Genome-Wide Analysis of mir-548 Gene Family Reveals Evolutionary and Functional Implications

mir-548 is a larger, poorly conserved primate-specific miRNA gene family. 69 human mir-548 genes located in almost all human chromosomes whose widespread distribution pattern implicates the evolutionary origin from transposable elements. Higher level of nucleotide divergence was detected between these human miRNA genes, which mainly derived from divergence of multicopy pre-miRNAs and homologous miRNA genes. Products of  mir-548, miR-548-5p, and miR-548-3p showed inconsistent evolutionary patterns, which partly contributed to larger genetic distances between pre-miRNAs. “Seed shifting” events could be detected among miR-548 sequences due to various 5′ ends. The events led to shift of seed sequences and target mRNAs, even generated to new target mRNAs. Additionally, the phenomenon of miRNA:miRNA interaction in the miRNA gene family was found. The potential interaction between miRNAs may be contributed to dynamic miRNA expression profiles by complementarily binding events to form miRNA:miRNA duplex with 5′-/3′-overhangs. The miRNA gene family had important roles in multiple biological processes, including signaling pathways and some cancers. The potential abundant roles and functional implication further led to the larger and poorly conserved gene family with genetic variation based on transposable elements. The evolutionary pattern of the primate-specific gene family might contribute to dynamic expression profiles and regulatory network

ROS-mediated TNF-α and MIP-2 gene expression in alveolar macrophages exposed to pine dust

BACKGROUND: Respiratory symptoms, impaired lung function, and asthma have been reported in workers exposed to wood dust in a number of epidemiological studies. The underlying pathomechanisms, however, are not well understood. Here, we studied the effects of dust from pine (PD) and heat-treated pine (HPD) on the release of reactive oxygen species (ROS) and inflammatory mediators in rat alveolar macrophages. METHODS: Tumour necrosis factor-alpha (TNF-α) and macrophage inflammatory protein-2 (MIP-2) protein release, TNF-α and MIP-2 mRNA expression, and generation of ROS were studied as end points after treatment of rat alveolar macrophages with PD or HPD. In a separate series of experiments, the antioxidants glutathione and N-acetyl-L-cysteine were included in combination with wood dust. To determine the endogenous oxidative and antioxidant capacity of wood dusts, electron spin resonance (ESR) spectroscopy was used. RESULTS: After 4 h incubation, both PD and HPD elicited a significantly (p < 0.05) increased mRNA expression of TNF-α and MIP-2 as well as a concentration-dependent release of TNF-α and MIP-2 protein. Interestingly, PD induced a significantly higher TNF-α and MIP-2 production than HPD. Moreover, a significantly increased ROS production was observed in alveolar macrophages exposed to both PD and HPD. In the presence of the antioxidants glutathione and N-acetyl-L-cysteine, the PD- and HPD-induced release of ROS, TNF-α, and MIP-2 was significantly reduced. Finally, electron spin resonance analyses demonstrated a higher endogenous antioxidant capacity of HPD compared to PD. Endotoxin was not present in either dust sample. CONCLUSION: These results indicate that pine dust is able to induce expression of TNF-α and MIP-2 in rat alveolar macrophages by a mechanism that is, at least in part, mediated by ROS

Bi-level dynamic scheduling architecture based on service unit digital twin agents

Pure reactive scheduling is one of the core technologies to solve the complex dynamic disturbance factors in real-time. The emergence of CPS, digital twin, cloud computing, big data and other new technologies based on the industrial Internet enables information acquisition and pure reactive scheduling more practical to some extent. However, how to build a new architecture to solve the problems which traditional dynamic scheduling methods cannot solve becomes a new research challenge. Therefore, this paper designs a new bi-level distributed dynamic workshop scheduling architecture, which is based on the workshop digital twin scheduling agent and multiple service unit digital twin scheduling agents. Within this architecture, scheduling a physical workshop is decomposed to the whole workshop scheduling in the first level and its service unit scheduling in the second level. On the first level, the whole workshop scheduling is executed by its virtual workshop coordination (scheduling) agent embedded with the workshop digital twin consisting of multi-service unit digital twins. On the second level, each service unit scheduling coordinated by the first level scheduling is executed in a distributed way by the corresponding service unit scheduling agent associated with its service unit digital twin. The benefits of the new architecture include (1) if a dynamic scheduling only requires a single service unit scheduling, it will then be performed in the corresponding service unit scheduling without involving other service units, which will make the scheduling locally, simply and robustly. (2) when a dynamic scheduling requires changes in multiple service units in a coordinated way, the first level scheduling will be executed and then coordinate the second level service unit scheduling accordingly. This divide-and-then-conquer strategy will make the scheduling easier and practical. The proposed architecture has been tested to illustrate its feasibility and practicality

