bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutations of L293 in transmembrane two of the mouse 5‐hydroxytryptamine3A receptor alter gating and alcohol modulatory actions
Authors: Hu Xiang‐Qun , Hayrapetyan Volodya , Gadhiya Jay J , Rhubottom Heather E , Lovinger David M , Machu Tina K 
Published: March 2006

The goal of this study was to determine whether mutations of L293 at the 15′ position of TM2 in the 5‐HT3A receptor alter macroscopic current kinetics, and if these changes could account for alterations in alcohol modulation. Receptor function was assessed in Xenopus oocytes under voltage‐clamp and in HEK293 cells with whole‐cell patch‐clamp recording and rapid drug application.
Examination of responses of L293C and L293S receptors to agonist alone revealed enhanced activation, deactivation, and desensitization rates relative to the wild‐type receptor. The L293G mutation produced marked slowing of deactivation and desensitization rates. Increased potency of 5‐HT and increased efficacy of the partial agonist, DA, was also observed in these mutant receptors.
Ethanol and trichloroethanol (TCEt) enhancement of receptor function was reduced or eliminated in receptors containing L293 mutations to C, G, or S. The L293I mutant receptor retained ethanol and TCEt sensitivity. Ethanol and TCEt enhanced activation rate in the wild‐type, but not the L293G and L293S receptors. No relationship was observed between any physicochemical property of the substituted amino acids and the change in alcohol potentiation of function.
The changes in receptor‐channel properties in the mutant receptors support the idea that the L293 residue has important roles in channel gating. Our findings indicate that loss of allosteric modulation by alcohols is not related in any simple way to changes in channel kinetic properties brought about by L293 mutants. We did not observe any evidence that L293 is part of an alcohol binding site.

British Journal of Pharmacology (2006) 148, 88–101. doi:10.1038/sj.bjp.0706685
Suppression of pancreatitis‐related allodynia/hyperalgesia by proteinase‐activated receptor‐2 in mice
Authors: Kawabata Atsufumi , Matsunami Maho , Tsutsumi Masahiro , Ishiki Tsuyoshi , Fukushima Osamu , Sekiguchi Fumiko , Kawao Naoyuki , Minami Takeshi , Kanke Toru , Saito Naohiro 
Published: March 2006

Proteinase‐activated receptor‐2 (PAR2), a receptor activated by trypsin and tryptase, is abundantly expressed in the gastrointestinal tract including the C‐fiber terminal, and might play a role in processing of visceral pain. In the present study, we examined and characterized the roles of PAR2 in pancreatitis‐related abdominal hyperalgesia/allodynia in mice.
Caerulein, administered i.p. once, caused a small increase in abdominal sensitivity to stimulation with von Frey hairs, without causing pancreatitis, in PAR2‐knockout (KO) mice, but not wild‐type (WT) mice.
Caerulein, given hourly six times in total, caused more profound abdominal hyperalgesia/allodynia in PAR2‐KO mice, as compared with WT mice, although no significant differences were detected in the severity of pancreatitis between the KO and WT animals.
The PAR2‐activating peptide, 2‐furoyl‐LIGRL‐NH2, coadministered repeatedly with caerulein six times in total, abolished the caerulein‐evoked abdominal hyperalgesia/allodynia in WT, but not PAR2‐KO, mice. Repeated doses of 2‐furoyl‐LIGRL‐NH2 moderately attenuated the severity of caerulein‐induced pancreatitis in WT animals.
Our data from experiments using PAR2‐KO mice provide evidence that PAR2 functions to attenuate pancreatitis‐related abdominal hyperalgesia/allodynia without affecting pancreatitis itself, although the PAR2AP applied exogenously is not only antinociceptive but also anti‐inflammatory.

