Tracing blastomere fate choices of early embryos in single cell culture

Blastomeres of early vertebrate embryos undergo numerous fate choices for division, motility, pluripotency maintenance and restriction culminating in various cell lineages. Tracing blastomere fate choices at the single cell level in vitro has not been possible because of the inability to isolate and cultivate early blastomeres as single cells. Here we report the establishment of single cell culture system in the fish medaka, enabling the isolation and cultivation of individual blastomeres from 16- to 64-cell embryos for fate tracing at the single cell level in vitro. Interestingly, these blastomeres immediately upon isolation exhibit motility, lose synchronous divisions and even stop dividing in ≥50% cases, suggesting that the widely accepted nucleocytoplasmic ratio controlling synchronous divisions in entire embryos does not operate on individual blastomeres. We even observed abortive division, endomitosis and cell fusion. Strikingly, ~5% of blastomeres in single cell culture generated extraembryonic yolk syncytial cells, embryonic stem cells and neural crest-derived pigment cells with timings mimicking their appearance in embryos. We revealed the maternal inheritance of key lineage regulators and their differential expression in cleavage embryos. Therefore, medaka blastomeres possess the accessibility for single cell culture, previously unidentified heterogeneity in motility, division, gene expression and intrinsic ability to generate major extraembryonic and embryonic lineages without positioning cues. Our data demonstrate the fidelity and potential of the single cell culture system for tracking blastomere fate decisions under defined conditions in vitro

Single Cell Sequencing Reveals Mechanisms of Persistent Truncus Arteriosus Formation after PDGFRα and PDGFRβ Double Knockout in Cardiac Neural Crest Cells

Persistent truncus arteriosus (PTA) is an uncommon and complex congenital cardiac malformation accounting for about 1.2% of all congenital heart diseases (CHDs), which is caused by a deficiency in the embryonic heart outflow tract’s (OFT) septation and remodeling. PDGFRα and PDGFRβ double knockout (DKO) in cardiac neural crest cells (CNCCs) has been reported to cause PTA, but the underlying mechanisms remain unclear. Here, we constructed a PTA mouse model with PDGFRα and PDGFRβ double knockout in Pax3+ CNCCs and described the condensation failure into OFT septum of CNCC-derived cells due to disturbance of cell polarity in the DKO group. In addition, we further explored the mechanism with single-cell RNA sequencing. We found that two main cell differentiation trajectories into vascular smooth muscle cells (VSMCs) from cardiomyocytes (CMs) and mesenchymal cells (MSs), respectively, were interrupted in the DKO group. The process of CM differentiation into VSMC stagnated in a transitional CM I-like state, which contributed to the failure of OFT remodeling and muscular septum formation. On the other hand, a Penk+ transitional MS II cluster closely related to cell condensation into the OFT septum disappeared, which led to the OFT’s septation absence directly. In conclusion, the disturbance of CNCC-derived cells caused by PDGFRα and PDGFRβ knockout can lead to the OFT septation disorder and the occurrence of PTA

Genetic characterization of dilated cardiomyopathy patients undergoing heart transplantation in the Chinese population by whole-exome sequencing

Abstract Background Dilated cardiomyopathy (DCM) is one of the most frequent causes of heart failure and heart transplantation (HTx). The genetic basis of DCM among patients undergoing HTx remains to be further studied. This study aimed to characterize the genetic basis of DCM HTx in the Chinese population. Methods In total, 208 unrelated DCM patients who underwent HTx at Fuwai Hospital between June 2004 and June 2017 were included in this study. Whole-exome sequencing (WES) was performed for all patients. Gene burden analysis, variant classification, and genotype–phenotype correlation analysis were subsequently performed. Results After completing the bioinformatics analysis, gene burden analysis suggested that titin (TTN), filamin C (FLNC) and lamin A/C (LMNA) were significantly enriched with rare protein-altering variants. The frequencies of TTN and FLNC truncating variants in our cohort were 18.8% and 8.7%, respectively. Among the 165 rare variants in high evidence DCM-related genes, 27 (16.4%) and 59 (35.8%) were interpreted as pathogenic (P) and likely pathogenic (LP), respectively. In addition, 41 (47.7%) and 16 (18.6%) of these 86 P/LP variants are located in TTN and FLNC, respectively. The FLNC group contained more patients with NYHA class IV than the P/LP-negative group (FLNC, 16/18 vs. P/LP-negative, 81/123, P = 0.049). Conclusions Based on WES, we provided a primary genetic spectrum of DCM patients undergoing HTx in the Chinese population. TTN and FLNC harbour the most P/LP variants. FLNC truncation may lead to severe clinical symptoms in DCM patients

