Towards Functional Annotation of the Preimplantation Transcriptome: An RNAi Screen in Mammalian Embryos

With readily available transcriptome-wide data, understanding the role of each expressed gene is an essential next step. Although RNAi technologies allow for genome-wide screens in cell culture, these approaches cannot replace strategies for discovery in the embryo. Here we present, for the first time, a knockdown screen in mouse preimplantation embryos. Early mammalian development encompasses dynamic cellular, molecular and epigenetic events that are largely conserved from mouse to man. We assayed 712 genes for requirements during preimplantation. We identified 59 genes required for successful development or outgrowth and implantation. We have characterized each phenotype and revealed cellular, molecular, and lineage specific defects following knockdown of transcript. Induced network analyses demonstrate this as a valid approach to identify networks of genes that play important roles during preimplantation. Our approach provides a robust and efficient strategy towards identification of novel phenotypes during mouse preimplantation and facilitates functional annotation of the mammalian transcriptome

Trmt112 Gene Expression in Mouse Embryonic Development

Mouse Trmt112, the homologous gene of yeast Trm112 (tRNA methyltransferase 11-2), was initially cloned from RIKEN with uncertain function. The yeast TRM112 is now known to play important roles in RNA methylation. Here, we studied the expression of Trmt112 by in situ hybridization and quantitative real-time RT-PCR (QRT-PCR). A higher expression level of Trmt112 was observed in the brain and nervous system by whole mount in situ hybridization from embryonic day 10.5 (E10.5) to E11.5. At later developmental stages E13.5 and E16.5, abundant expression was prominently found in various organs and tissues including developing brain, nervous system, thymus, lung, liver, intestine, kidney, and cartilage. Furthermore, Trmt112 was persistently expressed from E9.5 to E18.5 on whole embryos and highly expressed in multiple organs at E12.5, E15.5 and E18.5 by QRT-PCR. These results showed that Trmt112 gene was highly and ubiquitously expressed during mouse embryonic development, implying that it might be involved in the morphogenesis of diverse organs and tissues and numerous physiological functions

Integrative single-cell RNA sequencing and metabolomics decipher the imbalanced lipid-metabolism in maladaptive immune responses during sepsis

BackgroundTo identify differentially expressed lipid metabolism-related genes (DE-LMRGs) responsible for immune dysfunction in sepsis.MethodsThe lipid metabolism-related hub genes were screened using machine learning algorithms, and the immune cell infiltration of these hub genes were assessed by CIBERSORT and Single-sample GSEA. Next, the immune function of these hub genes at the single-cell level were validated by comparing multiregional immune landscapes between septic patients (SP) and healthy control (HC). Then, the support vector machine-recursive feature elimination (SVM-RFE) algorithm was conducted to compare the significantly altered metabolites critical to hub genes between SP and HC. Furthermore, the role of the key hub gene was verified in sepsis rats and LPS-induced cardiomyocytes, respectively.ResultsA total of 508 DE-LMRGs were identified between SP and HC, and 5 hub genes relevant to lipid metabolism (MAPK14, EPHX2, BMX, FCER1A, and PAFAH2) were screened. Then, we found an immunosuppressive microenvironment in sepsis. The role of hub genes in immune cells was further confirmed by the single-cell RNA landscape. Moreover, significantly altered metabolites were mainly enriched in lipid metabolism-related signaling pathways and were associated with MAPK14. Finally, inhibiting MAPK14 decreased the levels of inflammatory cytokines and improved the survival and myocardial injury of sepsis.ConclusionThe lipid metabolism-related hub genes may have great potential in prognosis prediction and precise treatment for sepsis patients

Enhanced polarization and abnormal flexural deformation in bent freestanding perovskite oxides

