Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs.

BACKGROUND: Asthma is a heterogeneous disease characterized by chronic airway inflammation. Long non-coding RNA can act as competing endogenous RNA to mRNA, and play significant role in many diseases. However, there is little known about the profiles of long non-coding RNA and the long non-coding RNA related competing endogenous RNA network in asthma. In current study, we aimed to explore the long non-coding RNA-microRNA-mRNA competing endogenous RNA network in asthma and their potential implications for therapy and prognosis. METHODS: Asthma-related gene expression profiles were downloaded from the Gene Expression Omnibus database, re-annotated with these genes and identified for asthma-associated differentially expressed mRNAs and long non-coding RNAs. The long non-coding RNA-miRNA interaction data and mRNA-miRNA interaction data were downloaded using the starBase database to construct a long non-coding RNA-miRNA-mRNA global competing endogenous RNA network and extract asthma-related differentially expressed competing endogenous RNA network. Finally, functional enrichment analysis and drug repositioning of asthma-associated differentially expressed competing endogenous RNA networks were performed to further identify key long non-coding RNAs and potential therapeutics associated with asthma. RESULTS: This study constructed an asthma-associated competing endogenous RNA network, determined 5 key long non-coding RNAs (MALAT1, MIR17HG, CASC2, MAGI2-AS3, DAPK1-IT1) and identified 8 potential new drugs (Tamoxifen, Ruxolitinib, Tretinoin, Quercetin, Dasatinib, Levocarnitine, Niflumic Acid, Glyburide). CONCLUSIONS: The results suggested that long non-coding RNA played an important role in asthma, and these novel long non-coding RNAs could be potential therapeutic target and prognostic biomarkers. At the same time, potential new drugs for asthma treatment have been discovered through drug repositioning techniques, providing a new direction for the treatment of asthma.

Corticosteroid therapy in pneumonia from swine-origin influenza A (H1N1) in China.

The first three cases of confirmed infection with the virus in China were documented between May 10 and May 15, 2009. Although the clinical characteristics of the H1N1 pneumonia were described in clinical reports, the therapy has few been described. Therefore, we report our experiences of 53 cases of the H1N1 pneumonia with treatment. We describe clinical characteristic of 53 patients who were hospitalized for laboratory-confirmed H1N1 pneumonia at the 2nd Clinical College of Harbin Medical University. In addition, we measure the role of corticosteroid, mechanical ventilation, and non-corticosteroid antiviral therapy in the management of pneumonia patients with novel H1N1 infection. Real-time reverse-transcriptase-polymerase chain (RT-PCR) testing was used to confirm infection. The outcome of therapy was compared in scores of PaO2 and CT. The data was statistical analyzed by the Shapiro-Wilk, anova, Student-Newman-Keuls Test, and Kruskal-Wallis Test. The most common symptoms were dyspnea. In moderate ill patients, the changes in the increased PaO2 were lower in the non-corticosteroid antiviral therapy group than in the combination of corticosteroid and non-corticosteroid antiviral therapy after 5 days' therapy. The therapy protocol of non-corticosteriod + mechanical ventilation played important role in the recovery of severe ill patients.

MLL1, a H3K4 methyltransferase, regulates the TNFα-stimulated activation of genes downstream of NF-κB.

Genes of the mixed lineage leukemia (MLL) family regulate transcription by methylating histone H3K4. Six members of the MLL family exist in humans, including SETD1A, SETD1B and MLL1-MLL4. Each of them plays non-redundant roles in development and disease genesis. MLL1 regulates the cell cycle and the oscillation of circadian gene expression. Its fusion proteins are involved in leukemogenesis. Here, we studied the role of MLL1 in innate immunity and found it selectively regulates the activation of genes downstream of NF-κB mediated by tumor necrosis factor (TNFα) and lipopolysaccharide (LPS). Real-time PCR and genome-wide gene expression profile analysis proved that the deficiency of MLL1 reduced the expression of a group of genes downstream of nuclear factor κB (NF-κB). However, the activation of NF-κB itself was not affected. The MLL1 complex is found both in the nucleus and cytoplasm and is associated with NF-κB. CHIP assays proved that the translocation of MLL1 to chromatin was dependent on NF-κB. Our results suggest that MLL1 is recruited to its target genes by activated NF-κB and regulates their transcription.

Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing.

MicroRNAs (miRNAs) play key regulatory roles in various biological processes and diseases. A comprehensive analysis of large scale small RNA sequencing data (smRNA-seq) will be very helpful to explore tissue or disease specific miRNA markers and uncover miRNA variants. Here, we systematically analyzed 410 human smRNA-seq datasets, which samples are from 24 tissue/disease/cell lines. We tested the mapping strategies and found that it was necessary to make multiple-round mappings with different mismatch parameters. miRNA expression profiles revealed that on average ∼70% of known miRNAs were expressed at low level or not expressed (RPM < 1) in a sample and only ∼9% of known miRNAs were relatively highly expressed (RPM > 100). About 30% known miRNAs were not expressed in all of our used samples. The miRNA expression profiles were compiled into an online database (HMED, http://bioinfo.life.hust.edu.cn/smallRNA/). Dozens of tissue/disease specific miRNAs, disease/control dysregulated miRNAs and miRNAs with arm switching events were discovered. Further, we identified some highly confident editing sites including 24 A-to-I sites and 23 C-to-U sites. About half of them were widespread miRNA editing sites in different tissues. We characterized that the 2 types of editing sites have different features with regard to location, editing level and frequency. Our analyses for expression profiles, specific miRNA markers, arm switching, and editing sites, may provide valuable information for further studies of miRNA function and biomarker finding.

Hydrazone-linked covalent organic framework functionalized with cysteine as a fluorescence sensor and Exploration of paper chip for p-nitrophenol detection.

The large use and emission of p-nitrophenol (p-NP) seriously pollute the environment and endanger human health. In this work, a hydrazone-linked fluorescent covalent organic framework (BATHz-COF) was simply synthesized at room temperature and covalently linked N-acetyl-L-cysteine (NALC) via the "thiol-ene" click reaction, where carboxyl groups were introduced to improve dispersion and fluorescence intensity. As a rapid, good selectivity and reusability fluorescence sensor, the obtained COF-NALC has been used for quantitative analysis of p-NP predicated on the internal filtering effect (IFE). Under optimal conditions, COF-NALC enabled quantitative detection of p-NP with a linear range of 5-50 µM and the detection limit was 1.46 µM. The application of COF-NALC to the detection of p-NP in river water samples was successful, and the satisfactory recoveries were 98.0%-109.3%. Furthermore, the fluorescent COF paper chips constructed by in situ growth were combined with a smartphone to build a visual platform for the quick and real-time detection of p-NP, providing an excellent illustration for the development of intelligent fluorescence sensing in environmental analysis.

The zona incerta modulates spontaneous spike-wave discharges in the rat.

The contribution of the zona incerta (ZI) of the thalamus on spike-wave discharges (SWDs) was investigated. Chronic recordings of bilateral cortices, bilateral vibrissa muscle, and unilateral ZI were performed in Long-Evans rats to examine the functional role of SWDs. Rhythmic ZI activity appeared at the beginning of SWD and was accompanied by higher-oscillation frequencies and larger spike magnitudes. Bilateral lidocaine injections into the mystacial pads led to a decreased oscillation frequency of SWDs, but the phenomenon of ZI-related spike magnitude enhancement was preserved. Moreover, 800-Hz ZI microstimulation terminates most of the SWDs and whisker twitching (WT; >80%). In contrast, 200-Hz ZI microstimulation selectively stops WTs but not SWDs. Stimulation of the thalamic ventroposteriomedial nucleus showed no obvious effect on terminating SWDs. A unilateral ZI lesion resulted in a significant reduction of 7- to 12-Hz power of both the ipsilateral cortical and contralateral vibrissae muscle activities during SWDs. Intraincertal microinfusion of muscimol showed a significant inhibition on SWDs. Our present data suggest that the ZI actively modulates the SWD magnitude and WT behavior.

CADgene: a comprehensive database for coronary artery disease genes.

