53 research outputs found
A tissue-specific landscape of sense/antisense transcription in the mouse intestine
<p>Abstract</p> <p>Background</p> <p>The intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the analysis of the RNA sequence space, the level of detail on the global architecture of the transcriptome reached a new order of magnitude compared to microarrays.</p> <p>Results</p> <p>We report the ultra-deep characterization of the polyadenylated transcriptome in two closely related, yet distinct regions of the mouse intestinal tract (small intestine and colon). We assessed tissue-specific transcriptomal architecture and the presence of novel transcriptionally active regions (nTARs). In the first step, signatures of 20,541 NCBI RefSeq transcripts could be identified in the intestine (74.1% of annotated genes), thereof 16,742 are common in both tissues. Although the majority of reads could be linked to annotated genes, 27,543 nTARs not consistent with current gene annotations in RefSeq or ENSEMBL were identified. By use of a second independent strand-specific RNA-Seq protocol, 20,966 of these nTARs were confirmed, most of them in vicinity of known genes. We further categorized our findings by their relative adjacency to described exonic elements and investigated regional differences of novel transcribed elements in small intestine and colon.</p> <p>Conclusions</p> <p>The current study demonstrates the complexity of an archetypal mammalian intestinal mRNA transcriptome in high resolution and identifies novel transcriptionally active regions at strand-specific, single base resolution. Our analysis for the first time shows a strand-specific comparative picture of nTARs in two tissues and represents a resource for further investigating the transcriptional processes that contribute to tissue identity.</p
Reactive oxygen species in phagocytic leukocytes
Phagocytic leukocytes consume oxygen and generate reactive oxygen species in response to appropriate stimuli. The phagocyte NADPH oxidase, a multiprotein complex, existing in the dissociated state in resting cells becomes assembled into the functional oxidase complex upon stimulation and then generates superoxide anions. Biochemical aspects of the NADPH oxidase are briefly discussed in this review; however, the major focus relates to the contributions of various modes of microscopy to our understanding of the NADPH oxidase and the cell biology of phagocytic leukocytes
Characterization of the Glass Transition of Water Predicted by Molecular Dynamics Simulations Using Nonpolarizable Intermolecular Potentials
Molecular dynamics
simulations allow detailed study of the experimentally
inaccessible liquid state of supercooled water below its homogeneous
nucleation temperature and the characterization of the glass transition.
Simple, nonpolarizable intermolecular potentials are commonly used
in classical molecular dynamics simulations of water and aqueous systems
due to their lower computational cost and their ability to reproduce
a wide range of properties. Because the quality of these predictions
varies between the potentials, the predicted glass transition of water
is likely to be influenced by the choice of potential. We have thus
conducted an extensive comparative investigation of various three-,
four-, five-, and six-point water potentials in both the NPT and NVT
ensembles. The <i>T</i><sub>g</sub> predicted from NPT simulations
is strongly correlated with the temperature of minimum density, whereas
the maximum in the heat capacity plot corresponds to the minimum in
the thermal expansion coefficient. In
the NVT ensemble, these points are instead related to the maximum
in the internal pressure and the minimum of its derivative, respectively.
A detailed analysis of the hydrogen-bonding properties at the glass
transition reveals that the extent of hydrogen-bonds lost upon the
melting of the glassy state is related to the height of the heat capacity
peak and varies between water potentials
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