AIMC Topic: RNA, Messenger
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Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues.
Methods (San Diego, Calif.)
Mar 12, 2024
N6-methyladenosine (m6A) is the most prevalent, abundant, and conserved internal modification in the eukaryotic messenger RNA (mRNAs) and plays a crucial role in the cellular process. Although more than ten methods were developed for m6A detection ov...
Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d.
BioTechniques
Feb 29, 2024
In this study, the authors compared the efficiency of automated robotic and manual injection methods for the CRISPR-RfxCas13d (CasRx) system for mRNA knockdown and Cas9-mediated DNA targeting in zebrafish embryos. They targeted the no tail () gene as...
Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression.
Molecular systems biology
Feb 14, 2024
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in...
miTDS: Uncovering miRNA-mRNA interactions with deep learning for functional target prediction.
Methods (San Diego, Calif.)
Jan 26, 2024
MicroRNAs (miRNAs) are vital in regulating gene expression through binding to specific target sites on messenger RNAs (mRNAs), a process closely tied to cancer pathogenesis. Identifying miRNA functional targets is essential but challenging, due to in...
Mechanism of TNF- α inducing apoptosis and autophagy of chondrocytes by activating NF- κ B signal pathway.
Cellular and molecular biology (Noisy-le-Grand, France)
Dec 31, 2023
This study aimed to explore the mechanism of apoptosis and autophagy of chondrocytes induced by tumor necrosis factor α (TNA-α) by activating the NF-κB signal pathway. For this purpose, 24 SD rats were selected for feeding. The knee cartilage was cut...
A deep learning model predicts the presence of diverse cancer types using circulating tumor cells.
Scientific reports
Nov 30, 2023
Circulating tumor cells (CTCs) are cancer cells that detach from the primary tumor and intravasate into the bloodstream. Thus, non-invasive liquid biopsies are being used to analyze CTC-expressed genes to identify potential cancer biomarkers. In this...
The water-soluble subfraction from Artemisia argyi alleviates LPS-induced inflammatory responses via multiple pathways and targets in vitro and in vivo.
Journal of ethnopharmacology
Oct 28, 2023
ETHNOPHARMACOLOGICAL RELEVANCE: As a traditional Chinese medicine, Artemisia argyi has been used medicinally and eaten for more than 2000 years in China. It is widely reported in treating inflammatory diseases such as eczema, dermatitis, arthritis, a...
Curcumin Modulates NOX Gene Expression and ROS Production via P-Smad3C in TGF-β-Activated Hepatic Stellate Cells.
Iranian biomedical journal
Oct 28, 2023
BACKGROUND: Liver fibrosis, associated with hepatic stellate cells (HSCs), occurs when a healthy liver sustains damage, thereby impairing its function. NADPH oxidases (NOXs), specifically isoforms 1, 2, and 4, play a role in reactive oxygen species (...
EMDL_m6Am: identifying N6,2'-O-dimethyladenosine sites based on stacking ensemble deep learning.
BMC bioinformatics
Oct 25, 2023
BACKGROUND: N6, 2'-O-dimethyladenosine (mAm) is an abundant RNA methylation modification on vertebrate mRNAs and is present in the transcription initiation region of mRNAs. It has recently been experimentally shown to be associated with several human...
NN-RNALoc: Neural network-based model for prediction of mRNA sub-cellular localization using distance-based sub-sequence profiles.
PloS one
Sep 14, 2023
The localization of messenger RNAs (mRNAs) is a frequently observed phenomenon and a crucial aspect of gene expression regulation. It is also a mechanism for targeting proteins to a specific cellular region. Moreover, prior research and studies have ...
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