Cmah deficiency may lead to age-related hearing loss by influencing miRNA-PPAR mediated signaling pathway

Background Previous evidence has indicated CMP-Neu5Ac hydroxylase (Cmah) disruption inducesaging-related hearing loss (AHL). However, its function mechanisms remain unclear. This study was to explore the mechanisms of AHL by using microarray analysis in the Cmah deficiency animal model. Methods Microarray dataset GSE70659 was available from the Gene Expression Omnibus database, including cochlear tissues from wild-type and Cmah-null C57BL/6J mice with old age (12 months, n = 3). Differentially expressed genes (DEGs) were identified using the Linear Models for Microarray data method and a protein–protein interaction (PPI) network was constructed using data from the Search Tool for the Retrieval of Interacting Genes database followed by module analysis. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery. The upstream miRNAs and potential small-molecule drugs were predicted by miRwalk2.0 and Connectivity Map, respectively. Results A total of 799 DEGs (449 upregulated and 350 downregulated) were identified. Upregulated DEGs were involved in Cell adhesion molecules (ICAM1, intercellular adhesion molecule 1) and tumor necrosis factor (TNF) signaling pathway (FOS, FBJ osteosarcoma oncogene; ICAM1), while downregulated DEGs participated in PPAR signaling pathway (PPARG, peroxisome proliferator-activated receptor gamma). A PPI network was constructed, in which FOS, ICAM1 and PPARG were ranked as hub genes and PPARG was a transcription factor to regulate other target genes (ICAM1, FOS). Function analysis of two significant modules further demonstrated PPAR signaling pathway was especially important. Furthermore, mmu-miR-130b-3p, mmu-miR-27a-3p, mmu-miR-27b-3p and mmu-miR-721 were predicted to regulate PPARG. Topiramate were speculated to be a potential small-molecule drug to reverse DEGs in AHL. Conclusions PPAR mediated signaling pathway may be an important mechanism for AHL. Downregulation of the above miRNAs and use of topiramate may be potential treatment strategies for ALH by upregulating PPARG

The odontoblastic differentiation of dental mesenchymal stem cells: molecular regulation mechanism and related genetic syndromes

Dental mesenchymal stem cells (DMSCs) are multipotent progenitor cells that can differentiate into multiple lineages including odontoblasts, osteoblasts, chondrocytes, neural cells, myocytes, cardiomyocytes, adipocytes, endothelial cells, melanocytes, and hepatocytes. Odontoblastic differentiation of DMSCs is pivotal in dentinogenesis, a delicate and dynamic process regulated at the molecular level by signaling pathways, transcription factors, and posttranscriptional and epigenetic regulation. Mutations or dysregulation of related genes may contribute to genetic diseases with dentin defects caused by impaired odontoblastic differentiation, including tricho-dento-osseous (TDO) syndrome, X-linked hypophosphatemic rickets (XLH), Raine syndrome (RS), hypophosphatasia (HPP), Schimke immuno-osseous dysplasia (SIOD), and Elsahy-Waters syndrome (EWS). Herein, recent progress in the molecular regulation of the odontoblastic differentiation of DMSCs is summarized. In addition, genetic syndromes associated with disorders of odontoblastic differentiation of DMSCs are discussed. An improved understanding of the molecular regulation and related genetic syndromes may help clinicians better understand the etiology and pathogenesis of dentin lesions in systematic diseases and identify novel treatment targets

A review of eco-friendly functional road materials

Extensive studies on traditional and novel engineering materials and the increasing demands by growing traffic have led to tremendous changes of the function of roads. Roads, as an important part of the human living environment, have evolved from structures that were designed and built for passing vehicles, to ecological assets with significant economic importance. In addition to structural stability and durability, functions such as noise reduction, urban heat island mitigation, de-icing and exhaust gas absorption, are also expected. This study focused on state-of-the-art research on the performance, applications and challenges of six environment-friendly functional road materials, namely the permeable asphalt concrete, noise-reducing pavement materials, low heat-absorbing pavement materials, exhaust gas-decomposing pavement materials, de-icing pavement materials, and energy harvesting pavement materials. With this study, we aim to provide references to the latest relevant literatures of the design and development of environment-friendly functional pavement, and promote innovation in materials science and pavement design principles. For this purpose, this review compiled extensive knowledge in modern road construction and related disciplines, in order to promote the development of modern pavement engineering technologies

A continuous fluorescence assay for the characterization of Nudix hydrolases.

