1,721,313 research outputs found
The Epithelial-Mesenchymal Transition, as Hacked by a microRNA Combinatorial Code
Full text linkA new study coupling bioinformatic and experimental investigations highlights the importance of combinatorial microRNA targeting in human EMT, a phenotypic program underlying normal and pathological processes
Conformal perturbation theory confronts lattice results in the vicinity of a critical point
Full text linkWe study the accuracy and predictive power of conformal perturbation theory by a comparison with lattice results in the neighborhood of the finite-temperature deconfinement transition of SU(2) Yang-Mills theory, assuming that the infrared properties of this non-Abelian gauge theory near criticality can be described by the Ising model. The results of this comparison show that conformal perturbation theory yields quantitatively accurate predictions in a broad temperature range. We discuss the implications of these findings for the description of the critical point (belonging to the same universality class) of another strongly coupled, non-supersymmetric non-Abelian gauge theory: the critical end-point in the phase diagram of QCD at finite temperature and finite quark chemical potential
MicroRNA-mediated regulatory circuits: outlook and perspectives
Full text linkMicroRNAs have been found to be necessary for regulating genes implicated in almost all signaling pathways, and consequently their dysfunction influences many diseases, including cancer. Understanding of the complexity of the microRNA-mediated regulatory network has grown in terms of size, connectivity and dynamics with the development of computational and, more recently, experimental high-throughput approaches for microRNA target identification. Newly developed studies on recurrent microRNA-mediated circuits in regulatory networks, also known as network motifs, have substantially contributed to addressing this complexity, and therefore to helping understand the ways by which microRNAs achieve their regulatory role. This review provides a summarizing view of the state-of-the-art, and perspectives of research efforts on microRNA-mediated regulatory motifs. In this review, we discuss the topological properties characterizing different types of circuits, and the regulatory features theoretically enabled by such properties, with a special emphasis on examples of circuits typifying their biological significance in experimentally validated contexts. Finally, we will consider possible future developments, in particular regarding microRNA-mediated circuits involving long non-coding RNAs and epigenetic regulators
Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes
Full text linkAbstract
Background
Protein-DNA recognition underlies fundamental biological processes ranging from transcription to replication and modification. Herein, we present a computational study of the sequence modulation of internal dynamic properties and of intraprotein networks of aminoacid interactions that determine the stability and specificity of protein-DNA complexes.
Results
To this aim, we apply novel theoretical approaches to analyze the dynamics and energetics of biological systems starting from MD trajectories. As model system, we chose different sequences of Zinc Fingers (ZF) of the Zif268 family bound with different sequences of DNA. The complexes differ for their experimental stability properties, but share the same overall 3 D structure and do not undergo structural modifications during the simulations. The results of our analysis suggest that the energy landscape for DNA binding may be populated by dynamically different states, even in the absence of major conformational changes. Energetic couplings between residues change in response to protein and/or DNA sequence variations thus modulating the selectivity of recognition and the relative importance of different regions for binding.
Conclusions
The results show differences in the organization of the intra-protein energy-networks responsible for the stabilization of the protein conformations recognizing and binding DNA. These, in turn, are reflected into different modulation of the ZF's internal dynamics. The results also show a correlation between energetic and dynamic properties of the different proteins and their specificity/selectivity for DNA sequences. Finally, a dynamic and energetic model for the recognition of DNA by Zinc Fingers is proposed.
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Identification of new AP-2alpha regulated genes: a biological and bioinformatic approach
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Universal signatures of the effective string in finite temperature lattice gauge theories
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The Unreasonable effectiveness of effective string theory: The case of the 3D SU(2) Higgs model
Full text linkWe study string breaking in the three-dimensional SU(2) Higgs model, using values of the gauge coupling for which the confinementlike and Higgs-like regions of the phase diagram are separated just by a smooth crossover. We show that even in the presence of string breaking, the confining part of the interquark potential is well described by the effective string theory and that also the fine details of the effective string, like the higher order terms of the Nambu-Goto action or the boundary correction, can be precisely extracted from the fits and agree with the effective string predictions. We comment on the implications of these results for QCD simulations with dynamical quarks
Thermodynamics of SU(N) gauge theories in 2+1 dimensions in the $T regime
No full textNon peer reviewe
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