The epigenome involves a complex set of cellular processes governing genomic activity. Dissecting this complexity necessitates the development of tools capable of specifically manipulating these ...processes. The repurposing of prokaryotic CRISPR systems has allowed for the development of diverse technologies for epigenome engineering. Here, we review the state of currently achievable epigenetic manipulations along with corresponding applications. With future optimization, CRISPR-based epigenomic editing stands as a set of powerful tools for understanding and controlling biological function.
Repurposed CRISPR-Cas molecules provide a useful tool set for broad applications of genomic editing and regulation of gene expression in prokaryotes and eukaryotes. Recent discovery of phage-derived ...proteins, anti-CRISPRs, which serve to abrogate natural CRISPR anti-phage activity, potentially expands the ability to build synthetic CRISPR-mediated circuits. Here, we characterize a panel of anti-CRISPR molecules for expanded applications to counteract CRISPR-mediated gene activation and repression of reporter and endogenous genes in various cell types. We demonstrate that cells pre-engineered with anti-CRISPR molecules become resistant to gene editing, thus providing a means to generate "write-protected" cells that prevent future gene editing. We further show that anti-CRISPRs can be used to control CRISPR-based gene regulation circuits, including implementation of a pulse generator circuit in mammalian cells. Our work suggests that anti-CRISPR proteins should serve as widely applicable tools for synthetic systems regulating the behavior of eukaryotic cells.
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•A novel sorbent (PEI-impregnated NKA-9) was firstly applied to biogas upgrading.•Adsorption, regeneration, and separation performance were comprehensively analyzed.•CH4 was ...effectively separated from biogas with the purity of above 95%.•Operation condition effects and potential degradation were discussed carefully.•Excellent chemical stability with undetectable urea formation by CO2 purging.
Biogas upgrading technology is important for increasing the heating value of biogas via separating CH4 and CO2, before biogas can be utilized as a vehicle fuel or for grid injection. In this work, using a porous polymeric resin (NKA-9), we prepared a new sorbent, namely polyethyleneimine (PEI)-impregnated NKA-9, for use in biogas upgrading to methane via CO2 sorption firstly. The adsorption performance, regeneration behavior, cyclic stability and CH4/CO2 separation performance were then evaluated in detail. The sorbent exhibited high adsorption capacity of up to 151.1 mg/g with negligible CH4 adsorbed, demonstrating its high selectivity towards CO2 over CH4. In column breakthrough experiments, binary mixtures were separated effectively under each set of reaction condition, where high CH4 purities of >95% could be obtained as the final product in the outlet gas. As tested, excessive PEI loading, high temperature and low CO2 concentration in biogas would result in unfavorable effects on biogas upgrading. In addition, we tested the regenerability of the sorbent using the two most common methods-N2 and CO2 purging, where the sorbent could be regenerated completely at temperatures above 85 °C and 155 °C, respectively. During the long-term operation, PEI-impregnated NKA-9 exhibited excellent cyclic stability, with 1.4% and 5.2% decreases in adsorption capacity after 30 adsorption-regeneration cycles. Detailed characterization revealed that the sorbent was chemically stable at 155 °C, in contrast to other conventional amine-modified sorbents. Therefore, the regenerable PEI-impregnated NKA-9 sorbent could be a promising choice for biogas upgrading to methane via CO2 sorption.
Eukaryotic chromosomes feature large regions of compact, repressed heterochromatin hallmarked by Heterochromatin Protein 1 (HP1). HP1 proteins play multi-faceted roles in shaping heterochromatin, and ...in cells, HP1 tethering to individual gene promoters leads to epigenetic modifications and silencing. However, emergent properties of HP1 at supranucleosomal scales remain difficult to study in cells because of a lack of appropriate tools. Here, we develop CRISPR-engineered chromatin organization (EChO), combining live-cell CRISPR imaging with inducible large-scale recruitment of chromatin proteins to native genomic targets. We demonstrate that human HP1α tiled across kilobase-scale genomic DNA form novel contacts with natural heterochromatin, integrates two distantly targeted regions, and reversibly changes chromatin from a diffuse to compact state. The compact state exhibits delayed disassembly kinetics and represses transcription across over 600 kb. These findings support a polymer model of HP1α-mediated chromatin regulation and highlight the utility of CRISPR-EChO in studying supranucleosomal chromatin organization in living cells.
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•CRISPR-dCas9 can be modified to tile chromatin proteins over large genomic regions•dCas9-HP1α tiling facilitates long-range chromatin interactions in cis and in trans•Polymers of HP1α impede distal transcription and confer structural stability•dCas9-HP1α tiling allows chromatin co-localization and compaction
Technologies to manipulate and study 3D genome organization in living cells remain scarce. Gao et al. develop a CRISPR-dCas9-based approach for inducibly tiling chromatin proteins across kilobase-scale regions of the chromosome, uncovering the direct role of HP1α in dynamically mediating long-range chromatin interactions, chromatin compaction, and transcriptional repression.
Abstract
Graphene has aroused great attention due to the intriguing properties associated with its low-energy Dirac Hamiltonian. When graphene is coupled with a correlated insulating substrate, ...electronic states that cannot be revealed in either individual layer may emerge in a synergistic manner. Here, we theoretically study the correlated and topological states in Coulomb-coupled and gate-tunable graphene-insulator heterostructures. By electrostatically aligning the electronic bands, charge carriers transferred between graphene and the insulator can yield a long-wavelength electronic crystal at the interface, exerting a superlattice Coulomb potential on graphene and generating topologically nontrivial subbands. This coupling can further boost electron-electron interaction effects in graphene, leading to a spontaneous bandgap formation at the Dirac point and interaction-enhanced Fermi velocity. Reciprocally, the electronic crystal at the interface is substantially stabilized with the help of cooperative interlayer Coulomb coupling. We propose a number of substrate candidates for graphene to experimentally demonstrate these effects.
