bluuebunny/crossref_metadata_2025 huggingface dataset:
Different Roles for AMPA and NMDA Receptors in Transmission at the Immature Retinogeniculate Synapse
Authors: Liu Xiaojin , Chen Chinfei
Published: November 2007

The relay of information at the retinogeniculate synapse, the connection between retina and visual thalamus, begins days before eye opening and is thought to play an important role in the maturation of neural circuits in the thalamus and visual cortex. Remarkably, during this period of development, the retinogeniculate synapse is immature, with single retinal ganglion cell inputs evoking an average peak excitatory postsynaptic current (EPSC) of only about 40 pA compared with 800 pA in mature synapses. Yet, at the mature synapse, EPSCs >400 pA are needed to drive relay neuron firing. This raises the question of how small-amplitude EPSCs can drive transmission at the immature retinogeniculate synapse. Here we find that several features of the immature synapse, compared with the mature synapse, contribute to synaptic transmission. First, although the peak amplitude of EPSC is small, the decay time course of both α-amino-3-hydroxy-5-methyl-4isoxazolepropionic acid receptor (AMPAR) and N-methyl-d-aspartate receptor (NMDAR) currents is significantly slower. The prolonged time course of NMDAR currents is a result of the presence of both NR2B and NR2C/D subunits. In addition, the extended presence of neurotransmitter released prolongs the synaptic current time course. Second, reduced sensitivity to magnesium block results in significantly greater synaptic charge transfer through NMDAR. Third, AMPAR currents contribute to the spike latency, but not to temporal precision, at the immature synapse. Furthermore, intrinsic excitability is greater. These properties enable immature synapses with predominantly NMDARs and little or no AMPARs to contribute to the relay of information from retina to visual cortex.
Increased Regulatory and Decreased CD8+ Cytotoxic T Cells in the Blood of Patients with Idiopathic Pulmonary Arterial Hypertension
Authors: Ulrich Silvia , Nicolls Mark R. , Taraseviciene Laima , Speich Rudolf , Voelkel Norbert
Published: November 2007

Background: An association between pulmonary arterial hypertension (PAH) and various immune disorders is well established. Recently, the role of an intact immune system in protecting against pulmonary angioproliferation was shown in an animal model. Objective: To elucidate the role of T cells in human PAH, we comparatively studied T cell subclasses with emphasis on regulatory T cells (Treg) in the peripheral blood of patients with idiopathic pulmonary arterial hypertension (IPAH) and healthy controls. Methods:Isolated peripheral blood mononuclear cells from 36 patients diagnosed with IPAH and 33 healthy controls were stained with fluorescently labeled monoclonal antibodies against superficial T cell markers (CD3, CD4, CD8, CD25) and FoxP3, the intracellular marker of Treg cells. The relative cell distribution was analyzed by flow cytometry. The functionality of patient and control Treg cells was assessed by coculture of Treg with nonregulatory T cells from the same individual. Results: Significantly less CD8+ T cells (p = 0.02) and more CD25hi+ and FoxP3+CD4+ T cells were found in the peripheral blood of patients compared with controls (p = 0.009 and p < 0.001, respectively). The percentage of FoxP3+ cells within the CD25hi+CD4+ Treg cells was similar. Treg cell functionality was equal in patients and controls. Conclusion: Our findings of decreased CD8+ T cells and increased Treg cells in the peripheral blood of patients with IPAH are novel and may have implications for directing future research in the field to elucidate the differential role of T cells and the immune system in IPAH.
Extracellular Matrix Fibronectin Mechanically Couples Skeletal Muscle Contraction With Local Vasodilation
Authors: Hocking Denise C. , Titus Patricia A. , Sumagin Ronen , Sarelius Ingrid H.
Published: November 2007

