Rapid reconstitution of ubiquitinated nucleosome using a non-denatured histone octamer ubiquitylation approach.

BACKGROUND: Histone ubiquitination modification is emerging as a critical epigenetic mechanism involved in a range of biological processes. In vitro reconstitution of ubiquitinated nucleosomes is pivotal for elucidating the influence of histone ubiquitination on chromatin dynamics. RESULTS: In this study, we introduce a Non-Denatured Histone Octamer Ubiquitylation (NDHOU) approach for generating ubiquitin or ubiquitin-like modified histone octamers. The method entails the co-expression and purification of histone octamers, followed by their chemical cross-linking to ubiquitin using 1,3-dibromoacetone. We demonstrate that nucleosomes reconstituted with these octamers display a high degree of homogeneity, rendering them highly compatible with in vitro biochemical assays. These ubiquitinated nucleosomes mimic physiological substrates in function and structure. Additionally, we have extended this method to cross-linking various histone octamers and three types of ubiquitin-like proteins. CONCLUSIONS: Overall, our findings offer an efficient strategy for producing ubiquitinated nucleosomes, advancing biochemical and biophysical studies in the field of chromatin biology.

Rural Spatial Differentiation and Revitalization Approaches in China: A Case Study of Qingdao City.

Rural revitalization, as a major strategy with the goal of realizing the overall development of strong agriculture industries, beautiful rural areas, and rich farmers, is an effective way of alleviating the loss of talent, land, capital, and other elements in rural areas and a possible cure for "rural diseases". However, "rural diseases" faced by villages are very different, and thus exploring suitable strategies for rural revitalization is beneficial to the implementation of rural revitalization strategies and the promotion of urban-rural integration. Based on location theory, this paper constructs a point-axis-domain three-dimensional spatial location theory model that integrates market location, traffic location, and natural location and combines the coupling coordination model to comprehensively study the vitality and development directions of Qingdao's rural areas. Results found that Qingdao's high-level and medium-high-level coupling coordination areas are the main types of coupling coordination, accounting for 45.19% and 47.48%, respectively. Based on the development status of Qingdao, this study explores development directions for rural revitalization poles as well as high-level, medium-high-level, and medium-level coupling coordination areas and suggests the following: rural revitalization poles should play a demonstration role in rural revitalization in terms of industrial development, rural civilization, social governance, public service construction, etc.; high-level coupling coordination areas should focus on building modern hi-tech agriculture and rural marine tourism industries; medium-high-level coupling coordination areas should strengthen the building of satellite towns and promote industrial transformation and upgrading; medium-level coupling coordination areas should actively develop ecological environment conservation models and establish a characteristic mountainous eco-tourism industry. Thus, the findings provide important scientific reference for the implementation of rural revitalization.

Wise Information Technology of Med: Human Pose Recognition in Elderly Care.

The growing problem of aging has led to a social concern on how to take care of the elderly living alone. Many traditional methods based on visual cameras have been used in elder monitoring. However, these methods are difficult to be applied in daily life, limited by high storage space with the camera, low-speed information processing, sensitivity to lighting, the blind area in vision, and the possibility of revealing privacy. Therefore, wise information technology of the Med System based on the micro-Doppler effect and Ultra Wide Band (UWB) radar for human pose recognition in the elderly living alone is proposed to effectively identify and classify the human poses in static and moving conditions. In recognition processing, an improved PCA-LSTM approach is proposed by combing with the Principal Component Analysis (PCA) and Long Short Term Memory (LSTM) to integrate the micro-Doppler features and time sequence of the human body to classify and recognize the human postures. Moreover, the classification accuracy with different kernel functions in the Support Vector Machine (SVM) is also studied. In the real experiment, there are two healthy men and one woman (22-26 years old) selected to imitate the movements of the elderly and slowly perform five postures (from sitting to standing, from standing to sitting, walking in place, falling and boxing). The experimental results show that the resolution of the entire system for the five actions reaches 99.1% in the case of using Gaussian kernel function, so the proposed method is effective and the Gaussian kernel function is suitable for human pose recognition.

Dynamic Nature of CTCF Tandem 11 Zinc Fingers in Multivalent Recognition of DNA As Revealed by NMR Spectroscopy.

