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As the genome is organized into a three-dimensional structure in intracellular space, epigenomic information also has a complex spatial arrangement. However, most epigenetic studies describe locations of methylation marks, chromatin accessibility regions, and histone modifications in the horizontal dimension. Proper spatial epigenomic information has rarely been obtained. In this study, we designed spatial chromatin accessibility sequencing (SCA-seq) to resolve the genome conformation by capturing the epigenetic information in single-molecular resolution while simultaneously resolving the genome conformation. Using SCA-seq, we are able to examine the spatial interaction of chromatin accessibility (e.g. enhancer–promoter contacts), CpG island methylation, and spatial insulating functions of the CCCTC-binding factor. We demonstrate that SCA-seq paves the way to explore the mechanism of epigenetic interactions and extends our knowledge in 3D packaging of DNA in the nucleus.

Abstract Aqueous zinc batteries are ideal candidates for grid-scale energy storage because of their safety and low-cost aspects. However, the production of large-format aqueous Zn batteries is hindered by electrolyte consumption, hydrogen gas evolution and accumulation, and Zn dendrites growth. To circumvent these issues, here we propose an “open” pouch cell design for large-format production of aqueous Zn batteries, which can release hydrogen gas and allow the refilling of the electrolyte components consumed during cell cycling. The cell uses a gel electrolyte containing crosslinked kappa (k)-carrageenan and chitosan. It bonds water molecules and hinders their side reaction with Zn, preventing electrolyte leakage and fast evaporation. As a proof-of-concept, we report the assembly and testing of a Zn | |ZnxV2O5·nH2O multi-layer “open” pouch cell using the carrageenan/chitosan gel electrolyte, which delivers an initial discharge capacity of 0.9 Ah and 84% capacity retention after 200 cycles at 200 mA g‒1, 370 kPa and 25 °C.

BackgroundChronic obstructive pulmonary disease (COPD) has become one of the most significant chronic diseases in China. According to conventional wisdom, smoking is the pathogenic factor. However, current research indicates that the pathophysiology of COPD may be associated with prior respiratory system events (e.g., childhood hospitalization for pneumonia, chronic bronchitis) and environmental exposure (e.g., dust from workplace, indoor combustion particles). Dyspnea, persistent wheezing, and other respiratory symptoms further point to the need for pulmonary function tests in this population. Reducing the burden of chronic diseases in China requires a thorough understanding of the various factors that influence the occurrence of COPD.MethodsUsing a cohort from the natural population, this study used nested case-control analysis. We carried out a number of researches, including questionnaire surveys and pulmonary function testing, in the Northwest and Southeast cohorts of China between 2014 and 2021. After removing any variations in the baseline data between patients and control subjects using propensity score matching analysis, the risk factors were examined using univariate or multivariate regression.ResultIt was discovered that prior history of chronic bronchitis, long-term wheezing symptoms, and environmental exposure—including smoking and biofuel combustion—were risk factors for COPD. Dyspnea, symptoms of mobility limitation, organic matter, and a history of hospitalization for pneumonia at an early age were not significant in the clinical model but their incidence in COPD group is higher than that in healthy population.DiscussionCOPD screening effectiveness can be increased by looking for individuals with chronic respiratory symptoms. Smokers should give up as soon as they can, and families that have been exposed to biofuels for a long time should convert to clean energy or upgrade their ventilation. Individuals who have previously been diagnosed with emphysema and chronic bronchitis ought to be extra mindful of the prevention or advancement of COPD.

Abstract Epigenetic modifications of histones are associated with development and pathogenesis of disease. Existing approaches cannot provide insights into long-range interactions and represent the average chromatin state. Here we describe BIND&MODIFY, a method using long-read sequencing for profiling histone modifications and transcription factors on individual DNA fibers. We use recombinant fused protein A-M.EcoGII to tether methyltransferase M.EcoGII to protein binding sites to label neighboring regions by methylation. Aggregated BIND&MODIFY signal matches bulk ChIP-seq and CUT&TAG. BIND&MODIFY can simultaneously measure histone modification status, transcription factor binding, and CpG 5mC methylation at single-molecule resolution and also quantifies correlation between local and distal elements.

Cu metal suffers from unavoidable and uncontrollable surface reconstruction during electrocatalysis. The authors here guide the reconstruction process in a favorable direction using trace amount of electrolyte additives, promoting CO2 electroreduction to CH4.

Abstract Background Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In most conventional sequencing studies, the high-throughput short-read sequencing largely ignores the epigenetic status of most ecDNA regions except for the junctional areas. Methods Here, we developed a method of sequencing enzyme-accessible chromatin in circular DNA (CCDA-seq) based on the use of methylase to label open chromatin without fragmentation and exonuclease to enrich ecDNA sequencing depth, followed by long-read nanopore sequencing. Results Using CCDA-seq, we observed significantly different patterns in nucleosome/regulator binding to ecDNA at a single-molecule resolution. Conclusions These results deepen the understanding of ecDNA regulatory mechanisms.

Nowadays more and more IoT devices, including a large number of IoT servers, have been deployed on the Internet. The security of IoT servers has always been a challenge. In this paper, a new model named addressless IoT server is proposed, which allows people to use the large IPv6 address space to protect IoT server security. The server is allocated an IPv6 prefix instead of an address. When the authenticated client initiates communication, it uses an encryption mechanism to generate a specific destination address under the prefix. The server verifies the destination address when receiving the packet, and discards the packet if the verification fails. In this way, the model can prevent attackers from perceiving the server and launching scans or attacks, while remains compatible with the current Internet. The prototype is implemented and an extensive set of experiments are conducted in this paper. The results demonstrate that the model can better protect server security.

Eliminating unnecessary exposure is a principle of server security. The huge IPv6 address space enhances security by making scanning infeasible, however, with recent advances of IPv6 scanning technologies, network scanning is again threatening server security. In this paper, we propose a new model named addressless server, which separates the server into an entrance module and a main service module, and assigns an IPv6 prefix instead of an IPv6 address to the main service module. The entrance module generates a legitimate IPv6 address under this prefix by encrypting the client address, so that the client can access the main server on a destination address that is different in each connection. In this way, the model provides isolation to the main server, prevents network scanning, and minimizes exposure. Moreover it provides a novel framework that supports flexible load balancing, high-availability, and other desirable features. The model is simple and does not require any modification to the client or the network. We implement a prototype and experiments show that our model can prevent the main server from being scanned at a slight performance cost.

The catalytic conversion of carbon dioxide into value-added products requires an understanding of the active species present under working conditions. Here, the authors discover copper-containing complexes to reversibly transform during electrocatalysis into methane-producing copper nanoclusters.

Rational design and synthesis are important for the development of materials for energy applications. Here, the authors sequentially synthesize pyrite structured cobalt phosphosulfide nanoparticles on carbon nanotubes, probing the role of phosphorous substitution on catalyst stability and durability.