Coronary artery disease (CAD) is a complex, multifactorial disease and a leading cause of mortality world wide. Over the past decades, great efforts have been made to elucidate the underlying genetic basis of CAD and massive data have been accumulated. To integrate these data together and to provide a useful resource for researchers, we developed the CADgene, a comprehensive database for CAD genes. We manually extracted CAD-related evidence for more than 300 candidate genes for CAD from over 1300 publications of genetic studies. We classified these candidate genes into 12 functional categories based on their roles in CAD. For each gene, we extracted detailed information from related studies (e.g. the size of case-control, population, SNP, odds ratio, P-value, etc.) and made useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein-protein interactions and others. Besides the statistical number of studies for each gene, CADgene also provides tools to search and show the most frequently studied candidate genes. In addition, CADgene provides cumulative data from 11 publications of CAD-related genome-wide association studies. CADgene has a user-friendly web interface with multiple browse and search functions. It is freely available at http://www.bioguo.org/CADgene/.

Acupuncture effect on dumping syndrome in esophagus cancer patients with feeding jejunostomy: A study protocol for a single blind randomized control trial.

INTRODUCTION: Esophagus cancer patients are at risk for malnourishment. Feeding jejunostomy is used in advanced esophagus cancer patients in order to support and supplement the patients' nutrition needs. In dumping syndrome, the food is rapidly introduced into the intestine at a rate that is faster than normal, it is associated with both digestive system and vasoactive symptoms. Dumping syndrome has an association with both esophagus cancer patients and feeding jejunostomy. In the mid and long term, dumping syndrome is an important issue that contributes to the risk of malnourishment in advanced esophagus cancer patients. In recent studies, acupuncture was effective in regulating digestive symptoms. Acupuncture is considered to be a safe intervention, that was previously shown to be effective in treating digestive-related symptoms. METHODS: Sixty advanced esophageal cancer patients post-feeding jejunostomy will be divided into 2 equal groups, an intervention group (n = 30) and a control group (n = 30). Patients in the intervention group will receive acupuncture using the following acupoints: ST36 (Zusanli), ST37 (Shangjuxu), ST39 (Xiajuxu), PC6 (Neiguan), LI4 (Hegu), and Liv 3 (Taichung). Patients in the control group will receive shallow acupuncture on 12 non-acupoints (sham points), 1 cm from the above mention points. Patients and assessors will be blind to trial allocation. Both groups will receive acupuncture twice a week for 6 weeks. The main outcome measurements are: body weight, BMI, Sigstad's score, and the Arts' dumping questionnaire. DISCUSSION: There are no previous studies that have examined the use of acupuncture on patients with dumping syndrome. This single-blind randomized control trial will investigate the effect of acupuncture on dumping syndrome in advanced esophagus cancer patients with feeding jejunostomy. The results will determine if verum acupuncture can affect dumping syndrome and prevent weight loss.

Involvement of the Cav3.2 T-type calcium channel in thalamic neuron discharge patterns.

BACKGROUND: Mice that have defects in their low-threshold T-type calcium channel (T-channel) genes show altered pain behaviors. The changes in the ratio of nociceptive neurons and the burst firing property of reticular thalamic (RT) and ventroposterior (VP) neurons in Cav3.2 knockout (KO) mice were studied to test the involvement of thalamic T-channel and burst firing activity in pain function. RESULTS: Under pentobarbital or urethane anesthesia, the patterns of tonic and burst firings were recorded in functionally characterized RT and VPL neurons of Cav3.2 KO mice. Many RT neurons were nociceptive (64% under pentobarbital anesthesia and 50% under urethane anesthesia). Compared to their wild-type (WT) controls, fewer nociceptive RT neurons were found in Cav3.2 KO mice. Both nociceptive and tactile RT neurons showed fewer bursts in Cav3.2 KO mice. Within a burst, RT neurons of Cav3.2 KO mice had a lower spike frequency and less-prominent accelerando-decelerando change. In contrast, VP neurons of Cav3.2 KO mice showed a higher ratio of bursts and a higher discharge rate within a burst than those of the WT control. In addition, the long-lasting tonic firing episodes in RT neurons of the Cav3.2 KO had less stereotypic regularity than their counterparts in WT mice. CONCLUSIONS: RT might be important in nociception of the mouse. In addition, we showed an important role of Cav3.2 subtype of T-channel in RT burst firing pattern. The decreased occurrence and slowing of the bursts in RT neurons might cause the increased VP bursts. These changes would be factors contributing to alternation of pain behavior in the Cav3.2 KO mice.

