Single-cell RNA sequencing reveals dynamic changes in A-to-I RNA editome during early human embryogenesis

BACKGROUND: A-to-I RNA-editing mediated by ADAR (adenosine deaminase acting on RNA) enzymes that converts adenosine to inosine in RNA sequence can generate mutations and alter gene regulation in metazoans. Previous studies have shown that A-to-I RNA-editing plays vital roles in mouse embryogenesis. However, the RNA-editing activities in early human embryonic development have not been investigated. RESULTS: Here, we characterized genome-wide A-to-I RNA-editing activities during human early embryogenesis by profiling 68 single cells from 29 human embryos spanning from oocyte to morula stages. We demonstrate dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion. In parallel with ADAR expression level changes, the genome-wide A-to-I RNA-editing levels in cells remained relatively stable until 4-cell stage, but dramatically decreased at 8-cell stage, continually decreased at morula stage. We detected 37 non-synonymously RNA-edited genes, of which 5 were frequently found in cells of multiple embryonic stages. Moreover, we found that A-to-I editings in miRNA-targeted regions of a substantial number of genes preferably occurred in one or two sequential stages. CONCLUSIONS: Our single-cell analysis reveals dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion, and provides important insights into early human embryogenesis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3115-2) contains supplementary material, which is available to authorized users

Metasurface-based Spectral Convolutional Neural Network for Matter Meta-imaging

Convolutional neural networks (CNNs) are representative models of artificial neural networks (ANNs), that form the backbone of modern computer vision. However, the considerable power consumption and limited computing speed of electrical computing platforms restrict further development of CNNs. Optical neural networks are considered the next-generation physical implementations of ANNs to break the bottleneck. This study proposes a spectral convolutional neural network (SCNN) with the function of matter meta-imaging, namely identifying the composition of matter and mapping its distribution in space. This SCNN includes an optical convolutional layer (OCL) and a reconfigurable electrical backend. The OCL is implemented by integrating very large-scale, pixel-aligned metasurfaces on a CMOS image sensor, which accepts 3D raw datacubes of natural images, containing two-spatial and one-spectral dimensions, at megapixels directly as input to realize the matter meta-imaging. This unique optoelectronic framework empowers in-sensor optical analog computing at extremely high energy efficiency eliminating the need for coherent light sources and greatly reducing the computing load of the electrical backend. We employed the SCNN framework on several real-world complex tasks. It achieved accuracies of 96.4% and 100% for pathological diagnosis and real-time face anti-spoofing at video rate, respectively. The SCNN framework, with an unprecedented new function of substance identification, provides a feasible optoelectronic and integrated optical CNN implementation for edge devices or cellphones with limited computing capabilities, facilitating diverse applications, such as intelligent robotics, industrial automation, medical diagnosis, and astronomy

Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes

Background/Aims: Intestinal morphology and the types of enterocytes are changed in piglets during the suckling period, but it is unclear whether these changes are associated with metabolic changes in epithelium. The present study was conducted to test the hypothesis that glucose, fatty acids, and amino acid metabolism in differentiated piglet enterocytes changed during suckling. Methods: Twenty-four piglets (Duroc × [Landrace × Yorkshire]) from 8 litters (3 piglets/litter) were selected. A single piglet from each litter was randomly selected and euthanized at days 7, 14, and 21. Differentiated enterocytes (DE) were isolated from their mid-jejunum. Isobaric tags for relative and absolute quantification and subsequent liquid chromatography-tandem mass spectrometry were used to identify and measure protein synthesis. Results: The results showed that various activities, including: cellular processes; metabolic processes; biological regulation; pigmentation; and, localization, in DEs changed during suckling. Metabolic process analyses revealed that protein expression related to glycolysis and citrate cycle was decreased from day 7 to day 14. The number of differentiated enterocytes of 21 d piglets increased compared to 7 d piglets. Most of the proteins involved in fatty acid and amino acids metabolism had decreased DE expression between day 7 and day 14. Some, but not all, detected proteins down-regulated in DEs of 21 day piglets compared to 7 day piglets. Conclusion: These results indicate that glucose, fatty acids, and amino acids metabolism changed during suckling. This may provide useful information for designing feed formulas and regulating piglet intestinal growth and development

Comprehensive analysis of the prognosis and immune effect of the oncogenic protein Four Jointed Box 1