During exercise, local mechanisms in tissues cause arterioles to rapidly dilate to increase blood flow to tissues to meet the metabolic demands of contracting muscle. Despite decades of study, the mechanisms underlying this important aspect of blood flow control are still far from clear. We now report a novel mechanism wherein fibronectin fibrils in connective tissue matrices transduce signals from contracting skeletal muscle to local blood vessels to increase blood flow. Using intravital microscopy, we show that local vasodilation in response to skeletal muscle contraction is specifically inhibited by an antibody that recognizes the matricryptic site in the first type III repeat of fibronectin (FNIII-1). In the absence of skeletal muscle contraction, direct application of FNIII-1–containing fibronectin fragments to cremaster muscle arterioles in situ, triggered a rapid, specific, and reversible local dilation that was mediated by nitric oxide and required the cryptic, heparin-binding sequence of FNIII-1. Furthermore, application of function-blocking FNIII-1 peptides to cremaster muscle arterioles rapidly and specifically decreased their diameter, indicating that the matricryptic site of fibronectin also contributes to resting vascular tone. Alexa fluor 488–labeled fibronectin, administered intravenously, was rapidly assembled into elongated, branching fibrils in the extracellular matrix of intact cremaster muscle, demonstrating active polymerization of fibronectin in areas adjacent to blood vessels. Together, these data provide the first evidence that a matricryptic, heparin-binding site within fibronectin fibrils of adult connective tissue plays a dynamic role in regulating both vascular responses and vascular tone.
Sex Differences in Heritability of Ischemic Stroke
Authors: Touzé Emmanuel , Rothwell Peter M.
Published: November 2007

Background and Purpose—

Using data from Oxfordshire, UK, we recently showed that women are more likely than men to have a family history of stroke in female versus male first degree relatives. To test the generalizability of this finding, we did a comprehensive systematic review of all available published and unpublished data.

Methods—

Studies were included in the present review if they reported the frequency of family history of stroke in relation to sex of parent or proband. Where necessary, we contacted authors of studies to obtain unpublished data. Data from the Oxford Vascular Study (OXVASC) and 3 other Oxford cohorts (1925 patients) were secondarily pooled with the data from other studies.

Results—

We obtained data from 18 studies (7941 patients), including unpublished data from 7 studies. Female probands were slightly more likely to have a parental history of stroke than male probands (pooled OR=1.15; 95% CI: 1.03 to 1.29;
P
(sig)
=0.028;
P
(het)
=0.45). Maternal history of stroke was more common than paternal history (pooled OR=1.25; 1.15 to 1.37;
P
(sig)
<0.00001;
P
(het)
=0.12). However, the maternal excess was only present in female probands (pooled OR=1.47; 1.27 to 1.70;
P
(sig)
<0.00001;
P
(het)
=0.11). In contrast, male probands were no more likely to have maternal than paternal history of stroke (pooled OR=1.02; 0.88 to 1.17,
P
(sig)
=0.43;
P
(het)
=0.09).

Conclusions—

Women with stroke are more likely than men to have a parental history of stroke, which is accounted for by an excess maternal history of stroke. This finding could be explained by sex-specific genetic, epigenetic, or nongenetic mechanisms.
Time Spent at Home Poststroke
Authors: Quinn Terence J. , Dawson Jesse , Lees Jennifer S. , Chang Tou-Pin , Walters Matthew R. , Lees Kennedy R.
Published: November 2007

Background and Purpose—

Stroke outcome assessment requires some measure of functional recovery. Several instruments are in common use but all have recognized limitations. We examined duration of stay in the patient’s own home over the first 90 days since stroke—“home-time”—as an alternative outcome likely to show graded response with improved reliability.

Methods—

We examined prospectively collected data from the GAIN International trial using analysis of variance with Bonferroni contrasts of adjacent modified Rankin scale score categories.

Results—

We had full outcome data from 1717 of 1788 patients. Increasing home-time was associated with improved modified Rankin scale scores (
P
<0.0001). The relationship held across all modified Rankin scale grades except 4 to 5.

Conclusions—

Home-time offers a robust, useful, and easily validated outcome measure for stroke, particularly across better recovery levels.
Production of A1 Based Composite Reinforced with SnO2 Coated SiC Particles
Authors: Tekmen C. , Ozvardar O. , Cocen U.
Published: November 2007

An investigation was carried out on SnO2 coating of SiC particles by sol-gel technique and the production of SnO2 coated 20 vol% SiC particle reinforced composite and unreinforced matrix alloy by squeeze casting. The morphology of the coating and microstructural, interfacial and mechanical properties of the composite were characterized by using an optical microscope, image analyzer, scanning electron microscope (SEM), energy dispersion spectroscopy (EDS), and X-ray diffraction (XRD). It has been found that the coating is not degraded during the fabrication process; in other words, SnO 2 coating by sol-gel technique is an effective way to improve the matrix/reinforcement interfacial properties.
Sociologists and `the Japanese model': a passing enthusiasm?
Authors: McCormick Kevin
Published: November 2007

