Non-coding RNAs identification and regulatory networks in pathogen-host interaction in the microsporidia congenital infection.

BACKGROUND: The interaction networks between coding and non-coding RNAs (ncRNAs) including long non-coding RNA (lncRNA), covalently closed circular RNA (circRNA) and miRNA are significant to elucidate molecular processes of biological activities and interactions between host and pathogen. Congenital infection caused by vertical transmission of microsporidia N. bombycis can result in severe economic losses in the silkworm-feeding industry. However, little is known about ncRNAs that take place in the microsporidia congenital infection. Here we conducted whole-transcriptome RNA-Seq analyses to identify ncRNAs and regulatory networks for both N. bombycis and host including silkworm embryos and larvae during the microsporidia congenital infection. RESULTS: A total of 4,171 mRNAs, 403 lncRNA, 62 circRNAs, and 284 miRNAs encoded by N. bombycis were identified, among which some differentially expressed genes formed cross-talk and are involved in N. bombycis proliferation and infection. For instance, a lncRNA/circRNA competing endogenous RNA (ceRNA) network including 18 lncRNAs, one circRNA, and 20 miRNAs was constructed to describe 14 key parasites genes regulation, such as polar tube protein 3 (PTP3), ricin-B-lectin, spore wall protein 4 (SWP4), and heat shock protein 90 (HSP90). Regarding host silkworm upon N. bombycis congenital infection, a total of 14,889 mRNAs, 3,038 lncRNAs, 19,039 circRNAs, and 3,413 miRNAs were predicted based on silkworm genome with many differentially expressed coding and non-coding genes during distinct developmental stages. Different species of RNAs form interacting network to modulate silkworm biological processes, such as growth, metamorphosis and immune responses. Furthermore, a lncRNA/circRNA ceRNA network consisting of 140 lncRNAs, five circRNA, and seven miRNAs are constructed hypothetically to describe eight key host genes regulation, such as Toll-6, Serpin-6, inducible nitric oxide synthase (iNOS) and Caspase-8. Notably, cross-species analyses indicate that parasite and host miRNAs play a vital role in pathogen-host interaction in the microsporidia congenital infection. CONCLUSION: This is the first comprehensive pan-transcriptome study inclusive of both N. bombycis and its host silkworm with a specific focus on the microsporidia congenital infection, and show that ncRNA-mediated regulation plays a vital role in the microsporidia congenital infection, which provides a new insight into understanding the basic biology of microsporidia and pathogen-host interaction.

PPAR γ/Nnat/NF-κB Axis Involved in Promoting Effects of Adiponectin on Preadipocyte Differentiation.

A previous study has demonstrated that adiponectin (APN) could promote preadipocyte differentiation, and the present study further explored its mechanism. 3T3-L1 cells were infected with adenovirus holding human adiponectin gene apM1 and mouse neuronatin (Nnat) shRNA and initiated differentiation while coculturing with mature adipocytes stimulated with LPS. After 8 days, preadipocyte differentiation was observed by Oil Red O staining. Real-time quantitative PCR was used to evaluate mRNA expression levels of monocyte chemoattractant protein-1 (MCP-1), interleukin- (IL-) 6, IL-8, and tumor necrosis factor α (TNF-α). The levels of reactive oxygen species (ROS), total antioxidant capacity (T-AOC), malondialdehyde (MDA), and superoxide dismutase (SOD) in 3T3-L1 cells were detected. Western blotting was done to quantify the protein expression levels of Nnat, peroxisome proliferator-activated receptor (PPAR) γ, p65, and inhibitor of nuclear factor κB (IκB) α. Results demonstrated that APN overexpression markedly increased preadipocyte differentiation; inhibited gene expression of MCP-1, IL-6, IL-8, and TNF-α; reduced ROS and MDA release; increased T-AOC and SOD levels; upregulated Nnat, PPAR γ, and IκB α protein expressions; and downregulated p65 protein expression under LPS stimulation. However, the effects of APN were markedly attenuated when Nnat expression was knocked down. Taken together, the present study provided evidences that the effects of APN on promoting preadipocyte differentiation under inflammatory conditions via anti-inflammation and antioxidative stress may be regulated by the PPAR γ/Nnat/NF-κB signaling pathway.

A bioinformatics analysis of the susceptibility genes in Stanford type A aortic dissection.

