Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes

<p>Abstract</p> <p>Background</p> <p>The true water bugs are grouped in infraorder Nepomorpha (Insecta: Hemiptera: Heteroptera) and are of great economic importance. The phylogenetic relationships within Nepomorpha and the taxonomic hierarchies of Pleoidea and Aphelocheiroidea are uncertain. Most of the previous studies were based on morphological characters without algorithmic assessment. In the latest study, the molecular markers employed in phylogenetic analyses were partial sequences of 16S rDNA and 18S rDNA with a total length about 1 kb. Up to now, no mitochondrial genome of the true water bugs has been sequenced, which is one of the largest data sets that could be compared across animal taxa. In this study we analyzed the unresolved problems in Nepomorpha using evidence from mitochondrial genomes.</p> <p>Results</p> <p>Nine mitochondrial genomes of Nepomorpha and five of other hemipterans were sequenced. These mitochondrial genomes contain the commonly found 37 genes without gene rearrangements. Based on the nucleotide sequences of mt-genomes, Pleoidea is not a member of the Nepomorpha and Aphelocheiroidea should be grouped back into Naucoroidea. Phylogenetic relationships among the superfamilies of Nepomorpha were resolved robustly.</p> <p>Conclusion</p> <p>The mt-genome is an effective data source for resolving intraordinal phylogenetic problems at the superfamily level within Heteroptera. The mitochondrial genomes of the true water bugs are typical insect mt-genomes. Based on the nucleotide sequences of the mt-genomes, we propose the Pleoidea to be a separate heteropteran infraorder. The infraorder Nepomorpha consists of five superfamilies with the relationships (Corixoidea + ((Naucoroidea + Notonectoidea) + (Ochteroidea + Nepoidea))).</p

Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)

<p>Abstract</p> <p>Background</p> <p>Nucleotide sequences and the gene arrangements of mitochondrial genomes are effective tools for resolving phylogenetic problems. Hemipteroid insects are known to possess highly reorganized mitochondrial genomes, but in the suborder Heteroptera (Insecta: Hemiptera), there was only one complete mitochondrial genome sequenced without gene rearrangement and the phylogeny of infraorder Pentatomomorpha in Heteroptera was still uncertain.</p> <p>Results</p> <p>Fifteen mitochondrial genomes of the suborder Heteroptera were sequenced. Gene rearrangements were found as follows: 1) <it>tRNA-I </it>and <it>tRNA-Q </it>switched positions in Aradidae, 2) <it>tRNA-T </it>and <it>tRNA-P </it>switched positions in Largidae and Pyrrhocoridae. Two recombination events were found in Alydidae and Malcidae. The other mt-genomes were organized in the same way as observed in <it>Drosophila yakuba</it>. The phylogenetic analyses of infraorder Pentatomomorpha based on the nucleotide sequence raised the hypothesis of (Aradoidea + (Pentatomoidea + (Pyrrhocoroidea + (Lygaeoidea + Coreoidea)))). The rearrangement of <it>tRNA-T </it>and <it>tRNA-P </it>also linked Largidae and Pyrrhocoridae together. Furthermore, the conserved sequence block in the unusual intergenic spacers between <it>tRNA-H </it>and <it>ND4 </it>favored the monophyly of Lygaeoidea. Tetranucleotide ATCA was inferred to be the initiation codon of <it>ND2 </it>in Cydnidae. No correlation was found between the rates of nucleotide substitution and gene rearrangement. CG content was significantly correlated with the nucleotide substitution rate of each gene. For ND1, there was a positive correlation (<it>P </it>< 0.01) between amino acids variations and hydrophobicity, but a negative correlation (<it>P </it>< 0.01) for ND6. No conserved sequence was found among the control regions and these regions were not always the most AT-rich region of the mt-genome.</p> <p>Conclusion</p> <p>Heteropteran insects are extremely complex groups worthy of further study because of the unusual tetranucleotide initiation codon and their great mt-genomic diversity, including gene rearrangements and recombinations. The mt-genome is a powerful molecular marker for resolving phylogeny at the level of the superfamily and family. Gene rearrangements were not correlated with nucleotide substitution rates. CG content variation caused the different evolutionary patterns among genes. For ND1, in many polar or nonpolar regions the specific identity of the amino acid residues might be more important than maintaining the polarity of these regions, while the opposite is true for ND6. Most sequences of the control regions did not appear to be important for regulatory functions. Finally, we suggest that the term "AT-rich regions" should not be used.</p

