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 The concept of RNA velocity has been recently developed that allowed to look at the otherwise static single-cell RNA sequencing data in a dynamic way, which permitted inferences about cell fates. However, the more precise parameters, such as the number of exons/introns, can also be determined using long-read methods. Comparing the numbers of exons and introns allows including more genes for downstream velocity analysis and resolves the precise cell fate. The recently developed concept of “RNA velocity” concerns with dynamic changes in mRNA expression and complements single-cell RNA sequencing (scRNA-seq) data, which are static snapshots of a certain cell state taken at a given time point 1 . RNA velocity measures the change in mRNA abundance by differentiating the newly transcribed unspliced pre-mRNAs from mature spliced mRNAs. The rapidly developing long-read sequencing technology lends itself for RNA velocity analysis of scRNA-seq data, which was previously performed primarily using second-generation sequencing.
Microbial-mediated utilization of particulate organic matter (POM) during its downward transport from the surface to the deep ocean constitutes a critical component of the global ocean carbon cycle. However, it remains unclear as to how high hydrostatic pressure (HHP) and low temperature (LT) with the sinking particles affects community structure and network interactions of the particle-attached microorganisms (PAM) and those free-living microorganisms (FLM) in the surrounding water. In this study, we investigated microbial succession and network interactions in experiments simulating POM sinking in the ocean. Diatom-derived 13C- and 12C-labeled POM were used to incubate surface water microbial communities from the East China Sea (ECS) under pressure (temperature) of 0.1 (25 °C), 20 (4 °C), and 40 (4 °C) MPa (megapascal). Our results show that the diversity and species richness of the PAM and FLM communities decreased significantly with HHP and LT. Microbial community analysis indicated an increase in the relative abundance of Bacteroidetes at high pressure (40 MPa), mostly at the expense of Gammaproteobacteria, Alphaproteobacteria, and Gracilibacteria at atmospheric pressure. Hydrostatic pressure and temperature affected lifestyle preferences between particle-attached (PA) and free-living (FL) microbes. Ecological network analysis showed that HHP and LT enhanced microbial network interactions and resulted in higher vulnerability to networks of the PAM communities and more resilience of those of the FLM communities. Most interestingly, the PAM communities occupied most of the module hubs of the networks, whereas the FLM communities mainly served as connectors of the modules, suggesting their different ecological roles of the two groups of microbes. These results provided novel insights into how HHP and LT affected microbial community dynamics, ecological networks during POM sinking, and the implications for carbon cycling in the ocean.
Hydrogen peroxide (H 2 O 2 ) is widely used in paper, food, textile, and wastewater treatment industries as a bleaching or microbicidal agent.Usually, H 2 O 2 used in these industries should be removed by catalase before further treatment.In this study, a piezotolerant Halomonas piezotolerans (strain NBT06E8 T ) was isolated from deep-sea sediment of New Britain Trench at depth of 8900 m.The strain was aerobic, motile, Gram-stain negative, rod-shaped, oxidase-positive and catalase-positive.Growth of the strain was observed at 4-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 8-9) and in 0.5-21% (w/v) NaCl (optimum, 3-7%).The optimal pressure for growth was 0.1-30 MPa with tolerance up to 60 MPa.Under optimal growth conditions, the strain could tolerate 15 mM H 2 O 2 .The purified catalase (KatE) was obtained by heterologous expression in Escherichia coli and Ni-NTA agarose gel column method.The enzymatic characteristics showed that the optimal substrate concentration was 60 mM, the optimal enzymatic activity temperature and pH were 20 °C and 7, respectively.The optimal salinity was between 2-4%.New findings on oxidative stress mechanisms of this strain will broaden our knowledge of stress adaptation of deep-sea bacteria and potentiate the biotechnological application of Halomonas species in the future.
Additional file 12: Table S12. The taxonomic assignment of the 1070 bacterial isolates. Their taxonomy was assigned based on 16S rRNA gene sequences using NCBI rRNA/ITS databases.
Underwater acoustic communication is an important wireless communication method for underwater information communication. However, the time-varying, frequency-varying, and space-varying characteristics of underwater acoustic channels pose great challenges to receiver design for underwater acoustic communications. The adaptive decision feedback iterative equalizer is an effective design method for underwater acoustic communication receivers. It adopts an adaptive method for symbol judgment, and uses the information interaction between the equalizer and the decoder to further improve the equalization reliability. A balanced design among balance accuracy, steady-state error, computational complexity, and system overhead can be achieved. This paper proposes a design method of underwater acoustic communication decision feedback iterative equalization receiver based on symbol-by-symbol posterior information soft decision. The receiver design method uses adaptive algorithm to calculate soft-decision symbols in a symbol-by-symbol manner, which can accurately obtain the equalization process Equalize the variation of symbol mean value and variance, thereby improving the accuracy of decoding and the reliability of the receiver. In this paper, the proposed receiver design method is verified by the measured data.
'/%3e%3cuse xlink:href='%23a' transform='rotate(23.036 .093 25.536)'/%3e%3cuse xlink:href='%23a' transform='rotate(45.87 1.273 16.18)'/%3e%3cuse xlink:href='%23a' transform='rotate(69.945 .996 12.078)'/%3e%3cuse xlink:href='%23a' transform='rotate(20.66 -19.689 31.932)'/%3e%3c/svg%3e)