Model independent study of the Dirac structure of the nucleon-nucleon interaction

Relativistic and non-relativistic modern nucleon-nucleon potentials are mapped on a relativistic operator basis using projection techniques. This allows to compare the various potentials at the level of covariant amplitudes were a remarkable agreement is found. In nuclear matter large scalar and vector mean fields of several hundred MeV magnitude are generated at tree level. This is found to be a model independent feature of the nucleon-nucleon interaction.Comment: 5 pages, 2 figures, results for V_lowk added, to appear in PR

Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements

Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape. We explored sets of randomly selected satDNA-harboring genomic fragments in four mollusc species to examine satDNA transition sites, and the nature of adjacent sequences. All examined junctions are characterized by abrupt transitions from satDNAs to other sequences. Among them, junctions of only one examined satDNA mapped non-randomly (within the palindrome), indicating that well-defined sequence feature is not a necessary prerequisite in the junction formation. In the studied sample, satDNA flanking sequences can be roughly classified into two groups. The first group is composed of anonymous DNA sequences which occasionally include short segments of transposable elements (TEs) as well as segments of other satDNA sequences. In the second group, satDNA repeats and the array flanking sequences are identified as parts of TEs of the Helitron superfamily. There, some array flanking regions hold fragmented satDNA monomers alternating with anonymous sequences of comparable length as missing monomer parts, suggesting a process of sequence reorganization by a mechanism able to excise short monomer parts and replace them with unrelated sequences. The observed architecture of satDNA transition sites can be explained as a result of insertion and/or recombination events involving short arrays of satDNA monomers and TEs, in combination with hypothetical transposition-related ability of satDNA monomers to be shuffled independently in the genome. We conclude that satDNAs and TEs can form a complex network of sequences which essentially share the propagation mechanisms and in synergy shape the genome

Conserved DNA motifs, including the CENP-B box-like, are involved in satellite DNA array rearrangements

Satellite DNAs (satDNAs), despite rapid evolution that continuously remodel the genomic landscape, occupy functionally essential centromeric regions. Difficult to be explored due to their repetitive nature and divergence, satDNAs are still hardly accessible frontiers of eukaryotic genomes and knowledge concerning functional significance of satellite DNAs is rather limited. In this work, we provide a comprehensive analysis of six satDNAs in the library of recently separated root-knot nematodes Meloidogyne chitwoodi and M. fallax. We disclosed two different conserved regions common for analyzed satDNAs. One appeared to be highly similar to the CENP-B box of human alpha satDNA, which emerged, in sequence alignment, as a conserved segment common for six divergent satDNAs shared by closely related genomes. Observed results emphasize it as the most prominent example of the CENP-B box-like motif out of mammals. The proposed feature of the CENP-B box-like motif is to act as a promoter in the hypothesized cut-and-paste transposition-related mechanism. This observation could represent a novel role of the CENP-B box, in addition to the known function in centromere protein binding. We propose that the second conserved sequence motif detected in explored satDNAs is involved in illegitimate recombination. In parallel to alpha satDNAs, we found organization of satDNA arrays in nematodes comparable to that found in human and primates, in the form of simple and complex higher order repeats (HORs). In contrast to human satDNA organization, characterized by phylogenetically distinct HOR and monomeric forms, organizational patterns observed in nematodes are consistent with frequent and continuous shuffling of sequences between HORs and monomeric arrays. Our results suggest the role of conserved domains in mechanisms that cause rapid shuffling of sequences among divergent satDNAs, on the level of short-segment tracts. In context of satDNA evolution, our finding provides, for the first time, an experimentally verified link between conserved domains and satDNA rearrangement events

Nuclear matter in the chiral limit and the in-medium chiral condensate

We investigate nuclear matter, i.e. the nuclear equation-of-state (EOS) as well as the relativistic mean fields in the chiral limit. The investigations are based on a chiral nucleon-nucleon EFT interaction where the explicit and implicit pion mass dependence is known up to next-to-leading order. The nuclear bulk properties are found to remain fairly stable in the chiral limit. Based on the same interaction the in-medium scalar condensate is derived, both in Hartree-Fock approximation as well as from the Brueckner G-matrix, making thereby use of the Hellman-Feynman theorem. Short distance physics which determines the reduction of the in-medium nucleon mass is found to play only a minor role for the reduction of the chiral condensate.Comment: 30 pages, 5 figs. To appear in Nuclear Physics

The relativistic self-energy in nuclear dynamics

It is a well known fact that Dirac phenomenology of nuclear forces predicts the existence of large scalar and vector mean fields in matter. To analyse the relativistic self-energy in a model independent way, modern high precision nucleon-nucleon ($NN$) potentials are mapped on a relativistic operator basis using projection techniques. This allows to compare the various potentials at the level of covariant amplitudes were a remarkable agreement is found. It allows further to calculate the relativistic self-energy in nuclear matter in Hartree-Fock approximation. Independent of the choice of the nucleon-nucleon interaction large scalar and vector mean fields of several hundred MeV magnitude are generated at tree level. In the framework of chiral EFT these fields are dominantly generated by contact terms which occur at next-to-leading order in the chiral expansion. Consistent with Dirac phenomenology the corresponding low energy constants which generate the large fields are closely connected to the spin-orbit interaction in $NN$ scattering. The connection to QCD sum rules is discussed as well.Comment: 49 pages, 13 figure