Evolution of conserved secondary structures and their function in transcriptional regulation networks

<p>Abstract</p> <p>Background</p> <p>Many conserved secondary structures have been identified within conserved elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations of these conserved secondary structures in human populations and their biological functions have not been fully studied.</p> <p>Results</p> <p>We searched for polymorphisms within conserved secondary structures and identified a number of SNPs within these elements even though they are highly conserved among species. The density of SNPs in conserved secondary structures is about 65% of that of their flanking, non-conserved, sequences. Classification of sites as stems or as loops/bulges revealed that the density of SNPs in stems is about 62% of that found in loops/bulges. Analysis of derived allele frequency data indicates that sites in stems are under stronger evolutionary constraint than sites in loops/bulges. Intergenic conserved secondary structures tend to associate with transcription factor-encoding genes with genetic distance being the measure of regulator-gene associations. A substantial fraction of intergenic conserved secondary structures overlap characterized binding sites for multiple transcription factors.</p> <p>Conclusion</p> <p>Strong purifying selection implies that secondary structures are probably important carriers of biological functions for conserved sequences. The overlap between intergenic conserved secondary structures and transcription factor binding sites further suggests that intergenic conserved secondary structures have essential roles in directing gene expression in transcriptional regulation networks.</p

Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair

Correction to Wu DD, Irwin DM, Zhang YP: Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair. BMC Evol Biol 2008, 8:241

Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats

The Nucleon-Nucleon Interaction in a Chiral Constituent Quark Model

We study the short-range nucleon-nucleon interaction in a chiral constituent quark model by diagonalizing a Hamiltonian comprising a linear confinement and a Goldstone boson exchange interaction between quarks. The six-quark harmonic oscillator basis contains up to two excitation quanta. We show that the highly dominant configuration is $\mid s^4p^2[42]_O [51]_{FS}>$ due to its specific flavour-spin symmetry. Using the Born-Oppenheimer approximation we find a strong effective repulsion at zero separation between nucleons in both $^3S_1$ and $^1S_0$ channels. The symmetry structure of the highly dominant configuration implies the existence of a node in the S-wave relative motion wave function at short distances. The amplitude of the oscillation of the wave function at short range will be however strongly suppressed. We discuss the mechanism leading to the effective short-range repulsion within the chiral constituent quark model as compared to that related with the one-gluon exchange interaction.Comment: 31 pages, LaTe

Large-deviation analysis for counting statistics in mesoscopic transports

We present an efficient approach, based on a number-conditioned master equation, for large-deviation analysis in mesoscopic transports. Beyond the conventional full-counting-statistics study, the large-deviation approach encodes complete information of both the typical trajectories and the rare ones, in terms of revealing a continuous change of the dynamical phase in trajectory space. The approach is illustrated with two examples: (i) transport through a single quantum dot, where we reveal the inhomogeneous distribution of trajectories in general case and find a particular scale invariance point in trajectory statistics; and (ii) transport through a double dots, where we find a dynamical phase transition between two distinct phases induced by the Coulomb correlation and quantum interference.Comment: 8 pages, 3 figure

The d' dibaryon in the quark-delocalization, color-screening model

We study the questions of the existence and mass of the proposed $d' (IJ^P=00^-)$ dibaryon in the quark-delocalization, color-screening model (QDCSM). The transformation between physical and symmetry bases has been extended to the cases beyond the SU(2) orbital symmetry. Using parameters fixed by baryon properties and $NN$ scattering, we find a mild attraction in the $IJ^P=00^-$ channel, but it is not strong enough to form a deeply bound state as proposed for the $d'$ state. Nor does the (isospin) I=2 N$\Delta$ configuration have a deeply bound state. These results show that if a narrow dibaryon $d'$ state does exist, it must have a more complicated structure.Comment: 12 pp. latex, no figs., 2 tables, additional refs., Report-no was adde