bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous determination of MK‐0767 and seven metabolites in rat urine using liquid chromatography/tandem mass spectrometry
Authors: Shen Zhongzhou , Kochansky Christopher , Bakhtiar Ray , Franklin Ronald B. , Vincent Stella H.
Published: September 2004

MK‐0767, 5‐[2,4‐dioxothiazolidin‐5‐yl)methyl]‐2‐methoxy‐N‐[[(4‐trifluoromethyl)phenyl]methyl]benzamide (I, Table 1), is a dual peroxisome proliferator‐activated receptor (PPAR) α/γ agonist previously studied for the treatment of type 2 diabetes and dyslipidemia. To support further toxicological studies in one of the animal species used in chronic testing of I, a liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the simultaneous quantification of I and seven metabolites in rat urine was developed and validated. In this method, urine samples were diluted with acetonitrile/methanol (50:50, v/v) and injected directly onto the column of an LC system. Detection was achieved by MS/MS using a turbo ion spray probe monitoring precursor → product ion combinations in selected reaction monitoring (SRM) mode. The linear range for I and three metabolites was 0.8–800 ng/mL, and 8–8000 ng/mL for four other metabolites found to be present in urine at higher concentrations than I. Intra‐day and inter‐day variation using this method were ≤13.0%. The method exhibited good linearity, reproducibility, specificity and sufficient sensitivity when used for the analysis of rat urine samples. Concentrations of I and its major metabolites in rat urine were determined in samples collected between 0–24 h after dosing on the last day of administration of nine daily oral doses to three male (1000 mg/kg/day) and three female (300 mg/kg/day) Sprague‐Dawley rats. The urinary concentrations of I and its metabolites were similar in male and female rats. The average concentrations of I were 0.51 and 0.33 μg/mL in male and female rats, respectively. Concentrations of four of the seven metabolites quantified were 6‐ to 45‐fold higher than those of I. The most abundant metabolite, with concentrations of 24.2 and 13.3 μg/mL in male and female rat urine, respectively, was a methyl sulfoxide derivative formed by oxidative cleavage of the thiazolidinedione ring, followed by S‐methylation and oxidation of the sulfide intermediate. Copyright © 2004 John Wiley & Sons, Ltd.

Molecular weight (MW), SRM transitions and structures of MK‐0767 (I) and its metabolites

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MS1, MS2, and SQT—three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
Authors: McDonald W. Hayes , Tabb David L. , Sadygov Rovshan G. , MacCoss Michael J. , Venable John , Graumann Johannes , Johnson Jeff R. , Cociorva Daniel , Yates John R.
Published: September 2004

As the speed with which proteomic labs generate data increases along with the scale of projects they are undertaking, the resulting data storage and data processing problems will continue to challenge computational resources. This is especially true for shotgun proteomic techniques that can generate tens of thousands of spectra per instrument each day. One design factor leading to many of these problems is caused by storing spectra and the database identifications for a given spectrum as individual files. While these problems can be addressed by storing all of the spectra and search results in large relational databases, the infrastructure to implement such a strategy can be beyond the means of academic labs. We report here a series of unified text file formats for storing spectral data (MS1 and MS2) and search results (SQT) that are compact, easily parsed by both machine and humans, and yet flexible enough to be coupled with new algorithms and data‐mining strategies. Copyright © 2004 John Wiley & Sons, Ltd.
Process modeling: A systems engineering tool for analyzing complex systems
Authors: Osmundson John S. , Gottfried Russell , Kum Chee Yang , Boon Lau Hui , Lian Lim Wei , Patrick Poh Seng Wee , Thye Tan Choo
Published: September 2004

This paper presents a method for performing architectural analyses of complex systems‐of‐systems using process modeling. A process is a series of actions undertaken by a system‐of‐systems to produce one or more end results, typically products and services. The method applies to systems‐of systems whose effectiveness and performance depend strongly on process timelines, such as distributed information systems, logistics systems, and manufacturing and distribution systems. A fundamental tool in this method is the development of a unified modeling language (UML) related view of the system‐of‐system processes of interest and the subsequent conversion of the UML related view into an end‐to‐end system‐of‐systems executable object‐oriented simulation model. This method is illustrated by applying process modeling and simulation to analysis of a military systems‐of‐systems, an expeditionary warfare system envisioned for the 2015–2020 time frame. Expeditionary warfare is the operation of an armed force in an area far from a supportable home base and supported by temporarily established means. The U.S. military has conducted expeditionary warfare in the past by building up forces, equipment, and supplies at a beachhead before moving on to an objective. There is current interest in the U.S. military to shift from the concept of establishing a beachhead and then movement to an objective to a concept of sea‐based launching and supporting forces and sea‐to‐objective maneuver for fighting forces. A fundamental tool in this analysis is an end‐to‐end object‐oriented simulation model emulating the full implementation of these force architectures and design factors as well as accounting for the impact of varying levels of operational intensity, attrition of personnel and transport vehicles, weather, mining sea lanes, transport vehicle operating and availability constraints, landing spot constraints, and transit and communications delays. This paper focuses on the framework of the simulation model and its most significant findings as applied to expeditionary warfare concepts as an example of the application of process modeling to architectural analyses of complex systems‐of‐systems. © 2004 Wiley Periodicals, Inc. Syst Eng 7: 320–337, 2004
Opioid analgesia in the newborn
Authors: Nandi R. , Fitzgerald M.
Published: September 2004

