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Chromatin dynamics and organization can be altered by condensin complexes. In turn, the molecular behavior of a condensin complex changes based on the tension of the substrate to which condensin is bound. This interplay between chromatin organization and condensin behavior demonstrates the need for tools that allows condensin complexes to be observed on a variety of chromatin organizations. We provide a method for simulating condensin complexes on a dynamic polymer substrate using the polymer dynamics simulator ChromoShake and the condensin simulator RotoStep. These simulations can be converted into simulated fluorescent images that are able to be directly compared to experimental images of condensin and fluorescently labeled chromatin. Our pipeline enables users to explore how changes in condensin behavior alters chromatin dynamics and vice versa while providing simulated image datasets that can be directly compared to experimental observations.
This article was published in the following journal.
Name: Methods in molecular biology (Clifton, N.J.)
Molecular dynamics simulation is a powerful tool used in modern molecular modeling, which enables a deeper comprehension of the physical behavior of atoms and molecules at a micro level. In this study...
Condensins are highly conserved proteins that are important for chromosome maintenance in nearly all forms of life. While many organisms employ two forms of the condensin complex, the condensin genes ...
Structural maintenance of chromosomes (SMC) complexes play pivotal roles in controlling chromatin organization. Condensin is an essential SMC complex that compacts chromatin to form condensed chromoso...
The condensin protein complex plays a key role in the structural organization of genomes. How the ATPase activity of its SMC subunits drives large-scale changes in chromosome topology has remained unk...
New training methods such as simulation have been introduced in cardiology as in other specialties; however, the development of effective simulation-based training programs is challenging. They are of...
Rapid technological advances in the last 20 years have led to the exponential adoption of simulation-based learning in nursing education.
Debriefing after simulation plays a crucial role in student learning and medical practice. This paper focuses on impact of computer debriefing technique on knowledge retention of midwives ...
The investigators hypothesise that simulation-based training will have initial educational benefits and in coherence with the traditional apprenticeship model will heighten the educational...
The investigators aim to test a curriculum of non-technical skills (NTS) training for simulation-based training of colonoscopy. There is no known literature to date on the optimal approach...
Prostate cancer (CAP) is one of the most common malignancies in men, both in Western countries and developing countries. Radiation therapy (RT) is an important therapeutic option. New tech...
A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.
A computer simulation developed to study the motion of molecules over a period of time.
Computer-based representation of physical systems and phenomena such as chemical processes.
Echocardiography amplified by the addition of depth to the conventional two-dimensional ECHOCARDIOGRAPHY visualizing only the length and width of the heart. Three-dimensional ultrasound imaging was first described in 1961 but its application to echocardiography did not take place until 1974. (Mayo Clin Proc 1993;68:221-40)
Descriptive anatomy based on three-dimensional imaging (IMAGING, THREE-DIMENSIONAL) of the body, organs, and structures using a series of computer multiplane sections, displayed by transverse, coronal, and sagittal analyses. It is essential to accurate interpretation by the radiologist of such techniques as ultrasonic diagnosis, MAGNETIC RESONANCE IMAGING, and computed tomography (TOMOGRAPHY, X-RAY COMPUTED). (From Lane & Sharfaei, Modern Sectional Anatomy, 1992, Preface)
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...