This article critiques the construction of `the Japanese model' of employment relations by sociologists in English language sociological research monographs, organization textbooks and introductory general textbooks. It demonstrates how marked differences emerged across the different genres and relates them to the different purposes of researchers and textbook writers.The article examines three particular puzzles. First, why did general textbooks adopt `the Japanese model' in the 1990s when media commentaries were announcing the demise of the Japanese model in Japan? Second, why did the 1990s textbooks use 1980s organization textbooks rather than research monographs for their sources? Third, why are general textbooks ready to distance themselves from the model in 2006 when researchers confirm continuing vitality in the Japanese model in large Japanese companies? Answering these questions reveals how sociological knowledge of Japanese employment has been generated, disseminated and used in research, teaching and policy debates.
Fostering Intuition in Management Education
Authors: Sadler-Smith Eugene , Burke Lisa A.
Published: November 2007

In business, there is little doubt that managers use their intuitions when making decisions. But in spite of the fact that intuition and rationality are two parallel systems of knowing, intuition is often considered the antithesis of rationality and is overlooked, disregarded, or acted on covertly by managers. What is also clear is that intuition is not typically a part of the traditional management education curriculum. The risk therefore exists that business school programs may be producing managers of the future who are unprepared with respect to the more intuitive aspects of management practice. In this article, the authors define intuition and explore various ways management educators can incorporate intuition in business curricula, along with specific teaching ideas that can be utilized in the classroom.
Detection of Free Radicals in Electron Beam-Irradiated Mucuna pruriens (L. DC.) Seeds by Electron Spin Resonance
Authors: Bhat R. , Sridhar K.R.
Published: November 2007

Electron spin resonance (ESR) spectroscopy was employed to detect free radicals in raw Mucuna pruriens (velvet bean) seeds after electron beam irradiation (Microtron source: 0, 2.5, 5, 7.5, 10, 15 and 30 kGy) and conventional processing (roasting, powdering and cooking). The ESR signal of irradiated seeds (g=2.0055±0.0001) was more prominent in the seed coat than cotyledon. Seed coat of irradiated samples showed dose-dependent linear increase of this signal (g = 2.0055) accompanied by a weak triplet (satellite peak; aH = 3 mT) produced exclusively by radiolysis and could be used as an indication of successful irradiation. Irradiated cotyledon portion devoid of satellite peak (triplet) showed a linear increase in signal intensity up to 10 kGy with a sharp decline at higher doses (15 and 30kGy). Stability of radiation-induced ESR signals after 6 months of storage (25 ± 1°C) revealed the presence of a weak triplet with a substantial loss of signal intensity. Thermal effects such as roasting and powdering of seeds increased the signal intensity (g = 2.0055) similar to or in greater proportion than irradiation. Phenolics in seeds, which contribute significantly to detect free radicals in vegetative parts of a plant showed a waning trend in seed coat, while it was vice versa in cotyledon. Textural studies revealed significant loss in firmness after irradiation (p<0.05), which might favour in minimising the cooking time. Results of the present study might help to divulge the beneficial effects of application of electron beam irradiation technology as a better alternative to fumigants in seed preservation for safety and quarantine purposes.
Effect of Physical and Chemical Treatments on Campylobacter Spiked into Food Samples
Authors: Bhavsar S.P. , Augustine S.K. , Kapadnis B.P.
Published: November 2007