Pain in neonates is now well established. Studies of the developmental neurobiology of pain have revealed that pain processing in the immature is very different from that in the mature nervous system. Neonates undergo considerable maturation of peripheral, spinal and supraspinal afferent pain transmission over the early postnatal period but are able to respond to tissue injury with specific behaviour and with autonomic, hormonal and metabolic signs of stress and distress. Opioid analgesia is now widely used in neonates. There is evidence that morphine requirements may be low in the youngest patients. Sensory threshold testing in rat pups has shown that the analgesic potency of systemic morphine mechanical stimulation is significantly greater in the neonate and declines with postnatal age. The changing morphine sensitivity in the postnatal period may be part of a general reorganisation in the structure and function of primary afferent synapses, neurotransmitter/receptor expression and function and excitatory and inhibitory modulation from higher brain centres. Importantly opioid receptor expression undergoes significant developmental regulation — mu opioid receptors, observed to be exuberantly expressed in the neonatal rat, have been found to be functional. These findings have important implications for the human neonate as they provide a possible explanation for the differences in morphine requirements observed in the youngest patients. The study of the underlying mechanisms of pain and analgesia in development has enabled important changes in clinical practice. However, pain in the newborn remains poorly understood and continued research and intensive study in this area is essential for further effective analgesic intervention and the discovery of new targets for therapy.
Severe acute maternal morbidity in rural South Africa
Authors: Gandhi M.N. , Welz T. , Ronsmans C.
Published: September 2004

Objective: Our objective was to identify the frequency, causes, and avoidable factors of severe acute maternal morbidity (SAMM) in four non‐specialist hospitals in rural South Africa. Method: We conducted a prospective audit using criteria for SAMM suited to the diagnostic and treatment facilities available in the primary hospital setting. For each case of SAMM, a local audit team assessed the standard of care against local management guidelines and examined avoidable factors. An external specialist also retrospectively examined avoidable factors. Result The facility‐based incidence of SAMM was 541 cases per 100,000 births (95% CI 368–767). The commonest organ systems involved were cerebral (42%), coagulation (19%), and vascular dysfunctions (16%). The commonest obstetric diagnoses were eclampsia (39%) and obstetric haemorrhage (32%). Approximately 65% of cases were avoidable. Conclusion: A qualitative case review audit of SAMM in a non‐specialist rural setting appears feasible and sustainable, and provides valuable information towards improving deficiencies in maternal care.
Chlorofluorocarbons in the Sea of Okhotsk: Ventilation of the intermediate water
Authors: Yamamoto‐Kawai Michiyo , Watanabe Shuichi , Tsunogai Shizuo , Wakatsuchi Masaaki
Published: September 2004

Ventilation of the intermediate layer in the Sea of Okhotsk is studied with regard to the ventilation of North Pacific Intermediate Water (NPIW). Measurements of chlorofluorocarbons (CFCs) from 1998 to 2000 reveal that the Okhotsk intermediate water is ventilated in two ways. The first consists of dense water formation in the polynyas that form on the northern shelves during winter. Measurements show that on the northwestern shelf, because of atmospheric cooling and brine rejection, the cold water that forms is dense enough to enter the intermediate layer. The CFC concentration in this dense shelf water (DSW) is high and almost saturated with respect to atmospheric CFCs, indicating that the DSW experiences active air‐water gas exchange during its formation. Away from the shelves, the CFC distribution shows that the DSW directly ventilates the upper level of the Okhotsk Sea Intermediate Water (OSIW). The second ventilation process is driven by the strong tidal mixing around the Bussol' Strait. The observed distribution of CFCs at the 27.4 σθ level suggest that diapycnal mixing around the strait transports CFCs from the surface to this deeper layer, ventilating the OSIW. Combination of both processes means that the OSIW is more ventilated than Pacific water at the same density levels.
Ensemble prediction of rainfall during the 2000–2002 Mei‐Yu seasons: Evaluation over the Taiwan area
Authors: Yang Ming‐Jen , Jou Ben J.‐D. , Wang Shi‐Chieh , Hong Jing‐Shan , Lin Pay‐Liam , Teng Jen‐Hsin , Lin Hui‐Chuan
Published: September 2004

This paper reports the first effort on real‐time ensemble predictions of precipitation during the 2000–2002 Mei‐Yu seasons (May to June) over the Taiwan area. Six members were included, each using the fifth‐generation Pennsylvania State University‐National Center for Atmospheric Research Mesoscale Model (MM5) nesting down to 15‐km grid size, with different combinations of cumulus and microphysics parameterizations. Rainfall forecasts were evaluated with the equitable threat score (ETS) and bias score (BS). On the basis of verifications on 15‐km grid points over three Mei‐Yu seasons, it was found that no one member persistently had the least root mean square error of 12–24 hours and 24–36 hours accumulated rainfalls. For rainfall occurrence, most members had better predictions over the northeastern mountainous area, the northwestern coastal plain, the central mountain slope, the southwestern coastal plan, and the southwestern mountainous area. These regions also corresponded to areas of more accumulated rainfalls during three Mei‐Yu seasons. An ensemble prediction, using a multiple linear regression (MLR) method which performed a least‐square fit between the predicted and observed rainfalls in postseason analysis, had the best ETS and BS skill. The MLR ensemble forecast outperformed the average forecast (for all six members), the average forecasts of cumulus (four‐member) and microphysics (three‐member) ensembles, and also a high‐resolution (5‐km) forecast; however, a high‐resolution forecast still had better skill for heavy rainfall events. The MLR ensemble forecast, using the weightings determined from previous Mei‐Yu seasons, still had similar ETS trend to that with weightings determined by current‐year Mei‐Yu season, albeit with less skill.
A new criterion for identifying breaks in monsoon conditions over the Indian subcontinent
Authors: Ramesh Kumar M. R. , Prabhu Dessai Uma R.
Published: September 2004