The protective effect of quercetin on retinal inflammation in mice: the involvement of tumor necrosis factor/nuclear factor-κB signaling pathways.

Quercetin is a natural flavonoid that occurs in fruits and vegetables. Retinal inflammation is an important cause of vision loss. This study was aimed to analyze the effects of oral administration of quercetin on retinal inflammation. Transgenic mice, carrying nuclear factor-κB (NF-κB)-driven luciferase genes, were injected with 1 mg per kg body weight of lipopolysaccharide (LPS). Various amounts (1, 10, and 100 mg per kg body weight) of quercetin were orally given to mice. LPS-induced retinal inflammation was evaluated by bioluminescence imaging and histological examination 4 hours later. RNA-Seq analysis of gene expression profiles was performed to explain the mechanisms of quercetin on eye inflammation. Our data showed that LPS enhanced luminescent signals on ocular tissues, while LPS-induced luminescence intensities were significantly suppressed by quercetin by 73.61 ± 21.74%. LPS significantly increased the thickness of retinal tissues by 1.52 ± 0.37 fold, in comparison with the mock, while quercetin reduced the LPS-induced retinal thickness and decreased the accumulation of infiltrating granulocytes. Biological pathway analysis showed that tumor necrosis factor (TNF), cytokine, and NF-κB signaling pathways were involved in the anti-inflammatory mechanisms of quercetin. Immunohistochemical staining further showed that quercetin reduced the activation of NF-κB, the expression of interleukin-1ß and TNF-α, and the infiltration of granulocytes in retinal tissues. In conclusion, this is the first study reporting the effects and mechanisms of orally administered quercetin against LPS-induced retinal inflammation in mice. Due to its safety, our study suggested that supplementation of quercetin has beneficial effects on the eyes.

Oral Administration of Vanillin Improves Imiquimod-Induced Psoriatic Skin Inflammation in Mice.

Vanillin is one of the most widely used flavoring products worldwide. Psoriasis is a chronic inflammatory skin disorder. The interleukin-23 (IL-23)/interleukin-17 (IL-17) axis plays a critical role in psoriasis. Here, we analyzed the effect of vanillin on imiquimod (IMQ)-induced psoriatic skin inflammation in mice. Mice were treated topically with IMQ on the back skin and orally with various amounts of vanillin for 7 consecutive days. Vanillin significantly improved IMQ-induced histopathological changes of skin in a dose-dependent manner. The thickness and number of cell layers of epidermis were reduced by 29 ± 14.4 and 27.8 ± 11%, respectively, in mice given 100 mg/kg of vanillin. A microarray showed that a total of 9042 IMQ-upregulated genes were downregulated by vanillin, and the biological pathways involved in the immune system and metabolism were significantly altered by vanillin. The upregulated expressions of IL-23, IL-17A, and IL-17F genes were suppressed by vanillin, with fold changes of -3.07 ± 0.08, -2.06 ± 0.21, and -1.62 ± 0.21, respectively. Moreover, vanillin significantly decreased both the amounts of IL-17A and IL-23 and the infiltration of immune cells in the skin tissues of IMQ-treated mice. In conclusion, our findings suggested that vanillin was an effective bioactive compound against psoriatic skin inflammation. Moreover, the downregulation of IL-23 and IL-17 expression suggested that vanillin was a novel regulator of the IL-23/IL-17 axis.

Integration of transcriptome, proteome and metabolism data reveals the alkaloids biosynthesis in Macleaya cordata and Macleaya microcarpa.

