scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse.

Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively found in eukaryotes. Investigating eccDNA at the single-cell level is crucial for understanding cellular heterogeneity, evolution, development, and specific cellular functions. However, high-throughput identification methods for single-cell eccDNA are complex, and the lack of mature, widely applicable technologies has resulted in limited resources.

The role of circRNAs and miRNAs in drug resistance and targeted therapy responses in breast cancer.

MicroRNAs (miRNAs) are small non-coding RNAs comprising 19-24 nucleotides that indirectly control gene expression. In contrast to other non-coding RNAs (ncRNAs), circular RNAs (circRNAs) are defined by their covalently closed loops, forming covalent bonds between the 3' and 5' ends. circRNAs regulate gene expression by interacting with miRNAs at transcriptional or post-transcriptional levels.

Laboratory-developed Droplet Digital PCR Assay for Quantification of the JAK2 Mutation.

Precise quantification of the JAK2 mutation using highly sensitive assays is crucial for diagnosis, treatment process monitoring, and prognostic prediction in myeloproliferative neoplasms' (MPNs) patients. Digital droplet polymerase chain reaction (ddPCR) enables precise quantification of low-level mutations amidst a high percentage of wild type alleles without the need for external calibrators or endogenous controls. The objective of this study was to optimize a ddPCR assay for detecting the JAK2 mutation and establish it as a laboratory-developed ddPCR assay in our center.

Maternal exposure to particulate matter from duck houses restricts fetal growth due to inflammatory damage and oxidative stress.

The composition of particulate matter (PM) in poultry farms differs significantly from that of atmospheric PM as there is a higher concentration of microbes on farms. To assess the health effects of PM from poultry farms on pregnant animals, we collected PM from duck houses using a particulate sampler, processed it via centrifugation and vacuum concentration, and subsequently exposed the mice to airborne PM at 0.48 mg/m (i.

Micro/nano topological modification of TiO nanotubes activates Thy-1 signaling to control osteogenic differentiation of stem cells.

Micro/nano topological modification is critical for improving the in vivo behaviors of bone implants, regulating multiple cellular functions. Titania (TiO) nanotubes show the capacity of promoting osteoblast-related cell differentiation and induce effective osseointegration, serving as a model material for studying the effects of micro/nano-topological modifications on cells. However, the intracellular signaling pathways by which TiO nanotubes regulate the osteogenic differentiation of stem cells are not fully defined.

Studies on the airborne bacterial communities and antimicrobial resistance genes in duck houses based on metagenome and PCR analysis.

The threat of antimicrobial resistance (AMR) is on the rise globally, especially with the development of animal husbandry and the increased demand for antibiotics. Livestock and poultry farms, as key sites for prevalence of antibiotic-resistant bacteria (ARB), can spread antimicrobial resistance genes (ARGs) through microbial aerosols and affect public health. In this study, total suspended particulate matter (TSP) and airborne culturable microorganisms were collected from duck houses in Tai'an, Shandong Province, and the bacterial communities and airborne ARGs were analyzed using metagenomics and PCR methods.

Methods, bioinformatics tools and databases in ecDNA research: An overview.

Extrachromosomal DNA (ecDNA), derived from chromosomes, is a cancer-specific circular DNA molecule. EcDNA drives tumor initiation and progression, which is associated with poor clinical outcomes and drug resistance in a wide range of cancers. Although ecDNA was first discovered in 1965, tremendous technological revolutions in recent years have provided crucial new insights into its key biological functions and regulatory mechanisms.

M1 polarization of chicken macrophage HD11 can be activated by duck Tembusu virus via MyD88-NF-κB-mediated signaling pathway.

Duck Tembusu virus (DTMUV) has caused significant economic losses to the global duck industry since its outbreak in 2010. The macrophages act as the key immune cell, and its polarization in different functional states is very important for host's immune responses and microbial infections. Avian macrophages are the main target cells of DTMUV, its polarization induced by DTMUV and the underlying mechanisms were explored in this study.

Efficacy, toxicity and prognostic factors of pyrotinib‑involved neoadjuvant therapy in HER2‑positive breast cancer: A retrospective study.

Pyrotinib is a novel irreversible tyrosine kinase inhibitor targeting the human epidermal growth factor receptor (HER), whose efficacy in treating metastatic HER2-positive (HER2) breast cancer has been confirmed. The present study aimed to explore the efficacy, safety and prognostic factors of pyrogenic-involved neoadjuvant therapy in patients with HER2 breast cancer. A total of 49 patients with HER2 breast cancer who received pyrotinib-neoadjuvant therapy were recruited.

Epidemiological investigation and drug resistance characteristics of Riemerella anatipestifer strains from large-scale duck farms in Shandong Province, China from March 2020 to March 2022.

Infectious serositis is a common disease caused by Riemerella anatipestifer (R. anatipestifer) in ducks, characterized by respiratory distress, septicemia, and neurological symptoms. In this study, 1,020 samples (brain and liver) were collected from ducks with suspected R.

