Cryptic transcripts from a ubiquitous plasmid origin of replication confound tests for cis-regulatory function.

A vast amount of research on the regulation of gene expression has relied on plasmid reporter assays. In this study, we show that plasmids widely used for this purpose constitutively produce substantial amounts of RNA from a TATA-containing cryptic promoter within the origin of replication. Readthrough of these RNAs into the intended transcriptional unit potently stimulated reporter activity when the inserted test sequence contained a 3' splice site (ss). We show that two human sequences, originally reported to be internal ribosome entry sites and later to instead be promoters, mimic both types of element in dicistronic reporter assays by causing these cryptic readthrough transcripts to splice in patterns that allow efficient translation of the downstream cistron. Introduction of test sequences containing 3' ss into monocistronic luciferase reporter vectors widely used in the study of transcriptional regulation also created the false appearance of promoter function via the same mechanism. Across a large number of variants of these plasmids, we found a very highly significant correlation between reporter activity and levels of such spliced readthrough transcripts. Computational estimation of the frequency of cryptic 3' ss in genomic sequences suggests that misattribution of cis-regulatory function may be a common occurrence

Anomalous quasiparticle transport in the superconducting state of CeCoIn5

We report on a study of thermal Hall conductivity k_xy in the superconducting state of CeCoIn_5. The scaling relation and the density of states of the delocalized quasiparticles, both obtained from k_xy, are consistent with d-wave superconducting symmetry. The onset of superconductivity is accompanied by a steep increase in the thermal Hall angle, pointing to a striking enhancement in the quasiparticle mean free path. This enhancement is drastically suppressed in a very weak magnetic field. These results highlight that CeCoIn_5 is unique among superconductors. A small Fermi energy, a large superconducting gap, a short coherence length, and a long mean free path all indicate that CeCoIn_5 is clearly in the superclean regime (E_F/Delta<<l/xi), in which peculiar vortex state is expected.Comment: 5 pages, 5 figure

Air Shower Simulation and Hadronic Interactions

The aim of this report of the Working Group on Hadronic Interactions and Air Shower Simulation is to give an overview of the status of the field, emphasizing open questions and a comparison of relevant results of the different experiments. It is shown that an approximate overall understanding of extensive air showers and the corresponding hadronic interactions has been reached. The simulations provide a qualitative description of the bulk of the air shower observables. Discrepancies are however found when the correlation between measurements of the longitudinal shower profile are compared to that of the lateral particle distributions at ground. The report concludes with a list of important problems that should be addressed to make progress in understanding hadronic interactions and, hence, improve the reliability of air shower simulations.Comment: Working Group report given at UHECR 2012 Symposium, CERN, Feb. 2012. Published in EPJ Web of Conferences 53, 01007 (2013