CISD1 Is a Breast Cancer Prognostic Biomarker Associated with Diabetes Mellitus

Women with diabetes mellitus are believed to have increased risk of developing breast cancer and lower life expectancies. This study aims to depict the association between the CISD1, the co-expressed genes, and diabetes mellitus to offer potential therapeutic targets for further mechanical research. The TCGA-BRCA RNAseq data is acquired. All the data and analyzed using R packages and web-based bioinformatics tools. CISD1 gene expression was evaluated between tumor bulk and adjacent tissue. Immune cell infiltration evaluation was performed. CISD1 expressed significantly higher in tumor tissue than that of the normal tissue, indicating poor overall survival rates. High expression level of CISD1 in tumor shows less pDC and NK cells penetration. There are 138 genes shared between CISD1 co-expressed gene pool in BRCA and diabetes mellitus related genes using “diabetes” as the term for text mining. These shared genes enrich in “cell cycle” and other pathways. MCODE analysis demonstrates that p53-independent G1/S DNA damage checkpoint, p53-independent DNA damage response, and ubiquitin mediated degradation of phosphorylated cdc25A are top-ranked than other terms. CISD1 and co-expressed genes, especially shared ones with diabetes mellitus, can be the focused genes considered when addressing clinical problems in breast cancer with a diabetes mellitus background

Identification of Key Pathways and Genes in Advanced Coronary Atherosclerosis Using Bioinformatics Analysis

Background. Coronary artery atherosclerosis is a chronic inflammatory disease. This study aimed to identify the key changes of gene expression between early and advanced carotid atherosclerotic plaque in human. Methods. Gene expression dataset GSE28829 was downloaded from Gene Expression Omnibus (GEO), including 16 advanced and 13 early stage atherosclerotic plaque samples from human carotid. Differentially expressed genes (DEGs) were analyzed. Results. 42,450 genes were obtained from the dataset. Top 100 up- and downregulated DEGs were listed. Functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) identification were performed. The result of functional and pathway enrichment analysis indicted that the immune system process played a critical role in the progression of carotid atherosclerotic plaque. Protein-protein interaction (PPI) networks were performed either. Top 10 hub genes were identified from PPI network and top 6 modules were inferred. These genes were mainly involved in chemokine signaling pathway, cell cycle, B cell receptor signaling pathway, focal adhesion, and regulation of actin cytoskeleton. Conclusion. The present study indicated that analysis of DEGs would make a deeper understanding of the molecular mechanisms of atherosclerosis development and they might be used as molecular targets and diagnostic biomarkers for the treatment of atherosclerosis

Toxic Effects of Acute Benzo[a]pyrene Exposure on Blood Clam Tegillarca granosa and Its Potential Coping Mechanism