BackgroundThe Four Jointed Box 1 (FJX1) gene has been implicated in the upregulation of various cancers, highlighting its crucial role in oncology and immunity. In order to better understand the biological function of FJX1 and identify new immunotherapy targets for cancer, we conducted a comprehensive analysis of this gene.MethodsWe analyzed the expression profiles and prognostic value of FJX1 using data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). Copy number alterations (CNAs), mutations, and DNA methylation were analyzed through cBioPortal. The Immune Cell Abundance Identifier (ImmuCellAI) was used to examine the correlation between FJX1 expression and immune cell infiltration. The relationship between FJX1 expression and immune-related genes and immunosuppressive pathway-related genes was analyzed using The Tumor Immune Estimation Resource version 2 (TIMER2). Tumor mutational burden (TMB) and microsatellite instability (MSI) were obtained from TCGA pan-cancer data. The effect of immunotherapy and the IC50 were assessed using IMvigor210CoreBiologies and Genomics For Drug Sensitivity in Cancer (GDSC). Finally, we evaluated the impact of FJX1 on colon cancer cell proliferation and migration through in vitro functional experiments.ResultsOur study indicated that FJX1 expression was high in most cancers and was significantly associated with poor prognosis. High FJX1 expression was also linked to significant alterations in CNA, DNA methylation, TMB, and MSI. Positive correlations were found between FJX1 expression and tumor-associated macrophages (TAMs) and with immune-related genes such as TGFB1 and IL-10 and immunosuppressive pathway-related genes such as TGFB1 and WNT1. On the other hand, FJX1 expression showed a negative relationship with CD8+ T cells. Furthermore, high FJX1 expression led to reduced effectiveness of immunotherapy and drug resistance. In colon cancer cells, FJX1 knockdown was found to decrease cell proliferation and migration.ConclusionOur research findings demonstrate that FJX1 is a new prognostic factor with a significant role in tumor immunity. Our results highlight the importance of further exploring the potential of targeting FJX1 as a therapeutic strategy in cancer

Root hairs facilitate rice root penetration into compacted layers

Compacted soil layers adversely affect rooting depth and access to deeper nutrient and water resources, thereby impacting climate resilience of crop production and global food security. Root hair plays well-known roles in facilitating water and nutrient acquisition. Here, we report that root hair also contributes to root penetration into compacted layers. We demonstrate that longer root hair, induced by elevated auxin response during a root compaction response, improves the ability of rice roots to penetrate harder layers. This compaction-induced auxin response in the root hair zone is dependent on the root apex-expressed auxin synthesis gene OsYUCCA8 (OsYUC8), which is induced by compaction stress. This auxin source for root hair elongation relies on the auxin influx carrier AUXIN RESISTANT 1 (OsAUX1), mobilizing this signal from the root apex to the root hair zone. Mutants disrupting OsYUC8 and OsAUX1 genes exhibit shorter root hairs and weaker penetration ability into harder layers compared with wild type (WT). Root-hair-specific mutants phenocopy these auxin-signaling mutants, as they also exhibit an attenuated root penetration ability. We conclude that compaction stress upregulates OsYUC8-mediated auxin biosynthesis in the root apex, which is subsequently mobilized to the root hair zone by OsAUX1, where auxin promotes root hair elongation, improving anchorage of root tips to their surrounding soil environment and aiding their penetration ability into harder layers

Emodin Alleviates Liver Fibrosis of Mice by Reducing Infiltration of Gr1 hi

Emodin, as a major active component of Rheum palmatum L. and Polygonum cuspidatum, has been reported to have antifibrotic effect. However, the mechanism of emodin on antifibrotic effect for liver fibrosis was still obscure. In the present study, we aimed to investigate whether emodin can alleviate carbon tetrachloride- (CCl4-) induced liver fibrosis through reducing infiltration of Gr1hi monocytes. Liver fibrosis was induced by intraperitoneal CCl4 injection in mice. Mice in the emodin group received emodin treatment by gavage. Pretreatment with emodin significantly protected mice from liver inflammation and fibrosis revealed by the decreased elevation of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST), as well as reduced hepatic necrosis and fibrosis by analysis of hematoxylin-eosin (HE) staining, Masson staining, α-smooth muscle actin (α-SMA), and collagen-I immunohistochemistry staining. Further, compared to CCl4 group, mice in the emodin group showed significantly less intrahepatic infiltration of Gr1hi monocytes. Moreover, emodin significantly inhibited hepatic expression of interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), transforming growth factor-β1 (TGF-β1), granulin (GRN), monocyte chemoattractant protein 1 (MCP-1), and chemokine ligand 7 (CCL7), which was in line with the decreased numbers of intrahepatic Gr1hi monocytes. In conclusion, emodin can alleviate the degree of liver fibrosis by reducing infiltration of Gr1hi monocytes. These results suggest that emodin is a promising candidate to prevent and treat liver fibrosis