The Current Situation and Development Prospect of Whole-Genome Screening.

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.

A New Generation of Lineage Tracing Dynamically Records Cell Fate Choices.

Reconstructing the development of lineage relationships and cell fate mapping has been a fundamental problem in biology. Using advanced molecular biology and single-cell RNA sequencing, we have profiled transcriptomes at the single-cell level and mapped cell fates during development. Recently, CRISPR/Cas9 barcode editing for large-scale lineage tracing has been used to reconstruct the pseudotime trajectory of cells and improve lineage tracing accuracy. This review presents the progress of the latest CbLT (CRISPR-based Lineage Tracing) and discusses the current limitations and potential technical pitfalls in their application and other emerging concepts.

Downregulation of S100 calcium binding protein A12 inhibits the growth of glioma cells.

BACKGROUND: S100 calcium binding protein A12 (S100A12) is a member of the S100 protein family and is widely expressed in neutrophil and low expressed in lymphocytes and monocyte. However, the role of S100A12 in glioma has not yet been identified. METHODS: In the present study, we carried out immunohistochemical investigation of S100A12 in 81 glioma tissues to determine the expression of S100A12 in glioma cells, and evaluate the clinical significance of S100A12 in glioma patients. Futher we knockdown the S100A12 by shRNA, and evaluated cell proliferation, cell migration and cell apoptosis by MTT, colony formation assay, transwell assay,flow cytometry assa and western blot. RESULTS: We found that S100A12 was upregulated in tissues of glioma patients and the expression was correlated to WHO stage and tumor size. Further, we found that knockdown S100A12 inhibits the proliferation, migration and invasion of glioma cells through regulating cell apoptosis and EMT. CONCLUSION: S100A12 plays a vital role in glioma progression, and may be an important regulatory molecule for biological behaviors of glioma cell lines.

MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation.

Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation. Furthermore, using Myogenin as a model locus, we elucidate the hierarchical and complex interactions among hotspots during the differentiation, demonstrating SE function is propelled by the physical and functional cooperation among hotspots. Finally, we show MyoD and FoxO3 are key in orchestrating the Myogenin hotspots interaction and activation. Altogether our results identify muscle-specific SEs and provide mechanistic insights into the functionality of SE.

Ribosomal RNA gene transcription mediated by the master genome regulator protein CCCTC-binding factor (CTCF) is negatively regulated by the condensin complex.

CCCTC-binding factor (CTCF) is a ubiquitously expressed "master weaver" and plays multiple functions in the genome, including transcriptional activation/repression, chromatin insulation, imprinting, X chromosome inactivation, and high-order chromatin organization. It has been shown that CTCF facilitates the recruitment of the upstream binding factor onto ribosomal DNA (rDNA) and regulates the local epigenetic state of rDNA repeats. However, the mechanism by which CTCF modulates rRNA gene transcription has not been well understood. Here we found that wild-type CTCF augments the pre-rRNA level, cell size, and cell growth in cervical cancer cells. In contrast, RNA interference-mediated knockdown of CTCF reduced pre-rRNA transcription. CTCF positively regulates rRNA gene transcription in a RNA polymerase I-dependent manner. We identified an RRGR motif as a putative nucleolar localization sequence in the C-terminal region of CTCF that is required for activating rRNA gene transcription. Using mass spectrometry, we identified SMC2 and SMC4, two subunits of condensin complexes that interact with CTCF. Condensin negatively regulates CTCF-mediated rRNA gene transcription. Knockdown of SMC2 expression significantly facilitates the loading of CTCF and the upstream binding factor onto the rDNA locus and increases histone acetylation across the rDNA locus. Taken together, our study suggests that condensin competes with CTCF in binding to a specific rDNA locus and negatively regulates CTCF-mediated rRNA gene transcription.

Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells.

Introduction: The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective: To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results: We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions: The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.

Improving the thermostability of Escherichia coli phytase, appA, by enhancement of glycosylation.

