrG and Cas9 components. Furthermore, we used the CRISPR-HDR tool box to knock out the 0 kb (protospacer only), 2 kb, 10 kb and even 50 kb gene fragments. This CRISPR-HDR tool box could also be used to simultaneously knock in multiple genes at the loci of two highly expressed extracellular secreted proteins, glucoamylase A (glaA) and alpha-amylase (amyA, two copies). In our study, two or three copies of glucose oxidase (goxC) were precisely knocked in at the loci of amyA and glaA, resulting in 4-fold increased enzyme activity (869.86 U/mL). This CRISPR-HDR tool box can be easily manipulated, and the AMA1-based plasmid can be easily removed under selective pressure of 5-fluoroorotic acid and uridine.

Identification and Characterization of a Novel Basic Helix-Loop-Helix Transcription Factor of Phospholipid Synthesis Regulation in Aspergillus niger.

The synthesis of phospholipids relies on a sort of genes, whose promoter regions contain inositol-sensitive upstream activation sequence (UASINO) and are regulated by the basic helix-loop-helix (bHLH)-type ino2/ino4 transcription factor (TF) pair. Ten putative bHLH TFs have been found through whole genome sequencing of Aspergillus niger, but none of these TFs have been characterized. In this study, we identified and characterized the bHLH-type TF ino2(An02g04350) in A. niger. Electrophoretic mobility shift assay (EMSA) and yeast two-hybrid assay demonstrated that ino2 functions as a homodimer in UASINO genes (e.g., ino1 and cho1) and binds to opi1(An1g02370) in vitro. Real-time quantitative PCR of ino1 and quantification of total phospholipid indicated that the ino2 disruptant downregulated the transcription of ino1 and the amount of total cellular phosphatidylinositol. In addition, phenotype analyses showed that a loss of ino2 led to resistance to cell wall interference and DNA damage. Comparative transcriptome analyses showed that more than 1000 genes and GO terms associated with UASINO, endoplasmic reticulum-associated protein degradation, phosphatidylinositol synthesis, chitin synthesis, and fatty acid synthesis were differentially expressed in Δino2 compared to the wild type (WT). Taken together, these observations indicate that the bHLH TF ino2 functions as a homodimer that regulates the synthesis of phosphatidylinositol, fatty acid, and chitin and influences the homeostasis of the endoplasmic reticulum membrane.

Association between IL-1 gene polymorphisms and tuberculosis susceptibility in the Chinese Tibetan population.

Interleukin-1 (IL-1) gene is known to be implicated in tuberculosis (TB). The present case-control study was designed to investigate whether IL-1 polymorphisms associated with TB susceptibility in a Chinese Tibetan cohort. 300 Tibetan tuberculosis patients and 300 healthy controls were recruited for 12 single-nucleotide polymorphisms (SNPs) genotyping of IL-1 gene via Sequenom MassARRAY analysis. The odds ratio (OR) and 95% confidence interval (CI) were analyzed by unconditional logistic regression to evaluate the effect of polymorphisms on the risk of tuberculosis. Among genotyped SNPs, a significant high risk between TB and SNP rs3783550 G/T, rs3783546 G/C, rs2856838 A/G, rs1609682 G/T, rs3783521 A/G genotype within IL-1α as well as rs1143623 G/G genotype within IL-1ß was found based on multiple model analysis. In addition, IL-1α SNPs mapped in a 10 kb LD block with D'>0.98, suggesting that a significant linkage disequilibrium presence among these SNPs, and "TCATG" haplotype of IL-1α SNPs with a 1.47-fold risk for TB was observed (P = 0.007). In conclusion, our data shed new light on how IL-1 SNPs may contribute to tuberculosis susceptibility in the Chinese Tibetan population.

Characteristics of coronary arterial lesions in patients with coronary heart disease and hypertension.

OBJECTIVE: The aim of this study was to investigate the correlations between risk factors such as hypertension and the complex degrees of coronary arterial lesions (CAL). METHODS: We selected 462 patients with coronary heart disease (CHD) with confirmed the stenosis (≥50 %) in at least one major coronary artery on coronary angiography and divided them into the "CHD with hypertension" group (CHD-HT, n = 306) and the CHD group (n = 156). The characteristics of CAL and the occurrence of 2-year postoperative major adverse cardiac cerebrovascular events (MACCE) in the two groups were observed. RESULTS: The mean SYNTAX scores (SS) was higher in the CHD-HT group than in the CHD group (P < 0.05). The proportions of complex, calcified, and diffused long lesions in the PCI patients' target vascular lesions, as well as the total MACCE incidence, were significantly higher in the CHD-HT group than in the CHD group (P < 0.05). Logistic multifactor regression analysis showed that age, male sex, hypertension, diabetes, hyperlipidemia, and previous history of myocardial infarction were positively correlated with the SS (P < 0.05). CONCLUSIONS: The patients with CHD-HT exhibited complicated and diffused CAL, and arterial hypertension can be considered as a risk factor for the complexity of coronary lesions in patients with ischemic heart disease.