Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder

BACKGROUND Major depressive disorder(MDD)is a common and serious mental illness.Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing.Recently,noncoding RNAs(ncRNAs)were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence;however,the interplay among RNA species,including protein-coding RNAs and ncRNAs,in MDD remains unclear.AIM To investigate the RNA expression datasets downloaded from a public database and construct a network based on differentially expressed long noncoding RNA(lncRNAs),microRNAs(miRNAs),and mRNAs between MDD and controls.METHODS Gene expression data were searched in NCBI Gene Expression Omnibus using the search term“major depressive disorder.”Six array datasets from humans were related to the search term:GSE19738,GSE32280,GSE38206,GSE52790,GSE76826,and GSE81152.These datasets were processed for initial assessment and subjected to quality control and differential expression analysis.Differentially expressed lncRNAs,miRNAs,and mRNAs were determined,Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed,and protein-protein interaction network was generated.The results were analyzed for their association with MDD.RESULTS After analysis,3 miRNAs,12 lncRNAs,and 33 mRNAs were identified in the competing endogenous RNA network.Two of these miRNAs were earlier shown to be involved in psychiatric disorders,and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The expression of hub gene fatty acid 2-hydroxylase was enriched,and the encoded protein was found to be involved in myelin formation,indicating that neurological development and signal transduction are involved in MDD pathogenesis.CONCLUSION The present study presents candidate nc RNAs involved in the neurogenesis and neuroplasticity pathways related to MDD.

Glutamate decarboxylase 1 gene polymorphisms are associated with respiratory symptoms in panic disorder

BACKGROUND Genetic factors play an important role in the pathogenesis of panic disorder(PD).However,the effect of genetic variants on PD remains controversial.AIM To evaluate the associations between glutamate decarboxylase 1(GAD1)gene polymorphisms and PD risk and assess the effect of GAD1 gene polymorphisms on the severity of clinical symptoms in PD.METHODS We recruited 230 PD patients and 224 healthy controls in this study.All participants were assessed for anxiety and panic symptom severity using the Hamilton Anxiety Rating Scale(HAM-A)and Panic Disorder Severity Scale(PDSS).GAD1 gene polymorphisms(rs1978340 and rs3749034)were genotyped and assessed for allele frequencies.RESULTS There were no significant differences between cases and controls in the genotype distributions or allele frequencies of GAD1(rs1978340 and rs3749034).In addition,the effect of GAD1(rs1978340 and rs3749034)on PD severity was not significant.However,regarding respiratory symptoms,patients with the GAD1 rs1978340 A/A genotype had significantly higher scores than those with the A/G or G/G genotype.CONCLUSION Here,we showed that the A/A genotype of GAD1 rs1978340 was associated with increased severity of respiratory symptoms in patients with PD.

Pilot study of genome-wide DNA methylation and gene expression for treatment response to escitalopram in panic disorder

BACKGROUND Antidepressants,particularly selective serotonin reuptake inhibitors,are currently considered the first-line treatment for panic disorder(PD).However,little is known about the relationship between the biomarkers that may predict better treatment.AIM To compare genome-wide methylation and gene expression patterns between responsive and non-responsive patients with PD after 4 wk of escitalopram treatment.METHODS Thirty patients with PD were enrolled in this study(responders=13;nonresponders=17).All patients were assessed using the PD Severity Scale-Chinese version before and after treatment.The Illumina Infinium MethylationEPIC(850k)BeadChip for genome-wide methylation screening and mRNA sequencing was used in all patients with PD.RESULTS A total of 701 differentially methylated positions(DMPs)were found between responders and non-responders(|Δβ|≥0.06,q<0.05),and the hyper-and hypomethylated CpG sites were 511(72.9%)and 190(27.1%),respectively.Relative to non-responders,there were 59 differential transcripts,of which 20 were downregulated and 39 were upregulated(q<0.05).However,no differen tially expressed genes were identified by mRNA sequencing after correcting for multiple testing(|log2(FC)|>1,q>0.05).CONCLUSION This preliminary study showed that DMPs might be associated with the treatment response to escitalopram in PD;however,these DMPs need to be verified in large samples.

Revisiting study on Boussinesq modeling of wave transformation over various reef profiles

To better understand the complex process of wave transformation and associated hydrodynamics over various fringing reef profiles, numerical experiments were conducted with a one-dimensional （1D） Boussinesq wave model. The model is based on higher-order Boussinesq equations and a higher-accuracy finite difference method. The dominant energy dissipation in the surf zone, wave breaking, and bottom friction were considered by use of the eddy viscosity concept and quadratic bottom friction law, respectively. Numerical simulation was conducted for a wide range of wave conditions and reef profiles. Good overall agreement between the computed results and the measurements shows that this model is capable of describing wave processes in the fringing reef environment. Numerical experiments were also conducted to track the source of underestimation of setup for highly nonlinear waves. Linear properties （including dispersion and shoaling） are found to contribute little to the underestimation; the low accuracy in nonlinearity and the ad hoc method for treating wave breaking may be the reason for the problem.

Experimental study on modulational instability and evolution of crescent waves

A series of experiments on the instability of steeP water wave trains in water with finite water depths and infinite water depths in a wide wave basin were performed. It was found that under the coupled development of modulational instability and class-Ⅱ instability, the initial two-dimensional steep wave trains evolved into three＇dimensional crescent waves, followed by the occurrence of disordered water surfaces, and that the wave energy transferred to sidebands in the amplitude spectrum of the water surface elevation. The results also show that water depth has a significant effect on the growth of modulational instability and the evolutiin of crescent waves. The larger the water depth, the more quickly the modulational instability suppresses class-II instability.

Application of power law to vertical distribution of longshore currents

The vertical profiles of longshore currents have been examined experimentally over plane and barred beaches. In most cases, the vertical profiles of longshore currents are expressed by the logarithmic law. The power law is not commonly used to describe the profile of longshore currents. In this paper, however, a power-type formula is proposed to describe the vertical profiles of longshore currents. The formula has two parameters: the power law index (a) and the depth-averaged velocity. Based on previous studies, power law indices were set as a=1/10 and a=1/7. Depth-averaged velocity can be obtained through measurement. The fitting of the measured velocity profiles to a=1/10 and a=1/7 was assessed for the vertical longshore profiles. The vertical profile of longshore currents is well described by the power-type formula with a=1/10 for a plane beach. However, for a barred beach, different values of a needed to be used for different regions. For the region from the bar trough to the offshore side of the bar crest, the vertical profiles of longshore currents given by the power-type formula with a=1/10 and a=1/7 fit the data well. However, the fit was slightly better with a=1/10 than that with a=1/7. For the data over the trough region of cross-shore distribution of the depth-averaged longshore currents, the power formula with a=1/3 provided a good fit. The formulas with a=1/10 and a=1/7 were further examined using published data from four sources covering laboratory and field experiments. The results indicate that the power-type formula fits the data well for the laboratory and field data with a=1/10.

Experimental research on unstable movements of sandbars under wave actions

This study is motivated by recognition of complex sandbar evolution patterns under wave actions inside the surf zone. A series of physical model experiments were conducted in a wave flume to investigate sandbar migration under various wave conditions, including wave groups, regular waves, and random waves. It was observed that under certain wave conditions sandbars move alternately shoreward and seaward rather than continuously in the same direction. The measurements show that the unstable movement of sandbars is closely related to the amplitude modulation of waves. Smaller amplitude modulation tends to produce more intense unstable bar movements. Data analysis further shows that the sandbar migration does not seem to be a passive response of the sea bed to wave forcing, but is most likely caused by the feedback interaction between waves and bed topography.