British Journal of Pharmacology (2006) 148, 54–60. doi:10.1038/sj.bjp.0706708
Cannabinoid 1 (CB1) receptors coupled to cholinergic motorneurones inhibit neurogenic circular muscle contractility in the human colon
Authors: Hinds Nicholas M , Ullrich Katja , Smid Scott D 
Published: March 2006

The effects of cannabinoid subtype 1 (CB1) receptor activation were determined on smooth muscle, inhibitory and excitatory motorneuronal function in strips of human colonic longitudinal muscle (LM) and circular muscle (CM) in vitro.
Electrical field stimulation (EFS; 0.5–20 Hz, 50 V) evoked a relaxation in LM and CM precontracted with a neurokinin‐2 (NK‐2) selective receptor agonist (β‐ala8‐neurokinin A; 10−6 M) in the presence of atropine (10−6 M); this was unaltered following pretreatment with the CB1‐receptor selective agonist arachidonyl‐2‐chloroethylamide (ACEA; 10−6 M).
In the presence of nitric oxide synthase blockade with N‐nitro‐L‐arginine (10−4 M), EFS evoked a frequency‐dependent ‘on‐contraction’ during stimulation and an ‘off‐contraction’ following stimulus cessation. On‐contractions were significantly inhibited in CM strips by pretreatment with ACEA (10−6 M). These inhibitory effects were reversed in the presence of the CB1 receptor‐selective antagonist N‐(piperidine‐1‐yl)‐5‐(4‐iodophenyl)‐1‐(2,4‐dichlorophenyl)‐4‐methyl‐1H‐pyrazole‐3‐carboxamide (10−7 M).
ACEA did not alter LM or CM contractile responses to acetylcholine or NK‐2 receptor‐evoked contraction.
Immunohistochemical studies revealed a colocalisation of CB1 receptors to cholinergic neurones in the human colon based on colabelling with choline acetyltransferase, in addition to CB1 receptor labelling in unidentified structures in the CM.
In conclusion, activation of CB1 receptors coupled to cholinergic motorneurones selectively and reversibly inhibits excitatory nerve transmission in colonic human colonic CM. These results provide evidence of a direct role for cannabinoids in the modulation of motor activity in the human colon by coupling to cholinergic motorneurones.

British Journal of Pharmacology (2006) 148, 191–199. doi:10.1038/sj.bjp.0706710
Ranolazine and late cardiac sodium current – a therapeutic target for angina, arrhythmia and more?
Authors: Makielski Jonathan C , Valdivia Carmen R 
Published: March 2006

Ranolazine is a new antianginal drug approved for clinical use in the United States in January 2006. A study published in this same issue of theBritish Journal of Pharmacologycharacterizes ranolazine block of late sodium current caused by the long QT syndrome 3 mutations. This commentary discusses the implications of that study and the background and implications for block of late cardiac sodium current in general.British Journal of Pharmacology(2006)148, 4–6. doi:10.1038/sj.bjp.0706713
Inhibition of Na+/H+‐exchanger with sabiporide attenuates the downregulation and uncoupling of the myocardialβ‐adrenoceptor system in failing rabbit hearts
Authors: Leineweber Kirsten , Aker Stephanie , Beilfuß Anja , Rekasi Heike , Konietzka Ina , Martin Claus , Heusch Gerd , Schulz Rainer 
Published: March 2006

Chronic heart failure (HF) is characterized by left ventricular (LV) structural remodeling, impaired function, increased circulating noradrenaline (NA) levels and impaired responsiveness of the myocardialβ‐adrenoceptor (βAR)‐adenylyl cyclase (AC) system. In failing hearts, inhibition of the sodium/proton‐exchanger (NHE)‐1 attenuates LV remodeling and improves LV function. The mechanism(s) involved in these cardioprotective effects remain(s) unclear, but might involve effects on the impairedβAR‐AC system.Therefore, we investigated whether NHE‐1 inhibition with sabiporide (SABI; 30 mg kg−1 day−1p.o.) might affect myocardialβAR density and AC activity in relation to changes in LV end‐diastolic diameter (LVEDD) and LV systolic fractional shortening (LVS‐FS) after 3 weeks of rapid LV pacing in rabbits.After 3 weeks of rapid LV pacing LVEDD was significantly increased (Shams 17±0.2 mm,n=9 vs 3wksHF 20±0.5 mm,n=8;P<0.05) and LVS‐FS decreased (Shams 31±1%,n=9 vs 3wksHF 10±1%,n=8;P<0.05). SABI treatment significantly improved LV function independent of whether rabbits were treated after 1 week of pacing (3wksHF+2wksSABI (n=7): LVEDD 18±1 mm; LVS‐FS 16±4%) or before pacing (3wksHF+3wksSABI (n=9): LVEDD 18±1 mm; LVS‐FS 18±6%). After 3 weeks of rapid LV pacing, SABI treatment significantly attenuated increases in serum NA content (Shams 0.83±0.19, 3wksHF 2.68±0.38, 3wksHF+2wksSABI 1.22±0.32, 3wksHF+3wksSABI 1.38±0.33 ng ml−1). Moreover,βAR density (Shams 64±5, 3wksHF 38±3, 3wksHF+2wksSABI 48±4, 3wksHF+3wksSABI 55±3 fmol mg−1protein) and responsiveness (isoprenaline‐stimulated AC activity. (Shams 57.6±4.9, 3wksHF 36.3±6.0, 3wksHF+2wksSABI 56.9±6.0, 3wksHF+3wksSABI 54.5±4.8 pmol cyclic AMP mg−1 protein−1 min−1) were significantly improved in SABI‐treated rabbits.From the present data we cannot address whether the improvedβAR‐AC system permitted improved LV function and/or whether the improved LV function resulted in less activation of the sympathetic nervous system and by this in a reduced stimulation of theβAR‐AC system. Accordingly, additional studies are needed to fully establish the cause‐and‐effect relationship between NHE‐1 inhibition and the restoration of the myocardialβAR system.British Journal of Pharmacology(2006)148, 137–146. doi:10.1038/sj.bjp.0706714
Impairment of PAR‐2‐mediated relaxation system in colonic smooth muscle after intestinal inflammation
Authors: Sato Koichi , Ninomiya Hiromichi , Ohkura Shinsuke , Ozaki Hiroshi , Nasu Tetsuyuki 
Published: March 2006

