Browsing Faculty/ Researcher Works by Subject "1.1 Normal biological development and functioning"
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Integrating TRPV1 Receptor Function with Capsaicin Psychophysics© 2016 Gregory Smutzer and Roni K. Devassy. Capsaicin is a naturally occurring vanilloid that causes a hot, pungent sensation in the human oral cavity. This trigeminal stimulus activates TRPV1 receptors and stimulates an influx of cations into sensory cells. TRPV1 receptors function as homotetramers that also respond to heat, proinflammatory substances, lipoxygenase products, resiniferatoxin, endocannabinoids, protons, and peptide toxins. Kinase-mediated phosphorylation of TRPV1 leads to increased sensitivity to both chemical and thermal stimuli. In contrast, desensitization occurs via a calcium-dependent mechanism that results in receptor dephosphorylation. Human psychophysical studies have shown that capsaicin is detected at nanomole amounts and causes desensitization in the oral cavity. Psychophysical studies further indicate that desensitization can be temporarily reversed in the oral cavity if stimulation with capsaicin is resumed at short interstimulus intervals. Pretreatment of lingual epithelium with capsaicin modulates the perception of several primary taste qualities. Also, sweet taste stimuli may decrease the intensity of capsaicin perception in the oral cavity. In addition, capsaicin perception and hedonic responses may be modified by diet. Psychophysical studies with capsaicin are consistent with recent findings that have identified TRPV1 channel modulation by phosphorylation and interactions with membrane inositol phospholipids. Future studies will further clarify the importance of capsaicin and its receptor in human health and nutrition.
Intrinsic disorder in putative protein sequences© 2012 Midic and Obradovic; licensee BioMed Central Ltd. Background: Intrinsically disordered proteins (IDPs) and regions (IDRs) perform a variety of crucial biological functions despite lacking stable tertiary structure under physiological conditions in vitro. State-of-the-art sequencebased predictors of intrinsic disorder are achieving per-residue accuracies over 80%. In a genome-wide study of intrinsic disorder in human genome we observed a big difference in predicted disorder content between confirmed and putative human proteins. We investigated a hypothesis that this discrepancy is not correct, and that it is due to incorrectly annotated parts of the putative protein sequences that exhibit some similarities to confirmed IDRs, which lead to high predicted disorder content. Methods: To test this hypothesis we trained a predictor to discriminate sequences of real proteins from synthetic sequences that mimic errors of gene finding algorithms. We developed a procedure to create synthetic peptide sequences by translation of non-coding regions of genomic sequences and translation of coding regions with incorrect codon alignment. Results: Application of the developed predictor to putative human protein sequences showed that they contain a substantial fraction of incorrectly assigned regions. These regions are predicted to have higher levels of disorder content than correctly assigned regions. This partially, albeit not completely, explains the observed discrepancy in predicted disorder content between confirmed and putative human proteins. Conclusions: Our findings provide the first evidence that current practice of predicting disorder content in putative sequences should be reconsidered, as such estimates may be biased.
Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal locationBackground: Members of the ribonuclease III superfamily of double-stranded(ds)-RNA-specific endoribonucleases participate in diverse RNA maturation and decay pathways in eukaryotic and prokaryotic cells. A human RNase III orthologue has been implicated in ribosomal RNA maturation. To better understand the structure and mechanism of mammalian RNase III and its involvement in RNA metabolism we determined the cDNA structure, chromosomal location, and expression patterns of mouse RNase III. Results: The predicted mouse RNase III polypeptide contains 1373 amino acids (∼160 kDa). The polypeptide exhibits a single C-terminal dsRNA-binding motif (dsRBM), tandem catalytic domains, a proline-rich region (PRR) and an RS domain. Northern analysis and RT-PCR reveal that the transcript (4487 nt) is expressed in all tissues examined, including extraembryonic tissues and the midgestation embryo. Northern analysis indicates the presence of an additional, shorter form of the transcript in testicular tissue. Fluorescent in situ hybridization demonstrates that the mouse RNase III gene maps to chromosome 15, region B, and that the human RNase III gene maps to a syntenic location on chromosome 5p13-p14. Conclusions: The broad transcript expression pattern indicates a conserved cellular role(s) for mouse RNase III. The putative polypeptide is highly similar to human RNase III (99% amino acid sequence identity for the two catalytic domains and dsRBM), but is distinct from other eukaryotic orthologues, including Dicer, which is involved in RNA interference. The mouse RNase III gene has a chromosomal location distinct from the Dicer gene. © 2002 Fortin et al; licensee BioMed Central Ltd.
Quasiparticle dynamics across the full Brillouin zone of Bi<inf>2</inf>Sr<inf>2</inf>CaCu<inf>2</inf>O<inf>8+δ</inf> traced with ultrafast time and angle-resolved photoemission spectroscopy© 2015 Author(s). A hallmark in the cuprate family of high-temperature superconductors is the nodal-antinodal dichotomy. In this regard, angle-resolved photoemission spectroscopy (ARPES) has proven especially powerful, providing band structure information directly in energy-momentum space. Time-resolved ARPES (trARPES) holds great promise of adding ultrafast temporal information, in an attempt to identify different interaction channels in the time domain. Previous studies of the cuprates using trARPES were handicapped by the low probing energy, which significantly limits the accessible momentum space. Using 20.15 eV, 12 fs pulses, we show for the first time the evolution of quasiparticles in the antinodal region of Bi2Sr2CaCu2O8+δ and demonstrate that non-monotonic relaxation dynamics dominates above a certain fluence threshold. The dynamics is heavily influenced by transient modification of the electron-phonon interaction and phase space restrictions, in stark contrast to the monotonic relaxation in the nodal and off-nodal regions.