Bioinformatics-Based Identification of lncRNA-miRNA-mRNA Network in Dilated Cardiomyopathy and Drug Prediction

Background. Dilated cardiomyopathy (DCM) is a cardiovascular disease of unknown etiology with progressive aggravation. More and more studies have shown that long noncoding RNAs (lncRNAs) play an essential role in dilated cardiomyopathy formation and development. The mechanism of action of competitive endogenous RNA (ceRNA) networks formed based on the principle that lncRNAs affect mRNAs’ expression level by competitively binding microRNAs (miRNAs) in dilated cardiomyopathy has rarely been reported. Objective. This study is aimed at constructing a lncRNA-miRNA-mRNA ceRNA network by bioinformatics analysis methods, discovering, and validating potential biomarkers of DCM in the ceRNA network and determining possible therapeutic targets from them for drug prediction. Methods. A lncRNA dataset and a mRNA microarray dataset were downloaded from the Gene Expression Omnibus Database (GEO). Gene expression was compared between blood samples from patients with dilated cardiomyopathy and blood samples from normal subjects to identify differential expression of lncRNAs and mRNAs. The lncRNA-miRNA-mRNA network was constructed using bioinformatics tools, and functional and pathway enrichment analysis and protein-protein interactions were performed. The mRNAs in the network and the proteins they encode are then used as targets for predicting drugs. Besides, the expression of lncRNAs in the ceRNA network was validated by real-time quantitative PCR (qRT-PCR) experiments in vitro. Results. The differentially expressed lncRNA-miRNA-mRNA ceRNA network in dilated cardiomyopathy was successfully established. Two differentially overexpressed key lncRNAs were found from the network: AC093817 and AC091062, and qRT-PCR experiments further validated the overexpression of AC093817 and AC091062. The mRNAs in the network and the proteins encoded by the mRNAs were used for drug prediction to get related drugs. Conclusion. This study supports a possible mechanism and drug development of dilated cardiomyopathy, AC093817 and AC091062 being potential biomarkers of dilated cardiomyopathy

Immune-Related Genes: Potential Regulators and Drug Therapeutic Targets in Hypertrophic Cardiomyopathy

Background. Accumulating evidence shows that the innate immune system is a key player in cardiovascular repair and regeneration, but little is known about the role of immune-related genes (IRGs) in hypertrophic cardiomyopathy (HCM). Methods. The differential mRNA expression profiles of HCM samples were downloaded from the Gene Expression Omnibus (GEO) dataset (GSE89714), and the IRG expression profile was obtained from the ImmPort database. The regulatory pathways of IRGs in HCM were screened out through discrepantly expressive genes (DEGs) analysis, enrichment of gene function/pathway analysis, and protein-protein interaction (PPI) network. Besides, hub IRGs in the PPI network were selected for drug prediction. Results. A total of 854 genes were differentially expressed in HCM, of which 88 were IRGs. Functional enrichment analysis revealed that 88 IRGs were mainly involved in the biological processes (BP) of SMAD protein pathway, smooth muscle cell proliferation, protein serine/threonine kinase, and mitogen-activated protein kinase (MAPK) cascade. Cytokine-cytokine receptor interaction, TGFβ signaling pathway, PI3K-Akt signaling pathway, and MAPK signaling pathway were enriched in the pathway enrichment analysis of these 88 IRGs. Furthermore, the PPI regulatory network of IRGs was constructed, and 10 hub IRGs were screened out to construct a regulatory network for HCM. 4 transcription factors (TFs) were the major regulator of 10 hub IRGs. Finally, these 10 hub IRGs were entered into the pharmacogenomics database for prediction, and the relevant drugs were obtained. Conclusions. In this study, 10 hub IRGs were coexpressed with 4 TFs to construct a regulatory network for HCM. Drug prediction of these 10 hub IRGs proposed potential therapeutic agents that could be used in HCM. These results indicate that IRGs are potential regulators and drug therapeutic targets in HCM

Long-term variations in ozone levels in the troposphere and lower stratosphere over Beijing: observations and model simulations