Protease‐activated receptor (PAR)‐2 plays important roles in intestinal inflammatory responses. Changes in PAR‐2‐mediated smooth muscle function may contribute pathophysiologically to the intestinal motility disorders often observed in inflammatory bowel disease (IBD).
Stimulation of PAR‐2 by trypsin‐induced relaxation of carbachol‐ and KCl‐induced contractions in normal rat colonic smooth muscle was completely resolved by tissue pretreatment with apamin, but not by pretreatment with l‐NMMA or a cocktail of neuronal blockers (tetrodotoxin, hexamethonium and propranolol).
In colon inflamed by dextran sodium sulphate (DSS), trypsin‐induced inhibitory effects were significantly reduced. Relaxation induced by SLIGRL‐NH2, a selective PAR‐2‐activating peptide, was also reduced in DSS‐treated rat colon. However, inhibitory effects of 1‐ethylbenzimidazolin‐2‐one, an activator of small conductance Ca2+‐activated K+ channel, were unaffected.
Expression of PAR‐2 mRNA in colonic muscularis externa was significantly lower in DSS‐treated rats than in control rats.
These results suggest that the PAR‐2 mediated relaxation system in colonic smooth muscle is suppressed in this experimental colitis rat model, and may contribute to motility disorders in IBD.

British Journal of Pharmacology (2006) 148, 200–207. doi:10.1038/sj.bjp.0706717
Constructing quantitative models from qualitative mutant phenotypes: preferences in selecting sensory organ precursors
Authors: Hsu Chao-Ping , Lee Pei-Hsuan , Chang Ching-Wei , Lee Cheng-Tsung 
Published: March 2006

Abstract
Motivation: To study biology from the systems level, mathematical models that describe the time-evolution of the system offer useful insights. Quantitative information is required for constructing such models, but such information is rarely provided.
Results: We propose a scheme—based on random searches over a parameter space, according to criteria set by qualitative experimental observations—for inferring quantitative parameters from qualitative experimental results. We used five mutant constraints to construct genetic network models for sensory organ precursor formation in Drosophila development. Most of the models were capable of generating expression patterns for the gene Enhancer of split that were compatible with experimental observations for wild type and two Notch mutants. We further examined factors differentiating the neural fate among cells in a proneural cluster, and found two opposite driving forces that bias the choice between middle cells and the peripheral cells. Therefore, it is possible to build numerical models from mutant screening and to study mechanisms behind the complicated network.
Contact: cherri@sinica.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
TOPAAS, a Tomato and Potato Assembly Assistance System for Selection and Finishing of Bacterial Artificial Chromosomes
Authors: Peters Sander A. , van Haarst Jan C. , Jesse Taco P. , Woltinge Dennis , Jansen Kim , Hesselink Thamara , van Staveren Marjo J. , Abma-Henkens Marleen H.C. , Klein-Lankhorst René M. 
Published: March 2006