The presence or absence of prolonged breaks over the Indian subcontinent during the mid monsoon months of July and August decides the fate of the monsoon rainfall. Using a new criterion for identifying the breaks, we have catalogued them for the period 1901 to 2002. We refer to a situation as a break, if the all India rainfall is less than 9 mm/day and the condition persists for a minimum of three days and if it occurs in the mid monsoon months of July and August. The majority of the breaks in the months of July and August were of 3–4 days duration (49%). Breaks identified by our method were in general consistent with those identified by the conventional methods. Further, the correlation between the seasonal monsoon rainfall and break (active) days identified by the present criteria is −0.80 (0.38) which is more robust than that of the previous studies.
Properties of jet engine combustion particles during the PartEmis experiment: Particle size spectra (d > 15 nm) and volatility
Authors: Nyeki S. , Gysel M. , Weingartner E. , Baltensperger U. , Hitzenberger R. , Petzold A. , Wilson C. W.
Published: September 2004

Size distributions (d > 15 nm) and volatile properties of combustion particles were measured during test‐rig experiments on a jet engine, consisting of a combustor and three simulated turbine stages (HES). The combustor was operated to simulate legacy (inlet temperature 300°C) and contemporary (500°C) cruise conditions, using kerosene with three different fuel sulfur contents (FSC; 50, 400 and 1300 μg g−1). Measurements found that contemporary cruise conditions resulted in lower number emission indices (EIN15) and higher geometric mean particle diameter (dG) than for legacy conditions. Increasing FSC resulted in an overall increase in EIN15 and decrease in dG. The HES stages or fuel additive (APA101) had little influence on EIN15 or dG, however, this is uncertain due to the measurement variability. EIN15 for non‐volatile particles was largely independent of all examined conditions.
A global water vapor data set obtained by merging the SSMI and MODIS data
Authors: Gao Bo‐Cai , Chan Pui K. , Li Rong‐Rong
Published: September 2004

At present, the column amount of atmospheric water vapor over clear land surfaces and over oceanic areas with sun glint is operationally retrieved from radiances measured with near‐IR channels of the Moderate Resolution Imaging SpectroRadiometer (MODIS) instruments on board the NASA Terra and Aqua Spacecraft platforms. TPW over oceans has also been derived operationally from radiances measured by the Special Sensor Microwave Imagers (SSMI) on board different spacecraft. We report in this letter that a global water vapor data product with improved quality can be obtained by merging the monthly‐mean MODIS near‐IR TPW data over land and the SSMI TPW data over water surfaces. Major characteristics of the seasonal variations of TPW are described. Examples of water vapor anomalies associated with the 2002 El Niño event are presented. We expect that the merged TPW data product will have useful applications for the study of the global hydrological cycle.
A cloud model interpretation of jumping cirrus above storm top
Authors: Wang Pao K.
Published: September 2004

A dynamically driven mechanism occurring above severe thunderstorms is described, which can explain the jumping cirrus phenomenon. A three‐dimensional, non‐hydrostatic cloud model is used to perform numerical simulation of a supercell that occurred in Montana in 1981. The jumping cirrus phenomenon is reproduced in the simulated storm. Analysis of the model results shows that the jumping cirrus phenomenon is produced by the breaking of the gravity waves excited by the strong convection inside the storm. The wave breaking process causes some moisture to detach from the storm cloud and jump into the stratosphere. The apparent upstream motion of the jumping cirrus is true only relative to the storm. The jumping cirrus phenomenon represents an irreversible transport mechanism of materials from the troposphere to the stratosphere.
Evidence of the effect of summertime midlatitude convection on the subtropical lower stratosphere from CRYSTAL‐FACE tracer measurements
Authors: Ray Eric A. , Rosenlof Karen H. , Richard Erik C. , Hudson P. K. , Cziczo D. J. , Loewenstein M. , Jost H.‐J. , Lopez J. , Ridley B. , Weinheimer A. , Montzka D. , Knapp D. , Wofsy S. C. , Daube B. C. , Gerbig C. , Xueref I. , Herman R. L.
Published: September 2004

Trace gas and particle measurements taken during the CRYSTAL‐FACE mission are used to examine mixing in the summer subtropical lower stratosphere. Vigorous convection in the central and eastern United States injected a significant amount of tropospheric air into the lower stratosphere, which was subsequently advected over the region sampled during the CRYSTAL‐FACE mission. Aerosols produced by biomass burning were observed over Florida during a time period with a large number of forest fires in the western United States and eastern Canada, providing evidence of convective injection of tropospheric air into the lower stratosphere. The circumstances of the large‐scale flow pattern in the upper troposphere and lower stratosphere, vigorous summertime convection, abundant forest fires, and the downstream sampling allow a unique view of mixing in the lower stratosphere. We calculate the fractions of midlatitude tropospheric air in the sampled lower stratosphere and mixing rates on the basis of consistency between a number of tracer‐tracer correlations. The tropospheric endpoints to the mixing estimates give an indication of midlatitude continental convective input into the lower stratosphere. We also discuss the possible impact of summertime midlatitude convection on the composition of the stratosphere as a whole.
Simulation of the Earth's radiation budget by the European Centre for Medium‐Range Weather Forecasts 40‐year reanalysis (ERA40)
Authors: Allan Richard P. , Ringer Mark A. , Pamment J. Alison , Slingo Anthony
Published: September 2004

