67 research outputs found
Expression-Dependent Folding of Interphase Chromatin
Multiple studies suggest that chromatin looping might play a crucial role in organizing eukaryotic genomes. To investigate the interplay between the conformation of interphase chromatin and its transcriptional activity, we include information from gene expression profiles into a polymer model for chromatin that incorporates genomic loops. By relating loop formation to transcriptional activity, we are able to generate chromosome conformations whose structural and topological properties are consistent with experimental data. The model particularly allows to reproduce the conformational variations that are known to occur between highly and lowly expressed chromatin regions. As previously observed in experiments, lowly expressed regions of the simulated polymers are much more compact. Due to the changes in loop formation, the distributions of chromatin loops are also expression-dependent and exhibit a steeper decay in highly active regions. As a results of entropic interaction between differently looped parts of the chromosome, we observe topological alterations leading to a preferential positioning of highly transcribed loci closer to the surface of the chromosome territory. Considering the diffusional behavior of the chromatin fibre, the simulations furthermore show that the higher the expression level of specific parts of the chromatin fibre is, the more dynamic they are. The results exhibit that variations of loop formation along the chromatin fibre, and the entropic changes that come along with it, do not only influence the structural parameters on the local scale, but also effect the global chromosome conformation and topology
Lifelong testicular differentiation in Pleurodeles waltl (Amphibia, Caudata)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens
The Putative Liquid-Liquid Transition is a Liquid-Solid Transition in Atomistic Models of Water
We use numerical simulation to examine the possibility of a reversible
liquid-liquid transition in supercooled water and related systems. In
particular, for two atomistic models of water, we have computed free energies
as functions of multiple order parameters, where one is density and another
distinguishes crystal from liquid. For a range of temperatures and pressures,
separate free energy basins for liquid and crystal are found, conditions of
phase coexistence between these phases are demonstrated, and time scales for
equilibration are determined. We find that at no range of temperatures and
pressures is there more than a single liquid basin, even at conditions where
amorphous behavior is unstable with respect to the crystal. We find a similar
result for a related model of silicon. This result excludes the possibility of
the proposed liquid-liquid critical point for the models we have studied.
Further, we argue that behaviors others have attributed to a liquid-liquid
transition in water and related systems are in fact reflections of transitions
between liquid and crystal
Visualisation and characterisation of mononuclear phagocytes in the chicken respiratory tract using CSF1R-transgenic chickens
Additional file 2. Location of B cells, T cells and follicular dendritic cells (FDC) in the lung of MacReporter chickens. The BALT region of 5 to 7 week old non-vaccination animals were analysed for B, T and FCD cells. Isotype controls were used to standardise the microscope and examine aspecific binding before acquiring images (A-B). The GC of MacReporter animals are tightly packed with Bu1-CSF1R-eGFP+ FDC cells and Bu1+CSF1R-eGFP- B cells (C) with few Bu1+ B cells found in the parabronchi (F). CD3+ T cells are disperse within and outside the GC (D) and parabronchi (G). CSF1R-eGFP+ FDC cells express Fc receptors and trap immunoglobulin by expressing IgY (E) and CSF1R-eGFP+ IgY+ FDC are rarely detected out with the GC, BALT region of the lung. GC are indicated by white dashed lines
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