Spilled petroleum pollution caused by seaborne oil transportation is a major marine environmental problem in the world. Petroleum pollutants contain significant amounts of low-molecular-weight alkanes and aromatics that induce toxic effects once taken up by marine organisms. Polycyclic aromatic hydrocarbons (PAHs) are a class of organic compounds with the most significant toxic environmental effects. As bivalves, which have a strong enrichment and tolerance capacity for PAHs in water, are widely distributed and easy to obtain, they are often used as model organisms for monitoring and evaluating offshore marine pollution. The blood clam (Tegillarca granosa), a bivalve with high economic value, is widely distributed in mudflats along the coast of Zhejiang Province. Blood clams have characteristics of benthic life, making them more likely to be exposed to petroleum pollutants. At present, there are few studies on the toxic effects of PAH exposure on blood clams. Herein, we chose benzo[a]pyrene (BaP), a typical PAH congener, as a contaminant, and investigated the toxic effects of acute BaP exposure on blood clams and their potential coping mechanisms.Blood clams required for the experiment were collected from Dongji Island and acclimated for a week in the laboratory. After acclimation, several healthy blood clams were randomly divided into the artificial sea water (ASW) (control group), dimethyl sulfoxide (DMSO) (solvent control group, 0.01% VDMSO/VASW), 10 μg/L BaP exposure group, and 100 μg/L BaP exposure groups based on the previous studies of our research group combined with the literature. Each group was set up with three replicates, each containing 40 individuals. The experiment lasted 96 h, and separate glass tanks were used to place all individuals in each replicate. One blood clam was randomly selected from each replicate of each concentration group at 0, 24, 48, and 96 h of exposure. After dissection on ice, the digestive gland was immediately separated using sterile forceps and scissors and stored at –80℃. The paraffin section was then used to observe the lesions of the digestive gland. A colorimetric assay was used to determine the activities of antioxidant enzymes and key enzymes involved in neurotransmission at different time points. The cell damage degree was also determined by measuring the levels of 8-hydroxy-2′- deoxyguanosine (8-OHdG) and malondialdehyde (MDA). In addition, enzyme-linked immunosorbent assays were used to determine DNA methylation levels. Finally, we measured the relative mRNA expression of antioxidant enzymes and performed a correlation analysis.Results showed prominent hemocyte infiltration and necrotic areas in the digestive gland of the blood clam after a total of 96 h of exposure to 10 and 100 μg/L BaP, indicating inflammation. The sloughing of digestive cells from the inner wall of the digestive tubule led to atrophy. Increased oxidative stress was indicated by elevated MDA and 8-OHdG content, leading to damage at the cellular level, such as lipid peroxidation and oxidative DNA damage. The activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and glutathione-S-transferase (GST), increased significantly 24 h post-exposure. This phenomenon further indicated that BaP exposure induced oxidative stress in the blood clam, with the antioxidant defense system actively regulating BaP-induced oxidative stress. The activities of two key neurotransmitter enzymes, acetylcholinesterase and acetylcholine transferase, were significantly reduced, indicating that the stress caused by BaP may induce neurotoxicity in the blood clam. In addition, we analyzed the changes in DNA methylation levels and gene expression of antioxidant enzymes in the blood clam under acute BaP exposure, finding that the DNA methylation levels were significantly decreased compared to pre-exposure, while the mRNA expression of SOD, CAT, and GST was significantly increased. Correlation analysis showed a negative correlation between DNA methylation and the gene expression of antioxidant enzymes, implying that blood clams may activate the antioxidant systems to fight against BaP toxicity by reducing DNA methylation levels. In conclusion, acute BaP exposure exerts a significant toxic effect on the blood clam, primarily characterized by histological damage, oxidative stress, and neurotoxicity. Moreover, changes in DNA methylation levels in the blood clam may be involved in the regulatory process of BaP toxic effects. This study is expected to provide new ideas for the in-depth exploration of the intrinsic regulatory mechanisms of bivalves in response to petroleum pollutant stress, and will be beneficial for resource conservation of the blood clam under the threat of petroleum pollution

An Interleukin-17 Isoform from Thick Shell Mussel <i>Mytilus coruscus</i> Serves as a Mediator of Inflammatory Response

The inflammatory cytokine interleukin-17 (IL17) plays an important role in innate immunity by binding to its receptors (IL17Rs) to activate immune defense signals. To date, information on members of the IL17 family is still very limited in molluscan species. Here, a novel member of the IL17 family was identified and characterized from thick shell mussel Mytilus coruscus, and this gene was designated as McIL17-1 by predicting structural domains and phylogenetic analysis. McIL17-1 transcripts existed in all examined tissues with high expression levels in gills, hemocytes and digestive glands. After the stimuli of different pathogen associated molecular patterns (PAMPs) for 72 h, transcriptional expression of McIL17-1 was significantly upregulated, except for poly I:C stimulation. Cytoplasm localization of McIL17-1 was shown in HEK293T cells by fluorescence microscopy. Further, in vivo and in vitro assays were performed to evaluate the potential function of McIL17-1 played in immune response. McIL17-1 was either knocked down or overexpressed in vivo through RNA inference (RNAi) and recombinant protein injection, respectively. With the infection of living Vibrio alginolyticus, a high mortality rate was exhibited in the McIL17-1 overexpressed group compared to the control group, while a lower mortality rate was observed in the McIL17-1 knocked down group than control group. In vitro, the flow cytometric analysis showed that the apoptosis rate of McIL17-1 inhibited hemocytes was significantly lower than that of the control group after lipopolysaccharide stimulation. These results collectively suggested that the newly identified IL17 isoform is involved in the inflammatory response to bacterial infection in M. coruscus

