2,700 research outputs found

    Phase Behavior of Melts of Diblock-Copolymers with One Charged Block

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    In this work we investigated the phase behavior of melts of block-copolymers with one charged block by means of dissipative particle dynamics with explicit electrostatic interactions. We assumed that all the Flory-Huggins \c{hi} parameters were equal to 0 and showed that the charge correlation attraction solely can cause microphase separation with long-range order; a phase diagram was constructed by varying the volume fraction of the uncharged block and the electrostatic interaction parameter {\lambda}. The obtained phase diagram was compared to the phase diagram of corresponding neutral diblock-copolymers. Surprisingly, the differences between these phase diagrams are rather subtle; the same phases are observed, and the positions of the ODT points are similar if the {\lambda}-parameter is considered as an "effective" \c{hi}-parameter. Next, we studied the position of the ODT for lamellar structure depending on the chain length N. It turned out that while for the uncharged diblock-copolymer the product \c{hi}crN was almost independent of N, for the diblock-copolymers with one charged block we observed a significant increase in {\lambda}crN upon increasing N. It can be attributed to the fact that the counterion entropy prevents the formation of ordered structures. This was supported by studying the ODT in diblock-copolymers with charged blocks and counterions cross-linked to the charged monomer units. The ODT for such systems was observed at significantly lower values of {\lambda} with the difference being more pronounced at longer chain lengths N. The diffusion of counterions in the obtained ordered structures was studied and compared to the case of a system with the same number of charged groups but homogeneous structure; the diffusion coefficient in a direction in the lamellar plane was found to be higher than in any direction in homogeneous structure

    Commutation relations on the covariant derivative

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    AbstractThe n-th order covariant derivative on a smooth manifold with affine connection is a differential operator which maps a function to a tensor field of type (0,n). In the paper the properties of this operator related to the permutations of indices are investigated by means of non-associative algebra. The general formula for commutation relations of this kind is obtained

    Early replication timing of the chicken α-globin gene domain correlates with its open chromatin state in cells of different lineages

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    AbstractThe vertebrate α-globin gene domain is an open chromatin domain overlapping a neighboring house-keeping gene. The tissue-specific cluster of α-globin genes and the overlapping housekeeping gene share the same replication origin. We have studied the replication timing of chicken α-globin genes in cells of different lineages using the FISH-based approach and found that α-globin genes replicate early both in erythroid and in non-erythroid cells, i.e. regardless of their transcriptional activity. Early replication timing of chicken α-globin genes in cells of different lineages was in good correlation with the open chromatin configuration of the α-globin gene domain in both erythroid and non-erythroid cells. We propose that active transcription of the housekeeping gene overlapping the α-globin gene domain enables an access of Origin Recognition Complex (ORC) proteins to the replication origin resulting in early replication of α-globin genes even in non-erythroid cells

    Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure

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    We have developed an experimental procedure to analyze the spatial proximity of nuclear matrix-bound DNA fragments. This protocol, referred to as Matrix 3C (M3C), includes a high salt extraction of nuclei, the removal of distal parts of unfolded DNA loops using restriction enzyme treatment, ligation of the nuclear matrix-bound DNA fragments and a subsequent analysis of ligation frequencies. Using the M3C procedure, we have demonstrated that CpG islands of at least three housekeeping genes that surround the chicken α-globin gene domain are assembled into a complex (presumably, a transcription factory) that is stabilized by the nuclear matrix in both erythroid and non-erythroid cells. In erythroid cells, the regulatory elements of the α-globin genes are attracted to this complex to form a new assembly: an active chromatin hub that is linked to the pre-existing transcription factory. The erythroid-specific part of the assembly is removed by high salt extraction. Based on these observations, we propose that mixed transcription factories that mediate the transcription of both housekeeping and tissue-specific genes are composed of a permanent compartment containing integrated into the nuclear matrix promoters of housekeeping genes and a ā€˜guest’ compartment where promoters and regulatory elements of tissue-specific genes can be temporarily recruited

    TMEM8 – a non-globin gene entrapped in the globin web

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    For more than 30 years it was believed that globin gene domains included only genes encoding globin chains. Here we show that in chickens, the domain of α-globin genes also harbor the non-globin gene TMEM8. It was relocated to the vicinity of the α-globin cluster due to inversion of an ∼170-kb genomic fragment. Although in humans TMEM8 is preferentially expressed in resting T-lymphocytes, in chickens it acquired an erythroid-specific expression profile and is upregulated upon terminal differentiation of erythroblasts. This correlates with the presence of erythroid-specific regulatory elements in the body of chicken TMEM8, which interact with regulatory elements of the α-globin genes. Surprisingly, TMEM8 is not simply recruited to the α-globin gene domain active chromatin hub. An alternative chromatin hub is assembled, which includes some of the regulatory elements essential for the activation of globin gene expression. These regulatory elements should thus shuttle between two different chromatin hubs
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