Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives

Abstract Background: Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. Findings: We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression–based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. Conclusions: These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments

Effects of Carbon Emission Trading on Companies’ Market Value: Evidence from Listed Companies in China

Emissions trading schemes (ETSs) are effective measures that facilitate economic growth and carbon mitigation, especially for developing countries such as China. These schemes can further affect the cash flow, production, and investment decisions of regulated companies. However, few empirical studies have explored how ETSs promote companies’ market value. We systematically evaluate the influence of the carbon emission trading (CET) policy on companies’ market value and explore the influential mechanism. We use the data of listed companies from the Chinese stock “A” markets and employ the difference-in-difference method to account for the unobserved cause of the CET policy regarding companies’ market value. Robust benchmark regression results reveal that the CET policy promotes companies’ market value significantly. The mechanism analysis reveals that the CET policy can improve the market value of listed companies by influencing the carbon price, innovative activities, and carbon disclosure. The results of the heterogeneity analysis show that the CET policy’s impact on companies’ market value is heterogeneous in terms of marketization degree, industry, firm ownership, and different regions. We suggest that the carbon pricing mechanism, degree of market perfection, carbon disclosure policy, and carbon finance should be optimized to improve the efficiency of ETSs

A case of SLE with COVID-19 and multiple infections

The coronavirus disease 2019 (COVID-19) has become a global pandemic, which is induced by infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients with systemic lupus erythematosus (SLE) are susceptible to infections due to the chronic use of immunosuppressive drugs and the autoimmune disorders. Now we report a case of SLE infected with SARS-CoV-2, influenza A virus and Mycoplasma pneumoniae concurrently. The patient used hydroxychloroquine and prednisone chronically to control the SLE. After infection of SARS-CoV-2, she was given higher dose of prednisone than before and the same dosage of hydroxychloroquine. Besides, some empirical treatments such as antiviral, antibiotic and immunity regulating therapies were also given. The patient finally recovered from COVID-19. This case indicated that hydroxychloroquine may not be able to fully protect SLE patient form SARS-CoV-2. Intravenous immunoglobulin therapies and increased dose of corticosteroids might be adoptable for patient with both COVID-19 and SLE. Physicians should consider SARS-CoV-2 virus test when SLE patient presented with suspected infection or SLE flare under the epidemic of COVID-19

Polyculture Affects the Growth, Antioxidant Status, Nutrient Content, and Flavor of Chinese Mitten Crabs (<i>Eriocheir sinensis</i>) and Largemouth Bass (<i>Micropterus salmoides</i>)

Chinese mitten crabs (Eriocheir sinensis) and largemouth bass (Micropterus salmoides) are popular with consumers in China. In recent years, the polyculture of these two species has received more attention, but little is known about how their interactions affect their commercially important traits. In this study, we set up an E. sinensis monoculture group (EM), a M. salmoides monoculture group (MM), and a polyculture group containing both species (EP) and compared the growth parameters, antioxidant statuses, nutritional compositions, and flavor qualities of crabs and fish between the different culture modes. Growth parameters in male crabs and largemouth bass were significantly higher in the EP group than in the EM and MM groups, respectively. Crabs in the EM and EP groups did not differ significantly in malondialdehyde content or glutathione peroxidase activity, regardless of the sampling time, which suggests that crabs in these groups had similar antioxidant and immunity capacities. Compared to the MM group, the activities of superoxide dismutase and catalase of largemouth bass in the EP group were higher, indicating the superior antioxidant capacity of fish in the polyculture mode. Alkaline phosphatase and acid phosphatase activities of both crabs and largemouth bass fluctuated with time in all groups, indicating their important roles in maintaining the health of these cultured species. The amino acid and fatty acid contents of edible tissues were similar between the EM and EP groups and the MM and EP groups, suggesting comparable flavor and quality of edible tissues in crabs and largemouth bass between culture modes. This study provides theoretical support for the polyculture of Chinese mitten crabs and largemouth bass