Danlou Recipe promotes cholesterol efflux in macrophages RAW264.7 and reverses cholesterol transport in mice with hyperlipidemia induced by P407

Abstract Introduction Liver X Receptor (LXR) agonists could attenuate the development of atherosclerosis but bring excess lipid accumulation in the liver. Danlou Recipe was believed to be a benefit for improving the lipid profile. Thus, it is unclear whether Danlou Recipe could attenuate hyperlipidemia without excess lipid accumulated in the liver of mice. This study aimed to clarify if Danlou Recipe could alleviate the progression of hyperlipidemia in mice without extra lipids accumulated in the liver. Methods Male murine macrophage RAW264.7 cells and murine peritoneal macrophages were used for the in vitro experiments. Cellular cholesterol efflux was determined using the fluorescent cholesterol labeling method. Those genes involved in lipid metabolism were evaluated by qRT‐PCR and western blotting respectively. In vivo, a mouse model of hyperlipidemia induced by P407 was used to figure out the effect of Danlou Recipe on reverse cholesterol transport (RCT) and hyperlipidemia. Ethanol extract of Danlou tablet (EEDL) was prepared by extracting the whole powder of Danlou Prescription from ethanol, and the chemical composition was analyzed by ultra-performance liquid chromatography (UPLC). Results EEDL inhibits the formation of RAW264.7 macrophage-derived foam cells, and promotes ABCA1/apoA1 conducted cholesterol efflux in RAW264.7 macrophages and mouse peritoneal macrophages. In the P407-induced hyperlipidemia mouse model, oral administration of EEDL can promote RCT in vivo and improve fatty liver induced by a high-fat diet. Consistent with the findings in vitro, EEDL promotes RCT by upregulating the LXR activities. Conclusion Our results demonstrate that EEDL has the potential for targeting RCT/LXR in the treatment of lipid metabolism disorders to be developed as a safe and effective therapy

Salidroside simultaneously reduces de novo lipogenesis and cholesterol biosynthesis to attenuate atherosclerosis in mice

Salidroside is a kind of phenylethanoid glycoside and widespread in the plants from Rhodiola and Ligustrum species. Our previous study has reported that salidroside can prevent atherosclerosis progression by ameliorating glyerolipid and glycerophospholipid metabolism in apoE-deficient (apoE−/−) mice. However, its effect on neutral lipids and underlying mechanism remains largely unclear. Here we investigated the molecular mechanism of salidroside action from the perspective of metabolic regulation by integrating metabonomics and transcriptomics pattern. The results showed that salidroside significantly reduced cholesterols, esterified cholesterols, fatty acids, unsaturated fatty acids and triacylclycerols biosynthesis in liver through down-regulating the genes expressions of sterol regulatory element-binding proteins (Srebf1 and Srebf2). The expressions of SREBPs targeted and downstream genes, such as the encoding genes of fatty acid synthase (Fasn), glycerol-3-phosphate acyltransferase (Gpam), stearoyl-CoA desaturase (Scd), 3-hydroxy-3-methylglutaryl-CoA reductase (Hmgcr), and proprotein convertase subtilisin/kexin type 9 (Pcsk9), were also inhibited after salidroside administration. ATP citrate lyase gene (Acly) that encodes an important enzyme producing acetyl-CoA for cholesterol and fatty acid biosynthesis significantly decreased after treatment as well. Moreover, one of ketone body products, 3-hydroxybutyrate, was significantly up-regulated in drug-treated group, indicating that fatty acid degradation was accelerated by salidroside at the same time. Our findings identify salidroside as a regulator of lipid homeostasis in atherosclerotic mice, suggesting its potential to be an alternative medicine for lowering the risks of atherosclerosis-related diseases