BACKGROUND: The Macleaya spp., including Macleaya cordata and Macleaya microcarpa, are traditional anti-virus, inflammation eliminating, and insecticide herb medicines for their isoquinoline alkaloids. They are also known as the basis of the popular natural animal food addictive in Europe. However, few studies especially at genomics level were conducted on them. Hence, we performed the Macleaya spp. transcriptome and integrated it with iTRAQ proteome analysis in order to identify potential genes involved in alkaloids biosynthesis. METHODOLOGY AND PRINCIPAL FINDINGS: We elaborately designed the transcriptome, proteome and metabolism profiling for 10 samples of both species to explore their alkaloids biosynthesis. From the transcriptome data, we obtained 69367 and 78255 unigenes for M. cordata and M. microcarpa, in which about two thirds of them were similar to sequences in public databases. By metabolism profiling, reverse patterns for alkaloids sanguinarine, chelerythrine, protopine, and allocryptopine were observed in different organs of two species. We characterized the expressions of enzymes in alkaloid biosynthesis pathways. We also identified more than 1000 proteins from iTRAQ proteome data. Our results strongly suggest that the root maybe the organ for major alkaloids biosynthesis of Macleaya spp. Except for biosynthesis, the alkaloids storage and transport were also important for their accumulation. The ultrastructure of laticifers by SEM helps us to prove the alkaloids maybe accumulated in the mature roots. CONCLUSIONS/SIGNIFICANCE: To our knowledge this is the first study to elucidate the genetic makeup of Macleaya spp. This work provides clues to the identification of the potential modulate genes involved in alkaloids biosynthesis in Macleaya spp., and sheds light on researches for non-model medicinal plants by integrating different high-throughput technologies.

A simple method for fabricating microwire tetrode with sufficient rigidity and integrity without a heat-fusing process.

Heat-fusing is a common process for fabricating microwire tetrodes. However, it is time-consuming, and the high-temperature treatment can easily cause the insulation of the microwire to overheat leading to short circuits. We herein provide a simple, fast method to fabricate microwire tetrodes without the heat-fusion process. By increasing the twisting density, we were able to fabricate tetrodes with good rigidity and integrity. This kind of tetrode showed good recording quality, penetrated the brain surface easily, and remained intact after chronic implantation. This method requires only general laboratory tools and is relatively simple even for inexperienced workers.

Relation between activities of the cortex and vibrissae muscles during high-voltage rhythmic spike discharges in rats.

Paroxysmal 5- to 12-Hz high-voltage rhythmic spike (HVRS) activities, which are accompanied by whisker twitching (WT), are found in Long Evans rats, but the function of these HVRS activities is still debated. In four major functional hypotheses of HVRS discharges, i.e., alpha tremor, attention/mu rhythm, idling/mu rhythm, and absence seizure, the first two hypotheses emphasize WT behavior in HVRS bouts. Whisker movement is primarily determined by activation of intrinsic and extrinsic muscles. To clarify the role of WT in HVRS activities, simultaneous recording of the activities from the cortex and intrinsic/extrinsic and neck muscles were performed. Most HVRS bouts (68.8%) revealed no time-locked WT behavior in a 2-h recording session. In addition, WT primarily arose from active protraction due to activation of intrinsic muscles followed by passive retraction. A small portion of WT resulted from activation of both vibrissae muscles with dynamic frequency-dependent phase shifts. Onset of the rhythmic vibrissae EMG significantly lagged behind HVRS onset, and the mean duration of vibrissae muscle activity was one-third to a one-half of a HVRS bout. Moreover, a greater number of HVRS bouts were associated with a longer HVRS duration and higher oscillation frequency. Oscillation frequencies of HVRS activities without WT behavior were significantly lower than those with WT. Under peripheral sensory/motor blockade by xylocaine injection, oscillation frequencies of HVRS bouts significantly decreased, but no remarkable changes in the number or duration of HVRS bouts were observed. Compared with vibrissa muscle activity during WT and exploratory whisking, the duration of muscular activity in each cycle was apparently longer during whisking bouts. Based on these results, overemphasis of the role of WT on HVRS activities might not be appropriate. Instead, HVRS discharges may be associated with absence seizure or idling state. In addition, peripheral inputs, including WT, may elevate the oscillation frequency of HVRS bouts. Moreover, different muscular controls may exist between WT and whisking.