An improved resource allocation method for mapping service function chains based on A3C

Abstract Network function virtualization (NFV) technology deploys network functions as software functions on a generalised hardware platform and provides customised network services in the form of service function chain (SFC), which improves the flexibility and scalability of network services and reduces network service costs. However, irrational resource allocation during service function chain mapping will cause problems such as low resource utilisation, long service request processing time and low mapping rate. To address the unreasonable problem of service mapping resource allocation, an improved service function chain mapping resource allocation method (SA3C) based on the Asynchronous advantageous action evaluation algorithm (A3C) is proposed. This study proposes an SFC mapping model and a mathematical model for joint allocation, which modeled the minimization of processing time as a Markov process. The main network was trained and multiple sub‐networks were generated in parallel using the ternary and deep reinforcement learning algorithm A3C, with the goal of identifying the optimal resource allocation strategy. The experimental simulation results show that compared with the Actor‐Critic (AC) and Policy Gradient (PG) methods, SA3C algorithm can improve the resource utilisation by 9.85%, reduce the total processing time by 10.72%, and improve the mapping rate by 6.72%, by reasonably allocating node computational resources and link bandwidth communication resources

The Landscape of Autophagy-Related (ATG) Genes and Functional Characterization of TaVAMP727 to Autophagy in Wheat

Autophagy is an indispensable biological process and plays crucial roles in plant growth and plant responses to both biotic and abiotic stresses. This study systematically identified autophagy-related proteins (ATGs) in wheat and its diploid and tetraploid progenitors and investigated their genomic organization, structure characteristics, expression patterns, genetic variation, and regulation network. We identified a total of 77, 51, 29, and 30 ATGs in wheat, wild emmer, T. urartu and A. tauschii, respectively, and grouped them into 19 subfamilies. We found that these autophagy-related genes (ATGs) suffered various degrees of selection during the wheat’s domestication and breeding processes. The genetic variations in the promoter region of Ta2A_ATG8a were associated with differences in seed size, which might be artificially selected for during the domestication process of tetraploid wheat. Overexpression of TaVAMP727 improved the cold, drought, and salt stresses resistance of the transgenic Arabidopsis and wheat. It also promoted wheat heading by regulating the expression of most ATGs. Our findings demonstrate how ATGs regulate wheat plant development and improve abiotic stress resistance. The results presented here provide the basis for wheat breeding programs for selecting varieties of higher yield which are capable of growing in colder, drier, and saltier areas

Additional file 1 of Genetic characterization of dilated cardiomyopathy patients undergoing heart transplantation in the Chinese population by whole-exome sequencing

Additional file 1: Figure S1. Variant filtering flowchart for PCA. DCM, dilated cardiomyopathy; MAF, minor allele frequency; PCA, principal component analysis

Recent progress in heterostructured materials for room‐temperature sodium‐sulfur batteries

