Here, we present a lysate-based split-luciferase assay for examining protein-protein interactions (PPIs) in HEK293T cell lysates, exemplified by interactions between subunits of protein phosphatase PP1. We describe steps for storing and re-using lysates, sensor design, assay setup/optimization, and high-throughput screening of compound libraries. We then detail procedures for applying the assay as a research tool to characterize the dynamics of PPIs, which we illustrate with specific examples. For complete details on the use and execution of this protocol, please refer to Claes and Bollen..
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http://dx.doi.org/10.1016/j.xpro.2024.103328 | DOI Listing |
Cancer Sci
January 2025
Department of colorectal surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China.
This study analyzed targeted sequencing data from 6530 tissue samples from patients with metastatic Chinese colorectal cancer (CRC) to identify low mutation frequency and subgroup-specific driver genes, using three algorithms for overall CRC as well as across different clinicopathological subgroups. We analyzed 425 cancer-related genes, identifying 101 potential driver genes, including 36 novel to CRC. Notably, some genes demonstrated subgroup specificity; for instance, ERBB4 was found as a male-specific driver gene and mutations of ERBB4 only influenced the prognosis of male patients with CRC.
View Article and Find Full Text PDFDatabase (Oxford)
January 2025
School of Computer Science and Technology, Xidian University, 266 Xinglong Section of Xifeng Road, Xi'an, Shaanxi 710126, China.
The pathogenesis of complex diseases is intricately linked to various genes and network medicine has enhanced understanding of diseases. However, most network-based approaches ignore interactions mediated by noncoding RNAs (ncRNAs) and most databases only focus on the association between genes and diseases. Based on the mentioned questions, we have developed DisGeNet, a database focuses not only on the disease-associated genes but also on the interactions among genes.
View Article and Find Full Text PDFCancers (Basel)
January 2025
Department of Dermatology, University of Florida College of Medicine, Gainesville, FL 32606, USA.
Despite significant strides in anti-melanoma therapies, resistance and recurrence remain major challenges. A deeper understanding of the underlying biology of these challenges is necessary for developing more effective treatment paradigms. Melanoma single-cell data were retrieved from the Broad Single Cell Portal (SCP11).
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China.
Melatonin is a hormone released by the pineal gland that regulates the sleep-wake cycle. It has been widely studied for its therapeutic effects on Alzheimer's disease (AD), particularly through the amyloidosis, oxidative stress, and neuroinflammation pathways. Nevertheless, the mechanisms through which it exerts its neuroprotective effects in AD are still largely unknown.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China.
Salt tolerance is a critical trait for plant survival and productivity in saline environments. Development of salt tolerant crops is a practical strategy for addressing soil salinity issues. In this study, RNA-Seq analysis was performed using two wheat cultivars with contrasting salt tolerance (Neixiang188, tolerant and Barra, sensitive) at 6 h and 24 h after salinity treatment to determine the genetic variations reflected in the RNA expression patterns and identify key genes associated with salt tolerance.
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