Abstract
We have developed the software package Tomato and Potato Assembly Assistance System (TOPAAS), which automates the assembly and scaffolding of contig sequences for low-coverage sequencing projects. The order of contigs predicted by TOPAAS is based on read pair information; alignments between genomic, expressed sequence tags, and bacterial artificial chromosome (BAC) end sequences; and annotated genes. The contig scaffold is used by TOPAAS for automated design of nonredundant sequence gap-flanking PCR primers. We show that TOPAAS builds reliable scaffolds for tomato (Solanum lycopersicum) and potato (Solanum tuberosum) BAC contigs that were assembled from shotgun sequences covering the target at 6- to 8-fold coverage. More than 90% of the gaps are closed by sequence PCR, based on the predicted ordering information. TOPAAS also assists the selection of large genomic insert clones from BAC libraries for walking. For this, tomato BACs are screened by automated BLAST analysis and in parallel, high-density nonselective amplified fragment length polymorphism fingerprinting is used for constructing a high-resolution BAC physical map. BLAST and amplified fragment length polymorphism analysis are then used together to determine the precise overlap. Assembly onto the seed BAC consensus confirms the BACs are properly selected for having an extremely short overlap and largest extending insert. This method will be particularly applicable where related or syntenic genomes are sequenced, as shown here for the Solanaceae, and potentially useful for the monocots Brassicaceae and Leguminosea.
Abundantly and Rarely Expressed Lhc Protein Genes Exhibit Distinct Regulation Patterns in Plants
Authors: Klimmek Frank , Sjödin Andreas , Noutsos Christos , Leister Dario , Jansson Stefan 
Published: March 2006

Abstract
We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.
How does activation loop phosphorylation modulate catalytic activity in the cAMP‐dependent protein kinase: A theoretical study
Authors: Cheng Yuhui , Zhang Yingkai , McCammon J. Andrew 
Published: March 2006

AbstractPhosphorylation mediates the function of many proteins and enzymes. In the catalytic subunit of cAMP‐dependent protein kinase, phosphorylation of Thr 197 in the activation loop strongly influences its catalytic activity. In order to provide theoretical understanding about this important regulatory process, classical molecular dynamics simulations and ab initio QM/MM calculations have been carried out on the wild‐type PKA–Mg2 ATP–substrate complex and its dephosphorylated mutant, T197A. It was found that pThr 197 not only facilitates the phosphoryl transfer reaction by stabilizing the transition state through electrostatic interactions but also strongly affects its essential protein dynamics as well as the active site conformation.
Computer‐aided NMR assay for detecting natively folded structural domains
Authors: Hondoh Takayuki , Kato Atsushi , Yokoyama Shigeyuki , Kuroda Yutaka 
Published: March 2006

AbstractStructural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. However, protein dissection essentially remains an empirical and often a tedious process. Here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. This approach combines the computational prediction of sequence regions corresponding to putative domains with an experimental assessment of their structures and stabilities by NMR and biochemical methods. We tested this approach with nine putative domains predicted from a set of 108 Thermus thermophilus HB8 sequences using PASS, a domain prediction program we previously reported. To facilitate the experimental assessment of the domain structures, we developed a generic 6‐hour His‐tag‐based purification protocol, which enables the sample quality evaluation of a putative structural domain in a single day. As a result, we observed that half of the predicted structural domains were indeed natively folded, as judged by their HSQC spectra. Furthermore, two of the natively folded domains were novel, without related sequences classified in the Pfam and SMART databases, which is a significant result with regard to the ability of structural genomics projects to uniformly cover the protein fold space.
Identification of phosphorylation sites in glycine N‐methyltransferase from rat liver
Authors: Luka Zigmund , Ham Amy‐Joan L. , Norris Jeremy L. , Yeo Eui‐Ju , Yermalitsky Valery , Glenn Byron , Caprioli Richard M. , Liebler Daniel C. , Wagner Conrad 
Published: March 2006

