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Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology.

ABSTRACT: Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process such as the topoisomerase-mediated preferential unknotting of DNA molecules. We model here topoisomerase-mediated passages of double-stranded DNA segments through each other using the formalism of grid diagrams. We show that this grid diagram-based modeling approach captures the essence of the preferential unknotting mechanism, based on topoisomerase selectivity of hooked DNA juxtapositions as the sites of intersegmental passages. We show that the grid diagram-based approach provides an important, new, and computationally convenient framework for investigating entanglement in biopolymers.

SUBMITTER: Barbensi A

PROVIDER: S-EPMC7043919 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology.

Barbensi Agnese A Celoria Daniele D Harrington Heather A HA Stasiak Andrzej A Buck Dorothy D

Science advances 20200226 9

Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process such as the topoisomerase-mediated preferential unknotting of DNA molecules. We model here topoisomerase-mediated passages of double-stranded DNA segments through each other using the formalism of grid diagrams. We show that this grid diagram-based modeling ap ...[more]

PMID: 32133398

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Project description:BackgroundThe integration of genomic and geospatial data into infectious disease transmission analyses typically includes residential locations and excludes other activity spaces where transmission may occur (e.g. work, school, or social venues). The objective of this analysis was to explore residential as well as other activity spaces of tuberculosis (TB) outbreaks to identify potential geospatial 'hotspots' of transmission.MethodsWe analyzed data that included geospatial coordinates for residence and other activity spaces collected during 2012-2016 for the Kopanyo Study, a population-based study of TB transmission in Botswana. We included participants with results from whole genome sequencing conducted on archived samples from the original study. We used a spatial log-Gaussian Cox process model to detect core areas of increased activity spaces of individuals belonging to TB outbreaks (genotypic groups with ≤5 single-nucleotide polymorphisms), which we compared to ungrouped participants (those not in a genotypic group of any size).FindingsWe analyzed data collected from 636 participants, including 70 participants belonging to six outbreak groups with a combined total of 293 locations, and 566 ungrouped participants with a combined total of 2289 locations. Core areas of activity space for each outbreak group were geographically distinct, and we found evidence of localized transmission in four of six outbreaks. For most of the outbreaks, including activity space data led to the detection of larger areas of higher spatial intensity and more focal points compared to residential location alone.InterpretationGeospatial analysis using activity space data (social gathering places as well as residence) may lead to improved understanding of areas of infectious disease transmission compared to using residential data alone.FundingThis work was supported by funding from the National Institute of Allergy and Infectious Diseases R01AI097045, R01AI147336, and R01AI170204.

Dataset Information

Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology.

Publications

Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology.

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