High glucose induces renal tubular epithelial cell senescence by inhibiting autophagic flux.

Autophagy, a cellular degradation process involving the formation and clearance of autophagosomes, is mediated by autophagic proteins, such as microtubule-associated protein 1 light chain 3 (LC3) and sequestosome 1 (p62), and modulated by 3-methyladenine (3-MA) as well as chloroquine (CQ). Senescence, characterised by permanent cell cycle arrest, is marked by proteins such as cyclin-dependent kinase inhibitor 1 (p21) and tumour protein 53 (p53). This study aims to investigate the relationship between cell senescence and renal function in diabetic kidney disease (DKD) and the effect of autophagy on high-glucose-induced cell senescence.

A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles.

Advances in three-dimensional (3D) genomics have revealed the spatial characteristics of chromatin interactions in gene expression regulation, which is crucial for understanding molecular mechanisms in biological processes. High-throughput technologies like ChIA-PET, Hi-C, and their derivatives methods have greatly enhanced our knowledge of 3D chromatin architecture. However, the chromatin interaction mechanisms remain largely unexplored.

Knowledge, attitude, and practice towards bacterial multidrug-resistance and structural equation modeling analysis among intensive care unit nurses and physicians.

Background: The intensive care unit (ICU) is a department with a high risk of MDR bacteria, and ICU nurses and physicians play critical roles in bacterial multidrug resistance (MDR) prevention.

Objectives: To explore the knowledge, attitudes, and practice (KAP) towards bacterial MDR among ICU nurses and physicians.

Methods: A self-designed questionnaire was administered to collect data.

AraENCODE: A comprehensive epigenomic database of Arabidopsis thaliana.

Arabidopsis is an important model organism in plant biology and genetics, and a large number of a chromatin conformation and epigenomic datasets have been generated to study the biology in Arabidopsis. To make it easier to access the accumulated epigenomic data, a user-friendly and reproducible epigenomic database, AraENCODE was developed. It contains various datasets and resources, including chromatin conformation, epigenomic, and transcriptome data, allowing researchers to investigate the regulation of epigenetic and chromatin interactions in Arabidopsis.

The role of HBV cccDNA in occult hepatitis B virus infection.

Occult hepatitis B virus (HBV) infection (OBI) refers to the presence of replication-competent HBV DNA in the liver, with or without HBV DNA in the blood, in individuals who tested negative for HBV surface antigen (HBsAg). In this peculiar phase of HBV infection, the covalently closed circular DNA (cccDNA) is in a low state of replication. Several advances have been made toward clarifying the mechanisms involved in such a suppression of viral activity, which seems to be mainly related to the host's immune control and epigenetic factors.

Improving the Transduction Efficiency and Antitumor Effect of Conditionally Replicative Adenovirus by Application of 6-cyclohexyl Methyl-β-D-maltoside.

As a tumor-targeting oncolytic adenovirus (Ad), conditionally replicating adenovirus (CRAd) can access the cell interior by binding to coxsackievirus-Ad receptors (CARs) and specifically replicate and destroy cancer cells without lethal effects on normal cells. The transduction efficiency of CRAd is highly dependent on the number of CARs on the cell membrane. However, not all tumor cells highly express CARs; therefore, improving the transduction efficiency of CRAd is beneficial for improving its antitumor effect.

Durability of Antibody Response Against Hepatitis B Virus for a Decreased Crowd: A Retrospective Polycentric Cohort Study from a 10-Year Follow-Up Clinical Study.

Aim: Hepatitis B surface antibody (HBsAb) plays an important role in the prevention of hepatitis B virus (HBV) infection, especially in immunocompromised individuals and in those infected with HBV.HBsAb levels often fluctuate and decrease.This study aimed to determine the regularity of HBsAb persistence among different populations.

DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.

Introduction: Polyploidy is a major force in plant evolution and the domestication of cultivated crops.

Objectives: The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication.

Methods: The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis.

Using Pandemic Data to Examine the Government's Pandemic Prevention Measures and Its Support Policies for Vulnerable Groups.

The outbreak of COVID-19 and the uncertainty it brings have created enormous pressure on governments to control the global pandemic and restore economic growth. It is an inevitable choice for governments of various countries to seek to control the pandemic and to provide support such as subsidies to people who lose their jobs or cannot work. However, governments should evaluate their pandemic policies to determine their effectiveness.

Exploiting the Fracture in Metal-Organic Frameworks: A General Strategy for Bifunctional Atom-Precise Nanocluster/ZIF-8(300 °C) Composites.

Atom-precise nanoclusters-metal-organic framework (APNC/MOF) composites, as bifunctional material with well-defined structures, have attracted considerable attention in recent years. Despite the progress made to date, there is an urgent need to develop a generic and scalable approach for all APNCs. Herein, the authors present the Exploiting Fracture Strategy (EFS) and successfully construct a super-stable bifunctional APNC/ZIF-8(300 °C) composite overcoming the limitations of previous strategies in selecting APNCs.

