Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected assembly outcomes, and there was no consensus on how to approach an optimal solution by selecting software tool and suitable strategy based on the properties of RNA-Seq data. To reveal the performance of different programs for transcriptome assembly, this work analyzed some important factors, including k-mer values, genome complexity, coverage depth, directional reads, etc. Seven program conditions, four single k-mer assemblers (SK: SOAPdenovo, ABySS, Oases and Trinity) and three multiple k-mer methods (MK: SOAPdenovo-MK, trans-ABySS and Oases-MK) were tested. While small and large k-mer values performed better for reconstructing lowly and highly expressed transcripts, respectively, MK strategy worked well for almost all ranges of expression quintiles. Among SK tools, Trinity performed well across various conditions but took the longest running time. Oases consumed the most memory whereas SOAPdenovo required the shortest runtime but worked poorly to reconstruct full-length CDS. ABySS showed some good balance between resource usage and quality of assemblies. Our work compared the performance of publicly available transcriptome assemblers, and analyzed important factors affecting de novo assembly. Some practical guidelines for transcript reconstruction from short-read RNA-Seq data were proposed. De novo assembly of C. sinensis transcriptome was greatly improved using some optimized methods

Nicorandil alleviates inflammation and oxidation in diabetic cardiomyopathy

Purpose: To examine the effect of nicorandil on high glucose-induced cardiomyocyte inflammation and oxidative stress.Methods: H9C2 cardiomyocytes were divided into control group, high glucose group and nicorandil group. The survival rate of cardiomyocytes was determined using the CCK-8 method. The contents of reactive oxygen species (ROS) of cardiomyocytes were determined by flow cytometry. The contents of MDA and LDH in cell supernatant were determined by kit. Western blot and real-time PCR were used to assess oxidative stress, inflammation and apoptosis related factors in each group of cardiomyocytes. The expression levels of IL-1β were determined by immunofluorescence. Tunnel staining was used to determine the apoptosis level of each group.Results: The expressions of SOD1 and SOD2 in the high glucose group were significantly decreased (p < 0.05). Also, the contents of MDA and LDH were significantly increased (p < 0.05). Furthermore, IL-1β, TNF-α, caspase 3 and Bax expressions were increased, while Bcl-2 expression was inhibited. IL-1β and Tunnel fluorescence also increased significantly. NF-κB and Ikkα were significantly increased, while IκB-α was inhibited. Furthermore, nicorandil inhibited oxidative stress and apoptosis, as well as NF-κB pathway and downstream factor Ikkα.Conclusion: Nicorandil ameliorates the inflammation and oxidative damage of cardiomyocytes induced by high glucose, by inhibiting NF-κB pathway, thereby lowering apoptosis. Thus, the findings provide new insight into the development of new agents for the treatment of diabetic cardiomyopathy

Experimental cyclic inter-conversion between Coherence and Quantum Correlations

Quantum resource theories seek to quantify sources of non-classicality that bestow quantum technologies their operational advantage. Chief among these are studies of quantum correlations and quantum coherence. The former to isolate non-classicality in the correlations between systems, the latter to capture non-classicality of quantum superpositions within a single physical system. Here we present a scheme that cyclically inter-converts between these resources without loss. The first stage converts coherence present in an input system into correlations with an ancilla. The second stage harnesses these correlations to restore coherence on the input system by measurement of the ancilla. We experimentally demonstrate this inter-conversion process using linear optics. Our experiment highlights the connection between non-classicality of correlations and non-classicality within local quantum systems, and provides potential flexibilities in exploiting one resource to perform tasks normally associated with the other.Comment: 8 pages, 4 figures, comments welcom

Analyzing Water Diffusion Properties in Dough Film Based on the Free Volume Theory

The water adsorption process by dough films at 20 and 40 ℃ was measured using a dynamic vapor sorption system under nine relative humidity (RH) levels. Water diffusivity was expressed as a function of water content and temperature according to the Vrentas & Duda free volume theory. The parameters of the free volume model were obtained by inversion of water content as a function of time. The results showed that the water diffusion coefficient determined based on the free volume theory could well simulate the water adsorption process by dough films at most water contents tested, but the predicted values were significantly lower than the actual ones at low water contents. Therefore, the Vrentas & Duda was improved by adding a free volume term as a function of water content. As the water content increased, the water diffusion coefficient slightly decreased initially, then increased, and finally increased rapidly. Finally, the mechanism of water diffusion at low water contents was discussed from the perspectives of β-transition and free volume changes

Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

Alternative splicing and trans-splicing events have not been systematically studied in the silkworm Bombyx mori. Here, the silkworm transcriptome was analyzed by RNA-seq. We identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans-splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is expressed sex-specifically in silkworm gonads. Trans-splicing of mod(mdg4) in silkworm was experimentally confirmed. We identified integrations from a common 5′-gene with 46 newly identified alternative 3′-exons that are located on both DNA strands over a 500-kb region. Other trans-splicing events in B. mori were predicted by bioinformatic analysis, in which 12 events were confirmed by RT-PCR, six events were further validated by chimeric SNPs, and two events were confirmed by allele-specific RT-PCR in F 1 hybrids from distinct silkworm lines of JS and L10, indicating that trans-splicing is more widespread in insects than previously thought. Analysis of the B. mori transcriptome by RNA-seq provides valuable information of regulatory alternative splicing events. The conservation of splicing events across species and newly identified trans-splicing events suggest that B. mori is a good model for future studies. Published by Cold Spring Harbor Laboratory Press. Copyrigh