The radiation budget simulated by the European Centre for Medium‐Range Weather Forecasts (ECMWF) 40‐year reanalysis (ERA40) is evaluated for the period 1979–2001 using independent satellite data and additional model data. This provides information on the quality of the radiation products and indirect evaluation of other aspects of the climate produced by ERA40. The climatology of clear‐sky outgoing longwave radiation (OLR) is well captured by ERA40. Underestimations of about 10 W m−2 in clear‐sky OLR over tropical convective regions by ERA40 compared to satellite data are substantially reduced when the satellite sampling is taken into account. The climatology of column‐integrated water vapor is well simulated by ERA40 compared to satellite data over the ocean, indicating that the simulation of downward clear‐sky longwave fluxes at the surface is likely to be good. Clear‐sky absorbed solar radiation (ASR) and clear‐sky OLR are overestimated by ERA40 over north Africa and high‐latitude land regions. The observed interannual changes in low‐latitude means are not well reproduced. Using ERA40 to analyze trends and climate feedbacks globally is therefore not recommended. The all‐sky radiation budget is poorly simulated by ERA40. OLR is overestimated by around 10 W m−2 over much of the globe. ASR is underestimated by around 30 W m−2 over tropical ocean regions. Away from marine stratocumulus regions, where cloud fraction is underestimated by ERA40, the poor radiation simulation by ERA40 appears to be related to inaccurate radiative properties of cloud rather than inaccurate cloud distributions.
Vanilloid TRPV1 receptor mediates the antihyperalgesic effect of the nonpsychoactive cannabinoid, cannabidiol, in a rat model of acute inflammation
Authors: Costa Barbara , Giagnoni Gabriella , Franke Chiara , Trovato Anna Elisa , Colleoni Mariapia
Published: September 2004

Cannabidiol (CBD), a nonpsychoactive marijuana constituent, was recently shown as an oral antihyperalgesic compound in a rat model of acute inflammation. We examined whether the CBD antihyperalgesic effect could be mediated by cannabinoid receptor type 1 (CB1) or cannabinoid receptor type 2 (CB2) and/or by transient receptor potential vanilloid type 1 (TRPV1). Rats received CBD (10 mg kg−1) and the selective antagonists: SR141716 (N‐(piperidin‐1‐yl)‐5‐(4‐chlorophenyl)‐1‐(2,4‐dichlorophenyl)‐4‐methyl‐1H‐pyrazole‐3‐carboxamide) for CB1, SR144528 (N‐[(1S)‐endo‐1,3,3‐trimethylbicyclo[2.2.1]heptan‐2‐yl]‐5‐(4‐chloro‐3‐methylphenyl)‐1‐(4‐methylbenzyl)pyrazole‐3 carboxamide) for CB2 and capsazepine (CPZ) for TRPV1 receptors. The intraplantar injection of carrageenan in rats induced a time‐dependent thermal hyperalgesia, which peaked at 3 h and decreased at the following times. CBD, administered 2 h after carrageenan, abolished the hyperalgesia to the thermal stimulus evaluated by plantar test. Neither SR141716 (0.5 mg kg−1) nor SR144528 (3 and 10 mg kg−1) modified the CBD‐induced antihyperalgesia; CPZ partially at the lowest dose (2 mg kg−1) and fully at the highest dose (10 mg kg−1) reversed this effect. These results demonstrate that TRPV1 receptor could be a molecular target of the CBD antihyperalgesic action.

British Journal of Pharmacology (2004) 143, 247–250. doi:10.1038/sj.bjp.0705920
Actions of two naturally occurring saturated N‐acyldopamines on transient receptor potential vanilloid 1 (TRPV1) channels
Authors: De Petrocellis Luciano , Chu Constance J , Moriello Aniello Schiano , Kellner Juliane C , Walker J Michael , Di Marzo Vincenzo
Published: September 2004

Four long‐chain, linear fatty acid dopamides (N‐acyldopamines) have been identified in nervous bovine and rat tissues. Two unsaturated members of this family of lipids, N‐arachidonoyl‐dopamine (NADA) and N‐oleoyl‐dopamine, were shown to potently activate the transient receptor potential channel type V1 (TRPV1), also known as the vanilloid receptor type 1 for capsaicin. However, the other two congeners, N‐palmitoyl‐ and N‐stearoyl‐dopamine (PALDA and STEARDA), are inactive on TRPV1. We have investigated here the possibility that the two compounds act by enhancing the effect of NADA on TRPV1 (‘entourage’ effect).

When pre‐incubated for 5 min with cells, both compounds dose‐dependently enhanced NADA's TRPV1‐mediated effect on intracellular Ca2+ in human embryonic kidney cells overexpressing the human TRPV1. In the presence of either PALDA or STEARDA (0.1–10 μM), the EC50 of NADA was lowered from ∼90 to ∼30 nM.

The effect on intracellular Ca2+ by another endovanilloid, N‐arachidonoyl‐ethanolamine (anandamide, 50 nM), was also enhanced dose‐dependently by both PALDA and STEARDA. PALDA and STEARDA also acted in synergy with low pH (6.0–6.7) to enhance intracellular Ca2+ via TRPV1.

When co‐injected with NADA (0.5 μg) in rat hind paws, STEARDA (5 μg) potentiated NADA's TRPV1‐mediated nociceptive effect by significantly shortening the withdrawal latencies from a radiant heat source. STEARDA (1 and 10 μg) also enhanced the nocifensive behavior induced by carrageenan in a typical test of inflammatory pain.

These data indicate that, despite their inactivity per se on TRPV1, PALDA and STEARDA may play a role as ‘entourage’ compounds on chemicophysical agents that interact with these receptors, with possible implications in inflammatory and neuropathic pain.

