Gene Family Evolution across 12 Drosophila Genomes

Comparison of whole genomes has revealed large and frequent changes in the size of gene families. These changes occur because of high rates of both gene gain (via duplication) and loss (via deletion or pseudogenization), as well as the evolution of entirely new genes. Here we use the genomes of 12 fully sequenced Drosophila species to study the gain and loss of genes at unprecedented resolution. We find large numbers of both gains and losses, with over 40% of all gene families differing in size among the Drosophila. Approximately 17 genes are estimated to be duplicated and fixed in a genome every million years, a rate on par with that previously found in both yeast and mammals. We find many instances of extreme expansions or contractions in the size of gene families, including the expansion of several sex- and spermatogenesis-related families in D. melanogaster that also evolve under positive selection at the nucleotide level. Newly evolved gene families in our dataset are associated with a class of testes-expressed genes known to have evolved de novo in a number of cases. Gene family comparisons also allow us to identify a number of annotated D. melanogaster genes that are unlikely to encode functional proteins, as well as to identify dozens of previously unannotated D. melanogaster genes with conserved homologs in the other Drosophila. Taken together, our results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this genomic revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species

Attribution of the Hemispheric Asymmetries in Trends of Stratospheric Trace Gases Inferred From Microwave Limb Sounder (MLS) Measurements

Using Microwave Limb Sounder (MLS) satellite observations, ERA‐Interim reanalysis data, and a chemistry transport model simulation, we analyze and investigate the causes of the asymmetric hemispheric trends of N2O, CH4, and HCl in the stratosphere during the period 2004–2012. We find significant hemispheric asymmetries in the trends of these trace gases in the midlatitude middle and lower stratosphere. With regard to N2O and CH4, the enhanced downwelling branch of the residual circulation in the Northern Hemisphere (NH) middle and upper stratosphere transports more N2O/CH4‐poor air from the upper stratosphere to the lower stratosphere. The enhanced poleward meridional branch of the residual circulation in the Southern Hemisphere (SH) stratosphere brings more N2O/CH4‐rich air from lower to middle latitudes. These processes therefore contribute to the negative trends of N2O and CH4 in the NH lower stratosphere and the positive trends in the SH middle stratosphere. A corresponding positive trend is found for HCl in the NH, where the deep branch of the residual circulation located in the middle and upper stratosphere strengthens, bringing more HCl‐rich air downward to the lower stratosphere, while the shallow branch of the residual circulation in the lower stratosphere weakens and leads to enhanced conversion of chlorine‐containing source gases of different lifetimes to HCl. A reversed picture emerges in the SH, where the deep branch of the residual circulation in the middle and upper stratosphere weakens, while the shallow branch in the lower stratosphere strengthens, resulting in less HCl there. In addition, the southward shift of the upwelling branch of the residual circulation in recent decades can partly explain trace gas trends above 20 hPa, while the eddy mixing has a small effect on the trends. Understanding these contributions from different processes to the hemispheric asymmetries in trends of these trace gases can help us to evaluate more accurately future changes in stratospheric composition

Sequence length dependence in arginine/phenylalanine oligopeptides: Implications for self-assembly and cytotoxicity

We present a detailed study on the self-assembly and cytotoxicity of arginine-rich fragments with general form [RF]n (n = 1–5). These highly simplified sequences, containing only two l-amino acids, provide suitable models for exploring both structure and cytotoxicity features of arginine-based oligopeptides. The organization of the sequences is revealed over a range of length scales, from the nanometer range down to the level of molecular packing, and their cytotoxicity toward C6 rat glioma and RAW264.7 macrophage cell lines is investigated. We found that the polymorphism is dependent on peptide length, with a progressive increase in crystalline ordering upon increasing the number of [RF] pairs along the backbone. A dependence on length was also found for other observables, including critical aggregation concentrations, formation of chiral assemblies and half maximum inhibitory concentrations (IC50). Whereas shorter peptides self-assemble into fractal-like aggregates, clear fibrillogenic capabilities are identified for longer sequences with octameric and decameric chains exhibiting crystalline phases organized into cross-β structures. Cell viability assays revealed dose-dependent cytotoxicity profiles with very similar behavior for both glioma and macrophage cell lines, which has been interpreted as evidence for a nonspecific mechanism involved in toxicity. We propose that structural organization of [RF]n peptides plays a paramount role regarding toxicity due to strong increase of local charge density induced by self-assemblies rich in cationic groups when interacting with cell membranes

A scoring system for the follow up study of nuclear receptor coactivator complexes