The 11 zinc fingers (ZFs) of the transcription factor CTCF play a versatile role in the regulation of gene expression. CTCF binds to numerous genomic sites to form chromatin loops and topologically associated domains and thus mediates the 3D architecture of chromatin. Although CTCF inter-ZF plasticity is essential for the recognition of multiple genomic sites, the dynamic nature of its 11 ZFs remains unknown. We assigned the chemical shifts of the CTCF ZFs 1-11 and solved the solution structures of each ZF. NMR backbone dynamics, residual dipolar couplings, and small-angle X-ray scattering experiments suggest a high inter-ZF plasticity of the free-form ZFs 1-11. As exemplified by two different protocadherin DNA sequences, the titration of DNAs to 15N-labeled CTCF ZFs 1-11 enabled systematic mapping of binding of CTCF ZFs to various chromatin sites. Our work paves the way for illustrating the molecular basis of the versatile DNA recognized by CTCF and has interesting implications for its conformational transition during DNA binding.

Ligand Proton Pseudocontact Shifts Determined from Paramagnetic Relaxation Dispersion in the Limit of NMR Intermediate Exchange.

Delineation of protein-ligand interaction modes is key for rational drug discovery. The availability of complex crystal structures is often limited by the aqueous solubility of the compounds, while lead-like compounds with micromolar affinities normally fall into the NMR intermediate exchange regime, in which severe line broadening to beyond the detection of interfacial resonances limits NMR applications. Here, we developed a new method to retrieve low-populated bound-state 1H pseudocontact shifts (PCSs) using paramagnetic relaxation dispersion (RD). We evaluated using a 1H PCS-RD approach in a BRM bromodomain lead-like inhibitor to filter molecular docking poses using multiple intermolecular structural restraints. Considering the universal presence of proton atoms in druglike compounds, our work will have wide application in structure-guided drug discovery even under an extreme condition of NMR intermediate exchange and low aqueous solubility of ligands.

[Spatio-temporal Variations in Phytoplankton Community in Shahe Reservoir, Tianmuhu, China].

Monthly investigations of the phytoplankton community and the associated environmental drivers during the past eight years in the Shahe Reservoir, Jiangsu Province, China revealed the spatial and temporal variations of phytoplankton and the associated driving factors in the reservoir. The results show that the concentrations of total nitrogen (TN), total phosphorous (TP), turbidity (Turb), suspended solids (SS), and chlorophyll-a (CHL) were the highest in the upstream tributaries and the lowest in the downstream-linked reservoir. In contrast, the highest Secchi disk depth (SDD) was recorded in the Shahe Reservoir and that the lowest in the upstream tributaries. Significant differences in water quality indices were recorded among the upstream tributaries, the transition region, and the downstream-linked reservoir area (ANOVA, P<0.05). The biomass of phytoplankton was the highest in the upstream tributaries and the lowest in the reservoir. The highest biomass of phytoplankton was recorded in the summer and the lowest in the winter. Synedra, Cyclotella, Cryptomonas, and Achnanthes were the dominant genera in the spring; Synedra, Cryptomonas, Raphidiopsis, and Phormidium were dominant in the summer; Cryptomonas, Synedra, Raphidiopsis, and Aphanizomenon were dominant in the autumn; and Cryptomonas, Synedra, Achnanthes, and Cyclotella were dominant in the winter. Synedra and Cryptomonas were the dominant genera throughout the year. The correlation analysis shows that TP, water temperature, and SDD were the most important driving factors for the spatial and temporal variations of phytoplankton. Notable spatial differences were recorded for Cryptomonas, while minimal variations were recorded for the remaining species. A smaller number sampling sites and a higher sampling frequency are needed to characterize the phytoplankton community in the Shahe Reservoir.

Interface-induced superconductivity and strain-dependent spin density waves in FeSe/SrTiO3 thin films.

The record superconducting transition temperature (T(c)) for the iron-based high-temperature superconductors (Fe-HTS) has long been 56 K. Recently, in single-layer FeSe films grown on SrTiO3 substrates, indications of a new record of 65 K have been reported. Using in situ photoemission measurements, we substantiate the presence of spin density waves (SDWs) in FeSe films--a key ingredient of Fe-HTS that was missed in FeSe before--and we find that this weakens with increased thickness or reduced strain. We demonstrate that the superconductivity occurs when the electrons transferred from the oxygen-vacant substrate suppress the otherwise pronounced SDWs in single-layer FeSe. Beyond providing a comprehensive understanding of FeSe films and directions to further enhance its T(c), we map out the phase diagram of FeSe as a function of lattice constant, which contains all the essential physics of Fe-HTS. With the simplest structure, cleanest composition and single tuning parameter, monolayer FeSe is an ideal system for testing theories of Fe-HTS.