De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda.

BackgroundThe Drosophila miranda neo-sex chromosome system is a useful resource for studying recently evolved sex chromosomes. However, the neo-Y genomic assembly is fragmented due to the accumulation of repetitive sequence. Furthermore, the separate assembly of the neo-X and neo-Y chromosomes into genomic scaffolds has proven to be difficult, due to their low level of sequence divergence, which in coding regions is about 1.5%. Here, we de novo assemble the transcriptome of D. miranda using RNA-seq data from several male and female tissues, and develop a bioinformatic pipeline to separately reconstruct neo-X and neo-Y transcripts.ResultsWe obtain 2,141 transcripts from the neo-X and 1,863 from the neo-Y. Neo-Y transcripts are generally shorter than their homologous neo-X transcripts (N50 of 2,048-bp vs. 2,775-bp) and expressed at lower levels. We find that 24% of expressed neo-Y transcripts harbor nonsense mutation within their open reading frames, yet most non-functional neo-Y genes are expressed throughout all of their length. We find evidence of gene loss of male-specific genes on the neo-X chromosome, and transcriptional silencing of testis-specific genes from the neo-X.ConclusionsNonsense mediated decay (NMD) has been implicated to degrade transcripts containing pre-mature termination codons (PTC) in Drosophila, but rampant description of neo-Y genes with pre-mature stop codons suggests that it does not play a major role in down-regulating transcripts from the neo-Y. Loss or transcriptional down-regulation of genes from the neo-X with male-biased function provides evidence for beginning demasculinization of the neo-X. Thus, evolving sex chromosomes can rapidly shift their gene content or patterns of gene expression in response to their sex-biased transmission, supporting the idea that sex-specific or sexually antagonistic selection plays a major role in the evolution of heteromorphic sex chromosomes

Nonlinear interaction of spin and charge currents in graphene

We describe a nonlinear interaction between charge currents and spin currents which arises from the energy dependence of the conductivity. This allows nonmagnetic contacts to be used for measuring and controlling spin signals. We choose graphene as a model system to study these effects and predict its magnitudes in nonlocal spin valve devices. The ambipolar behavior of graphene is used to demonstrate amplification of spin accumulation in p-n junctions by applying a charge current through nonmagnetic contacts.Comment: minor changes, 4 pages, 3 figure

Applications of Lipatov's high energy effective action to NLO BFKL jet phenomenology

We report on recent progress in the evaluation of next-to-leading order (NLO) observables using Lipatov's QCD high energy effective action. We calculate both real and virtual corrections to the quark induced forward jet vertex at NLO, making use of a new regularization method and a subtraction mechanism. As a new result we determine the real part of the NLO Mueller-Tang impact factor which is the only missing element for a complete NLO BFKL description of dijet events with a rapidity gap.Comment: 4 pages, 29 figures, proceedings of the XX Workshop on Deep-Inelastic Scattering and Related Subjects, 26-30 March, University of Bonn (2012

Legendrian and transverse twist knots

In 1997, Chekanov gave the first example of a Legendrian nonsimple knot type: the $m(5_2)$ knot. Epstein, Fuchs, and Meyer extended his result by showing that there are at least $n$ different Legendrian representatives with maximal Thurston--Bennequin number of the twist knot $K_{-2n}$ with crossing number $2n+1$. In this paper we give a complete classification of Legendrian and transverse representatives of twist knots. In particular, we show that $K_{-2n}$ has exactly $\lceil\frac{n^2}2\rceil$ Legendrian representatives with maximal Thurston--Bennequin number, and $\lceil\frac{n}{2}\rceil$ transverse representatives with maximal self-linking number. Our techniques include convex surface theory, Legendrian ruling invariants, and Heegaard Floer homology.Comment: 27 pages, v3: added figure, other minor changes, to appear in JEM