Campylobacter spp. were isolated from rivers Mula, Mutha and Pavana by preT-Kapadnis Baseri and Preston enrichment-modified charcoal cefoperazone deoxycholate agar methods. Survival studies were conducted in fresh skim cow milk, chicken meat extract and mushroom extract at various temperatures. The sensitivity of Campylobacter strains inoculated in the food samples, to chemical preservatives, gamma radiation, microwave heating and water bath heating was studied. Campylobacter strains survived well in milk and chicken extract; however, temperature significantly affected their survival in those food samples. Although most of the chemical preservatives were effective against Campylobacter isolates, the sub-inhibitory values of acetic acid and lactic acid were relatively lower against these isolates. All the strains investigated for the effect of gamma radiation, were sensitive to doses less than 3 kGy. In case of heat preservation, around 9 min was required to eliminate Campylobacter spp. by heating in water bath at 50°C while approximately 13 s from food samples exposed to heating in a microwave oven. The effect of food preservation techniques on Campylobacter varied with the temperature and type of the food. Microwave treatment appeared to be much more effective than water bath heating and that chicken meat extract conferred an additional protection to Campylobacter as compared to milk or PBS.
Effects of Culture, pH and Fat Concentration on Melting Rate and Sensory Characteristics of Probiotic Fermented Yellow Mombin (Spondias mombin L) Ice Creams
Authors: Favaro-Trindade C.S. , de Carvalho Balieiro J.C. , Dias P. Felix , Amaral Sanino F. , Boschini C.
Published: November 2007

Twelve fermented yellow mombin ice creams were produced with different starter cultures (Lactobacillus acidophilus 74-2, L. acidophilus LAC 4 and yoghurt starter culture), final pH (4.5 and 5) and concentrations of added cream (5 and 10%). Probiotic culture stability, melting properties and sensory acceptance were evaluated in ice cream samples. The mixes were frozen and stored for 105 days at -18°C. The melting rates were lower for samples with a pH of 4.5. Both probiotic cultures resisted the freezing process and, although a tendency for the counts to decrease during storage was detected, they were still higher than 10 6 cfu/g after 105 days, even in products with a pH of 4.5. A pH 4.5, 5% cream and L. acidophilus LAC 4 ice cream received significantly higher sensory scores when compared with pH 5, 10% cream and L. acidophilus 74-2 ice cream. The fermented yellow mombin ice cream was a suitable food for the delivery of L. acidophilus strains, with excellent viability and acceptable sensory characteristics.
Diagnosis and Minimally Invasive Treatment of Salivary Gland Obstruction
Authors: Drage Nicholas A , Brown Jackie E
Published: November 2007

Salivary obstruction is usually due to either calculi or strictures. These may be diagnosed using a combination of sialography and high resolution ultrasound. Minimally invasive techniques such as fluoroscopy guided basket retrieval of calculi or balloon dilation of strictures are successful techniques and may be carried out in a general hospital setting. These techniques may be developed for use under ultrasound guidance.
Congenital Absence of the Internal Carotid Artery – a Rare Case Identified by Ultrasound
Authors: Beardshall Matthew
Published: November 2007

Absence or hypoplasia of one or both internal carotid arteries is a rare condition that may remain asymptomatic and is usually diagnosed incidentally while investigating for other pathology. Knowledge of the anomaly should prompt further clinical evaluation, as it is associated with a high incidence of cerebral aneurysms. This case describes the use of ultrasound in the diagnosis of the condition, confirmed by magnetic resonance imaging, in a female patient with symptoms suggestive of transient ischaemic attacks.
Lentiviral (HIV)-based RNA interference screen in human B-cell receptor regulatory networks reveals MCL1-induced oncogenic pathways
Authors: Ruiz-Vela Antonio , Aggarwal Mohit , de la Cueva Paloma , Treda Cezary , Herreros Beatriz , Martín-Pérez Daniel , Dominguez Orlando , Piris Miguel A.
Published: November 2007

Aberrant inhibition of B-cell receptor (BCR)-induced programmed cell death pathways is frequently associated with the development of human auto-reactive B-cell lymphomas. Here, we integrated loss-of-function, genomic, and bioinformatics approaches for the identification of oncogenic mechanisms linked to the inhibition of BCR-induced clonal deletion pathways in human B-cell lymphomas. Lentiviral (HIV)-based RNA interference screen identified MCL1 as a key survival molecule linked to BCR signaling. Loss of MCL1 by RNA interference rendered human B-cell lymphomas sensitive to BCR-induced programmed cell death. Conversely, MCL1 overexpression blocked programmed cell death on BCR stimulation. To get insight into the mechanisms of MCL1-induced survival and transformation, we screened 41 000 human genes in a genome-wide gene expression profile analysis of MCL1-overexpressing B-cell lymphomas. Bioinformatic gene network reconstruction illustrated reprogramming of relevant oncoproteins within β-catenin–T-cell factor signaling pathways induced by enforced MCL1 expression. Overall, our findings not only illustrate MCL1 as an aberrantly expressed reprogramming oncoprotein in follicular lymphomas but also highlight MCL1 as key therapeutic target.
Exercise training reduces pulmonary ischaemia–reperfusion-induced inflammatory responses
Authors: Mussi R. K. , Camargo E. A. , Ferreira T. , De Moraes C. , Delbin M. A. , Toro I. F. C. , Brancher S. , Landucci E. C. T. , Zanesco A. , Antunes E.
Published: November 2007