Genipin Reverses HFD-Induced Liver Damage and Inhibits UCP2-Mediated Pyroptosis in Mice

Background/Aims: Liver damage is a typical manifestation of nonalcoholic fatty liver disease (NAFLD). It originates from excessive fat accumulation, leading to hepatocyte death, inflammation, and fibrosis. Nonalcoholic steatohepatitis (NASH) is a type of NAFLD with a prevalence of 49% in morbidly obese patients. Pyroptosis plays an important role in the development of NASH; thus, it is important to elucidate the effect of lipid accumulation on pyroptosis. Genipin (GNP), a natural water-soluble cross-linking agent, has hepatoprotective effects and decreases lipid accumulation in the liver; however, the mechanisms underlying these effects are unknown. Methods: In this study, qPCR and Western blot were used to examine pyroptotic gene expression in high-fat diet (HFD) induced obese mice and free fatty acids (FFAs) treated hepatocytes. At the same time, relative lactate dehydrogenase (LDH) release and Hoechst &#38; propidium iodide (PI) staining were done to verify cell death. To explore the molecular mechanism, cell transfection were constructed with siRNA or plasmid to obtain knockdown or overexpression hepatocytes. Results: We found that HFD-fed mice and FFAs-treated hepatocytes had obvious pyroptosis, and addition of GNP reversed liver damage and inhibited pyroptosis both in vitro and in vivo. Besides, UCP2 knockdown cells showed suppressed FFAs-mediated pyroptosis, as determined by decreased pyroptotic gene expression, reduced lactate dehydrogenase (LDH) release, and reduced cell death. Consistent with this, cells transfected with UCP2 had upregulated pyroptotic gene expression, increased LDH release, and increased cell death. Conclusion: GNP reverses HFD-induced liver damage and inhibits UCP2-mediated pyroptosis. Thus, GNP may serve as a potential therapeutic candidate for NAFLD

Comparison of Oxidative Properties, Light Absorbance, and Total and Elemental Mass Concentration of Ambient PM(2.5) Collected at 20 European Sites

OBJECTIVE: It has been proposed that the redox activity of particles may represent a major determinant of their toxicity. We measured the in vitro ability of ambient fine particles [particulate matter with aerodynamic diameters ≤2.5 μm (PM(2.5))] to form hydroxyl radicals ((•)OH) in an oxidant environment, as well as to deplete physiologic antioxidants (ascorbic acid, glutathione) in the naturally reducing environment of the respiratory tract lining fluid (RTLF). The objective was to examine how these toxicologically relevant measures were related to other PM characteristics, such as total and elemental mass concentration and light absorbance. DESIGN: Gravimetric PM(2.5) samples (n = 716) collected over 1 year from 20 centers participating in the European Community Respiratory Health Survey were available. Light absorbance of these filters was measured with reflectometry. PM suspensions were recovered from filters by vortexing and sonication before dilution to a standard concentration. The oxidative activity of these particle suspensions was then assessed by measuring their ability to generate (•)OH in the presence of hydrogen peroxide, using electron spin resonance and 5,5-dimethyl-1-pyrroline-N-oxide as spin trap, or by establishing their capacity to deplete antioxidants from a synthetic model of the RTLF. RESULTS AND CONCLUSION: PM oxidative activity varied significantly among European sampling sites. Correlations between oxidative activity and all other characteristics of PM were low, both within centers (temporal correlation) and across communities (annual mean). Thus, no single surrogate measure of PM redox activity could be identified. Because these novel measures are suggested to reflect crucial biologic mechanisms of PM, their use may be pertinent in epidemiologic studies. Therefore, it is important to define the appropriate methods to determine oxidative activity of PM

