Impact of resonance decays on critical point signals in net-proton fluctuations

The non-monotonic beam energy dependence of the higher cumulants of net-proton fluctuations is a widely studied signature of the conjectured presence of a critical point in the QCD phase diagram. In this work we study the effect of resonance decays on critical fluctuations. We show that resonance effects reduce the signatures of critical fluctuations, but that for reasonable parameter choices critical effects in the net-proton cumulants survive. The relative role of resonance decays has a weak dependence on the order of the cumulants studied with a slightly stronger suppression of critical effects for higher-order cumulants

Fluctuations of Particle Yield Ratios in Heavy-Ion Collisions

We study the dynamical fluctuations of various particle yield ratios at different incident energies. Assuming that the particle production yields in the hydronic final state are due to equilibrium chemical processes ($\gamma=1$), the experimental results available so far are compared with the hadron resonance gas model (HRG) taking into account the limited momentum acceptance in heavy-ion collisions experiments. Degenerated light and conserved strange quarks are presumed at all incident energies. At the SPS energies, the HRG with $\gamma=1$ provides a good description for the measured dynamical fluctuations in $(K^++K^-)/(\pi^++\pi^-)$. To reproduce the RHIC results, $\gamma$ should be larger than one. We also studied the dynamical fluctuations of $(p+\bar{p})/(\pi^++\pi^-)$. It is obvious that the energy-dependence of these dynamical fluctuations is non-monotonic.Comment: 8 pages, 2 eps figures and 1 tabl

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>All sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. Despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. As more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing.</p> <p>Results</p> <p>This study provides a comprehensive analysis of the origins of lineage-specific genes (LSGs) in <it>Arabidopsis thaliana </it>that are restricted to the Brassicaceae family. In this study, lineage-specific genes within the nuclear (1761 genes) and mitochondrial (28 genes) genomes are identified. The evolutionary origins of two thirds of the lineage-specific genes within the <it>Arabidopsis thaliana </it>genome are also identified. Almost a quarter of lineage-specific genes originate from non-lineage-specific paralogs, while the origins of ~10% of lineage-specific genes are partly derived from DNA exapted from transposable elements (twice the proportion observed for non-lineage-specific genes). Lineage-specific genes are also enriched in genes that have overlapping CDS, which is consistent with such novel genes arising from overprinting. Over half of the subset of the 958 lineage-specific genes found only in <it>Arabidopsis thaliana </it>have alignments to intergenic regions in <it>Arabidopsis lyrata</it>, consistent with either <it>de novo </it>origination or differential gene loss and retention, with both evolutionary scenarios explaining the lineage-specific status of these genes. A smaller number of lineage-specific genes with an incomplete open reading frame across different <it>Arabidopsis thaliana </it>accessions are further identified as accession-specific genes, most likely of recent origin in <it>Arabidopsis thaliana</it>. Putative <it>de novo </it>origination for two of the <it>Arabidopsis thaliana</it>-only genes is identified via additional sequencing across accessions of <it>Arabidopsis thaliana </it>and closely related sister species lineages. We demonstrate that lineage-specific genes have high tissue specificity and low expression levels across multiple tissues and developmental stages. Finally, stress responsiveness is identified as a distinct feature of Brassicaceae-specific genes; where these LSGs are enriched for genes responsive to a wide range of abiotic stresses.</p> <p>Conclusion</p> <p>Improving our understanding of the origins of lineage-specific genes is key to gaining insights regarding how novel genes can arise and acquire functionality in different lineages. This study comprehensively identifies all of the Brassicaceae-specific genes in <it>Arabidopsis thaliana </it>and identifies how the majority of such lineage-specific genes have arisen. The analysis allows the relative importance (and prevalence) of different evolutionary routes to the genesis of novel ORFs within lineages to be assessed. Insights regarding the functional roles of lineage-specific genes are further advanced through identification of enrichment for stress responsiveness in lineage-specific genes, highlighting their likely importance for environmental adaptation strategies.</p

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

Transposable elements (TEs) are mobile genetic elements that parasitize genomes by semi-autonomously increasing their own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performing unbiased genome-wide surveys of TE variation in natural populations have been lacking. Here, we describe a novel and cost-effective approach for estimating population frequencies of TE insertions using paired-end Illumina reads from a pooled population sample. Importantly, the method treats insertions present in and absent from the reference genome identically, allowing unbiased TE population frequency estimates. We apply this method to data from a natural Drosophila melanogaster population from Portugal. Consistent with previous reports, we show that low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions. We conservatively estimate that there are almost twice as many “novel” TE insertion sites as sites known from the reference sequence in our population sample (6,824 novel versus 3,639 reference sites, with on average a 31-fold coverage per insertion site). Different families of transposable elements show large differences in their insertion densities and population frequencies. Our analyses suggest that the history of TE activity significantly contributes to this pattern, with recently active families segregating at lower frequencies than those active in the more distant past. Finally, using our high-resolution TE abundance measurements, we identified 13 candidate positively selected TE insertions based on their high population frequencies and on low Tajima's D values in their neighborhoods

K∗(892)0K^{*}(892)^0 production in p++p interactions from NA61/SHINE

The measurement of $K^*(892)^0$ resonance production via its $K^+ \pi ^-$ decay mode in inelastic p$+$p collisions at beam momenta 40–158 GeV/c ($\sqrt{s_{\text {NN}}}=8.8-17.3$ GeV) is presented. The data were recorded by the NA61/SHINENA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. The analysis of $K^*(892)^0$ was done with the template method. The results include the double differential spectra $d^2 n/(dydp_{\text {T}})$, $d^2 n/(m_{\text {T}} dm_{\text {T}}dy)$ as well as dn/dy spectra.The measurement of $K^*(892)^0$ resonance production via its $K^+ \pi^-$ decay mode in inelastic p+p collisions at beam momenta 40$-$158 GeV/c ($\sqrt{s_{NN}}$=8.8$-$17.3 GeV) is presented. The data were recorded by the NA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. The analysis of $K^*(892)^0$ was done with the template method. The results include the double differential spectra $d^2 n/(dydp_T)$, $d^2 n/(m_T dm_T dy)$ as well as dn/dy spectra