Pseudo-messenger RNA: Phantoms of the transcriptome

The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein- coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo - messenger RNAs ( approximately half of which are transposonassociated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein- coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense- mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non- standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level.

Transfer of nonclassical properties from a microscopic superposition to macroscopic thermal states in the high temperature limit

We present several examples where prominent quantum properties are transferred from a microscopic superposition to thermal states at high temperatures. Our work is motivated by an analogy of Schrodinger's cat paradox, where the state corresponding to the virtual cat is a mixed thermal state with a large average photon number. Remarkably, quantum entanglement can be produced between thermal states with nearly the maximum Bell-inequality violation even when the temperatures of both modes approach infinity.

Proinsulin is encoded by an RNA splice variant in human blood myeloid cells

Genes for peripheral tissue-restricted self-antigens are expressed in thymic and hematopoietic cells. In thymic medullary epithelial cells, self-antigen expression imposes selection on developing autoreactive T cells and regulates susceptibility to autoimmune disease in mouse models. Less is known about the role of self-antigen expression by hematopoietic cells. Here we demonstrate that one of the endocrine self-antigens expressed by human blood myeloid cells, proinsulin, is encoded by an RNA splice variant. The surface expression of immunoreactive proinsulin was significantly decreased after transfection of monocytes with small interfering RNA to proinsulin. Furthermore, analogous to proinsulin transcripts in the thymus, the abundance of the proinsulin RNA splice variant in blood cells corresponded with the length of the variable number of tandem repeats 5' of the proinsulin gene, known to be associated with type 1 diabetes susceptibility. Self-antigen expression by peripheral myeloid cells extends the umbrella of immunological self and, by analogy with the thymus, may be implicated in peripheral immune tolerance.

Exact eigenvalue correspondences between laminated plate theories via membrane vibration

Based on Reddy's third-order theory, the first-order theory and the classical theory, exact explicit eigenvalues are found for compression buckling, thermal buckling and vibration of laminated plates via analogy with membrane vibration, These results apply to symmetrically laminated composite plates with transversely isotropic laminae and simply supported polygonal edges, Comprehensive consideration of a Winkler-Pasternak elastic foundation, a hydrostatic inplane force, an initial temperature increment and rotary inertias is incorporated. Bridged by the vibrating membrane, exact correspondences are readily established between any pairs of buckling and vibration eigenvalues associated with different theories. Positive definiteness of the critical hydrostatic pressure at buckling, the thermobukling temperature increment and, in the range of either tension loading or compression loading prior to occurrence of buckling, the natural vibration frequency is proved. (C) 2000 Elsevier Science Ltd. All rights reserved.

Mixed-state entanglement in the light of pure-state entanglement constrained by superselection rules

We show that the classification of bi-partite pure entangled states when local quantum operations are restricted, e.g., constrained by local superselection rules, yields a structure that is analogous in many respects to that of mixed-state entanglement, including such exotic phenomena as bound entanglement and activation. This analogy aids in resolving several conceptual puzzles in the study of entanglement under restricted operations. Specifically, we demonstrate that several types of quantum optical states that possess confusing entanglement properties are analogous to bound entangled states. Also, the classification of pure-state entanglement under restricted operations can be much simpler than for mixed state entanglement. For instance, in the case of local Abelian superselection rules all questions concerning distillability can be resolved.