Cross-Mapping Events in miRNAs Reveal Potential miRNA-Mimics and Evolutionary Implications

MicroRNAs (miRNAs) have important roles in various biological processes. miRNA cross-mapping is a prevalent phenomenon where miRNA sequence originating from one genomic region is mapped to another location. To have a better understanding of this phenomenon in the human genome, we performed a detailed analysis in this paper using public miRNA high-throughput sequencing data and all known human miRNAs. We observed widespread cross-mapping events between miRNA precursors (pre-miRNAs), other non-coding RNAs (ncRNAs) and the opposite strands of pre-miRNAs by analyzing the high-throughput sequencing data. Computational analysis on all known human miRNAs also confirmed that many of them could be involved in cross-mapping events. The processing or decay of both ncRNAs and pre-miRNA opposite strand transcripts may contribute to miRNA enrichment, although some might be miRNA-mimics due to miRNA mis-annotation. Comparing to canonical miRNAs, miRNAs involved in cross-mapping events between pre-miRNAs and other ncRNAs normally had shorter lengths (17–19 nt), lower prediction scores and were classified as pseudo miRNA precursors. Notably, 4.9% of all human miRNAs could be accurately mapped to the opposite strands of pre-miRNAs, which showed that both strands of the same genomic region had the potential to produce mature miRNAs and simultaneously implied some potential miRNA precursors. We proposed that the cross-mapping events are more complex than we previously thought. Sequence similarity between other ncRNAs and pre-miRNAs and the specific stem-loop structures of pre-miRNAs may provide evolutionary implications

Adsorption de molécules organiques aromatiques à base de chalcogènure sur les surfaces métalliques et diélectriques par auto-assemblage et épitaxie par jets moléculaires

