Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

Binary and Millisecond Pulsars at the New Millennium

We review the properties and applications of binary and millisecond pulsars. Our knowledge of these exciting objects has greatly increased in recent years, mainly due to successful surveys which have brought the known pulsar population to over 1300. There are now 56 binary and millisecond pulsars in the Galactic disk and a further 47 in globular clusters. This review is concerned primarily with the results and spin-offs from these surveys which are of particular interest to the relativity community.Comment: 59 pages, 26 figures, 5 tables. Accepted for publication in Living Reviews in Relativity (http://www.livingreviews.org

PPS, a Large Multidomain Protein, Functions with Sex-Lethal to Regulate Alternative Splicing in Drosophila

Alternative splicing controls the expression of many genes, including the Drosophila sex determination gene Sex-lethal (Sxl). Sxl expression is controlled via a negative regulatory mechanism where inclusion of the translation-terminating male exon is blocked in females. Previous studies have shown that the mechanism leading to exon skipping is autoregulatory and requires the SXL protein to antagonize exon inclusion by interacting with core spliceosomal proteins, including the U1 snRNP protein Sans-fille (SNF). In studies begun by screening for proteins that interact with SNF, we identified PPS, a previously uncharacterized protein, as a novel component of the machinery required for Sxl male exon skipping. PPS encodes a large protein with four signature motifs, PHD, BRK, TFS2M, and SPOC, typically found in proteins involved in transcription. We demonstrate that PPS has a direct role in Sxl male exon skipping by showing first that loss of function mutations have phenotypes indicative of Sxl misregulation and second that the PPS protein forms a complex with SXL and the unspliced Sxl RNA. In addition, we mapped the recruitment of PPS, SXL, and SNF along the Sxl gene using chromatin immunoprecipitation (ChIP), which revealed that, like many other splicing factors, these proteins bind their RNA targets while in close proximity to the DNA. Interestingly, while SNF and SXL are specifically recruited to their predicted binding sites, PPS has a distinct pattern of accumulation along the Sxl gene, associating with a region that includes, but is not limited to, the SxlPm promoter. Together, these data indicate that PPS is different from other splicing factors involved in male-exon skipping and suggest, for the first time, a functional link between transcription and SXL–mediated alternative splicing. Loss of zygotic PPS function, however, is lethal to both sexes, indicating that its role may be of broad significance

Optical Properties of Heavily Fluorinated Lanthanide Tris beta-Diketonate Phosphine Oxide Adducts

The construction of lanthanide(III) chelates that exhibit superior photophysical properties holds great importance in biological and materials science. One strategy to increase the luminescence properties of lanthanide(III) chelates is to hinder competitive non-radiative decay processes through perfluorination of the chelating ligands. Here, the synthesis of two families of heavily fluorinated lanthanide(III) β-diketonate complexes bearing monodentate perfluorinated tris phenyl phosphine oxide ligands have been prepared through a facile one pot reaction [Ln(hfac)3{(ArF)3PO}(H2O)] and [Ln(F7-acac)3{(ArF)3PO}2] (where Ln = Sm3+, Eu3+, Tb3+, Er3+ and Yb3+). Single crystal X-ray diffraction analysis in combination with photophysical studies have been performed to investigate the factors responsible for the differences in the luminescence lifetimes and intrinsic quantum yields of the complexes. Replacement of both bound H2O and C–H oscillators in the ligand backbone has a dramatic effect on the photophysical properties of the complexes, particularly for the near infra-red emitting ion Yb3+, where a five fold increase in luminescence lifetime and quantum yield is observed. The complexes [Sm(hfac)3{(ArF)3PO}(H2O)] (1), [Yb(hfac)3{(ArF)3PO}(H2O)] (5), [Sm(F7-acac)3{(ArF)3PO}2] (6) and [Yb(F7-acac)3{(ArF)3PO}2] (10) exhibit unusually long luminescence lifetimes and attractive intrinsic quantum yields of emission in fluid solution (ΦLn = 3.4% (1); 1.4% (10)) and in the solid state (ΦLn = 8.5% (1); 2.0% (5); 26% (6); 11% (10)), which are amongst the largest values for this class of compounds to date

Ab Initio Models of Dislocations

International audienceThis chapter reviews the different methodological aspects of the ab ini-tio modeling of dislocations. Such simulations are now frequently used to study the dislocation core, i.e. the region in the immediate vicinity of the line defect where the crystal is so strongly distorted that an atomic description is needed. This core region controls some dislocation fundamental properties, like their ability to glide in different crystallographic planes. Ab initio calculations based on the density functional theory offer a predictive way to model this core region. Because dislocations break the periodicity of the crystal and induce long range elastic fields, several specific approaches relying on different boundary conditions have been developed to allow for the atomistic modeling of these defects in simulation cells having a size compatible with ab initio calculations. We describe these different approaches which can be used to study dislocations with ab initio calculations and introduce the different analyses which are currently performed to characterize the core structure, before discussing how meaningful energy properties can be extracted from such simulations

The Fine-Tuning Argument: Exploring the Improbability of Our Existence

Contains fulltext : 158161.pdf (publisher's version ) (Open Access

Reconsidering the Inverse Gambler's Fallacy Charge Against the Fine-Tuning Argument for the Multiverse

Does the claimed fine-tuning of the constants of nature for life give reason to think that there are many other universes in which the constants have different values (a "multiverse")? Or does the inference from fine-tuning to a multiverse commit what Hacking calls the inverse gambler's fallacy? The present paper considers two fine-tuning problems that seem promising to consider because they are in many respects analogous to the problem of the fine-tuned constants. Reasoning that parallels the inference from fine-tuning to a multiverse seems prima facie adequate in these problems. However, it turns out that in both cases there are independent empirical reasons to believe the hypotheses that are analogous to the multiverse hypothesis. In the absence of such evidence, it would be coherent to raise the inverse gambler's fallacy charge against the inference from fine-tuning to these multiverse-type hypotheses. In response to this finding, I suggest taking the possibility seriously that established standards of rationality may not allow us to decide whether the inference from fine-tuning to a multiverse is fallacious or not. The paper concludes by sceptically assessing the prospects for obtaining independent empirical evidence for concrete multiverse theories