British Journal of Pharmacology (2004) 143, 251–256. doi:10.1038/sj.bjp.0705924
Effects of inhaled thrombin receptor agonists in mice
Authors: Moffatt James D , Lever Rebecca , Page Clive P
Published: September 2004

Active thrombin is found in the airways of patients with a variety of inflammatory lung diseases. However, whether thrombin contributes to the pathologies of these diseases is unknown, although thrombin is a potent inflammatory mediator in other organ systems. In the present study we have assessed the acute inflammatory effect of inhaled thrombin and investigated the possible receptors mediating any effects in mice.

Thrombin (200–2000 U kg−1 intranasally), induced the recruitment of a small, but significant, number of neutrophils into the airways as assessed by differential counts of cells retrieved by bronchoalveolar lavage (BAL). This small response was mimicked by peptide agonists of proteinase‐activated receptor‐4 (PAR4; GYPGKF, AYPGKF; 2–20 mg kg−1), but not PAR1 (SFLLRN; 2–20 mg kg−1). By contrast, trypsin (200–2000 U kg−1) caused profound inflammation and lung damage.

Concentrations of tumour necrosis factor‐α (TNF‐α) were elevated in BAL fluid from thrombin‐treated mice, and a TNF‐α‐neutralising antibody inhibited the influx of neutrophils in response to thrombin.

Although isolated alveolar macrophages appeared to express PAR1‐ and PAR4‐immunoreactivity, these cells failed to release TNF‐α above baseline levels in response to thrombin, trypsin or any of the peptide PAR agonists.

Neither thrombin (2000 U kg−1) nor trypsin (200 U kg−1) modified the airway neutrophilia in response to intranasal bacterial lipopolysaccharide (LPS; 100 μg kg−1).

In conclusion, exogenous thrombin has only a modest acute inflammatory action in the lung that appears to be mediated by PAR4 and involve release of TNF‐α from an unknown source.

British Journal of Pharmacology (2004) 143, 269–275. doi:10.1038/sj.bjp.0705926
The evolving role of lipid rafts and caveolae in G protein‐coupled receptor signaling: implications for molecular pharmacology
Authors: Ostrom Rennolds S , Insel Paul A
Published: September 2004

The many components of G‐protein‐coupled receptor (GPCR) signal transduction provide cells with numerous combinations with which to customize their responses to hormones, neurotransmitters, and pharmacologic agonists. GPCRs function as guanine nucleotide exchange factors for heterotrimeric (α, β, γ) G proteins, thereby promoting exchange of GTP for GDP and, in turn, the activation of ‘downstream’ signaling components. Recent data indicate that individual cells express mRNA for perhaps over 100 different GPCRs (out of a total of nearly a thousand GPCR genes), several different combinations of G‐protein subunits, multiple regulators of G‐protein signaling proteins (which function as GTPase activating proteins), and various isoforms of downstream effector molecules. The differential expression of such protein combinations allows for modulation of signals that are customized for a specific cell type, perhaps at different states of maturation or differentiation. In addition, in the linear arrangement of molecular interactions involved in a given GPCR–G‐protein–effector pathway, one needs to consider the localization of receptors and post‐receptor components in subcellular compartments, microdomains, and molecular complexes, and to understand the movement of proteins between these compartments. Co‐localization of signaling components, many of which are expressed at low overall concentrations, allows cells to tailor their responses by arranging, or spatially organizing in unique and kinetically favorable ways, the molecules involved in GPCR signal transduction. This review focuses on the role of lipid rafts and a subpopulation of such rafts, caveolae, as a key spatial compartment enriched in components of GPCR signal transduction. Recent data suggest cell‐specific patterns for expression of those components in lipid rafts and caveolae. Such domains likely define functionally important, cell‐specific regions of signaling by GPCRs and drugs active at those GPCRs.

British Journal of Pharmacology (2004) 143, 235–245. doi:10.1038/sj.bjp.0705930
Investigation of the effect of the farnesyl protein transferase inhibitor R115777 on isoprenylation and intracellular signalling by the prostacyclin receptor
Authors: O'Meara Sarah J , Kinsella B Therese
Published: September 2004

The human (h) and mouse (m) prostacyclin receptors (IPs) undergo isoprenylation through attachment of a C‐15 farnesyl moiety within their conserved carboxyl terminal ‐CSLC sequences.

Herein, the effects of a novel farnesyl transferase inhibitor R115777 on signalling by the hIP and mIP, overexpressed in human embryonic kidney 293 cells, and by the hIP endogenously expressed in human erythroleukaemia cells were investigated.

R115777 significantly impaired IP‐mediated cyclic AMP generation (IC50 0.37–0.60 nM) and intracellular calcium ([Ca2+]i) mobilization (IC50 37–65 nM), but had no effect on signalling by the control nonisoprenylated β2 adrenergic receptor or the α or β isoforms of the human thromboxane A2 receptor (TP).

Additionally, R115777 significantly reduced IP‐mediated cross‐desensitization of signalling by the TPα, but not by the TPβ, isoform of the human TP and impaired the farnesylation‐dependent processing of the chaperone HDJ‐2 protein (IC50 4.5 nM).

Furthermore, R115777 fully impaired isoprenylation of both the Ha‐RasWT and Ha‐RasCSLC in vitro and in whole cells confirming that, unlike N‐Ras and Ki‐Ras, the ‐CSLC motif associated with the IP cannot support alternative geranylgeranylation in the presence of R115777 and does not act as a substrate for geranylgeranyl transferase 1 in vitro or in whole cells.