Tropospheric ozone is both a major pollutant and a short-lived greenhouse gas and has therefore caused much concern in recent years. The ozone profile in the troposphere and lower stratosphere over Beijing has been observed since 2002 by ozonesondes developed by the Institute of Atmospheric Physics. Increasing concentrations of tropospheric ozone from 2002 to 2010 measured by these balloon-based observations have been reported previously. As more observations are now available, we used these data to analyse the long-term variability of ozone over Beijing during the whole period from 2002 to 2018. The ozonesondes measured increasing concentrations of ozone from 2002 to 2012 in both the troposphere and lower stratosphere. There was a sudden decrease in observed ozone between 2011 and 2012. After this decrease, the increasing trend in ozone concentrations slowed down, especially in the mid-troposphere, where the positive trend became neutral. We used the Chemical Lagrangian Model of the Stratosphere (CLaMS) to determine the influence of the transport of ozone from the stratosphere to the troposphere on the observed ozone profiles. CLaMS showed a weak increase in the contribution of stratospheric ozone before the decrease in 2011–2012 and a much more pronounced decrease after this time. Because there is no tropospheric chemistry in CLaMS, the sudden decrease simulated by CLaMS indicates that a smaller downward transport of ozone from the stratosphere after 2012 may explain a significant part of the observed decrease in ozone in the mid-troposphere and lower stratosphere. However, the influence of stratospheric ozone in the lower troposphere is negligible in CLaMS, and the hiatus in the positive trend after 2012 can be attributed to a reduction in ozone precursors as a result of stronger pollution control measures in Beijing

Multiple Domestication Centers Revealed by the Geographical Distribution of Chinese Native Pigs

Previous studies have shown that Southeast Asian pigs were independently domesticated from local wild boars. However, the domestication of Chinese native pigs remains a subject of debate. In the present study, phylogenetic analysis of Chinese native pigs was performed by screening for haplotypes inferred from a phylogenetic tree of pig mitochondrial DNA (mtDNA) sequences based on sequence-specific mutations. A total of 2466 domestic pigs formed 124 haplotypes and were assigned to four clades. Clade A comprised pigs distributed mainly in the Qinghai-Tibet Plateau and its surrounding areas; these pigs clustered into three groups. The pigs of clade B were mainly from the Mekong River Basin in Yunnan Province and had been exposed to genetic infiltration from European populations. Clade C comprised pigs mainly from the middle and lower reaches of the Yangtze River. The pigs of clade D were distributed mainly at the intersection of Yunnan, Sichuan, and Gansu provinces east of the Hengduan Mountains (YSGH). Compared with wild boar, at least three domestication centers and one expansion center of pigs in China were detected. Among the four centers detected, two were for Tibetan pigs and were in the Qinghai-Tibet Plateau and at the YSGH intersection, and the other two were in the Mekong River Basin in Yunnan Province and the middle and downstream regions of the Yangtze River

Effects of cultivation and agricultural abandonment on soil carbon, nitrogen and phosphorus in a meadow steppe in eastern Inner Mongolia

Grassland conversion into cropland and further into abandoned land may result in substantial changes when such conversion neglects the historical context of the land use pattern in question in most cases. The objectives of this study were to examine the effects of land use shifts on soil organic carbon (OC), total nitrogen (TN) and total phosphorus (TP) in a meadow steppe in eastern Inner Mongolia. Four sites within 50 km were selected as replicates, and within each of the four sites, the plant and soil properties were investigated separately for three land use types, grassland, cropland and abandoned land from cropland, to reveal the effect of land use changes on soil nutrient contents and stocks. We found that cropland had the highest canopy biomass, whereas grassland maintained the highest root biomass. Significant decreases in OC and TN contents occurred mainly in the 0-20 cm soil layer with the conversion of grassland into cropland, whereas TP contents significantly increased in the 10-30 cm soil profile. Abandonment obviously increased the soil OC and TN contents in the 0-20 cm soil layer compared with cropland, although the levels of native grassland were not reached. The C:N, C:P and N:P ratios were highest in the entire soil profile for the grassland followed by the abandoned land and then the cropland. Changes in nutrient stocks with land use shifts showed similar trends as those in the relevant nutrient contents, but the change ratios of stocks among different land use types could be significantly underestimated due to the cultivation-compaction effect. Thus, we concluded that the abandonment and maintenance of native grasslands should be adopted to protect and maintain the soil organic matter and nitrogen in the meadow steppe of Inner Mongolia

Characterization of a complete mitochondrial genome of Turdus ruficollis (Passeriformes: Turdidae)