A codon-optimized Escherichia coli appA phytase gene was synthesized and expressed in Pichia pastoris. Two residue substitutions (Q258N, Q349N) were sequentially introduced to enhance its glycosylation activity. Secretion of appA-Q258N/Q349N was approx. 0.3 mg ml(-1) and enzyme activity reached 1,030 U ml(-1). Purified appA-Q258N/Q349N had a specific activity of 3,137 U mg(-1) with an MW of approx. 53 kDa. Compared with appA-WT, appA-Q258N/Q349N showed over 40 % enhancement in thermostability (85 °C for 10 min) and 4-5 °C increases in the melting temperatures (Tm). The Km and Kcat of appA-Q258N/Q349N were 0.43 mM and 3,058 s(-1), respectively, which are similar with that of appA-WT. The mutant appA-Q258N/Q349N obtained in this study could be used for the large-scale commercial production of phytase.

Graph-Collaborated Auto-Encoder Hashing for Multiview Binary Clustering.

Unsupervised hashing methods have attracted widespread attention with the explosive growth of large-scale data, which can greatly reduce storage and computation by learning compact binary codes. Existing unsupervised hashing methods attempt to exploit the valuable information from samples, which fails to take the local geometric structure of unlabeled samples into consideration. Moreover, hashing based on auto-encoders aims to minimize the reconstruction loss between the input data and binary codes, which ignores the potential consistency and complementarity of multiple sources data. To address the above issues, we propose a hashing algorithm based on auto-encoders for multiview binary clustering, which dynamically learns affinity graphs with low-rank constraints and adopts collaboratively learning between auto-encoders and affinity graphs to learn a unified binary code, called graph-collaborated auto-encoder (GCAE) hashing for multiview binary clustering. Specifically, we propose a multiview affinity graphs' learning model with low-rank constraint, which can mine the underlying geometric information from multiview data. Then, we design an encoder-decoder paradigm to collaborate the multiple affinity graphs, which can learn a unified binary code effectively. Notably, we impose the decorrelation and code balance constraints on binary codes to reduce the quantization errors. Finally, we use an alternating iterative optimization scheme to obtain the multiview clustering results. Extensive experimental results on five public datasets are provided to reveal the effectiveness of the algorithm and its superior performance over other state-of-the-art alternatives.

Loss of Dip2b leads to abnormal neural differentiation from mESCs.

BACKGROUND: Disco-interacting protein 2 homolog B is a member of the Dip2 family encoded by the Dip2b gene. Dip2b is widely expressed in neuro-related tissues and is essential in axonal outgrowth during embryogenesis. METHODS: Dip2b knockout mouse embryonic stem cell line was established by CRISPR/Cas9 gene-editing technology. The commercial kits were utilized to detect cell cycle and growth rate. Flow cytometry, qRT-PCR, immunofluorescence, and RNA-seq were employed for phenotype and molecular mechanism assessment. RESULTS: Our results suggested that Dip2b is dispensable for the pluripotency maintenance of mESCs. Dip2b knockout could not alter the cell cycle and proliferation of mECSs, or the ability to differentiate into three germ layers in vitro. Furthermore, genes associated with axon guidance, channel activity, and synaptic membrane were significantly downregulated during neural differentiation upon Dip2b knockout. CONCLUSIONS: Our results suggest that Dip2b plays an important role in neural differentiation, which will provide a valuable model for studying the exact mechanisms of Dip2b during neural differentiation.

Stem cell competition driven by the Axin2-p53 axis controls brain size during murine development.

Cell competition acts as a quality-control mechanism that eliminates cells less fit than their neighbors to optimize organ development. Whether and how competitive interactions occur between neural progenitor cells (NPCs) in the developing brain remains unknown. Here, we show that endogenous cell competition occurs and intrinsically correlates with the Axin2 expression level during normal brain development. Induction of genetic mosaicism predisposes Axin2-deficient NPCs to behave as "losers" in mice and undergo apoptotic elimination, but homogeneous ablation of Axin2 does not promote cell death. Mechanistically, Axin2 suppresses the p53 signaling pathway at the post-transcriptional level to maintain cell fitness, and Axin2-deficient cell elimination requires p53-dependent signaling. Furthermore, mosaic Trp53 deletion confers a "winner" status to p53-deficient cells that outcompete their neighbors. Conditional loss of both Axin2 and Trp53 increases cortical area and thickness, suggesting that the Axin2-p53 axis may coordinate to survey cell fitness, regulate natural cell competition, and optimize brain size during neurodevelopment.

Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells.

Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP-vPRC1 or YAF2-vPRC1 catalyzes H2AK119ub through a positive-feedback model; however, whether RYBP and YAF2 have different regulatory functions is still unclear. Here, we show that the expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Taken together, this study reveals that RYBP and YAF2 function differentially in regulating mESC neural differentiation.

Prediction of the Maturity of Greenhouse Grapes Based on Imaging Technology.

To predict grape maturity in solar greenhouses, a plant phenotype-monitoring platform (Phenofix, France) was used to obtain RGB images of grapes from expansion to maturity. Horizontal and longitudinal diameters, compactness, soluble solid content (SSC), titratable acid content, and the SSC/acid of grapes were measured and evaluated. The color values (R, G, B, H, S, and I) of the grape skin were determined and subjected to a back-propagation neural network algorithm (BPNN) to predict grape maturity. The results showed that the physical and chemical properties (PCP) of the three varieties of grapes changed significantly during the berry expansion stage and the color-changing maturity stage. According to the normalized rate of change of the PCP indicators, the ripening process of the three varieties of grapes could be divided into two stages: an immature stage (maturity coefficient Mc < 0.7) and a mature stage (after which color changes occurred) (0.7 ≤ Mc < 1). When predicting grape maturity based on the R, G, B, H, I, and S color values, the R, G, and I as well as G, H, and I performed well for Drunk Incense, Muscat Hamburg, and Xiang Yue grape maturity prediction. The GPI ranked in the top three (up to 0.87) when the above indicators were used in combination with BPNN to predict the grape Mc by single-factor and combined-factor analysis. The results showed that the prediction accuracy (RG and HI) of the two-factor combination was better for Drunk Incense, Muscat Hamburg, and Xiang Yue grapes (with recognition accuracies of 79.3%, 78.2%, and 79.4%, respectively), and all of the predictive values were higher than those of the single-factor predictions. Using a confusion matrix to compare the accuracy of the Mc's predictive ability under the two-factor combination method, the prediction accuracies were in the following order: Xiang Yue (88%) > Muscat Hamburg (81.3%) > Drunk Incense (76%). The results of this study provide an effective way to predict the ripeness of grapes in the greenhouse.

Generation of an mESC model with a human hemophilia B nonsense mutation via CRISPR/Cas9 technology.

BACKGROUND: Hemophilia B is a rare inherited genetic bleeding disorder caused by a deficiency or lack of coagulation factor IX, the gene for which (F9) is located on the X chromosome. Hemophilia B is currently incurable and the standard treatment is coagulation factor replacement therapy. Although gene therapy has the potential to cure hemophilia, significant barriers are still needed to be overcome, e.g., off-target effects and immunoreactivity, so new approaches must be explored. Nonsense mutations account for 8% of all the hemophilia B mutation types and can result in the development of coagulation factor inhibitors. In this study, CRISPR/Cas9 technology was used to construct a mouse embryonic stem cell model with a hemophilia B nonsense mutation (F9 c.223C > T) in humans to investigate the pathogenesis and treatment of nonsense mutations in hemophilia B. METHODS: First, a donor plasmid with a mutation (F9 c.223 C > T) and sgRNAs were constructed. Second, both the donor plasmid and the px330-sgRNA were electroporated into mouse embryonic stem cell, and the mutant cells were then screened using puromycin and red fluorescence. Third, the mutant cell lines were tested for pluripotency and the ability to differentiate into three layers. Finally, the effect of mutation on gene function was studied in the differentiation system. RESULTS: The mutant vector and effective sgRNA were constructed, and the mutant cell line was screened. This mutant cell line exhibited pluripotency and the ability to differentiate into three layers. This point mutation affects F9 expression at both the RNA and protein levels in the differentiation system. CONCLUSIONS: The mutant cell line obtained in the current study had a single-base mutation rather than a base deletion or insertion in the exon, which is more similar to clinical cases. In addition, the mutant has the characteristics of mouse embryonic stem cells, and this point mutation affects F9 gene transcription and translation, which can be used as a disease model for studying the pathogenesis and treatment of hemophilia at the stem cell level.

A low voltage-powered soft electromechanical stimulation patch for haptics feedback in human-machine interfaces.