Background: The expression levels of long noncoding RNAs (lncRNAs) and mRNAs in human acute Stanford type A aortic dissecting aneurysm and normal active vascular tissues were compared using the array lncRNA/mRNA expression profile chip technology. Methods: The tissue samples of 5 patients who presented with Stanford type A aortic dissections and the normal ascending aorta tissues from 5 donor heart transplantation patients receiving surgical treatment in Ganzhou People's Hospital were collected. Hematoxylin and eosin (HE) staining were performed to investigate the structural features of the ascending aortic vascular tissue. Nanodropnd-100 was used to detect the surface level of RNA in 10 samples included in the experiment, to ensure that the quality of the standard was consistent with the core plate detection. NanoDrop ND-1000 was used to detect the RNA expression levels in 10 specimens included in the experiment to ensure that the quality of specimens satisfied the requirements of the microarray detection experiment. The Arraystar Human LncRNA/mRNAV3.0 expression profile chip (8×60K, Arraystar) was used to detect the expression levels of lncRNAs and mRNAs in the tissue samples. Results: A total of 29,198 lncRNAs and 22,959 mRNA target genes could be detected in the above tissue samples after the initial data were standardized and low-expression information was filtered. The data in the middle of the range of 50% value consistency was higher. The scatterplot results preliminarily suggested that there were large numbers of lncRNAs with increased and decreased expression in Stanford type A aortic dissection tissues compared with normal aortic tissues. The differentially expressed lncRNAs were enriched in BPs including apoptosis, nitric oxide synthesis, estradiol response, angiogenesis, inflammatory response, oxidative stress, and acute response; cell components (CCs) including cytoplasm, nucleus, cytoplasmic matrix, extracellular space, protein complex, and platelet α granule lumen; and MFs including protease binding, zinc ion binding, steroid compound binding, steroid hormone receptor activity, heme binding, protein kinase, cytokine, superoxide dismutase, and nitric oxide synthase activities. Conclusions: Gene ontology analysis demonstrated that many genes in Stanford type A aortic dissection were involved in cell biological functions, cell components, and molecular functions through upregulating and downregulating the levels of expression.

Prevalence and genotyping distribution of Enterocytozoon bieneusi in diarrheic pigs in Chongqing and Sichuan provinces, China.

The microsporidian fungal pathogen Enterocytozoon bieneusi is a unicellular parasite that infects humans and various animals, including pigs. Currently, there are few data on E. bieneusi infection a in diarrheic pigs in Chongqing and Sichuan Provinces, China. This study aims to determine the prevalence and genotype distribution of E. bieneusi in diarrheic pigs. In total, 514 fecal samples from diarrheic pigs were obtained from 14 large-scale farms in Chongqing and Sichuan Provinces (326 suckling pigs, 17 weaned pigs, 65 fattening pigs, and 106 sows). To identify the E. bieneusi genotypes, genomic DNA was isolated from the samples and tested by nested PCR, targeting the internal transcribed spacer region of the rRNA followed by DNA sequence analysis. The overall prevalence of E. bieneusi was 79.8% (410/514), with rates of 84.9% (90/106) in sows and 64.7% (11/17) in weaned pigs. We found 61 different genotypes, including seven known genotypes (E, F, CHG1, Peru8, CAF1, B, and BEB17) and 54 novel genotypes. These 54 new genotypes are variants of eight known genotypes (SDD2, A, B, HLJD-IV, PigSpEb1, O, JLD-I, and BEB17) based on their sequence similarities. Phylogenetically, all of the identified genotypes clustered with counterparts belonging to Group 1 and Group 2 of E. bieneusi. Therefore, we found a higher prevalence of E. bieneusi in sows than in preweaned and weaned pigs. These findings indicate that diarrheic pigs could be a potential reservoir host, which can contaminate the environment and be a source of microsporidia in humans and other animals.

Self-doping synthesis of trivalent Ni2O3 as a hole transport layer for high fill factor and efficient inverted perovskite solar cells.

