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 Angular Dependence of the Dynamic Structure Factor near Bragg Reflections: Graphite

The electron energy-loss function of graphite is studied for momentum transfers q beyond the first Brillouin zone. We find that near Bragg reflections the spectra can change drastically for very small variations in q. The effect is investigated by means of first principle calculations in the random phase approximation and confirmed by inelastic x-ray scattering measurements of the dynamic structure factor S(q,\omega). We demonstrate that this effect is governed by crystal local field effects and the stacking of graphite. It is traced back to a strong coupling between excitations at small and large momentum transfers

Quantized representation of some nonlinear integrable evolution equations on the soliton sector

The Hirota algorithm for solving several integrable nonlinear evolution equations is suggestive of a simple quantized representation of these equations and their soliton solutions over a Fock space of bosons or of fermions. The classical nonlinear wave equation becomes a nonlinear equation for an operator. The solution of this equation is constructed through the operator analog of the Hirota transformation. The classical N-solitons solution is the expectation value of the solution operator in an N-particle state in the Fock space.Comment: 12 page

Chromium at High Pressures: Weak Coupling and Strong Fluctuations in an Itinerant Antiferromagnet

The spin- and charge-density-wave order parameters of the itinerant antiferromagnet chromium are measured directly with non-resonant x-ray diffraction as the system is driven towards its quantum critical point with high pressure using a diamond anvil cell. The exponential decrease of the spin and charge diffraction intensities with pressure confirms the harmonic scaling of spin and charge, while the evolution of the incommensurate ordering vector provides important insight into the difference between pressure and chemical doping as means of driving quantum phase transitions. Measurement of the charge density wave over more than two orders of magnitude of diffraction intensity provides the clearest demonstration to date of a weakly-coupled, BCS-like ground state. Evidence for the coexistence of this weakly-coupled ground state with high-energy excitations and pseudogap formation above the ordering temperature in chromium, the charge-ordered perovskite manganites, and the blue bronzes, among other such systems, raises fundamental questions about the distinctions between weak and strong coupling.Comment: 11 pages, 9 figures (8 in color