相关论文: Topology Regulation during Replication of the Kine…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The evolution, replication and self-assembly of this structure…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
Polymer composites are ubiquitous in biology and industry alike, owing to their emergent desirable mechanical properties not attainable in single-species systems. At the same time, polymer topology has been shown to play a key role in…
The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
We use graph theory simulations and single molecule experiments to investigate percolation properties of kinetoplasts, the topologically linked mitochondrial DNA from trypanosome parasites. The edges of some kinetoplast networks contain a…
In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed", or specified, at the end of the M and the beginning of G1 phases of the cell…
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in biophysics. Most of the existing models neglect the dynamics of TopoII which is characteristics for…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…