A theory of baryon resonances at large N_c

At large number of colors, N_c quarks in baryons are in a mean field of definite space and flavor symmetry. We write down the general Lorentz and flavor structure of the mean field, and derive the Dirac equation for quarks in that field. The resulting baryon resonances exhibit an hierarchy of scales: The crude mass is O(N_c), the intrinsic quark excitations are O(1), and each intrinsic quark state entails a finite band of collective excitations that are split as O(1/N_c). We build a (new) theory of those collective excitations, where full dynamics is represented by only a few constants. In a limiting (but unrealistic) case when the mean field is spherically-and flavor-symmetric, our classification of resonances reduces to the SU(6) classification of the old non-relativistic quark model. Although in the real world N_c is only three, we obtain a good accordance with the observed resonance spectrum up to 2 GeV.Comment: 27 pages, 4 figures, minor changes, resembles published versio

Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation

Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum likelihood approach to determine the history of substitution patterns in the human genome. This approach utilizes the vast amount of repetitive sequence deposited in the human genome over the past ~250 MYR. Using this approach we estimate the frequencies of seven types of substitutions: the four transversions, two transitions, and the methyl-assisted transition of cytosine in CpG. Comparing substitutional patterns in repetitive elements of various ages, we reconstruct the history of the base-substitutional process in the different isochores for the past 250 Myr. At around 90 Myr ago (around the time of the mammalian radiation), we find an abrupt 4- to 8-fold increase of the cytosine transition rate in CpG pairs compared to that of the reptilian ancestor. Further analysis of nucleotide substitutions in regions with different GC-content reveals concurrent changes in the substitutional patterns. While the substitutional pattern was dependent on the regional GC-content in such ways that it preserved the regional GC-content before the mammalian radiation, it lost this dependence afterwards. The substitutional pattern changed from an isochore-preserving to an isochore-degrading one. We conclude that isochores have been established before the radiation of the eutherian mammals and have been subject to the process of homogenization since then

Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specific effects

This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since the mammalian radiation, yielding a number of results that would have been difficult to obtain using the more conventional comparative method of analysis. This analysis revealed substantial and consistent variability of rates of substitution, with the variability ranging up to 2-fold among different regions. The rates of substitutions of C or G nucleotides with A or T nucleotides vary much more sharply than the reverse rates suggesting that much of that variation is due to differences in mutation rates rather than in the probabilities of fixation of C/G vs. A/T nucleotides across the genome. For all types of substitution we observe substantially more hotspots than coldspots, with hotspots showing substantial clustering over tens of Mbp's. Our analysis revealed that GC-content of surrounding sequences is the best predictor of the rates of substitution. The pattern of substitution appears very different near telomeres compared to the rest of the genome and cannot be explained by the genome-wide correlations of the substitution rates with GC content or exon density. The telomere pattern of substitution is consistent with natural selection or biased gene conversion acting to increase the GC-content of the sequences that are within 10-15 Mbp away from the telomere.Comment: 35 pages, 6 figure

Strong Purifying Selection at Synonymous Sites in D. melanogaster

Synonymous sites are generally assumed to be subject to weak selective constraint. For this reason, they are often neglected as a possible source of important functional variation. We use site frequency spectra from deep population sequencing data to show that, contrary to this expectation, 22% of four-fold synonymous (4D) sites in D. melanogaster evolve under very strong selective constraint while few, if any, appear to be under weak constraint. Linking polymorphism with divergence data, we further find that the fraction of synonymous sites exposed to strong purifying selection is higher for those positions that show slower evolution on the Drosophila phylogeny. The function underlying the inferred strong constraint appears to be separate from splicing enhancers, nucleosome positioning, and the translational optimization generating canonical codon bias. The fraction of synonymous sites under strong constraint within a gene correlates well with gene expression, particularly in the mid-late embryo, pupae, and adult developmental stages. Genes enriched in strongly constrained synonymous sites tend to be particularly functionally important and are often involved in key developmental pathways. Given that the observed widespread constraint acting on synonymous sites is likely not limited to Drosophila, the role of synonymous sites in genetic disease and adaptation should be reevaluated

