Mapping the strand-specific transcriptome of fission yeast

Pervasive genome-wide transcription is widespread in eukaryotic cells, but key features of the transcriptome have yet to be fully characterized. a new study using antibody-based detection of RNA-DNA duplexes on tiling arrays now reveals a complex, strand-specific transcriptional world in fission yeast

Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics

<p>Abstract</p> <p>Background</p> <p>Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics have not been well investigated in most invertebrates. Here, we performed genome survey for key defensome genes in <it>Oikopleura dioica </it>genome, and explored genome-wide gene expression using high density tiling arrays with over 2 million probes, in response to two model xenobiotic chemicals - the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) the pharmaceutical compound Clofibrate (Clo).</p> <p>Results</p> <p><it>Oikopleura </it>genome surveys for key genes of the chemical defensome suggested a reduced repertoire. Not more than 23 cytochrome P450 (CYP) genes could be identified, and neither CYP1 family genes nor their transcriptional activator AhR was detected. These two genes were present in deuterostome ancestors. As in vertebrates, the genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR) signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways.</p> <p>Conclusions</p> <p><it>Oikopleura </it>has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates.</p

Transcriptional landscape of the human and fly genomes: Nonlinear and multifunctional modular model of transcriptomes

Regions of the genome not coding for proteins or not involved in cis-acting regulatory activities are frequently viewed as lacking in functional value. However, a number of recent large-scale studies have revealed significant regulated transcription of unannotated portions of a variety of plant and animal genomes, allowing a new appreciation of the widespread transcription of large portions of the genome. High-resolution mapping of the sites of transcription of the human and fly genomes has provided an alternative picture of the extent and organization of transcription and has offered insights for biological functions of some of the newly identified unannotated transcripts. Considerable portions of the unannotated transcription observed are developmental or cell-type-specific parts of protein-coding transcripts, often serving as novel, alternative 5′ transcriptional start sites. These distal 5′ portions are often situated at significant distances from the annotated gene and alternatively join with or ignore portions of other intervening genes to comprise novel unannotated protein-coding transcripts. These data support an interlaced model of the genome in which many regions serve multifunctional purposes and are highly modular in their utilization. This model illustrates the underappreciated organizational complexity of the genome and one of the functional roles of transcription from unannotated portions of the genome. Copyright 2006, Cold Spring Harbor Laboratory Press © 2006 Cold Spring Harbor Laboratory Press

Observation of Pseudoscalar and Axial Vector Resonances in pi- p -> K+ K- pi0 n at 18 GeV

A new measurement of the reaction pi- p -> K+ K- pi0 n has been made at a beam energy of 18 GeV. A partial wave analysis of the K+ K- pi0 system shows evidence for three pseudoscalar resonances, eta(1295), eta(1416), and eta(1485), as well as two axial vectors, f1(1285), and f1(1420). Their observed masses, widths and decay properties are reported. No signal was observed for C(1480), an IG J{PC} = 1+ 1{--} state previously reported in phi pi0 decay.Comment: 7 pages, 6 figs, to be submitted to Phys. Let

УСТРОЙСТВО ДЛЯ ОПРЕДЕЛЕНИЯ ФИЗИКО-МЕХАНИЧЕСКИХ СВОЙСТВ ЭЛАСТОМЕРНЫХ МАТЕРИАЛОВ

Developed the device for determining the physical and mechanical properties of elastomeric materials. In contrast to the well-known device that operates on the method of Shore, used to measure only the hardness of elastomeric materials, developed the device can measure not only hardness, but also the relative deformation of the samples made of elastomeric materials, as well as the ability of these materials to restore the original dimensions after deformation. The device has a simple design includes coaxial with the direction of the force transducer strain into an electrical signal that provides a sensitivity of at least 3 mV/μm.Разработано устройство для определения физико-механических свойств эластомерных материалов. В отличие от известного прибора, работающего по методу Шора, применяемого для измерения только твердости эластомерных материалов, разработанное устройство позволяет измерять не только твердость, но и относительные деформации образцов из эластомерных материалов, а также способность этих материалов к восстановлению первоначальных размеров после деформации. Устройство имеет простую конструкцию, содержит соосный с направлением приложения силы преобразователь деформации в электрический сигнал, что обеспечивает чувствительность не менее 3 мВ/мкм

Search for Exotic Mesons in pi- P Interactions at 18 GeV/c

The recent search for non $q \bar{q}$ mesons in $\pi^{-}p$ interactions at Brookhaven National Laboratory is summarized. Many final states such as $\eta \pi$, $\eta' \pi^{-}$, $a_{0} \pi$, $f_{1} \pi$, $a_{2} \pi$, $b_{1} \pi$, which are favored decay modes of exotics, are under investigation.Comment: 9 pages, PostScript, Presented at the International School of Nuclear Physics, Erice, Sicily, Italy, September 199

Properties of ρ\rho and ω\omega Mesons at Finite Temperature and Density as Inferred from Experiment

The mass shift, width broadening, and spectral density for the $\rho$ and $\omega$ mesons in a heat bath of nucleons and pions are calculated using a general formula which relates the self-energy to the real and imaginary parts of the forward scattering amplitude. We use experimental data to saturate the scattering amplitude at low energies with resonances and include a background Pomeron term, while at high energies a Regge parameterization is used. The real part obtained directly is compared with the result of a dispersion integral over the imaginary part. The peaks of the spectral densities are little shifted from their vacuum positions, but the widths are considerably increased due to collisional broadening. Where possible we compare with the UrQMD model and find quite good agreement. At normal nuclear matter density and a temperature of 150 MeV the spectral density of the $\rho$ meson has a width of 345 MeV, while that for the $\omega$ is in the range 90--150 MeV.Comment: 21 pages revtex + 9 postscript figure