Dynamic insights into increasing antibiotic resistance in Staphylococcus aureus by label-free SERS using a portable Raman spectrometer.

Rapid and quantitative detection of bacterial antibiotic resistance is of great significance for the prevention and treatment of infections and understanding drug-resistant mechanism. In this study, label-free surface-enhanced Raman spectroscopy (SERS) technology was applied to dynamically explore oxacillin/cefazolin-derived resistance in Staphylococcus aureus using a portable Raman spectrometer. The results showed that S.

Rapid, Label-Free Prediction of Antibiotic Resistance in by Surface-Enhanced Raman Spectroscopy.

The rapid identification of bacterial antibiotic susceptibility is pivotal to the rational administration of antibacterial drugs. In this study, cefotaxime (CTX)-derived resistance in (abbr. CTX-) during 3 months of exposure was rapidly recorded using a portable Raman spectrometer.

TAD boundary and strength prediction by integrating sequence and epigenetic profile information.

Topologically associated domains (TADs) are one of the important higher order chromatin structures with various sizes in the eukaryotic genomes. TAD boundaries, as the flanking regions between adjacent domains, can restrict the interactions of regulatory elements, including enhancers and promoters, and are generally dynamic and variable in different cells. However, the influence of sequence and epigenetic profile-based features in the identification of TAD boundaries is largely unknown.

Insight into the Mechanism of the CuAAC Reaction by Capturing the Crucial AuCu-π-Alkyne Intermediate.

The classic Fokin mechanism of the CuAAC reaction of terminal alkynes using a variety of Cu(I) catalysts is well-known to include alkyne deprotonation involving a bimetallic σ,π-alkynyl intermediate. In this study, we have designed a CNT-supported atomically precise nanocluster AuCu (noted AuCu/CNT) that heterogeneously catalyzes the CuAAC reaction of terminal alkynes σ,π. Therefore, three nanocluster-π-alkyne intermediates [AuCu(π-CH≡C-p-CHR)], R = H, Cl, and CH, have been captured and characterized by MALDI-MS.

Rapid and label-free identification of different cancer types based on surface-enhanced Raman scattering profiles and multivariate statistical analysis.

Rapid detection and classification of cancer cells with label-free and non-destructive methods are helpful for rapid screening of cancer patients in clinical settings. Here, surface-enhanced Raman scattering (SERS) was used for rapid, unlabeled, and non-destructive detection of seven different cell types, including human cancer cells and non-tumorous cells. Au nanoparticles were used as enhanced substrates and directly added to cell surfaces.

Copper stress induces zebrafish central neural system myelin defects via WNT/NOTCH-hoxb5b signaling and pou3f1/fam168a/fam168b DNA methylation.

Unbalanced copper (Cu) homeostasis is associated with neurological development defects and diseases. However, the molecular mechanisms remain elusive. Here, central neural system (CNS) myelin defects and the down-regulated expression of WNT/NOTCH signaling and its down-stream mediator hoxb5b were observed in Cu stressed zebrafish larvae.

Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.

Background: Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and promoters in linear DNA (1D). Enhancers and promoters are fundamental non-coding elements enriched with transcription factors (TFs) to form chromatin loops.

Evaluation of the effects of sequence length and microsatellite instability on single-guide RNA activity and specificity.

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology is effective for genome editing and now widely used in life science research. However, the key factors determining its editing efficiency and off-target cleavage activity for single-guide RNA (sgRNA) are poorly documented. Here, we systematically evaluated the effects of sgRNA length on genome editing efficiency and specificity.

Label-Free Exosomal Detection and Classification in Rapid Discriminating Different Cancer Types Based on Specific Raman Phenotypes and Multivariate Statistical Analysis.

Exosomes contain different functional bimolecular characteristics related to physiological or pathological processes and are now recognized as new biomarkers in different human cancers. Rapid detection and classification of cancer-related exosomes might be helpful in the rapid screening of patients that may have cancer. Here, we report a surface enhanced Raman scattering technology for rapid and label-free exosomal detection (Exo-SERS) to aid in the discrimination of different cancer cells based on specific Raman phenotypes and multivariate statistical analysis.

The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation.

Autopolyploidy is widespread in higher plants and important for agricultural yield and quality. However, the effects of genome duplication on the chromatin organization and transcriptional regulation are largely unknown in plants. Using High-throughput Chromosome Conformation Capture (Hi-C), we showed that autotetraploid Arabidopsis presented more inter-chromosomal interactions and fewer short-range chromatin interactions compared with its diploid progenitor.

sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs.

Motivation: Small non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), play key roles in many biological processes. However, only a few tools can be used to develop the optimal primer or probe design for the expression profile of small ncRNAs. Here, we developed sRNAPrimerDB, the first automated primer designing and query web service for small ncRNAs.

Detecting the Population Structure and Scanning for Signatures of Selection in Horses () From Whole-Genome Sequencing Data.

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses.