Search

High-throughput transcriptomics has revolutionised the field of transcriptome research by offering a cost-effective and powerful screening tool. Standard bulk RNA sequencing (RNA-Seq) enables characterisation of the average expression profiles for individual samples and facilitates identification of the molecular functions associated with genes differentially expressed across conditions. RNA-Seq can also be applied to disentangle splicing variants and discover novel transcripts, thus contributing to a comprehensive understanding of the transcriptome landscape. A closely related technique, single-cell RNA-Seq, has enabled the study of cell-type-specific gene expressions in hundreds to thousands of cells, aiding the exploration of cell heterogeneity. Nowadays, bulk RNA-Seq and single-cell RNA-Seq serve as complementary tools to advance and accelerate the development of transcriptome-based resources. This Collection illustrates how the current global research community makes use of these techniques to address a broad range of questions in life sciences. It demonstrates the usefulness and popularity of high-throughput transcriptomics and presents the best practices and potential issues for the benefit of future end-users. [ABSTRACT FROM AUTHOR]

The common management practices of dairy calves leads to increased starch concentration in feed, which subsequently may cause rumen acidosis while on milk and during weaning. Until recently, few attempts were undertaken to understand the health risks of prolonged ruminal acidosis in post weaning calves. Resultantly, the molecular changes in the digestive tracts in post-weaning calves with ruminal acidosis remain largely unexplored. In this study, we investigated the liver transcriptome changes along with its correlation with the rumen microbial rRNA expression changes in young calves using our model of feed induced ruminal acidosis. In this model, new born calves were fed a highly processed, starch-rich diet starting from one week of age through 16 weeks. A total of eight calves were involved in this study. Four of them were fed the acidosis-inducing diet (Treated) and the rest of the four were fed a standard starter diet (Control). Liver and rumen epithelial tissues were collected at necropsy at 17 weeks of age. Transcriptome analyses were carried out in the liver tissues and rRNA meta-transcriptome analysis were done using the rumen epithelial tissues. The correlation analysis was performed by comparing the liver mRNA expression with the rumen epithelial rRNA abundance at genus level. Calves with induced ruminal acidosis had significantly lower ruminal pH in comparison to the control group, in addition to significantly less weight-gain over the course of the experiment. In liver tissues, a total of 428 differentially expressed genes (DEGs) (fold-change, FC ≥ 1.5; adjusted P ≤ 0.1) were identified in treated group in comparison to control. Biological pathways enriched by these DEGs included cellular component organization, indicating the impact of ruminal acidosis on liver development in young calves. Specifically, the up-regulated genes were enriched in acute phase response (P < 0.01), pyruvate metabolic process (P < 0.01) and proton-acceptors (P ≪ 0.001), indicating the liver's response to feed induced acidosis at the transcriptome level. Twelve transferase activity related genes had significant correlation with rumen microbial rRNA expression changes. Among these genes, two up-regulated genes were reported with involvement in lipid metabolism in the liver, implying the direct effect of feed-induced acidosis on both the rumen microbial community and liver metabolism. Our study provides insight into the physiological remodeling in the liver resultant from the prolonged acidosis in post weaning calves, which may facilitate future RNA-seq based diagnosis and precision management of rumen acidosis in dairy calves. [ABSTRACT FROM AUTHOR]

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. [ABSTRACT FROM AUTHOR]

In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle. In this study, we dosed young calves with exogenous rumen fluid obtained from an adult donor cow, starting at birth, and repeated every other week until six weeks of age. Eight Holstein bull calves were included in this study and were separated into two groups of four: the first group was treated with rumen content freshly extracted from an adult cow, and the second group was treated with sterilized rumen content. Using whole-transcriptome RNA-sequencing, we investigated the transcriptional changes in the host liver, which is a major metabolic organ and vital to the calf's growth performance. Additionally, the comparison of rumen epimural microbial communities between the treatment groups was performed using the rRNA reads generated by sequencing. Liver transcriptome changes were enriched with genes involved in cell signaling and protein phosphorylation. Specifically, up-regulation of SGPL1 suggests a potential increase in the metabolism of sphingolipids, an essential molecular signal for bacterial survival in digestive tracts. Notably, eight genera, belonging to four phyla, had significant increases in abundance in treated calves. Our study provides insight into host liver transcriptome changes associated with early colonization of the microbial communities in neonatal calves. Such knowledge provides a foundation for future probiotics-based research in microbial organism mediated rumen development and nutrition in ruminants. [ABSTRACT FROM AUTHOR]

