Mathematical models can integrate different types of experimental datasets, reconstitute biological systems in silico, and identify previously unknown molecular mechanisms. Over the past decade, mathematical models have been developed based on quantitative observations, such as live-cell imaging and biochemical assays. However, it is difficult to directly integrate next-generation sequencing (NGS) data. Although highly dimensional, NGS data mostly only provides a "snapshot" of cellular states. Nevertheless, the development of various methods for NGS analysis has led to much more accurate predictions of transcription factor activity and has revealed various concepts regarding transcriptional regulation. Therefore, fluorescence live-cell imaging of transcription factors can help alleviate the limitations in NGS data by supplementing temporal information, linking NGS to mathematical modeling. This chapter introduces an analytical method for quantifying dynamics of nuclear factor kappaB (NF-κB) which forms aggregates in the nucleus. The method may also be applicable to other transcription factors regulated in a similar fashion.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-0716-3008-2_11 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Epidemiology and outcomes of carbapenem-resistant infections in patients with hematological malignancies from 2014 to 2022.
Front Microbiol
January 2025
Department of Infection Management and Disease Control, The First Medical Center of Chinese PLA General Hospital, Beijing, China.
Background: We aimed to describe the epidemiology, cross-transmission, interventions, and outcomes of carbapenem-resistant (CRKP) infections in the hematological malignancies (HM) department of a hospital in China.
Methods: This prospective study was divided into three stages from 2014 to 2022: Period 1 (from 1 January 2014 to 4 March 2021), Period 2 (from 5 March 2021 to 31 December 2021), and Period 3 (from 1 January 2022 to 31 December 2022), with different measures implemented at each stage to evaluate the rate of new infections. The risk factors, epidemiological characteristics, data from all patients with CRKP, NGS gene sequencing molecular epidemiology analysis, and cross-transmission were described.
Improved ChIP Sequencing for H3K27ac Profiling and Super-Enhancer Analysis Assisted by Fluorescence-Activated Sorting of Formalin-Fixed Paraffin-Embedded Tissues.
Biol Proced Online
January 2025
Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, 610041, China.
Archived clinical formalin-fixed paraffin-embedded tissue (FFPE) is valuable for the study of tumor epigenetics. Although protocol of chromatin immunoprecipitation coupled with next generation sequencing (NGS) (ChIP-seq) using FFPE samples has been established, removal of interference signals from non-target cell components in the samples is still needed. In this study, the protocol of ChIP-seq with purified cells from FFPE lymphoid tissue of nodal T follicular helper cell lymphoma, angioimmunoblastic type (nTFHL-AI) after fluorescence-activated cell sorting (FACS) was established and optimized.
View Article and Find Full Text PDFHow to combine multiple tools for the genetic diagnosis work-up of pediatric B-cell acute lymphoblastic leukemia.
Ann Hematol
January 2025
Hematology Service, Experimental Hematology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.
This study investigated the importance of comprehensive genetic diagnosis in pediatric B-cell acute lymphoblastic leukemia (B-ALL). We analyzed 175 B-ALL employing karyotyping, FISH, MLPA, targeted next-generation sequencing (t-NGS), and Optical Genome Mapping (OGM). This approach achieved an 83% classification rate, identifying 17 distinct genetic subtypes.
View Article and Find Full Text PDFIntroduction: Cytomegalovirus (CMV) is a DNA-containing virus that is widespread worldwide and is of great importance in infectious pathology of children and adults. The aim of this study is to evaluate the prevalence of CMV among children and immunocompromised patients in the Nizhny Novgorod region (central Russia) and to perform a phylogenetic analysis of the identified strains.
Materials And Methods: DNA samples of CMV detected in frequently ill children and adult recipients of solid organs were studied.
High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine.
Funct Integr Genomics
January 2025
Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, Lucknow, 226002, India.
High-resolution insights into the nucleotide arrangement within an organism's genome are pivotal for deciphering its genetic composition, function, and evolutionary trajectory. Over the years, nucleic acid sequencing has been instrumental in driving significant advancements in genomics and molecular biology. The advent of high-throughput or next-generation sequencing (NGS) technologies has revolutionized whole genome sequencing, revealing novel and intriguing features of genomes, such as single nucleotide polymorphisms and lethal mutations in both coding and non-coding regions.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!