In conclusion, these data confirm that R115777 potently impairs IP isoprenylation and signalling, and suggest that clinically it may not only target Ras proteins but may also disrupt IP isoprenylation, events which could impact on physiologic processes in which prostacyclin and its receptor are implicated.

British Journal of Pharmacology (2004) 143, 318–330. doi:10.1038/sj.bjp.0705956
Pharmacological evidence for a key role of voltage‐gated K+ channels in the function of rat aortic smooth muscle cells
Authors: Tammaro Paolo , Smith Amy L , Hutchings Simon R , Smirnov Sergey V
Published: September 2004

The role of voltage‐dependent (IKv) and large conductance Ca2+‐activated (BKCa) K+ currents in the function of the rat aorta was investigated using specific BKCa and KV channel inhibitors in single rat aortic myocytes (RAMs) with patch‐clamp technique and in endothelium‐denuded aortic rings with isometric tension measurements.

The whole‐cell K+ currents were recorded in RAMs dialysed with 200 and 444 nM Ca2+ and in perforated‐patch configuration. Electrophysiological analysis demonstrated that IKv appeared at −40 mV, while BKCa (isolated using 1 μM paxilline) were seen positive to −20 mV in all conditions.

Voltage‐dependent characteristics, but not maximal conductance, of IKv was significantly altered in increased [Ca2+]i. Correolide (1 μM) (a KV1 channel blocker) did not inhibit the IKv, whereas millimolar concentration of TEA (IC50=3.1±0.6 mM, n=5) and 4‐aminopyridine (4‐AP, IC50=5.9±1.9 mM, n=7) suppressed IKv. These results and immunocytochemical analysis suggest the KV2.1 channel to be a molecular correlate for IKv.

In nonstimulated aortic rings 1–5 mM TEA and 4‐AP (inhibitors of IKv), but not paxilline (1 μM), caused contraction. The frequency of contractile responses to TEA and 4‐AP was increased in the presence of 10 mM KCl, which itself did not significantly affect the aortic basal tone.

Phenylephrine (15–40 nM) induced sustained tension with superimposed slow oscillatory contractions (termed OWs). OWs were blocked by diltiazem, ryanodine and cyclopiazonic acid, suggesting the involvement of L‐type Ca2+ channels and ryanodine‐sensitive Ca2+ stores in this process.

TEA and 4‐AP, but not IbTX, paxilline or correolide, increased the duration and amplitude of OWs, indicating that IKv is involved in the control of oscillatory activity.

In conclusion, our findings suggest that the KV2.1‐mediated IKv, and not BKCa, plays an important role in the regulation of the excitability and contractility of rat aorta.

British Journal of Pharmacology (2004) 143, 303–317. doi:10.1038/sj.bjp.0705957
The two membrane segments of leader peptidase partition one by one into the lipid bilayer via a Sec/YidC interface
Authors: Houben Edith N. G. , ten Hagen‐Jongman Corinne M. , Brunner Josef , Oudega Bauke , Luirink Joen
Published: September 2004

We have addressed the mechanism of insertion of both transmembrane segments (TMs) of leader peptidase, a double‐spanning protein, into the Escherichia coli inner membrane. Using photo‐crosslinking, the first TM (H1) was shown to insert at a Sec‐translocon/YidC interface in a fixed orientation. H1 lost its contacts with the Sec‐translocon and gained access to lipids near YidC soon after complete exposure outside the ribosome. Following lipid integration, it moved away from the Sec/YidC insertion site. The second TM (H2) inserted and interacted with SecY and YidC in a similar transient fashion. The data are consistent with a linear integration model in which the TMs of polytopic inner membrane proteins move one by one from a Sec/YidC insertion site into the lipid bilayer. We propose that YidC assists the lipid partitioning of single TMs.
The Effect of Ultraviolet Radiation on Ultrastructure and Photosynthesis in the Red Macroalgae Palmaria palmata and Odonthalia dentata from Arctic Waters
Authors: Holzinger A. , Lütz C. , Karsten U. , Wiencke C.
Published: September 2004

Abstract: In radiation exposure experiments, the effects of mild artificial UV conditions (4.7 W m‐2 UV‐A and 0.20 W m‐2 UV‐B) plus PAR (25 ‐ 30 μmol photons m‐2 s‐1) on photosynthesis and ultrastructure of two red algal species from the Arctic have been investigated. While Palmaria palmata was collected from the upper sublittoral of the Kongsfjord (Spitsbergen, Norway), Odonthalia dentata represents a typical deepwater species at this high latitude. After 6 h and 24 h exposure to UV, chlorophyll fluorescence of photosystem II (PS II efficiency, Fv/Fm) was determined as an indicator for photosynthetic performance, and the relative electron transport rates in response to increasing photon fluence rates were recorded. In parallel, tissue samples were prepared for the transmission electron microscope (TEM). The presented data clearly demonstrate a significant influence of experimental UV on photosynthetic performance. Photochemical efficiency of PS II of both red algal species decreased to about one third of the initial value under UV. While the PI (photosynthesis‐irradiance) curve parameter α (positive slope at limiting photon fluence rates) strongly decreased in both plants, the Ik values (initial value of light‐saturated photosynthetic rate) increased 3 ‐ 5‐fold. Palmaria palmata does not appear to become photoinhibited under these conditions, but O. dentata showed strong photoinhibition. The TEM results demonstrated that the photosynthetic apparatus was severely influenced by UV in both species, because thylakoid membranes appeared wrinkled, lumen dilatations occurred, and the outer membranes were altered. Moreover, mitochondria were damaged, and numerous plasma vesicles were observed. In conclusion, both red algal species are negatively affected by UV on the physiological and ultrastructural level. However, the differences in photoinhibitory responses correlate well with the vertical depth zonation of P. palmata and O. dentata in the Arctic Kongsfjord.
Changes in Vegetation and Soil Characteristics in Coastal Sand Dunes along a Gradient of Atmospheric Nitrogen Deposition
Authors: Jones M. L. M. , Wallace H. L. , Norris D. , Brittain S. A. , Haria S. , Jones R. E. , Rhind P. M. , Reynolds B. R. , Emmett B. A.
Published: September 2004