Physical exercise reduces the deleterious effects of cardiovascular and inflammatory disorders. The purpose of the present study was to evaluate the beneficial effects of physical training on the inflammatory responses following lung ischaemia–reperfusion (IR) in rats.

Male Wistar rats were divided into sham-operated animals and sedentary and trained animals submitted to lung IR. The run training programme consisted of 5 sessions·week−1, each lasting 60 min·day−1, at 66% of maximal oxygen consumption for 8 weeks. The left pulmonary artery, bronchus and pulmonary vein were occluded for 90 min and reperfused for 2 h. Lung protein extravasation was measured as125I-human albumin accumulation, whereas lung neutrophil infiltration was measured as myeloperoxidase activity.

Lung IR in sedentary rats resulted in marked increases in protein extravasation and neutrophil influx, and in significant elevations of serum tumour necrosis factor (TNF)-α and interleukin (IL)-1β levels. Physical preconditioning attenuated the increased IR-induced protein leakage without affecting neutrophil influx. It also reduced serum TNF-α (and IL-1β) levels, but had no effect on IL-10 levels. Plasma superoxide dismutase activity was significantly increased in trained IR rats.

The present data show that physical preconditioning protects the rat lung from ischaemia–reperfusion injury by attenuating the pulmonary vascular permeability that may be a consequence of reduced levels of tumour necrosis factor-α and interleukin-1β and elevated superoxide dismutase activity.
Neoalveolarisation contributes to compensatory lung growth following pneumonectomy in mice
Authors: Fehrenbach H. , Voswinckel R. , Michl V. , Mehling T. , Fehrenbach A. , Seeger W. , Nyengaard J. R.
Published: November 2007

Regeneration of the gas exchange area by induction of neoalveolarisation would greatly improve therapeutic options in destructive pulmonary diseases. Unilateral pneumonectomy is an established model to remove defined portions of gas exchange area and study mechanisms of compensatory lung growth. The question of whether new alveoli are added to the residual lung after pneumonectomy in mice was addressed.

Left-sided pneumonectomy was performed in 11 adult C57BL/6 mice. Alveolar numbers were analysed in lungs fixed at days 6 and 20 after pneumonectomy and in 10 age-matched controls using design-based stereology based on a physical fractionator. Post-fixation lung volume was determined by fluid displacement.

Complete restoration of lung volume was observed 20 days after pneumonectomy. Alveolar numbers were significantly increased by 33% in residual right lungs at day 20 in comparison with control right lungs. In control left lungs, an average of 471±162×103 alveoli was estimated, 49% of which were regenerated by residual lungs at day 20. Of the newly formed alveoli seen at day 20, 74% were already present at day 6.

The present data demonstrate that, in addition to growth in size of existing alveoli, neoalveolarisation contributes to restoration of the gas exchange area in adult mice and is induced early after pneumonectomy.
The role of the UPS in cystic fibrosis
Authors: Turnbull Emma L , Rosser Meredith FN , Cyr Douglas M
Published: November 2007

CF is an inherited autosomal recessive disease whose lethality arises from malfunction of CFTR, a single chloride (Cl-) ion channel protein. CF patients harbor mutations in theCFTRgene that lead to misfolding of the resulting CFTR protein, rendering it inactive and mislocalized. Hundreds of CF-related mutations have been identified, many of which abrogate CFTR folding in the endoplasmic reticulum (ER). More than 70% of patients harbor the ΔF508 CFTR mutation that causes misfolding of the CFTR proteins. Consequently, mutant CFTR is unable to reach the apical plasma membrane of epithelial cells that line the lungs and gut, and is instead targeted for degradation by the UPS. Proteins located in both the cytoplasm and ER membrane are believed to identify misfolded CFTR for UPS-mediated degradation. The aberrantly folded CFTR protein then undergoes polyubiquitylation, carried out by an E1-E2-E3 ubiquitin ligase system, leading to degradation by the 26S proteasome. This ubiquitin-dependent loss of misfolded CFTR protein can be inhibited by the application of ‘corrector’ drugs that aid CFTR folding, shielding it from the UPS machinery. Corrector molecules elevate cellular CFTR protein levels by protecting the protein from degradation and aiding folding, promoting its maturation and localization to the apical plasma membrane. Combinatory application of corrector drugs with activator molecules that enhance CFTR Cl-ion channel activity offers significant potential for treatment of CF patients.