AbstractPrevious studies have shown that rat glycine N‐methyltransferase (GNMT) is phosphorylated in vivo, and could be phosphorylated in vitro on serine residues with a significant increase of enzyme activity, but no phosphorylation sites were identified. In this work the identification of the specific phosphorylation sites of rat GNMT is reported. Three different preparations of rat GNMT were analyzed: (1) purified from liver by standard methods of protein purification, (2) prepared from isolated hepatocytes and from liver tissue by immunoprecipitation, and (3) recombinant protein expressed in Escherichia coli. We measured the molecular weights of protein isoforms using electrospray mass spectrometry and used liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) of peptides resulting from tryptic and chymotryptic digests. We also performed chemical analysis of phosphoamino acids and protein sequencing. In all samples, the phosphorylated serine residues 71, 182, and 241 were found. In GNMT prepared from liver tissue and hepatocytes an S9 additional residue was found to be phosphorylated. In hepatocytes and in recombinant GNMT S139 was detected. Serine 9 was also identified as a target for cAMP‐dependent protein kinase in vitro. The positions of these phosphorylated residues in the tertiary structure of GNMT indicate their possible effect on enzyme conformation and activity.
Repeat protein architectures predicted by a continuum representation of fold space
Authors: Hausrath Andrew C. , Goriely Alain 
Published: March 2006

AbstractIt is an open question whether nature has utilized all possible protein folds. For a simple protein architecture, the helical repeats, we report a method to address this question based on a mapping between the set of repetitive curves and a space of parameters specifying the curve. The exploration of the parameter space for a particular architecture enables a systematic exploration of the fold space for that protein architecture. In a planar subspace of the parameter space of helical repeats we have identified points corresponding to both naturally occurring folds and potential folds not observed so far.
Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae
Authors: Shin Dong Hae , Kim Jeong‐Sun , Yokota Hisao , Kim Rosalind , Kim Sung‐Hou 
Published: March 2006

AbstractWe have determined the crystal structure of the DUF16 domain of unknown function encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 Å resolution. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled‐coils. The shorter one consists of 11 highly conserved residues. The sequence comprises noncanonical heptad repeats that induce a right‐handed coiled‐coil structure. The longer one is composed of approximately nine heptad repeats. In this coiled‐coil structure, there are three distinguishable regions that confer unique structural properties compared with other known homotrimeric coiled‐coils. The first part, containing one stutter, is an unusual phenylalanine‐rich region that is not found in any other coiled‐coil structures. The second part is a highly conserved glutamine‐rich region, frequently found in other trimeric coiled‐coil structures. The last part is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16 family together with a secondary structure prediction shows that the DUF16 family can be classified into five subclasses according to N‐terminal sequences. Based on the structural comparison with other coiled‐coil structures, a probable molecular function of the DUF16 family is discussed.
Stagonospora nodorum: cause of stagonospora nodorum blotch of wheat
Authors: SOLOMON PETER S. , LOWE ROHAN G. T. , TAN KAR‐CHUN , WATERS ORMONDE D. C. , OLIVER RICHARD P. 
Published: March 2006

SUMMARY Stagonospora nodorum is an important pathogen of wheat and related cereals, causing both a leaf and glume blotch. This review summarizes recent advances in our understanding of taxonomy, control and pathogenicity of this species.Taxonomy:   Stagonospora (syn. Septoria) nodorum (Berk.) Castell. and Germano [teleomorph: Phaeosphaeria (syn. Leptosphaeria) nodorum (Müll.) Hedjar.], kingdom Fungi, phylum Ascomycota, subphylum Euascomycota, class Dothideomycetes, order Pleosporales, family Phaeosphaeriaceae, genus Phaeosphaeria, species nodorum.Host range:   Wheat, Triticum aestivum, T. durum, Triticale, are the main hosts but other cereals and wild grasses have been reported to harbour S. nodorum. Disease symptoms are lens‐shaped necrotic lesions on leaves, girdling necrosis on stems (especially the nodes, hence ‘nodorum’) and lesions on glumes. Mature lesions produce pycnidia scattered throughout the lesions, especially as tissue senesces.Useful websites:   http://ocid.nacse.org/research/deephyphae/htmls/asco_taxlist_spat.html (taxonomic information), http://ohioline.osu.edu/ac‐fact/0002.html (disease information), http://wwwacnfp.murdoch.edu.au/ (ACNFP homepage), http://www.broad.mit.edu/annotation/fungi/stagonospora_nodorum/index.html (genome sequence homepage), http://cogeme.ex.ac.uk/efungi/ (genome sequence annotation and analysis).