A clinical study of C arm-guided selective spinal nerve block combined with low-temperature plasma radiofrequency ablation of dorsal root ganglion in the treatment of zoster-related neuralgia

BackgroundThis study evaluated the analgesic efficacy and psychological response of low-temperature plasma ablation of dorsal root ganglion (DRG) combined with selective spinal nerve block in patients with acute or subacute zoster-related neuralgia (ZRN).MethodsTotally 90 ZRN patients were randomly and evenly divided into three groups. Treatment was given to Group A using C arm-guided selective spinal nerve block (C-SSVB), Group B using C-SSVB and pulsed radiofrequency (PRF), and Group C using C-SSVB and low-temperature plasma ablation of the DRG. The outcomes were examined using the Visual Analog Scale (VAS). Anxiety and depression of patients were evaluated using the Self-rating Anxiety Scale (SAS) and Self-rating Depression Scale (SDS). Quality of life was assessed using the Pittsburgh Sleep Quality Index (PSQI) and postoperative Satisfaction scale. In addition, data on adverse events and medication usage rates were collected.ResultsThe 90 patients were eligible for this study. The three treatments reduced VAS scores with no significant difference between groups A and B at the same time points; however, group B tended to have numerically lower VAS scores. Comparatively, group C had significantly reduced VAS scores on day 1 and 1 month after treatment compared with the other two groups. In terms of the decreasing SAS, SDS and PSQI scores, all the three treatments improved the anxiety, depression and sleep quality of the patients. In addition, significant alleviation in anxiety was found in group C compared with group A at all- time points. However, there was no statistically significant difference among the three groups in treatment-related adverse events that mainly focused on puncture pain at the surgical-site, skin numbness and medication usage rates.ConclusionsC-SSVB and LTPRA of DRG will be considered as a promising treatment option for ZRN patients if those results can be confirmed after further validation

Lower serum insulin-like growth factor 2 level in patients with bipolar disorder is associated with the severity of manic symptoms during manic episodes

ObjectiveAccumulating evidence has indicated that neurodevelopmental defects may underlie the pathophysiology of bipolar disorder (BD). Insulin-like growth factors (IGFs) are a family of neurotrophic factors that are essential for the survival and development of neurons. The present study aims to investigate whether IGF-2 signaling is implicated in the pathophysiological processes of BD.Method50 healthy controls and 78 patients with BD, including 23 patients who diagnosed acute depressive episode and 55 patients who diagnosed acute manic episode, were recruited in this study. The 17-item Hamilton Depression Rating Scale (HAMD-17) and the Young Mania Rating Scale (YMRS) were used to assess the severity of the depressive and manic symptoms, respectively. The serum IGF-2 level was determined by an enzyme-linked immunosorbent assay (ELISA). The Kolmogorov-Smirnov and Mann-Whitney U tests were used for between-group comparisons and spearman analysis was used to analyze correlations.ResultsPatients with BD had lower serum IGF-2 levels (66.08 ± 21.22 ng/ml) when compared to healthy controls (88.72 ± 31.55 ng/ml). BD patients were divided into manic episode and depressive episode subgroups. We found that serum IGF-2 levels were reduced in both the mania and depression subgroups (mania: 67.19 ± 21.52 ng/ml, depression: 63.43 ± 20.67 ng/ml; P < 0.001), while no significant difference was observed between two groups (P > 0.05). Spearman correlation analyses revealed that the levels of serum IGF-2 were negatively correlated with the YMRS scores in BD patients (r = -0.522, P < 0.001). Furthermore, IGF-2 was found to be an independent contributor to the severity of symptoms in patients with manic episodes (B = -0.610, t = -5.299, P < 0.001).ConclusionLower serum IGF-2 levels were found in BD patients and correlated with the severity of the manic symptoms in these patients during manic episodes. These results suggest that reduced IGF-2 levels might be involved in the pathophysiology of BD, and serum IGF-2 could be a peripheral biomarker for the evaluation of the severity of manic symptoms in BD patients

Purification of neural precursor cells reveals the presence of distinct, stimulus-specific subpopulations of quiescent precursors in the adult mouse hippocampus

The activity of neural precursor cells in the adult hippocampus is regulated by various stimuli; however, whether these stimuli regulate the same or different precursor populations remains unknown. Here, we developed a novel cell-sorting protocol that allows the purification to homogeneity of neurosphere-forming neural precursors from the adult mouse hippocampus and examined the responsiveness of individual precursors to various stimuli using a clonal assay. We show that within the Hes5-GFP(+) /Nestin-GFP(+) /EGFR(+) cell population, which comprises the majority of neurosphere-forming precursors, there are two distinct subpopulations of quiescent precursor cells, one directly activated by high-KCl depolarization, and the other activated by norepinephrine (NE). We then demonstrate that these two populations are differentially distributed along the septotemporal axis of the hippocampus, and show that the NE-responsive precursors are selectively regulated by GABA, whereas the KCl-responsive precursors are selectively modulated by corticosterone. Finally, based on RNAseq analysis by deep sequencing, we show that the progeny generated by activating NE-responsive versus KCl-responsive quiescent precursors are molecularly different. These results demonstrate that the adult hippocampus contains phenotypically similar but stimulus-specific populations of quiescent precursors, which may give rise to neural progeny with different functional capacity