Publication history:Republished from Current BioData's Targeted Proteins database (TPdb;http://www.targetedproteinsdb.com).
The ubiquitin proteasome system in Huntington's disease and the spinocerebellar ataxias
Authors: Davies Janet E , Sarkar Sovan , Rubinsztein David C
Published: November 2007

Huntington's disease and several of the spinocerebellar ataxias are caused by the abnormal expansion of a CAG repeat within the coding region of the disease gene. This results in the production of a mutant protein with an abnormally expanded polyglutamine tract. Although these disorders have a clear monogenic cause, each polyglutamine expansion mutation is likely to cause the dysfunction of many pathways and processes within the cell. It has been proposed that the ubiquitin proteasome system is impaired in polyglutamine expansion disorders and that this contributes to pathology. However, this is controversial with some groups demonstrating decreased proteasome activity in polyglutamine expansion disorders, some showing no change in activity and others demonstrating an increase in proteasome activity. It remains unknown whether the ubiquitin proteasome system is a feasible therapeutic target in these disorders. Here we review the conflicting results obtained from different assays performed in a variety of different systems.

Publication history:Republished from Current BioData's Targeted Proteins database (TPdb;http://www.targetedproteinsdb.com).
Randomised controlled comparison of the Health Survey Short Form (SF-12) and the Graded Chronic Pain Scale (GCPS) in telephone interviews versus self-administered questionnaires. Are the results equivalent?
Authors: Lungenhausen Margitta , Lange Stefan , Maier Christoph , Schaub Claudia , Trampisch Hans J , Endres Heinz G
Published: November 2007

Background

The most commonly used survey methods are self-administered questionnaires, telephone interviews, and a mixture of both. But until now evidence out of randomised controlled trials as to whether patient responses differ depending on the survey mode is lacking. Therefore this study assessed whether patient responses to surveys depend on the mode of survey administration. The comparison was between mailed, self-administered questionnaires and telephone interviews.

Methods

A four-armed, randomised controlled two-period change-over design. Each patient responded to the same survey twice, once in written form and once by telephone interview, separated by at least a fortnight. The study was conducted in 2003/2004 in Germany. 1087 patients taking part in the German Acupuncture Trials (GERAC cohort study), who agreed to participate in a survey after completing acupuncture treatment from an acupuncture-certified family physician for headache, were randomised. Of these, 823 (664 women) from the ages of 18 to 83 (mean 51.7) completed both parts of the study. The main outcome measure was the comparison of the scores on the 12-Item Short-Form Health Survey (SF-12) and the Graded Chronic Pain Scale (GCPS) questionnaire for the two survey modes.

Results

Computer-aided telephone interviews (CATI) resulted in significantly fewer missing data (0.5%) than did mailed questionnaires (2.8%; p < 0.001). The analysis of equivalence revealed a difference between the survey modes only for the SF-12 mental scales. On average, reported mental status score was 3.5 score points (2.9 to 4.0) lower on the self-administered questionnaire compared to the telephone interview. The order of administration affected results. Patients who responded to the telephone interview first reported better mental health in the subsequent paper questionnaire (mean difference 2.8 score points) compared to those who responded to the paper questionnaire first (mean difference 4.1 score points).