Recent realizations of ultrathin freestanding perovskite oxides offer a unique platform to probe novel properties in two-dimensional oxides. Here, we observe a giant flexoelectric response in freestanding BiFeO3 and SrTiO3 in their bent state arising from strain gradients up to 3.5 × 107 m−1, suggesting a promising approach for realizing ultra-large polarizations. Additionally, a substantial change in membrane thickness is discovered in bent freestanding BiFeO3, which implies an unusual bending-expansion/shrinkage effect in the ferroelectric membrane that has never been seen before in crystalline materials. Our theoretical model reveals that this unprecedented flexural deformation within the membrane is attributable to a flexoelectricity–piezoelectricity interplay. The finding unveils intriguing nanoscale electromechanical properties and provides guidance for their practical applications in flexible nanoelectromechanical systems

Numerical simulation for resistance of trimaran small waterplane area center hull based on STAR-CCM+

[Objectives] Due to its excellent seakeeping, rapidity and stability, Trimaran Small Waterplane Area Center Hull(TriSWACH)has an increasing number of applications in both civil vessels and warships. However, the laws of resistance of different submerged body shapes and side-hull configurations at different speeds still require research. As model tests are time-consuming and expensive, and cannot cover all potential hulls, numerical calculation based on STAR-CCM + is becoming increasingly preferred.[Methods] With the free surface effect consideration,STAR-CCM+ is validated to be practical for TriSWACH resistance prediction. The resistance performance is calculated with different side-hull configurations,including longitudinal and transverse,of circular submerged body shapes under the Fr series.[Results] As the results indicate,with the increase of speed,when the side-hull is arranged behind and moves closer to the main hull,the total resistance of TriSWACH is significantly lower than that of traditional trimarans,in the range of Fr=0.338~0.494.[Conclusions] The findings in this paper can provide useful references for future TriSWACH design

FUNCTIONAL IMAGING OF MATRIX STRUCTURE OF CRYOPRESERVED ENGINEERED TISSUES USING BACK-DIRECTIONAL GATED MESOSCOPIC IMAGING

Successful cryopreservation of engineered tissues (ETs) can greatly advance the access and availability of cell/tissue engineering products for clinical use. One of the key challenges in cryopreserving ETs is that the functionality of ETs should be maintained throughout the preservation process. Many of the functionalities are associated with the extracellular matrix (ECM) microstructure, which in turn can be a crucial marker for the post-thaw functionality. Recent studies also reported that the ECM microstructure can be affected by freezing-induced cell-fluid-matrix interactions.1–3 Thus, it is critical to assess three-dimensional (3-D) matrix structure of cryopreserved ETs in a non-destructive, non-invasive, and rapid manner.</jats:p

<i>Meg8</i>-DMR as the Secondary Regulatory Region Regulates the Expression of MicroRNAs While It Does Not Affect Embryonic Development in Mice

Meg8-DMR is the first maternal methylated DMR to be discovered in the imprinted Dlk1-Dio3 domain. The deletion of Meg8-DMR enhances the migration and invasion of MLTC-1 depending on the CTCF binding sites. However, the biological function of Meg8-DMR during mouse development remains unknown. In this study, a CRISPR/Cas9 system was used to generate 434 bp genomic deletions of Meg8-DMR in mice. High-throughput and bioinformatics profiling revealed that Meg8-DMR is involved in the regulation of microRNA: when the deletion was inherited from the mother (Mat-KO), the expression of microRNA was unchanged. However, when the deletion occurred from the father (Pat-KO) and homozygous (Homo-KO), the expression was upregulated. Then, differentially expressed microRNAs (DEGs) were identified between WT with Pat-KO, Mat-KO, and Homo-KO, respectively. Subsequently, these DEGs were subjected to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) term enrichment analysis to explore the functional roles of these genes. In total, 502, 128, and 165 DEGs were determined. GO analysis showed that these DEGs were mainly enriched in axonogenesis in Pat-KO and Home-KO, while forebrain development was enriched in Mat-KO. Finally, the methylation levels of IG-DMR, Gtl2-DMR, and Meg8-DMR, and the imprinting status of Dlk1, Gtl2, and Rian were not affected. These findings suggest that Meg8-DMR, as a secondary regulatory region, could regulate the expression of microRNAs while not affecting the normal embryonic development of mice