Nickel oxide (NiOx) as a hole transport layer has been vastly investigated in perovskite solar cells (PSCs) due to the nature of p-type doping, highly transparent materials, and deep-lying valence bands. In this paper, a new phase based on trivalent Ni2O3 is synthesized by low temperature solution processing of mixed nickel (acetate/nitrate). In comparison, high-temperature solution-processing of divalent NiOx resulted in novel Ni2O3 thin films that display better consistency and superior energy compatibility with perovskite thin films. In this respect, high-performance perovskite solar cells are efficiently produced utilizing MA0.85FA0.15PbI0.9Cl0.1 perovskite with a power conversion efficiency (PCE) reaching 17.89% and negligible hysteresis comparable to 14.37% for NiOx. The Ni2O3-based PSCs reported the highest fill factor (FF) (82.66%) compared to that of divalent NiOx (67.53%). Different characterization studies and analyses supply proof of improved film quality, increased transport and extraction of charges, and suppressed charge recombination. Meanwhile, the device exhibits low hysteresis compared to sol-gel-processed NiOx.

Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves.

Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3' splice sites (23.75%), alternative 5' splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.

Coordinated Optical Matching of a Texture Interface Made from Demixing Blended Polymers for High-Performance Inverted Perovskite Solar Cells.

The continuing increase of the efficiency of perovskite solar cells has pushed the internal quantum efficiency approaching 100%, which means the light-to-carrier and then the following carrier transportation and extraction are no longer limiting factors in photoelectric conversion efficiency of perovskite solar cells. However, the optimal efficiency is still far lower than the Shockley-Queisser efficiency limit, especially for those inverted perovskite solar cells, indicating that a significant fraction of light does not transmit into the active perovskite layer to be absorbed there. Here, a planar inverted perovskite solar cell (ITO/PTAA/perovskite/PC61BM/bathocuproine (BCP)/Ag) is chosen as an example, and we show that its external quantum efficiency (EQE) can be significantly improved by simply texturing the poly[bis (4-phenyl)(2,4,6-trimethylphenyl)amine] (PTAA) layer. By washing the film prepared from a mixed polymer solution of PTAA and polystyrene (PS), a textured PTAA/perovskite interface is introduced on the light-input side of perovskite to inhibit internal optical reflection. The reduction of optical loss by this simple texture method increases the EQE and then the photocurrent of the ITO/PTAA/perovskite/PC61BM/BCP/Ag device with the magnitude of about 10%. At the same time, this textured PTAA benefits the band edge absorption in this planar solar cell. The large increase of the short-circuit current together with the increase of fill factor pushes the efficiency of this inverted perovskite solar cell from 18.3% up to an efficiency over 20.8%. By using an antireflection coating on glass to let more light into the device, the efficiency is further improved to 21.6%, further demonstrating the importance of light management in perovskite solar cells.

Efficient and Stable Planar n-i-p Perovskite Solar Cells with Negligible Hysteresis through Solution-Processed Cu2 O Nanocubes as a Low-Cost Hole-Transport Material.

Organic-inorganic halide perovskite solar cells (PSCs) have reached certified efficiencies of over 23 % with expensive organic hole-transporting materials. However, the use of an inorganic hole-transport layer (HTL) remains crucial as it would reduce cost combined with higher mobility and stability. In this direction, the application of Cu2 O as the top layer in PSCs is still complicated owing to the difficulty of solution processing. Herein, a solution-processing method is reported for preparing Cu2 O nanocubes as a p-type HTL in regular structure (n-i-p) PSCs. The controlled synthesis of Cu2 O nanocubes in a size range of 60-80 nm is achieved without using any surfactants, which are usually toxic and tricky to remove. The new structure of these Cu2 O nanocubes enhances the carrier mobility with preferable energy alignment to the perovskite layer and superb stability. The PSCs based on these Cu2 O nanocubes HTMs could achieve an efficiency exceeding 17 % with high stability, whereas organic P3HT-based PSCs display an efficiency of 15.59 % with a poorer running stability. This indicates that Cu2 O nanocubes are a promising HTM for efficient and stable PSCs.

Functional analysis of the mRNA profile of neutrophil gelatinase­associated lipocalin overexpression in esophageal squamous cell carcinoma using multiple bioinformatic tools.