Abstract Room‐temperature sodium‐sulfur (RT Na‐S) batteries are a promising next‐generation energy storage device due to their low cost, high energy density (1274 Wh kg−1), and environmental friendliness. However, RT Na‐S batteries face a series of vital challenges from sulfur cathode and sodium anode: (i) sluggish reaction kinetics of S and Na2S/Na2S2; (ii) severe shuttle effect from the dissolved intermediate sodium polysulfides (NaPSs); (iii) huge volume expansion induced by the change from S to Na2S; (iv) continuous growth of sodium metal dendrites, leading to short‐circuiting of the battery; (v) huge volume expansion/contraction of sodium anode upon sodium plating/stripping, causing uncontrollable solid‐state electrolyte interphase growth and “dead sodium” formation. Various strategies have been proposed to address these issues, including physical/chemical adsorption of NaPSs, catalysts to facilitate the rapid conversion of NaPSs, high‐conductive materials to promote ion/electron transfer, good sodiophilic Na anode hetero‐interface homogenized Na ions flux and three‐dimensional porous anode host to buffer the volume expansion of sodium. Heterostructure materials can combine these merits into one material to realize multifunctionality. Herein, the recent development of heterostructure as the host for sulfur cathode and Na anode has been reviewed. First of all, the electrochemical mechanisms of sulfur cathode/sodium anode and principles of heterostructures reinforced Na‐S batteries are described. Then, the application of heterostructures in Na‐S batteries is comprehensively examined. Finally, the current primary avenues of employing heterostructures in Na‐S batteries are summarized. Opinions and prospects are put forward regarding the existing problems in current research, aiming to inspire the design of advanced and improved next‐generation Na‐S batteries

Additional file 3 of Genetic characterization of dilated cardiomyopathy patients undergoing heart transplantation in the Chinese population by whole-exome sequencing

Additional file 3: Table S1. Quality control statistics for sequencing. DCM, dilated cardiomyopathy; Q20, percentage of bases with a Phred score greater than 20 to the total bases; Q30, percentage of bases with a Phred score greater than 30 to the total bases. Table S2. The number of variants carried by each DCM patient before and after filtering. DCM, dilated cardiomyopathy. Table S3. Rare variants in high evidence genes identified in the Fuwai DCM HTx cohort. One TTN variant (NM_133379:exon46:c.C12949T:p.Q4317X) was predicted to be VUS since it affects only the Novex-3 isoform. Bold PMID represents the paper focused on the HTx patients. ACMG/AMP, American College of Medical Genetics and Genomics and the Association for Molecular Pathology; ACTC1, actin alpha cardiac muscle 1; ACTN2, actinin alpha 2; B, benign; BAG3, BAG cochaperone 3; DCM, dilated cardiomyopathy; DES, desmin; DSP, desmoplakin; FLNC, filamin C; HTx, heart transplantation; JPH2, junctophilin 2; LB, likely benign; LMNA, lamin A/C; LP, likely pathogenic; MYH7, myosin heavy chain 7; NEXN, nexilin F-actin binding protein; P, pathogenic; PLN, phospholamban; RBM20, RNA binding motif protein 20; SCN5A, sodium voltage-gated channel alpha subunit 5; TNNT2, troponin T2, cardiac type; TTN, titin; VUS, variant of unknown significance. Table S4. The clinical characterization of DCM in relation to P/LP variant status. Continuous variables are expressed as the mean ± SD values, and all categorical variables are depicted using relative frequency distributions. Disease course: months from symptom onset to heart transplantation. AF, atrial fibrillation; BAG3, BAG cochaperone 3; BMI, body mass index; DCM, dilated cardiomyopathy; FLNC, filamin C; IVS, interventricular septum; LAD, left atrial diameter; LMNA, lamin A/C; LP, likely pathogenic; LVEDD, left ventricular end-diastolic dimension; LVEF, left ventricular ejection fraction; NYHA, New York Heart Association classification; P, pathogenic; RVD, right ventricle diameter; TTN, titin. P value < 0.05 = *, < 0.01 = **. Table S5. Clinical characterization of DCM in patients with one P/LP variant and those with more than one P/LP variant. Continuous variables are expressed as the mean ± SD values, and all categorical variables are depicted using relative frequency distributions. Disease course: months from symptom onset to heart transplantation. AF, atrial fibrillation; BMI, body mass index; DCM, dilated cardiomyopathy; IVS, interventricular septum; LAD, left atrial diameter; LP, likely pathogenic; LVEDD, left ventricular end-diastolic dimension; LVEF, left ventricular ejection fraction; NYHA, New York Heart Association classification; P, pathogenic; RVD, right ventricle diameter