Abstract: A field survey was conducted to detect signals of atmospheric nitrogen (N) in 11 dune systems along a nitrogen deposition gradient in the United Kingdom. In the mobile and semi‐fixed dunes, above‐ground biomass was positively related to N inputs. This increase was largely due to increased height and cover of Ammophila arenaria. In the long term, this increased biomass may lead to increased organic matter accumulation and consequently accelerated soil development. In the fixed dunes, above ground biomass also showed a positive relationship with N inputs as did soil C: N ratio while soil available N was negatively related to N inputs. Plant species richness was negatively related to N inputs. In the dune slacks, while soil and bulk vegetation parameters showed no relationship with N inputs, cover of Carex arenaria and Hypochaeris radicata increased. Site mean Ellenberg N numbers showed no relationship with N deposition either within habitats or across the whole dataset. Neither abundance‐weighting nor inclusion of the Siebel numbers for bryophytes improved the relationship. The survey reveals that the relationships of soil and vegetation with atmospheric N deposition vary between sand dune habitats but, despite this variability, clear correlations with N inputs exist. While this survey cannot establish causality, on the basis of the relationships observed we suggest a critical load range of 10 ‐ 20 kg N ha‐1 yr‐1 for coastal sand dunes in the UK.
Specific Intra‐Tissue Responses to Manganese in the Floating Lamina of Trapa natans L.
Authors: Baldisserotto C. , Ferroni L. , Medici V. , Pagnoni A. , Pellizzari M. , Fasulo M. P. , Fagioli F. , Bonora A. , Pancaldi S.
Published: September 2004

Abstract: Plant tolerance to heavy metals requires morpho‐physiological mechanisms that are still poorly understood, especially in hydrophytes. This study focuses on the young floating lamina of the rhyzophyte Trapa natans exposed for 10 d to 130 μM Mn. The lamina has the ability to bioaccumulate Mn (> 3000 μg g‐1). X‐ray microanalysis of Mn cellular distribution revealed accumulation in the upper epidermis, in the first palisade layer, and in the idioblasts of the spongy tissue, which were shown with electron microscopy to contain osmiophilic vacuolar deposits, also observed to a minor extent in the control leaves. On the basis of biochemical and histochemical tests, these deposits were attributed to phenolic compounds that were probably able to chelate Mn. Net photosynthesis, photosynthetic pigments, room temperature microspectrofluorimetric analyses, and ultrastructural studies of plastids were performed to evaluate the status of the photosynthetic apparatus. A greater development of thylakoid membranes was observed in plastids of the second palisade and spongy tissue, which, however, did not accumulate Mn. Only the spongy tissue experienced inadequate assembly of PS II, but this did not significantly influence the photosynthetic yield of the whole lamina. It was concluded that T. natans can optimise productivity in the presence of Mn by means of specific intra‐tissue responses within the framework of the floating lamina.
A Logical (Discrete) Formulation for the Storage and Recall of Environmental Signals in Plants
Authors: Thellier M. , Demongeot J. , Norris V. , Guespin J. , Ripoll C. , Thomas R.
Published: September 2004

Abstract:When subjected to an appropriate asymmetric stimulus, seedlings ofBidens pilosaL. “store” a symmetry‐breaking instruction that will finally take effect (in the form of a differential growth of the cotyledonary buds) only if the plants are in a state in which they can “recall” this information. The ability of the plants to recall the stored symmetry‐breaking instruction may be switched “on” or “off” by the application of a variety of stimuli. Although its detailed phenomenology is rather complicated, the overall behaviour of the plant storage/recall system can be modelled by use of an asynchronous, logical (discrete) description involving positive and negative feedback circuits, which are required for the existence of multi‐stationarity and stability, respectively. The state tables, as used in this formalism, give a concise and easy‐to‐handle description of the evolution of the system and make it particularly easy to determine its stable states. This modelling approach may be extended to the formulation of many other experimental systems.
Pollination Effectiveness and Pollen Dispersal in a Rhododendron ferrugineum (Ericaceae) Population
Authors: Escaravage N. , Wagner J.
Published: September 2004

Abstract: Many alpine plants are predominantly outcrossing, thus plant reproductive success is highly dependent on effectiveness of pollinators. How pollinators transfer pollen from one flower to another is of great interest in understanding the genetic structure in plant populations. We studied (1) the role and effectiveness of insect visitors for pollination, and (2) their contribution as pollen vectors for gene dispersal in a Rhododendron ferrugineum population. Various insect visitors were recorded, including Hymenoptera, Diptera, Coleoptera, and Lepidoptera. The most frequent and effective insects were honey bees and bumblebees. Muscid flies were considered as important pollinators, particularly due to their relatively high visitation rate. Syrphid flies, Formicidae, and Coleoptera were ineffective in transporting pollen, while the effectiveness of Lepidoptera and Empididae was negligible. A fluorescence labelling experiment revealed that pollen dispersal was restricted (0 ‐ 2 m) in a dense R. ferrugineum stand and decreased in a leptokurtic fashion. This might lead to geitonogamous self‐pollination that could explain the close relationship between individuals found in genetic studies of R. ferrugineum. However, some pollen grains may travel 40 ‐ 45 m, which implies the occurrence of cross‐pollination through the foraging activities of bumblebees and honey bees.
Molecular Evolution of the trnTUGU‐trnFGAA Region in Bryophytes
Authors: Quandt D. , Stech M.
Published: September 2004