Adiabatic processes realized with a trapped Brownian particle

We experimentally realize quasistatic adiabatic processes using a single optically-trapped micro- sphere immersed in water whose effective temperature is controlled by an external random electric field. A full energetic characterization of adiabatic processes that preserve either the position dis- tribution or the full phase space volume is presented. We show that only in the latter case the exchanged heat and the change in the entropy of the particle vanish when averaging over many repetitions. We provide analytical expressions for the distributions of the fluctuating heat and en- tropy, which we verify experimentally. We show that the heat distribution is asymmetric for any non-isothermal quasistatic process. Moreover, the shape of the distribution of the system entropy change in the adiabatic processes depends significantly on the number of degrees of freedom that are considered for the calculation of system entropy

Singular point characterization in microscopic flows

We suggest an approach to microrheology based on optical traps in order to measure fluid fluxes around singular points of fluid flows. We experimentally demonstrate this technique, applying it to the characterization of controlled flows produced by a set of birefringent spheres spinning due to the transfer of light angular momentum. Unlike the previous techniques, this method is able to distinguish between a singular point in a complex flow and the absence of flow at all; furthermore it permits us to characterize the stability of the singular point.Comment: 4 pages and 4 figure

Pervasive Natural Selection in the <i>Drosophila</i> Genome?

Over the past four decades, the predominant view of molecular evolution saw little connection between natural selection and genome evolution, assuming that the functionally constrained fraction of the genome is relatively small and that adaptation is sufficiently infrequent to play little role in shaping patterns of variation within and even between species. Recent evidence from Drosophila, reviewed here, suggests that this view may be invalid. Analyses of genetic variation within and between species reveal that much of the Drosophila genome is under purifying selection, and thus of functional importance, and that a large fraction of coding and noncoding differences between species are adaptive. The findings further indicate that, in Drosophila, adaptations may be both common and strong enough that the fate of neutral mutations depends on their chance linkage to adaptive mutations as much as on the vagaries of genetic drift. The emerging evidence has implications for a wide variety of fields, from conservation genetics to bioinformatics, and presents challenges to modelers and experimentalists alike.</p

Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogastergenome

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Recent analysis of the human and mouse genomes has shown that a substantial proportion of protein coding genes and cis-regulatory elements contain transposable element (TE) sequences, implicating TE domestication as a mechanism for the origin of genetic novelty. To understand the general role of TE domestication in eukaryotic genome evolution, it is important to assess the acquisition of functional TE sequences by host genomes in a variety of different species, and to understand in greater depth the population dynamics of these mutational events. Results Using an in silico screen for host genes that contain TE sequences, we identified a set of 63 mature "chimeric" transcripts supported by expressed sequence tag (EST) evidence in the Drosophila melanogaster genome. We found a paucity of chimeric TEs relative to expectations derived from non-chimeric TEs, indicating that the majority (~80%) of TEs that generate chimeric transcripts are deleterious and are not observed in the genome sequence. Using a pooled-PCR strategy to assay the presence of gene-TE chimeras in wild strains, we found that over half of the observed chimeric TE insertions are restricted to the sequenced strain, and ~15% are found at high frequencies in North American D. melanogaster populations. Estimated population frequencies of chimeric TEs did not differ significantly from non-chimeric TEs, suggesting that the distribution of fitness effects for the observed subset of chimeric TEs is indistinguishable from the general set of TEs in the genome sequence. Conclusion In contrast to mammalian genomes, we found that fewer than 1% of Drosophila genes produce mRNAs that include bona fide TE sequences. This observation can be explained by the results of our population genomic analysis, which indicates that most potential chimeric TEs in D. melanogaster are deleterious but that a small proportion may contribute to the evolution of novel gene sequences such as nested or intercalated gene structures. Our results highlight the need to establish the fixity of putative cases of TE domestication identified using genome sequences in order to demonstrate their functional importance, and reveal that the contribution of TE domestication to genome evolution may vary drastically among animal taxa.Published versio