The common substrate structure for the functionally diverse Nudix protein superfamily is nucleotide-diphosphate-X, where X is a large variety of leaving groups. The substrate specificity is known for less than 1% of the 29,400 known members. Most activities result in the release of an inorganic phosphate ion or of a product bearing a terminal phosphate moiety. Reactions have typically been monitored by a modification of the discontinuous Fiske-SubbaRow assay, which is relatively insensitive and slow. We report here the development of a continuous fluorescence assay that enables the rapid and accurate determination of substrate specificities in a 96-well format. We used this novel assay to confirm the reported substrate characterizations of MutT and NudD of Escherichia coli and to characterize DR_1025 of Deinococcus radiodurans and MM_0920 of Methanosarcina mazei. Novel findings enabled by the new assay include the following. First, in addition to the well-characterized hydrolysis of 8-oxo-dGTP at the α-β position, MutT cleaves at the β-γ phosphate bond at a rate of 3% of that recorded for hydrolysis at the α-β position. Second, MutT also catalyzes the hydrolysis of 5-methyl-dCTP. Third, 8-oxo-dGTP was observed to be the best substrate for DR_1025 of the 41 compounds screened

A continuous fluorescence assay for the characterization of Nudix hydrolases.

The common substrate structure for the functionally diverse Nudix protein superfamily is nucleotide-diphosphate-X, where X is a large variety of leaving groups. The substrate specificity is known for less than 1% of the 29,400 known members. Most activities result in the release of an inorganic phosphate ion or of a product bearing a terminal phosphate moiety. Reactions have typically been monitored by a modification of the discontinuous Fiske-SubbaRow assay, which is relatively insensitive and slow. We report here the development of a continuous fluorescence assay that enables the rapid and accurate determination of substrate specificities in a 96-well format. We used this novel assay to confirm the reported substrate characterizations of MutT and NudD of Escherichia coli and to characterize DR_1025 of Deinococcus radiodurans and MM_0920 of Methanosarcina mazei. Novel findings enabled by the new assay include the following. First, in addition to the well-characterized hydrolysis of 8-oxo-dGTP at the α-β position, MutT cleaves at the β-γ phosphate bond at a rate of 3% of that recorded for hydrolysis at the α-β position. Second, MutT also catalyzes the hydrolysis of 5-methyl-dCTP. Third, 8-oxo-dGTP was observed to be the best substrate for DR_1025 of the 41 compounds screened

Resolution Enhancement of Spherical Wave-Based Holographic Stereogram with Large Depth Range

The resolution-priority holographic stereogram uses spherical waves focusing on the central depth plane (CDP) to reconstruct 3D images. The image resolution near the CDP can be easily enhanced by modifying three parameters: the capturing depth, the pixel size of elemental image and the focal length of lens array. However, the depth range may decrease as a result. In this paper, the resolution characteristics were analyzed in a geometrical imaging model, and three corresponding methods were proposed: a numerical method was proposed to find the proper capturing depth; a partial aperture filtering technique was proposed after reducing pixel size; the moving array lenslet technique was introduced after increasing focal length and partial aperture filtering. Each method can enhance resolution within the total depth range. Simulation and optical experiments were performed to verify the proposed methods