Abstract: Structure, variability, and molecular evolution of the trnT‐F region in the Bryophyta (mosses and liverworts) is analyzed based on about 200 sequences of the trnT‐L spacer and trnL 5′ exon, 1000 sequences of the trnL intron, and 800 sequences of the trnL 3′ exon and trnL‐F spacer, including comparisons of lengths, GC contents, sequence similarities, and functional elements. Mutations occurring in the trnL 5′ and 3′ exons, including compensatory base pair changes, and a transition in the trnL anticodon in Takakia lepidozioides, are discussed. All three non‐coding regions display a mosaic structure of highly variable elements (V1 ‐ V3 in the trnT‐L spacer, V4/V5 corresponding to stem‐loop regions P6/P8 in the trnL intron, and V6/V7 in the trnL‐F spacer) and more conserved elements. In the trnL intron this structure is a consequence of the defined secondary structure necessary for correct splicing, whereas in both spacers conserved regions are restricted to promoter elements. At least the highly variable regions in the trnT‐L spacer and stem‐loop region P8 of the trnL intron seem to evolve independently in the major bryophyte lineages and are therefore not suitable for high taxonomic level phylogenetic reconstructions. In mosses, a trend of length reduction towards the more derived lineages is observed in all three non‐coding regions. GC contents are mostly linked to sequence variability, with the conserved regions being more GC rich and the more variable AT rich. The lowest GC values (< 10 %) are found in the trnT‐L spacer of mosses. In addition to two putative sigma70‐type promoters in the trnT‐L spacer, a third putative promoter is present in the trnL‐F spacer, although trnL and trnF are assumed to be co‐transcribed. Consensus sequences are provided for the ‐35 and ‐10 sequences of the major bryophyte lineages. The third promoter is part of a hairpin secondary structure, whose loop region is highly homoplastic in mosses due to an inversion occurring independently in non‐related taxa, even at the intraspecific level.
Origin and Evolution of the Light‐Dependent Protochlorophyllide Oxidoreductase (LPOR) Genes
Authors: Yang J. , Cheng Q.
Published: September 2004

Abstract: Light‐dependent NADPH‐protochlorophyllide oxidoreductase (LPOR) is a nuclear‐encoded chloroplast protein in green algae and higher plants which catalyzes the light‐dependent reduction of protochlorophyllide to chlorophyllide. Light‐dependent chlorophyll biosynthesis occurs in all oxygenic photosynthetic organisms. With the exception of angiosperms, this pathway coexists with a separate light‐independent chlorophyll biosynthetic pathway, which is catalyzed by light‐independent protochlorophyllide reductase (DPOR) in the dark. In contrast, the light‐dependent function of chlorophyll biosynthesis is absent from anoxygenic photosynthetic bacteria. Consequently, the question is whether cyanobacteria are the ancestors of all organisms that conduct light‐dependent chlorophyll biosynthesis. If so, how did photosynthetic eukaryotes acquire the homologous genes of LPOR in their nuclear genomes? The large number of complete genome sequences now available allow us to detect the evolutionary history of LPOR genes by conducting a genome‐wide sequence comparison and phylogenetic analysis. Here, we show the results of a detailed phylogenetic analysis of LPOR and other functionally related enzymes in the short chain dehydrogenase/reductase (SDR) family. We propose that the LPOR gene originated in the cyanobacterial genome before the divergence of eukaryotic photosynthetic organisms. We postulated that the photosynthetic eukaryotes obtained their LPOR homologues through endosymbiotic gene transfer.
Directional emission from asymmetric microlaser resonators of π-conjugated polymers
Authors: Polson R. C. , Vardeny Z. V.
Published: September 2004

A π-conjugated polymer film was fabricated into an asymmetric microlaser resonator having a quadrapole deformation with irregular boundaries and a Q factor of 600. At high excitation intensities above the threshold for lasing, we observed multimode laser emission spectra and directional emission at four different angles. Chaotic ray dynamics explains the observed emission pattern.
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detection of vibrationally excited HCO produced by the O(3P)+C2H4 reaction
Authors: Gardner Jennifer L. , Miller Steven M.
Published: September 2004

The distribution of rotational and vibrational energy in HCO produced by the O(3P)+C2H4 reaction has been measured using laser-induced fluorescence detection via the B̃2A′-X̃2A′ transition. Over a detection wavelength range of 248–290 nm, our experiments have shown that HCO is formed in both the ground state and in at least six vibrationally excited states with up to two quanta of energy in the C-O stretch and the bending mode. Dispersed fluorescence experiments were conducted to positively assign all of the HCO vibrational bands. The experiments confirmed that many bands, including the B̃(000)-X̃(000) band, are affected by overlap with other HCO bands. Spectral modeling was used to separate the contributions of overlapping HCO B̃-X̃ bands and to determine a nascent HCO rotational temperature of ∼600 K, corresponding to ∼6% of the total energy from the O(3P)+C2H4 reaction. HCO vibrational distributions were determined for two different average collision energies and were fit with vibrational temperatures of 1850±80 K and 2000±100 K, corresponding to ∼15% of the total energy. The observed Boltzmann distribution of vibrational energy in HCO indicates that HCO and CH3 are formed by the dissociation of an energized intermediate complex.