Genomic Characteristics and Phylogenetic Analyses of a Multiple Drug-Resistant Harboring Plasmid-Mediated Isolated from Tai'an City, China.

is a clinically common opportunistic pathogen that causes pneumonia and upper respiratory tract infection in humans as well as community-and hospital-acquired infections, posing significant threats to public health. Moreover, the insertion of a plasmid carrying the mobile colistin resistance (MCR) genes brings obstacles to the clinical treatment of infection. In this study, a strain of colistin-resistant (CRKP) was isolated from sputum samples of a patient who was admitted to a tertiary hospital in Tai'an city, China, and tested for drug sensitivity.

eccDNA Atlas: a comprehensive resource of eccDNA catalog.

Extrachromosomal circular DNA (eccDNA) represents a large category of non-mitochondrial and non-plasmid circular extrachromosomal DNA, playing an indispensable role in various aspects such as tumorigenesis, immune responses. However, the information of characteristics and functions about eccDNA is fragmented, hiding behind abundant literatures and massive whole-genome sequencing (WGS) data, which has not been sufficiently used for the identification of eccDNAs. Therefore, establishing an integrated repository portal is essential for identifying and analyzing eccDNAs.

Primary hepatic paraganglioma mimicking hepatocellular carcinoma: a case report.

Background: Primary hepatic paraganglioma (HPGL) originates from sympathetic nervous tissue in the liver. It is one of an exceedingly rare kind of sympathetic paragangliomas. The radiological features and clinical characters of HPGL can be easily confused with hepatocellular carcinoma (HCC).

Identification and characteristic analysis of enhancers across 13 major cancer types.

Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the function annotation of the mammalian genome (FANTOM) enhancers expression profiles and RNA-seq data from The Cancer Genome Atlas (TCGA) of 13 cancers and their corresponding -cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed (DE) enhancers. Furthermore, a total of 1036 DE genes regulated by DE enhancers were identified.

Tauroursodeoxycholic acid inhibits TGF-β1-induced renal fibrosis markers in cultured renal mesangial cells by regulating endoplasmic reticulum stress.

Chronic kidney disease (CKD) has a worldwide prevalence of higher than 10% with an increasing mortality rate. As it involves the deterioration of renal function, it represents a serious risk to human health and, if left untreated, significantly lowers the quality of the patient's life. CKD is characterized by renal fibrosis.

Non-Structural Protein 3 of Duck Tembusu Virus Induces Autophagy the ERK and PI3K-AKT-mTOR Signaling Pathways.

Despite autophagy's pivotal role in the replication of viruses such as duck Tembusu virus (DTMUV), which has caused massive economic losses to the poultry industry in the world, the specific relationships between DTMUV and cellular autophagy remain largely unknown. In response, we investigated the interactions between autophagy and DTMUV, the effects of the structural and non-structural proteins of DTMUV on autophagy, and the autophagy-related signaling pathways induced by DTMUV. Among the results, DTMUV increased the autophagy flux in duck embryo fibroblasts (DEF) and BHK-21 cells, while autophagy facilitated viral replication.

Tfcancer: a manually curated database of transcription factors associated with human cancers.

Summary: Transcription factors (TFs) are critical regulation elements and its dysregulation can lead to a variety of cancers. However, currently, there are no such online resources for large-scale collection, storage and analysis of TF-cancer associations in those cancers. To fill this gap, we present a database called TFcancer (http://lcbb.

EnhFFL: A database of enhancer mediated feed-forward loops for human and mouse.

Feed-forward loops (FFLs) are thought to be one of the most common and important classes of transcriptional network motifs involved in various diseases. Enhancers are cis-regulatory elements that positively regulate protein-coding genes or microRNAs (miRNAs) by recruiting DNA-binding transcription factors (TFs). However, a comprehensive resource to identify, store, and analyze the FFLs of typical enhancer and super-enhancer FFLs is not currently available.

Identification and Analysis of p53-Regulated Enhancers in Hepatic Carcinoma.

Enhancers can act as cis-regulatory elements to control transcriptional regulation by recruiting transcription factors (TFs) in a distance and orientation-independent manner. However, it is still unclear how p53 participates in the enhancer network as TF in hepatic carcinoma under the condition of DNA damage. A total of 14,286 active enhancers were identified through the integration of stable and unstable enhancer RNAs (eRNAs) captured by CAGE and GRO-seq, respectively.

EnhancerDB: a resource of transcriptional regulation in the context of enhancers.

Enhancers can act as cis-regulatory elements to control transcriptional regulation by recruiting DNA-binding transcription factors (TFs) in a tissue-specific manner. Recent studies show that enhancers regulate not only protein-coding genes but also microRNAs (miRNAs), and mutations within the TF binding sites (TFBSs) located on enhancers will cause a variety of diseases such as cancer. However, a comprehensive resource to integrate these regulation elements for revealing transcriptional regulations in the context of enhancers is not currently available.

An APOE-independent cis-eSNP on chromosome 19q13.32 influences tau levels and late-onset Alzheimer's disease risk.

Although multiple susceptibility loci for late-onset Alzheimer's disease (LOAD) have been identified, a large portion of the genetic risk for this disease remains unexplained. LOAD risk may be associated with single-nucleotide polymorphisms responsible for changes in gene expression (eSNPs). To detect eSNPs associated with LOAD, we integrated data from LOAD genome-wide association studies and expression quantitative trait loci using Sherlock (a Bayesian statistical method).