One grand challenge in haptic human-machine interface devices is to electromechanically stimulate sensations on the human skin wirelessly by thin and soft patches under a low driving voltage. Here, we propose a soft haptics-feedback system using highly charged, polymeric electret films with an annulus-shape bump structure to induce mechanical sensations on the fingertip of volunteers under an applied voltage range of 5-20 V. As an application demonstration, a 3 × 3 actuators array is used for transmitting patterned haptic information, such as letters of 'T', 'H', 'U' letters and numbers of '0', '1', '2'. Moreover, together with flexible lithium batteries and a flexible circuit board, an untethered stimulation patch is constructed for operations of 1 h. The analytical model, design principle, and performance characterizations can be applicable for the integration of other wearable electronics toward practical applications in the fields of AR (augmented reality), VR (virtual reality) and robotics.

Cascade diversification directs generation of neuronal diversity in the hypothalamus.

The hypothalamus contains an astounding heterogeneity of neurons that regulate endocrine, autonomic, and behavioral functions. However, its molecular developmental trajectory and origin of neuronal diversity remain unclear. Here, we profile the transcriptome of 43,261 cells derived from Rax+ hypothalamic neuroepithelium to map the developmental landscape of the mouse hypothalamus and trajectory of radial glial cells (RGCs), intermediate progenitor cells (IPCs), nascent neurons, and peptidergic neurons. We show that RGCs adopt a conserved strategy for multipotential differentiation but generate Ascl1+ and Neurog2+ IPCs. Ascl1+ IPCs differ from their telencephalic counterpart by displaying fate bifurcation, and postmitotic nascent neurons resolve into multiple peptidergic neuronal subtypes. Clonal analysis further demonstrates that single RGCs can produce multiple neuronal subtypes. Our study reveals that multiple cell types along the lineage hierarchy contribute to fate diversification of hypothalamic neurons in a stepwise fashion, suggesting a cascade diversification model that deconstructs the origin of neuronal diversity.

Knockout of Dip2c in murine ES cell line IBMSe001-B-1 by CRISPR/Cas9 genome editing technology.

DIP2 protein contains three members: DIP2A, DIP2B and DIP2C, and are broadly expressed in the nervous system from Drosophila to human during embryonic development. Dip2c gene-associated mutations have been reported in tumors and neuronal diseases. However, the role ofDip2cin the context of mouse embryonic stem (mES) cells has not been explored.To investigate the biological function of Dip2c during early embryo development, we generated Dip2c-/- mES line using a CRISPR/Cas9 system. This cell line has contributed to further investigation of molecular mechanism of Dip2c during cell differentiation, as well as a cell model for screening for neurogenic drug and cancer clinical cure.

Prognostic Nomograms for Primary High-Grade Glioma Patients in Adult: A Retrospective Study Based on the SEER Database.

PURPOSE: In our study, we aimed to screen the risk factors that affect overall survival (OS) and cancer-specific survival (CSS) in adult glioma patients and to develop and evaluate nomograms. METHODS: Primary high-grade gliomas patients being retrieved from the surveillance, epidemiology and end results (SEER) database, between 2004 and 2015, then they randomly assigned to a training group and a validation group. Univariate and multivariate Cox analysis models were used to choose the variables significantly correlated with the prognosis of high-grade glioma patients. And these variables were used to construct the nomograms. Next, concordance index (C-index), calibration plot and receiver operating characteristics (ROCs) curve were used to evaluate the accuracy of the nomogram model. In addition, the decision curve analysis (DCA) was used to analyze the benefit of nomogram and prognostic indicators commonly used in clinical practice. RESULTS: A total of 6395 confirmed glioma patients were selected from the SEER database, divided into training set (n =3166) and validation set (n =3229). Age at diagnosis, tumor grade, tumor size, histological type, surgical type, radiotherapy and chemotherapy were screened out by Cox analysis model. For OS nomogram, the C-index of the training set was 0.741 (95% CI: 0.751-0.731), and the validation set was 0.738 (95% CI: 0.748-0.728). For CSS nomogram, the C-index of the training set was 0.739 (95% CI: 0.749-0.729), and the validation set was 0.738 (95% CI: 0.748-0.728). The net benefit and net reduction in inverventions of nomograms in the decision curve analysis (DCA) was higher than histological type. CONCLUSIONS: We developed nomograms to predict 3- and 5-year OS rates and 3- and 5-year CSS rates in adult high-grade glioma patients. Both the training set and the validation set showed good calibration and validation, indicating the clinical applicability of the nomogram and good predictive results.