Conclusion

Despite the comparatively high cost of telephone interviews, they offer clear advantages over mailed self-administered questionnaires as regards completeness of data. Only items concerning mental status were dependent on the survey mode and sequence of administration. Items on physical status were not affected. Normative data for standardized telephone questionnaires could contribute to a better comparability with the results of the corresponding standardized paper questionnaires.
Structural analysis of the carboxy terminal PH domain of pleckstrin bound to D-myo-inositol 1,2,3,5,6-pentakisphosphate
Authors: Jackson Sean G , Zhang Yi , Haslam Richard J , Junop Murray S
Published: November 2007

Background

Pleckstrin homology (PH) domains are one of the most prevalent domains in the human proteome and represent the major phosphoinositide-binding module. These domains are often found in signaling proteins and function predominately by targeting their host proteins to the cell membrane. Inositol phosphates, which are structurally similar to phosphoinositides, are not only known to play a role as signaling molecules but are also capable of being bound by PH domains.

Results

In the work presented here it is shown that the addition of commercial myo-inositol hexakisphosphate (IP6) inhibited the binding of the carboxy terminal PH domain of pleckstrin (C-PH) to phosphatidylinositol 3,4-bisphosphate with an IC50 of 7.5 μM. In an attempt to characterize this binding structurally, C-PH was crystallized in the presence of IP6 and the structure was determined to 1.35 Å. Examination of the resulting electron density unexpectedly revealed the bound ligand to be D-myo-inositol 1,2,3,5,6-pentakisphosphate.

Conclusion

The discovery of D-myo-inositol 1,2,3,5,6-pentakisphosphate in the crystal structure suggests that the inhibitory effects observed in the binding studies may be due to this ligand rather than IP6. Analysis of the protein-ligand interaction demonstrated that this myo-inositol pentakisphosphate isomer interacts specifically with protein residues known to be involved in phosphoinositide binding. In addition to this, a structural alignment of other PH domains bound to inositol phosphates containing either four or five phosphate groups revealed that the majority of phosphate groups occupy conserved locations in the binding pockets of PH domains. These findings, taken together with other recently reported studies suggest that myo- inositol pentakisphosphates could act to regulate PH domain-phosphoinositide interactions by directly competing for binding, thus playing an important role as signaling molecules.
Inorganic pyrophosphate generation by transforming growth factor-beta-1 is mainly dependent on ANK induction by Ras/Raf-1/extracellular signal-regulated kinase pathways in chondrocytes
Authors: Cailotto Frederic , Bianchi Arnaud , Sebillaud Sylvie , Venkatesan Narayanan , Moulin David , Jouzeau Jean-Yves , Netter Patrick
Published: November 2007

ANK is a multipass transmembrane protein transporter thought to play a role in the export of intracellular inorganic pyrophosphate and so to contribute to the pathophysiology of chondrocalcinosis. As transforming growth factor-beta-1 (TGF-β1) was shown to favor calcium pyrophosphate dihydrate deposition, we investigated the contribution of ANK to the production of extracellular inorganic pyrophosphate (ePPi) by chondrocytes and the signaling pathways involved in the regulation of Ank expression by TGF-β1. Chondrocytes were exposed to 10 ng/mL of TGF-β1, and Ank expression was measured by quantitative polymerase chain reaction and Western blot. ePPi was quantified in cell supernatants. RNA silencing was used to define the respective roles of Ank and PC-1 in TGF-β1-induced ePPi generation. Finally, selective kinase inhibitors and dominant-negative/overexpression plasmid strategies were used to explore the contribution of several signaling pathways to Ank induction by TGF-β1. TGF-β1 strongly increased Ank expression at the mRNA and protein levels, as well as ePPi production. Using small interfering RNA technology, we showed that Ank contributed approximately 60% and PC-1 nearly 20% to TGF-β1-induced ePPi generation. Induction of Ank by TGF-β1 required activation of the extracellular signal-regulated kinase (ERK) pathway but not of p38-mitogen-activated protein kinase or of protein kinase A. In line with the general protein kinase C (PKC) inhibitor calphostin C, Gö6976 (a Ca2+-dependent PKC inhibitor) diminished TGF-β1-induced Ank expression by 60%, whereas a 10% inhibition was observed with rottlerin (a PKCδ inhibitor). These data suggest a regulatory role for calcium in TGF-β1-induced Ank expression. Finally, we demonstrated that the stimulatory effect of TGF-β1 on Ank expression was inhibited by the suppression of the Ras/Raf-1 pathway, while being enhanced by their constitutive activation. Transient overexpression of Smad 7, an inhibitory Smad, failed to affect the inducing effect of TGF-β1 on Ank mRNA level. These data show that TGF-β1 increases ePPi levels, mainly by the induction of the Ank gene, which requires activation of Ras, Raf-1, ERK, and Ca2+-dependent PKC pathways in chondrocytes.
Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa
Authors: Loscher Carol J , Hokamp Karsten , Kenna Paul F , Ivens Alasdair C , Humphries Peter , Palfi Arpad , Farrar G Jane
Published: November 2007