Ultrasonic wave is a powerful tool for many applications, such as structural health monitoring, medical diagnosis and partial discharges (PDs) detection. The fiber optic extrinsic Fabry–Perot interferometric (EFPI) sensor has become an ideal candidate for detecting weak ultrasonic signals due to its inherent advantages, and each time with a performance enhancement, it can bring great application potential in broadened fields. Herein, an EFPI ultrasonic sensor for PDs detection is proposed. The sensing diaphragm uses a 5-μm-thickness and beam-supported structure to improve the responsive sensitivity of the sensor at the resonant frequency. Furthermore, the ability of the sensor to detect characteristic ultrasonic signal of PDs is further enhanced by assembling a Fresnel-zone-plate (FZP)-based ultrasonic lens with the sensing probe to amplify the ultrasonic wave before it excites the sensing diaphragm. The final testing results show that the originally developed sensor owns the sensitivity of − 19.8 dB re. 1 V/Pa at resonant frequency. While, when the FZP is assembled with the probe, the sensitivity reaches to − 12.4 dB re. 1 V/Pa, and leads to a narrower frequency band, which indicates that the proposed method has a great potential to enhance the detection ability of sensor to characteristic ultrasonic wave of PDs. [ABSTRACT FROM AUTHOR]

We present an in-depth and systematical investigation on the plasmon Talbot effect of finite-sized two-dimensional (2D) periodic metallic nanoaperture arrays. The nanoaperture shapes, fill factor, lattice distribution, array size, film thickness, material property and polarization state of the incident light are considered, and the inherent influencing rules are summarized via the three-dimensional (3D) finite-difference time-domain (FDTD) numerical simulations. The nanoaperture shapes, fill factor or array size seems to express a tiny influence on Talbot effect, which shows a good agreement with our previously reported experimental results. Besides, square lattice brings out a much more uniform Talbot pattern than the triangular distribution, and the smaller array period should be taken to estimate the Talbot distance when it comes to a rectangular distribution. Furthermore, the thickness of Au film is suggested to within the range of 50~100 nm, which gives a broadest Talbot contour. It is also found out that the elliptical shape of hotspots is closely related to the linearly polarization state of the light source, showing an asymmetric electromagnetic field. The research contributes to a better understanding of the optical transmission features through periodic metallic nanoaperture arrays, which provides opportunities for the potential applications such as nanofabrication, optoelectronics, and imaging. [ABSTRACT FROM AUTHOR]

Current reports on the changes in peripheral blood regulatory T cell (Tregs) to CD4+ T cell ratio in systemic sclerosis (SSc) patients are varied in their conclusions. We therefore performed a meta-analysis to identify the actual change in the proportion of peripheral Tregs in SSc. Three databases, namely EMBASE, ISI web of knowledge, and Pubmed were systematically searched for relevant literature. Approximately 250 SSc patients and controls from several studies were included in this analysis. Comprehensive Meta Analysis Version 2.0 software was used to conduct the meta-analysis. Six studies were included in the meta-analysis. Results of the meta-analysis showed high degree of heterogeneity (I2 = 96.98), and a random-effect model was used in the subsequent analysis. The ratio of circulating Tregs to CD4+ T cell in SSc was lower than in controls, but not statistically significantly so (−0.61 ± 0.94, P = 0.52). Subgroup analysis did not identify any potential source of heterogeneity. This meta-analysis indicated that Tregs might play a less prominent immunosuppressive role in the immune system in SSc patients, but needs further confirmation. [ABSTRACT FROM AUTHOR]

Many individual herbs and herbal formulae have been demonstrated to provide safe and effective treatment for pancreatic ductal adenocarcinoma (PDAC); however, the therapeutic mechanisms underlying their effects have not been fully elucidated. A total of 114 herbal formulae comprising 216 single herbal medicines used to treat PDAC were identified. Cluster analysis revealed a core prescription including four herbs [Glycyrrhizae Radix et Rhizome (Gan Cao), Codonopsis Radix (Dang Shen), Citri Reticulatae Pericarpium (Chen Pi), and Pinelliae Rhizoma (Ban Xia)] in combination to treat PDAC, and 295, 256, 141, and 365 potential targets were screened for each of these four herbs, respectively. PDAC-related proteins (n = 2940) were identified from the DisGeNET database. Finally, 44 overlapping targets of herbs and PDAC were obtained, representing potential targets of the herbal medicines for PDAC treatment. GO enrichment analysis indicated that targets common to herbs and PDAC primarily functioned in response to steroid hormones. KEGG pathway enrichment analysis indicated that the herbs may prevent PDAC by influencing apoptotic, p53, and PI3K/Akt signaling pathways. Further, molecular docking analysis indicated that of identified bioactive compounds, stigmasterol, phaseol, perlolyrine, shinpterocarpin, and licopyranocoumarin have good binding ability with proteins involved in responses to steroid hormones, while stigmasterol, phaseol, perlolyrine, and DIOP have good binding ability with PTGS2(also known as COX-2), ESR1, ESR2, AR, and PGR. The anti-PDAC activity of herbal medicines may be mediated via regulation of proteins with roles in responses to steroid hormones. This study provides further evidence supporting the potential for use of herbal medicines to treat PDAC. [ABSTRACT FROM AUTHOR]