Optical control of CRISPR-Cas9-derived proteins would be useful for restricting gene editing or transcriptional regulation to desired times and places. Optical control of Cas9 functions has been ...achieved with photouncageable unnatural amino acids or by using light-induced protein interactions to reconstitute Cas9-mediated functions from two polypeptides. However, these methods have only been applied to one Cas9 species and have not been used for optical control of different perturbations at two genes. Here, we use photodissociable dimeric fluorescent protein domains to engineer single-chain photoswitchable Cas9 (ps-Cas9) proteins in which the DNA-binding cleft is occluded at baseline and opened upon illumination. This design successfully controlled different species and functional variants of Cas9, mediated transcriptional activation more robustly than previous optogenetic methods, and enabled light-induced transcription of one gene and editing of another in the same cells. Thus, a single-chain photoswitchable architecture provides a general method to control a variety of Cas9-mediated functions.
Chronic inflammation plays a pivotal role in cancer development. Cancer cells interact with adjacent cellular components (pro-inflammatory cells, intrinsic immune cells, stromal cells, etc.) and ...non-cellular components to form the inflammatory tumor microenvironment (TME). Interleukin 6 (IL-6), macrophage migration inhibitory factor (MIF), immune checkpoint factors and other pro-inflammatory cytokines produced by intrinsic immune cells in TME are the main mediators of intercellular communication in TME, which link chronic inflammation to cancer by stimulating different oncogenic signaling pathways and improving immune escape to promote cancer development. In parallel, the ability of monocytes, T regulatory cells (Tregs) and B regulatory cells (Bregs) to perform homeostatic tolerogenic functions is hijacked by cancer cells, leading to local or systemic immunosuppression. Standard treatments for advanced malignancies such as chemotherapy and radiotherapy have improved in the last decades. However, clinical outcomes of certain malignant cancers are not satisfactory due to drug resistance and side effects. The clinical application of immune checkpoint therapy (ICT) has brought hope to cancer treatment, although therapeutic efficacy are still limited due to the immunosuppressive microenvironment. Emerging evidences reveal that ideal therapies including clearance of tumor cells, disruption of tumor-induced immunosuppression by targeting suppressive TME as well as reactivation of anti-tumor T cells by ICT. Here, we review the impacts of the major pro-inflammatory cells, mediators and their downstream signaling molecules in TME on cancer development. We also discuss the application of targeting important components in the TME in the clinical management of cancer.
In the process of charging and using electric vehicles, lithium battery may cause hazards such as fire or even explosion due to thermal runaway. Therefore, a target detection model based on the ...improved YOLOv5 (You Only Look Once) algorithm is proposed for the features generated by lithium battery combustion, using the K-means algorithm to cluster and analyse the target locations within the dataset, while adjusting the residual structure and the number of convolutional kernels in the network and embedding a convolutional block attention module (CBAM) to improve the detection accuracy without affecting the detection speed. The experimental results show that the improved algorithm has an overall mAP evaluation index of 94.09%, an average F1 value of 90.00%, and a real-time detection FPS (frames per second) of 42.09, which can meet certain real-time monitoring requirements and can be deployed in various electric vehicle charging stations and production platforms for safety detection and will provide a guarantee for the safe production and development of electric vehicles in the future.
G-protein-coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors in eukaryotes and detect a wide array of cues in the human body. Here we describe a molecular device ...that couples CRISPR-dCas9 genome regulation to diverse natural and synthetic extracellular signals via GPCRs. We generate alternative architectures for fusing CRISPR to GPCRs utilizing the previously reported design, Tango, and our design, ChaCha. Mathematical modeling suggests that for the CRISPR ChaCha design, multiple dCas9 molecules can be released across the lifetime of a GPCR. The CRISPR ChaCha is dose-dependent, reversible, and can activate multiple endogenous genes simultaneously in response to extracellular ligands. We adopt the design to diverse GPCRs that sense a broad spectrum of ligands, including synthetic compounds, chemokines, mitogens, fatty acids, and hormones. This toolkit of CRISPR-coupled GPCRs provides a modular platform for rewiring diverse ligand sensing to targeted genome regulation for engineering cellular functions.
Rivers play a key role in regulating urban ecology, which can improve urban climate while slowing the heat island effect. As one of embodied energy in the field of ecology, emergy theory can be used ...to quantitatively evaluate the ecological characteristics of a system. This will help to further explore urban ecological sustainability in this article. In this study, four ecological riverbank reconstruction projects have been executed to restore the ecology along the banks of the Jinchuan River in Nanjing, China, which focus on the key river–lakeside and waterfront space in the main urban area. The LCA–emergy–carbon emission method was applied through a series of indicators, including emergy indexes and carbon emission indicators. It is important to distinguish prior research, and few have utilized this approach on urban waterways and waterscapes. The results illustrate that the reconstruction system has obvious improvement significance to the whole river ecology. This change can also be seen when using LCA–emergy analysis. In a 20-year cycle, the emergy of the material production stage and maintenance phase account for a major emergy share, followed by the construction stage, transportation process, and design process stage. The sustainability (ESI indicator) has been improved after carrying out the reconstruction projects. By choosing water and gravel as the primary material, the carbon emission can be reduced. The water treatment process accounts for the vast majority of carbon emissions. Secondly, gravel also plays an important role in carbon emission. Finally, an improved measure (clean energy reuse) was conducted to enhance the ecology of the reconstruction projects and obtained a significant ecological sustainability boost.
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