The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441796 | PMC |
| http://dx.doi.org/10.1093/nar/gkn192 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Identification of key regulators in pancreatic ductal adenocarcinoma using network theoretical approach.
PLoS One
January 2025
Department of Chemistry, Ashoka University, Sonipat, Haryana, India.
Pancreatic Ductal Adenocarcinoma (PDAC) is a devastating disease with poor clinical outcomes, which is mainly because of delayed disease detection, resistance to chemotherapy, and lack of specific targeted therapies. The disease's development involves complex interactions among immunological, genetic, and environmental factors, yet its molecular mechanism remains elusive. A major challenge in understanding PDAC etiology lies in unraveling the genetic profiling that governs the PDAC network.
View Article and Find Full Text PDFPhotooxidation Cross-Linked, Glutaraldehyde Cross-Linked, or Enzyme and Hydrostatic Pressure Processed Decellularized Biomaterials for Cardiovascular Repair Do Not Affect Host Response in a Rat Right Ventricular Outflow Flow Tract Reconstruction (RVOT) Model.
J Biomed Mater Res B Appl Biomater
February 2025
McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania, USA.
Cardiovascular diseases (CVDs) were responsible for approximately 19 million deaths in 2020, marking an increase of 18.7% since 2010. Biological decellularized patches are common therapeutic solutions for CVD such as cardiac and valve defects.
View Article and Find Full Text PDFBioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction.
Brief Bioinform
November 2024
Suzhou Key Lab of Multi-modal Data Fusion and Intelligent Healthcare, No. 1188 Wuzhong Avenue, Wuzhong District Suzhou, Suzhou 215004, China.
The automatic and accurate extraction of diverse biomedical relations from literature constitutes the core elements of medical knowledge graphs, which are indispensable for healthcare artificial intelligence. Currently, fine-tuning through stacking various neural networks on pre-trained language models (PLMs) represents a common framework for end-to-end resolution of the biomedical relation extraction (RE) problem. Nevertheless, sequence-based PLMs, to a certain extent, fail to fully exploit the connections between semantics and the topological features formed by these connections.
View Article and Find Full Text PDFA deep learning tissue classifier based on differential Co-expression genes predicts the pregnancy outcomes of cattle.
Biol Reprod
January 2025
Inner Mongolia SK·Xing Animal Breeding and Breeding Biotechnology Research Institute Co., Ltd, Hohhot 011517, China.
Economic losses in cattle farms are frequently associated with failed pregnancies. Some studies found that the transcriptomic profiles of blood and endometrial tissues in cattle with varying pregnancy outcomes display discrepancies even before artificial insemination (AI) or embryo transfer (ET). In the study, 330 samples from seven distinct sources and two tissue types were integrated and divided into two groups based on the ability to establish and maintain pregnancy after AI or ET: P (pregnant) and NP (nonpregnant).
View Article and Find Full Text PDFTopological importance of CD8 T-cell enrichment in the tumor microenvironment of classic Hodgkin lymphoma.
Ann Hematol
January 2025
Department of Medicine Division of Hematology and Rheumatology, Nihon University School of Medicine, Tokyo, Japan.
Classic Hodgkin lymphoma (CHL) histologically consists of Hodgkin Reed-Sternberg (HRS) cells and the tumor microenvironment (TME), but the relationship between TME characteristics and clinical features of CHL remains unclear. We aimed to investigate the effects of the TME structure on the outcomes of patients with CHL. We performed a high-throughput analysis of HRS cells and their topological relationship with the reactive immune cells in the TME.
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!