Compositions and Sources of Organic Aerosol in PM_2.5 in Nanjing in China

Organic aerosols are harmful to the environment because of their impact on air quality and visibility. They have serious effects not only on living beings and ecosystems because of their biological toxicity, but they also have an indirect effect on regional climate change as cloud condensation nuclei and radiation force. Many measures have been applied to decrease air pollution. Although the air quality has greatly improved, the standard of the World Health Organization (WHO) is far from being met at present. In this study, fine particulates were collected in Nanjing throughout 2019, and high-performance liquid chromatography–electrospray ion–mass spectrometry/mass spectrometry (HPLC-ESI-MS/MS) was carried out to determine 14 organic acids, 10 nitrated phenols, 1 aldehyde, and 1 ketone in aerosol samples. In this study, we further determined the changes in the pollutants in Nanjing in recent years compared to previous studies and characterized more kinds of species in the air. We found that different kinds of nitrated phenols showed similar trends of being abundant in winter and substituted in spring, autumn, and summer. 4-Nitrophenol was the most abundant species (2.83 ng m−3) among the nitrated phenols. p-Coumaric acid presented the highest level in summer with an average concentration of 1.55 ng m−3, indicating that grass burning was significant in summer, possibly due to wheat stalk and perennial ryegrass burning. The positive matrix fraction (PMF) model was applied to identify the sources of aerosols in Nanjing, including coal burning, grass burning, softwood burning, hardwood burning, anthropogenic secondary organic aerosols (SOAs), and biogenic SOAs. Coal burning and softwood burning contributed much more to the total determined species with values of 20.3% and 18.2%, respectively. Anthropogenic SOAs contributed 17.1%, and hardwood burning contributed 16.7%. The contribution of biogenic SOAs was 15%, and the grass-burning source contribution was the lowest, with 12.6%. With consideration of the large contribution from anthropogenic combustion activities, more strict measures are required to reduce emission pollutants in the future

The evolution of function within the Nudix homology clan

ABSTRACT The Nudix homology clan encompasses over 80,000 protein domains from all three domains of life, defined by homology to each other. Proteins with a domain from this clan fall into four general functional classes: pyrophosphohydrolases, isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch‐specific adenine glycosylases (A/G‐specific adenine glycosylases), and nonenzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally‐based annotations. We manually constructed a structure‐guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix homology domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix homology clan revealed general monophyly with regard to function and a few instances of probable homoplasy. Proteins 2017; 85:775–811. © 2016 Wiley Periodicals, Inc

Identification of Key Modules, Hub Genes, and Noncoding RNAs in Chronic Rhinosinusitis with Nasal Polyps by Weighted Gene Coexpression Network Analysis

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic inflammatory disease with relatively easy recurrence. However, the precise molecular mechanisms of this disease are poorly known. Based on gene sequencing data obtained from the Gene Expression Omnibus (GEO) database, we constructed coexpression networks by weighted gene coexpression network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The core gene of pathogenesis, CRSwNP, was screened by protein-protein interaction data (PPI) from the HPRD database. Unsupervised clustering was applied to screen hub genes related to the phenotype of CRSwNP. Blue and turquoise modules were found to be most significantly related to the pathogenicity of CRSwNP. Functional enrichment analysis showed that cell proliferation in the blue modules, the apoptotic process in the turquoise module, and the cancer pathway in both modules were mostly significantly correlated with the development of CRSwNP. The noncoding RNAs (long noncoding RNA and microRNA) and the top 10 core genes in each module were found to be associated with the pathogenesis of CRSwNP. A total of nine hub genes were identified to be related to the CRSwNP phenotype. By qRT-PCR analysis, AKT1, CDH1, PIK3R1, CBL, LRP1, MALAT1, and XIST were proven to be associated with the pathogenesis of CRSwNP. AGR2, FAM3D, PIP, DSE, and TMC were identified to be related to the CRSwNP phenotype. Further exploration of these genes will reveal more important information about the mechanisms of CRSwNP