We have systematically isolated a variety of coactivator complexes from HeLa S3 cells using proteomic approaches. In the present report, we have evaluated twelve coactivator complexes involved in nuclear receptor-dependent gene transcription that have been purified by using an immunoprecipitation method. The twelve purified coactivator complexes are SRC-1, SRC-2, SRC-3, CBP, p300, CAPER, E6-AP, ASC-1, CoREST, CRSP3, CRSP2, and CDK7 containing complexes. We have identified 153 protein components associated with these coactivator complexes using mass spectrometry. In order to systematically characterize the functional roles for these components in nuclear receptor-dependent gene transcription and their investigative potential, we have developed a scoring system. This scoring system is comprised of biological and experimental parameters. The biological evaluation considers aspects such as intrinsic enzymatic activity of a protein component, cellular signaling processes in which protein components may be involved, associations with human disease, specific protein motifs, and the known biological roles of other interacting partners of the identified protein. In the experimental evaluation, we include parameters, such as the availability of research materials for the functional study of the identified protein component; such as full-length cDNA clones, antibodies, and commercially available knock-out embryonic stem (ES) cells. Each scoring parameter has been assigned an arbitrary number of points according to perceived relative importance. On the basis of this scoring system, we prioritized each of the protein components in terms of the likelihood of their importance for coactivator complex networking in nuclear receptor-dependent gene transcription

Numerical renormalization group study of the symmetric Anderson-Holstein model: phonon and electron spectral functions

We study the symmetric Anderson-Holstein (AH) model at zero temperature with Wilson's numerical renormalization group (NRG) technique to study the interplay between the electron-electron and electron-phonon interactions. An improved method for calculating the phonon propagator using the NRG technique is presented, which turns out to be more accurate and reliable than the previous works in that it calculates the phonon renormalization explicitly and satisfies the boson sum rule better. The method is applied to calculate the renormalized phonon propagators along with the electron propagators as the onsite Coulomb repulsion $U$ and electron-phonon coupling constant $g$ are varied. As $g$ is increased, the phonon mode is successively renormalized, and for $g \gtrsim g_{co}$ crosses over to the regime where the mode splits into two components, one of which approaches back to the bare frequency and the other develops into a soft mode. The initial renormalization of the phonon mode, as $g$ is increased from 0, depends on $U$ and the hybridization $\Delta$; it gets softened (hardened) for $U \gtrsim (\lesssim) U_s (\Delta)$. Correlated with the emergence of the soft mode is the central peak of the electron spectral function severely suppressed. These NRG calculations will be compared with the standard Green's function results for the weak coupling regime to understand the phonon renormalization and soft mode.Comment: 18 pages, 4 figures. Submitted to Phys. Rev.

Gut microbiota-derived short-chain fatty acids protect against the progression of endometriosis

Worldwide, ∼196 million are afflicted with endometriosis, a painful disease in which endometrial tissue implants and proliferates on abdominal peritoneal surfaces. Theories on the origin of endometriosis remained inconclusive. Whereas up to 90% of women experience retrograde menstruation, only 10% develop endometriosis, suggesting that factors that alter peritoneal environment might contribute to endometriosis. Herein, we report that whereas some gut bacteria promote endometriosis, others protect against endometriosis by fermenting fiber to produce short-chain fatty acids. Specifically, we found that altered gut microbiota drives endometriotic lesion growth and feces from mice with endometriosis contained less of short-chain fatty acid and n-butyrate than feces from mice without endometriosis. Treatment with n-butyrate reduced growth of both mouse endometriotic lesions and human endometriotic lesions in a pre-clinical mouse model. Mechanistic studies revealed that n-butyrate inhibited human endometriotic cell survival and lesion growth through G-protein-coupled receptors, histone deacetylases, and a GTPase activating protein, RAP1GAP. Our findings will enable future studies aimed at developing diagnostic tests, gut bacteria metabolites and treatment strategies, dietary supplements, n-butyrate analogs, or probiotics for endometriosis

KMT-2016-BLG-1107: A New Hollywood-Planet Close/Wide Degeneracy

We show that microlensing event KMT-2016-BLG-1107 displays a new type of degeneracy between wide-binary and close-binary Hollywood events in which a giant-star source envelops the planetary caustic. The planetary anomaly takes the form of a smooth, two-day "bump" far out on the falling wing of the light curve, which can be interpreted either as the source completely enveloping a minor-image caustic due to a close companion with mass ratio $q=0.036$, or partially enveloping a major-image caustic due to a wide companion with $q=0.004$. The best estimates of the companion masses are both in the planetary regime ($3.3^{+3.5}_{-1.8}\,M_{\rm jup}$ and $0.090^{+0.096}_{-0.037}\,M_{\rm jup}$) but differ by an even larger factor than the mass ratios due to different inferred host masses. We show that the two solutions can be distinguished by high-resolution imaging at first light on next-generation ("30m") telescopes. We provide analytic guidance to understand the conditions under which this new type of degeneracy can appear.Comment: 23 pages, 7 figures, accepted for publication in A