Dans cette thèse, on a étudié la formation de monocouches auto-assemblées de différentes molécules de chalcogénure et de films minces de semiconducteurs organiques. Leurs caractéristiques électroniques et structurelles ont été étudiées principalement par la spectroscopie de photoélectron à rayons X à base de rayonnement synchrotron, la spectroscopie d’adsorption de rayons X à proximité de seuil, la microscopie à force atomique et la diffraction d'électrons à faible énergie. En outre, les caractéristiques d'adsorption du sélénium et du soufre ont été étudiées comme complément à l'étude des adsorptions des molécules comportant des atomes de chalcogène. Le XPS à haute résolution a été utilisé pour enquêter sur les monocouches auto-assemblées de benzèneselénol et de sélénophène sur Cu (111). L'étude détaillée des pics caractéristiques des niveaux du coeur a démontré l'existence de différents sites d'absorption des molécules et aussi avec les mesures NEXAFS l'apparition du clivage de la liaison Se-C. Ces conclusions sont étayées par l'étude de l’adsorption de sélénium atomique montrant également différents sites d'absorption pour le sélénium atomique avec différents environnements chimiques basés sur une étude XPS haute résolution des spectres caractéristiques Se3d, Se3p et l'imagerie LEED. On a étudié les adsorptions de molécules de polythiophène (nT, n = 1-4, 6) ainsi que pour le α, ω-diquaterthiophène (DH4T) et le dihexylsexithiophène (DH6T) sur les films Au (111) et films de Au sur le mica. Les résultats indiquent que les pics XPS S2p ont des contributions de molécules intactes sur différents sites d'adsorption et des molécules cassées. Ces conclusions sont étayées par les calculs DFT existants. La dissociation spontanée apparaît dans une mesure variable dans différents cas, ce qui pourrait être lié à différentes morphologies de surface, à l'existence de défauts et à la réactivité différentes liés a ces défauts. Des films ultra-minces d'α-sexithiophène (6T) ont été déposés sur des surfaces planes de CaF2 (111) / Si (111) et sur des surfaces striées de CaF2 (110) / Si (001) par épitaxie par faisceau moléculaire. L'image AFM de 6T sur CaF2 (111) montre de grandes îles avec des terrasses plates sans préférence dans le plan, tandis que des îlots étroits et allongés suivant l'ondulation du substrat sont formés pour 6T sur CaF2 (110). Les spectres XPS et NEXAFS indiquent que les interactions entre 6T et les surfaces sont négligeables et que les molécules s'alignent avec leur long axe perpendiculaire aux surfaces pour les deux cas.In this thesis, formation of self-assembled monolayers of different chalcogenide molecules and organic semiconductor thin films was investigated. Their electronic and structural characteristics have been investigated primarily by synchrotron based X-ray photoelectron, near edge X-ray absorption fine structure spectroscopy, Atomic force microscopy and low energy electron diffraction. In addition, the adsorption characteristics of selenium and sulfur were studied as a complement to the study of adsorptions of chalcogen headgroup molecules. The high resolution XPS was employed to investigate the self assembled monolayers of benzeneselenol and selenophene on Cu(111). The detailed study of characteristic core level peaks demonstrated the existence of different absorption sites of the molecules and also along with NEXAFS measurements the occurrence of Se-C bond cleavage. These conclusions are supported by the study of atomic selenium adsorptions showing also different absorption sites for the atomic selenium with different chemical environments based on high resolution XPS study of characteristic Se3d, Se3p spectra and LEED imaging. The adsorptions of polythiophene molecules (nT, n=1-4, 6) as well as for α, ω-diquaterthiophene (DH4T) and dihexylsexithiophene (DH6T) on Au(111) and Au films grown on mica was studied. The results indicate that the XPS S2p peaks have contributions from intact molecules on different adsorption sites and broken molecules complemented. These conclusions are supported by existing DFT calculations. Spontaneous dissociation appears to a variable extent in different cases, which could be related to different surface morphologies, existence of defects and ensuing differences reactivity.α-Sexithiophene (6T) ultrathin films were grown on CaF2(111)/Si(111) planar surfaces and on CaF2(110)/Si(001) ridged surfaces by molecular beam epitaxy. The AFM image of 6T on CaF2(111) shows large islands with flat terraces without in-plane preference, while narrow and elongated islands following the substrate corrugation are formed for 6T on CaF2(110). XPS and NEXAFS spectra indicate that the interactions between 6T and surfaces are negligible, and the molecules align with their long axis perpendicular to the surfaces for both cases

Deep sequencing of small RNA repertoires in mice reveals metabolic disorders-associated hepatic miRNAs.

Obesity and associated metabolic disorders contribute importantly to the metabolic syndrome. On the other hand, microRNAs (miRNAs) are a class of small non-coding RNAs that repress target gene expression by inducing mRNA degradation and/or translation repression. Dysregulation of specific miRNAs in obesity may influence energy metabolism and cause insulin resistance, which leads to dyslipidemia, steatosis hepatis and type 2 diabetes. In the present study, we comprehensively analyzed and validated dysregulated miRNAs in ob/ob mouse liver, as well as miRNA groups based on miRNA gene cluster and gene family by using deep sequencing miRNA datasets. We found that over 13.8% of the total analyzed miRNAs were dysregulated, of which 37 miRNA species showed significantly differential expression. Further RT-qPCR analysis in some selected miRNAs validated the similar expression patterns observed in deep sequencing. Interestingly, we found that miRNA gene cluster and family always showed consistent dysregulation patterns in ob/ob mouse liver, although they had various enrichment levels. Functional enrichment analysis revealed the versatile physiological roles (over six signal pathways and five human diseases) of these miRNAs. Biological studies indicated that overexpression of miR-126 or inhibition of miR-24 in AML-12 cells attenuated free fatty acids-induced fat accumulation. Taken together, our data strongly suggest that obesity and metabolic disturbance are tightly associated with functional miRNAs. We also identified hepatic miRNA candidates serving as potential biomarkers for the diagnose of the metabolic syndrome