Turdus ruficollis is mainly found in China and Northeast Asia. So far, the mitochondrial genome of more than 20 species from the genus Turdus has been studied. However, the relevant information of T. ruficollis has not been reported. To grasp a better comprehension on the molecular basis of T. ruficollis, we obtained the complete mitochondrial DNA genome sequences of this species. The mitogenome was 16,737 bp in length, which consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. A phylogenetic tree based on complete mitogenome sequences revealed that, within the genus Turdidae, T. ruficollis is closely related to T. naumanni and T. eumomus. The complete mitochondrial genome of T. ruficollis would be of great utility for population genetics and phylogeography of the Turdidae family and would also provide meritorious insights for future studies on conservation, genetics, and phylogeny of the Passeriformes family

Aerosol variations in the upper troposphere and lower stratosphere over the Tibetan Plateau

Satellite measurements and model simulations indicate the existence of the Asian tropopause aerosol layer (ATAL)—an enhanced aerosol layer in the upper troposphere and lower stratosphere (UTLS) associated with the Asian summer monsoon (ASM)—although it has rarely been evidenced by snapshots of balloon-borne in situ measurements. To better understand how the ATAL evolves, a portable optical particle counter (POPS) onboard a stratospheric balloon was released over the Tibetan Plateau (TP) during the ASM period of 2019. The POPS detected the ATAL in the UTLS during the ascending, descending periods, as well as during its quasi-horizontal floating periods. The aerosol number density in the ATAL showed obvious vertical variability. The peak aerosol number density in the ATAL was 180 cm ^−3 around the tropopause during the ascending and descending period and the maximum aerosol number density was 290 cm ^−3 around the tropopause during the floating period. And the aerosol concentration observed over the TP in the 2019 summer was approximately five times larger than that in the 2018 summer. Lagrangian simulations reveal that the minority of the observed aerosol particles were directly elevated in a region of uplift south of the Himalayas, and the majority of the particles were transported from the UTLS region situated approximately between the isentropic surfaces of 370 and 460 K. Up to 14% of the observed aerosol particles were directly influenced by the volcanic plumes from the eruption of the volcano Raikoke in June 2019

Field study of monotonic and cyclic lateral behaviour of piles in soft soils improved with and without vacuum preloading

Project Oufei is the largest individual reclamation project in Wenzhou city, China, and the main infrastructure consists of seawalls, sluices and separation dikes. These infrastructures face repeated horizontal forces from wind and waves; thus, it is essential to evaluate the lateral bearing of single pile used for sluice gates. This paper presents a case study on lateral monotonic and cyclic behaviour of bored piles in soft soils. Four instrumented piles were loaded monotonically and cyclically to assess the contribution of soil improvement by vacuum preloading with prefabricated vertical drains. The test results show that the ultimate horizontal capacities were 200 kPa and 100 kPa for piles in the treated zone and untreated zone, respectively, under monotonic loading and up to 220 kPa and 120 kPa for piles in the treated zone and untreated zone, respectively, under cyclic loading, indicating that the ultimate horizontal capacity of piles in the treated zone can meet the design requirement of 130 kPa. Moreover, soil improvement decreased the maximum bending moment of the bored piles and enhanced the pile head stiffness, and the influence depth of soil improvement is up to 10 m. This indicates that soil improvement by vacuum preloading with prefabricated vertical drains is effective and can be used for lateral loading in reclamation project

Potential and Distribution of Natural Gas Hydrate Resources in the South China Sea

The amount of natural gas contained in the world’s gas hydrate accumulations is enormous, but these estimates remain highly speculative. So far, it is still challenging to locate spatial distribution of marine gas hydrate and quantitatively characterize the evaluation parameters and systematic improvement of evaluation systems. Considering the systematic review of the key accumulation factors, such as heat flow, deposition rate and total organic carbon in the typical passive continental margin, the evaluation results of global marine gas hydrate resources were analyzed based on the characteristics of gas hydrate geology, geophysics and geochemistry anomalies in the South China Sea. We analyze the problems on the evaluation of marine gas hydrate resources, probing into the geological characteristics and distribution laws of marine gas hydrate resources in the South China Sea, and estimate the parameters for in-place resource evaluation, in which the volume method based on Monte Carlo probability was used to evaluate the gas hydrate potential resources in the South China Sea. The probability distribution ranges from 37.6 billion (with 90% probability) to 117.7 billion (with 10% probability) tons of oil equivalent, with an expected value of 74.4 billion tons of oil equivalent. The study results show that the gas hydrate resource density in the South China Sea is similar to that in the typical sea areas, and the estimated global resources are basically consistent with the assessment results at this stag; this shows that the South China Sea has great potential for gas hydrate resources. The research results can provide guidance for the evaluation of global climate change and the exploration and development of hydrate resources