Oxidant-Free Electrochemical Direct Oxidative Benzyl Alcohols to Benzyl Aldehydes Using Three-Dimensional Printing PPAR Polyoxometalate

The oxidation of benzyl alcohols is an important reaction in organic synthesis. Traditional methods for benzyl alcohol oxidation have not been widely utilized due to the use of significant amounts of precious metals and environmentally unfriendly reagents. In recent years, electrocatalytic oxidation has gained significant attention, particularly electrochemical anodic oxidation, which offers a sustainable alternative for oxidation without the need for external oxidants or reducing agents. Here, a copper monosubstituted phosphotungstate-based polyacrylate resins (Cu-LPOMs@PPAR) catalyst has been fabricated with immobilization and recyclability using 3D printing technology that can be successfully applied in the electrocatalytic oxidation of benzyl alcohol to benzaldehyde, achieving atom economy and reducing pollution. In this protocol, we obtain benzaldehyde in good yields with excellent functional group toleration under metal-free and oxidant-free conditions. This strategy could provide a new avenue for heterogeneous catalysts in application for enhancing the efficiency and selectivity of electrocatalytic oxidation processes

Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs

Lung tissue plays an important role in the respiratory system of mammals after birth. Early lung development includes six key stages, of which the saccular stage spans the pre- and neonatal periods and prepares the distal lung for alveolarization and gas-exchange. However, little is known about the changes in gene expression between fetal and neonatal lungs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in the lung tissue of fetal and neonatal piglets. A total of 19,310 lncRNAs and 14,579 mRNAs were identified and substantially expressed. Furthermore, 3248 mRNAs were significantly (FDR-adjusted p value &le; 0.05, FDR: False Discovery Rate) differentially expressed and were mainly enriched in categories related to cell proliferation, immune response, hypoxia response, and mitochondrial activation. For example, CCNA2, an important gene involved in the cell cycle and DNA replication, was upregulated in neonatal lungs. We also identified 452 significantly (FDR-adjusted p value &le; 0.05) differentially expressed lncRNAs, which might function in cell proliferation, mitochondrial activation, and immune response, similar to the differentially expressed mRNAs. These results suggest that differentially expressed mRNAs and lncRNAs might co-regulate lung development in early postnatal pigs. Notably, the TU64359 lncRNA might promote distal lung development by up-regulating the heparin-binding epidermal growth factor-like (HB-EGF) expression. Our research provides basic lung development datasets and will accelerate clinical researches of newborn lung diseases with pig models

Hemicastration induced spermatogenesis-related DNA methylation and gene expression changes in mice testis

Objective Hemicastration is a unilateral orchiectomy to remove an injured testis, which can induce hormonal changes and compensatory hypertrophy of the remaining testis, and may influence spermatogenesis. However, the underlying molecular mechanisms are poorly understood. Here, we investigated the impact of hemicastration on remaining testicular function. Methods Prepubertal mice (age 24 days) were hemicastrated, and their growth was monitored until they reached physical maturity (age 72 days). Subsequently, we determined testis DNA methylation patterns using reduced representation bisulfite sequencing of normal and hemicastrated mice. Moreover, we profiled the testicular gene expression patterns by RNA sequencing (RNA-seq) to examine whether methylation changes affected gene expression in hemicastrated mice. Results Hemicastration did not significantly affect growth or testosterone (p>0.05) compared with control. The genome-wide DNA methylation pattern of remaining testis suggested that substantial genes harbored differentially methylated regions (1,139) in gene bodies, which were enriched in process of protein binding and cell adhesion. Moreover, RNA-seq results indicated that 46 differentially expressed genes (DEGs) involved in meiotic cell cycle, synaptonemal complex assembly and spermatogenesis were upregulated in the hemicastration group, while 197 DEGs were downregulated, which were related to arachidonic acid metabolism. Integrative analysis revealed that proteasome 26S subunit ATPase 3 interacting protein gene, which encodes a protein crucial for homologous recombination in spermatocytes, exhibited promoter hypomethylation and higher expression level in hemicastrated mice. Conclusion Global profiling of DNA methylation and gene expression demonstrated that hemicastration-induced compensatory response maintained normal growth and testicular morphological structure in mice

