Rampant Adaptive Evolution in Regions of Proteins with Unknown Function in Drosophila simulans

Adaptive protein evolution is pervasive in Drosophila. Genomic studies, thus far, have analyzed each protein as a single entity. However, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. We compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. Interestingly, we find that non-domain regions of proteins are more frequent targets of directional selection. Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions. Non-domain regions of proteins clearly play a major role in adaptive protein evolution on a genomic scale and merit future investigations of their functional properties

Multiplicity fluctuations in relativistic nuclear collisions

Multiplicity distributions of hadrons produced in central nucleus-nucleus collisions are studied within the hadron-resonance gas model in the large volume limit. In the canonical ensemble conservation of three charges (baryon number, electric charge, and strangeness) is enforced. In addition, in the micro-canonical ensemble energy conservation is included. An analytical method is used to account for resonance decays. Multiplicity distributions and scaled variances for negatively charged hadrons are presented along the chemical freeze-out line of central Pb+Pb (Au+Au) collisions from SIS to LHC energies. Predictions obtained within different statistical ensembles are compared with preliminary NA49 experimental results on central Pb+Pb collisions in the SPS energy range. The measured fluctuations are significantly narrower than a Poisson reference distribution, and clearly favor expectations for the micro-canonical ensemble.Comment: 6 pages, 3 figure

One-pot synthesis of pH-responsive Eudragit-mesoporous silica nanocomposites enable colonic delivery of glucocorticoids for the treatment of inflammatory bowel disease

Oral glucocorticoids are backbones for the acute management of inflammatory bowel disease (IBD). However, the clinical effectiveness of conventional oral dosage forms of glucocorticoids is hindered by their low delivery efficiency and systemic side effects. To overcome this problem, a smart drug delivery system with high loading capacity and colonic release by coating functionalized mesoporous silica nanoparticles (MSNs) with a pH‐responsive polymer Eudragit S100 is proposed. In vitro dissolution tests show that Eudragit‐coated MSNs can limit the burst release of loaded prednisolone and budesonide in the gastric environment with more than 60% of the drugs released only at colonic pH (i.e., pH ≥ 7). In vivo therapeutic efficacy of budesonide‐loaded nanoparticles is tested in a murine model of dextran sodium sulfate‐induced colitis. An oral budesonide dose of 0.2 mg kg−1 nanoparticles with Eudragit coating improves the disease activity index compared to other groups. Interestingly, both coated and uncoated nanoparticles show pathological improvements demonstrated by similar levels of histological colitis score. However, coated nanoparticles significantly decrease mRNA expression of the cytokines (Il‐1β, Il‐17, and Il‐10) particularly in proximal colon, indicating colonic delivery. Overall, this study demonstrates the effectiveness of a simple method to fabricate targeted nanomedicine for the treatment of IBD.Peer reviewe

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

De Novo Origin of Human Protein-Coding Genes

The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence. RNA–seq data indicate that these genes have their highest expression levels in the cerebral cortex and testes, which might suggest that these genes contribute to phenotypic traits that are unique to humans, such as improved cognitive ability. Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes

Quantifying Adaptive Evolution in the Drosophila Immune System

It is estimated that a large proportion of amino acid substitutions in Drosophila have been fixed by natural selection, and as organisms are faced with an ever-changing array of pathogens and parasites to which they must adapt, we have investigated the role of parasite-mediated selection as a likely cause. To quantify the effect, and to identify which genes and pathways are most likely to be involved in the host–parasite arms race, we have re-sequenced population samples of 136 immunity and 287 position-matched non-immunity genes in two species of Drosophila. Using these data, and a new extension of the McDonald-Kreitman approach, we estimate that natural selection fixes advantageous amino acid changes in immunity genes at nearly double the rate of other genes. We find the rate of adaptive evolution in immunity genes is also more variable than other genes, with a small subset of immune genes evolving under intense selection. These genes, which are likely to represent hotspots of host–parasite coevolution, tend to share similar functions or belong to the same pathways, such as the antiviral RNAi pathway and the IMD signalling pathway. These patterns appear to be general features of immune system evolution in both species, as rates of adaptive evolution are correlated between the D. melanogaster and D. simulans lineages. In summary, our data provide quantitative estimates of the elevated rate of adaptive evolution in immune system genes relative to the rest of the genome, and they suggest that adaptation to parasites is an important force driving molecular evolution

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response

How defense genes originated with the evolution of their specific pathogen-responsive traits remains an important problem. It is generally known that a form of duplication can generate new genes, suggesting that a new gene usually evolves from an ancestral gene. However, we show that a new defense gene in plants may evolve by de novo origination, resulting in sophisticated disease-resistant functions in rice. Analyses of gene evolution showed that this new gene, OsDR10, had homologs only in the closest relative, Leersia genus, but not other subfamilies of the grass family; therefore, it is a rice tribe-specific gene that may have originated de novo in the tribe. We further show that this gene may evolve a highly conservative rice-specific function that contributes to the regulation difference between rice and other plant species in response to pathogen infections. Biologic analyses including gene silencing, pathologic analysis, and mutant characterization by transformation showed that the OsDR10-suppressed plants enhanced resistance to a broad spectrum of Xanthomonas oryzae pv. oryzae strains, which cause bacterial blight disease. This enhanced disease resistance was accompanied by increased accumulation of endogenous salicylic acid (SA) and suppressed accumulation of endogenous jasmonic acid (JA) as well as modified expression of a subset of defense-responsive genes functioning both upstream and downstream of SA and JA. These data and analyses provide fresh insights into the new biologic and evolutionary processes of a de novo gene recruited rapidly

Local IRBs vs. Federal Agencies: Shifting Dynamics, Systems, and Relationships

How IRBs relate to federal agencies, and the implications of these relationships, have received little, if any, systematic study. I interviewed 46 IRB chairs, directors, administrators, and members, contacting the leadership of 60 U.S. IRBs (every fourth one in the list of the top 240 institutions by NIH funding), interviewing IRB leaders from 34 (response rate=55%). IRBs describe complex direct and indirect relationships with federal agencies that affect IRBs through audits, guidance documents, and other communications, and can generate problems and challenges. Researchers often blame IRBs for frustrations, but IRBs often serve as the “local face” of federal regulations and agencies and are “stuck in the middle.” These data have critical implications for policy, practice, and research