Neutrophil gelatinase-associated lipocalin (NGAL) is a member of the lipocalin superfamily; dysregulated expression of NGAL has been observed in several benign and malignant diseases. In the present study, differentially expressed genes, in comparison with those of control cells, in the mRNA expression profile of EC109 esophageal squamous cell carcinoma (ESCC) cells following NGAL overexpression were analyzed by multiple bioinformatic tools for a comprehensive understanding. A total of 29 gene ontology (GO) terms associated with immune function, chromatin structure and gene transcription were identified among the differentially expressed genes (DEGs) in NGAL overexpressing cells. In addition to the detected GO categories, the results from the functional annotation chart revealed that the differentially expressed genes were also associated with 101 functional annotation category terms. A total of 59 subpathways associated locally with the differentially expressed genes were identified by subpathway analysis, a markedly greater total that detected by traditional pathway enrichment analysis only. Promoter analysis indicated that the potential transcription factors Snail, deltaEF1, Mycn, Arnt, MNB1A, PBF, E74A, Ubx, SPI1 and GATA2 were unique to the downregulated DEG promoters, while bZIP910, ZNF42 and SOX9 were unique for the upregulated DEG promoters. In conclusion, the understanding of the role of NGAL overexpression in ESCC has been improved through the present bioinformatic analysis.

Biochemical properties and comparative pharmacology of a coagulant from Deinagkistrodon acutus snake venom.

A number of snake venom thrombin-like enzymes (TLEs) have already been characterized. Some TLEs play significant roles in vessel injury hemostasis. A novel TLE (Agacutase) was purified from Deinagkistrodon acutus snake venom by the means of Sephadex G-75, DEAE-Sepharose FF, and Sephadex G-25 column chromatography. Structural analysis indicated that Agacutase is a single-chain glycoprotein with a molecular mass of 31,084 Da, isoelectric point of 4.38, optimal activity at 37 °C and pH 6.6, sugar content of 7.6%. Its N-terminal 44 amino acid sequence was determined to be VIGGNECDTNEHRFLAAFFTSRPWIFQCAGTLIHEEWVLAAAHC, showing maximum identity of 80% with that of Dav-X protease. The Agacutase-induced clotting activity was not influenced by heparin, hirudin, or Dextran 40, but activated by Ca(2+) and inhibited by PMSF or lactose, which suggests that Agacutase is a serine protease and the coagulation activity is independent of Thrombin. Agacutase with arginine esterase activity specifically cleaves the α-chain of fibrinogen. Agacutase iv (0.03-0.12 U/kg) shortened 16-68% of the rabbit blood clotting time. No significant influence was indicated on platelet, Factor II and XIII, or fibrinolytic system. It converts fibrinogen into the soluble fibrin that accelerates hemostasis at wound. Pharmacological comparison showed the hemostatic effect of Agacutase lasted 24h while Reptilase did 8h. Its maximum tolerated, abnormal toxicity, allergic, and hemorrhagin doses were 80 U/kg, 1 U, 2 U, and 50 U, respectively, whereas those of Reptilase or Agacutin were 35 U/kg, 0.25 U, 0.25 U, and 0.2 U, respectively. The results indicated that Agacutase may be a predominant coagulant.

Comprehensive bioinformation analysis of the mRNA profile of fascin knockdown in esophageal squamous cell carcinoma.

BACKGROUND: Fascin, an actin-bundling protein forming actin bundles including filopodia and stress fibers, is overexpressed in multiple human epithelial cancers including esophageal squamous cell carcinoma (ESCC). Previously we conducted a microarray experiment to analyze fascin knockdown by RNAi in ESCC. METHOD: In this study, the differentially expressed genes from mRNA expression profilomg of fascin knockdown were analyzed by multiple bioinformatics methods for a comprehensive understanding of the role of fascin. RESULTS: Gene Ontology enrichment found terms associated with cytoskeleton organization, including cell adhesion, actin filament binding and actin cytoskeleton, which might be related to fascin function. Except GO categories, the differentially expressed genes were annotated by 45 functional categories from the Functional Annotation Chart of DAVID. Subpathway analysis showed thirty-nine pathways were disturbed by the differentially expressed genes, providing more detailed information than traditional pathway enrichment analysis. Two subpathways derivated from regulation of the actin cytoskeleton were shown. Promoter analysis results indicated distinguishing sequence patterns and transcription factors in response to the co-expression of downregulated or upregulated differentially expressed genes. MNB1A, c-ETS, GATA2 and Prrx2 potentially regulate the transcription of the downregulated gene set, while Arnt-Ahr, ZNF42, Ubx and TCF11-MafG might co-regulate the upregulated genes. CONCLUSIONS: This multiple bioinformatic analysis helps provide a comprehensive understanding of the roles of fascin after its knockdown in ESCC.