Analysis of mRNA and lncRNA Expression Profiles of Breast Muscle during Pigeon (<i>Columba</i> <i>livia</i>) Development

The breast muscle is essential for flight and determines the meat yield and quality of the meat type in pigeons. At present, studies about long non-coding RNA (lncRNA) expression profiles in skeletal muscles across the postnatal development of pigeons have not been reported. Here, we used transcriptome sequencing to examine the White-King pigeon breast muscle at four different ages (1 day, 14 days, 28 days, and 2 years old). We identified 12,918 mRNAs and 9158 lncRNAs (5492 known lncRNAs and 3666 novel lncRNAs) in the breast muscle, and 7352 mRNAs and 4494 lncRNAs were differentially expressed in the process of development. We found that highly expressed mRNAs were mainly related to cell-basic and muscle-specific functions. Differential expression and time-series analysis showed that differentially expressed genes were primarily associated with muscle development and functions, blood vessel development, cell cycle, and energy metabolism. To further predict the possible role of lncRNAs, we also conducted the WGCNA and trans/cis analyses. We found that differentially expressed lncRNAs such as lncRNA-LOC102093252, lncRNA-G12653, lncRNA-LOC110357465, lncRNA-G14790, and lncRNA-LOC110360188 might respectively target UBE2B, Pax7, AGTR2, HDAC1, Sox8 and participate in the development of the muscle. Our study provides a valuable resource for studying the lncRNAs and mRNAs of pigeon muscles and for improving the understanding of molecular mechanisms in muscle development

DataSheet1_Landscape of immune infiltration in entorhinal cortex of patients with Alzheimerʼs disease.PDF

Alzheimer’s disease (AD) is one of the most common neurodegenerative diseases and manifests as progressive memory loss and cognitive dysfunction. Neuroinflammation plays an important role in the development of Alzheimer’s disease and anti-inflammatory drugs reduce the risk of the disease. However, the immune microenvironment in the brains of patients with Alzheimer’s disease remains unclear, and the mechanisms by which anti-inflammatory drugs improve Alzheimer’s disease have not been clearly elucidated. This study aimed to provide an overview of the immune cell composition in the entorhinal cortex of patients with Alzheimer’s disease based on the transcriptomes and signature genes of different immune cells and to explore potential therapeutic targets based on the relevance of drug targets. Transcriptomics data from the entorhinal cortex tissue, derived from GSE118553, were used to support our study. We compared the immune-related differentially expressed genes (irDEGs) between patients and controls by using the limma R package. The difference in immune cell composition between patients and controls was detected via the xCell algorithm based on the marker genes in immune cells. The correlation between marker genes and immune cells and the interaction between genes and drug targets were evaluated to explore potential therapeutic target genes and drugs. There were 81 irDEGs between patients and controls that participated in several immune-related pathways. xCell analysis showed that most lymphocyte scores decreased in Alzheimer’s disease, including CD4+ Tc, CD4+ Te, Th1, natural killer (NK), natural killer T (NKT), pro-B cells, eosinophils, and regulatory T cells, except for Th2 cells. In contrast, most myeloid cell scores increased in patients, except in dendritic cells. They included basophils, mast cells, plasma cells, and macrophages. Correlation analysis suggested that 37 genes were associated with these cells involved in innate immunity, of which eight genes were drug targets. Taken together, these results delineate the profile of the immune components of the entorhinal cortex in Alzheimer’s diseases, providing a new perspective on the development and treatment of Alzheimer’s disease.</p