Comprehensive MicroRNA Expression Profile of the Mammary Gland in Lactating Dairy Cows With Extremely Different Milk Protein and Fat Percentages.

A total of 31 differentially expressed genes in the mammary glands were identified in our previous study using RNA sequencing (RNA-Seq), for lactating cows with extremely high and low milk protein and fat percentages. To determine the regulation of milk composition traits, we herein investigated the expression profiles of microRNA (miRNA) using small RNA sequencing based on the same samples as in the previous RNA-Seq experiment. A total of 497 known miRNAs (miRBase, release 22.1) and 49 novel miRNAs among the reads were identified. Among these miRNAs, 71 were found differentially expressed between the high and low groups (p < 0.05, q < 0.05). Furthermore, 21 of the differentially expressed genes reported in our previous RNA-Seq study were predicted as target genes for some of the 71 miRNAs. Gene ontology and KEGG pathway analyses showed that these targets were enriched for functions such as metabolism of protein and fat, and development of mammary gland, which indicating the critical role of these miRNAs in regulating the formation of milk protein and fat. With dual luciferase report assay, we further validated the regulatory role of 7 differentially expressed miRNAs through interaction with the specific sequences in 3'UTR of the targets. In conclusion, the current study investigated the complexity of the mammary gland transcriptome in dairy cattle using small RNA-seq. Comprehensive analysis of differential miRNAs expression and the data from previous study RNA-seq provided the opportunity to identify the key candidate genes for milk composition traits.

[Effects of irrigation lower limit and straw returning amount on yield, quality and water use efficiency of greenhouse tomato]. / 灌水下限及秸秆还田对温室番茄产量、品质和水分利用效率的影响.

A split plot experiment was conducted in greenhouse to investigate the effects of irrigation lower limit and maize straw returning on the yield, quality, and water use efficiency (WUE) of tomato. Maize straw was applied for 1 (2018, A1), 2(2017, A2), and 3 (2016, A3) years at different amounts (0, 1.5×104, 3×104, 4.5×104 kg·hm-2) and different irrigation lower limits (50%θf, 60%θf, 70%θf, 80%θf, θf was the field water capacity). Variance analysis, entropy-weight and TOPSIS methods were used to examine the responses of yield, quality and water use efficiency (WUE) of tomato. The results showed that tomato yield was enhanced by the increases of irrigation lower limit. The maximum value of yield was observed in the 80%θf treatments, with the maximum average yield of 93.55 t·hm-2 in A1, 87.23 t·hm-2 in A2, and 99.34 t·hm-2 in A3, respectively. WUE and quality of tomato decreased with increasing irrigation lower limit. In the first year of straw returning, the maximum average yield of tomato was 99.60 t·hm-2 in straw returning 1.5×104 kg·hm-2 . In the second and third years, 4.5×104 kg·hm-2 straw returning had the highest average yield of tomato, which was 92.50 and 107.75 t·hm-2, respectively. The maximum WUE was observed with the straw returning of 1.5×104 kg·hm-2 in A1 and A2, while in the A3 treatment it happened in straw returning of 4.5×104 kg·hm-2. The quality index of tomato showed different trends with the increases of straw returning years and amount.

Generation of Dip2a homozygous knockout murine ES cell line IBMSe001-A-1 via CRISPR/Cas9 technology.

DIP2A mutation is associated with abnormal brain development and diseases including dyslexia, autism and Alzheimer's disease. However, the role and the involved mechanisms remain unknown. To study the biological function of DIP2A during mESCs neural differentiation in early neural development, we generated a Dip2a homozygous knockout 46C ESC cell line using CRISPR/Cas9 genome editing technology. The eighth exon of Dip2a gene was replaced with PGK-Puro-P2A-mCherry. This 46C-Dip2a KO cell line offers a useful resource to investigate the molecular mechanisms of DIP2A in the process of cell fate determination, as well as a potential source of building disease mouse model.