Background

The role played by microRNAs (miRs) as common regulators in physiologic processes such as development and various disease states was recently highlighted. Retinitis pigmentosa (RP) linked to RHO (which encodes rhodopsin) is the most frequent form of inherited retinal degeneration that leads to blindness, for which there are no current therapies. Little is known about the cellular mechanisms that connect mutations within RHO to eventual photoreceptor cell death by apoptosis.

Results

Global miR expression profiling using miR microarray technology and quantitative real-time RT-PCR (qPCR) was performed in mouse retinas. RNA samples from retina of a mouse model of RP carrying a mutant Pro347Ser RHO transgene and from wild-type retina, brain and a whole-body representation (prepared by pooling total RNA from eight different mouse organs) exhibited notably different miR profiles. Expression of retina-specific and recently described retinal miRs was semi-quantitatively demonstrated in wild-type mouse retina. Alterations greater than twofold were found in the expression of nine miRs in Pro347Ser as compared with wild-type retina (P < 0.05). Expression of miR-1 and miR-133 decreased by more than 2.5-fold (P < 0.001), whereas expression of miR-96 and miR-183 increased by more than 3-fold (P < 0.001) in Pro347Ser retinas, as validated by qPCR. Potential retinal targets for these miRs were predicted in silico.

Conclusion

This is the first miR microarray study to focus on evaluating altered miR expression in retinal disease. Additionally, novel retinal preference for miR-376a and miR-691 was identified. The results obtained contribute toward elucidating the function of miRs in normal and diseased retina. Modulation of expression of retinal miRs may represent a future therapeutic strategy for retinopathies such as RP.
MADS-complexes regulate transcriptome dynamics during pollen maturation
Authors: Verelst Wim , Twell David , de Folter Stefan , Immink Richard , Saedler Heinz , Münster Thomas
Published: November 2007

Background

Differentiation processes are responsible for the diversity and functional specialization of the cell types that compose an organism. The outcome of these processes can be studied at molecular, physiologic, and biochemical levels by comparing different cell types, but the complexity and dynamics of the regulatory processes that specify the differentiation are largely unexplored.

Results

Here we identified the pollen-specific MIKC* class of MADS-domain transcription factors as major regulators of transcriptome dynamics during male reproductive cell development in Arabidopsis thaliana. Pollen transcript profiling of mutants deficient in different MIKC* protein complexes revealed that they control a transcriptional switch that directs pollen maturation and that is essential for pollen competitive ability. We resolved the functional redundancy among the MIKC* proteins and uncovered part of the underlying network by identifying the non-MIKC* MADS-box genes AGL18 and AGL29 as downstream regulators of a subset of the MIKC* MADS-controlled genes.

Conclusion

Our results provide a first, unique, and compelling insight into the complexity of a transcription factor network that directs cellular differentiation during pollen maturation, a process that is essential for male reproductive fitness in flowering plants.
Early events in the recognition of danger signals after tissue injury
Authors: Kaczorowski David J , Mollen Kevin P , Edmonds Rebecca , Billiar Timothy R
Published: November 2007

The systemic inflammatory response observed in the setting of overwhelming infection bears striking similarities to that observed in the setting of severe traumatic injury from a clinical and physiologic standpoint. Recent observations have demonstrated that these disparate clinical entities share common mediators on a molecular level. TLRs, specifically TLR4, and the endogenous molecule high-mobility group box 1 are among the mediators that are known to play a role in inflammation in the setting of sepsis. Evidence is accumulating that demonstrates that these mediators also play a role in the host response to tissue injury. Here, we highlight findings from the 7th World Conference on Trauma, Shock, Inflammation and Sepsis in Munich, Germany, in the context of this growing body of literature.
Improving Protein–Protein Interaction Prediction Based on Phylogenetic Information Using a Least‐Squares Support Vector Machine
Authors: CRAIG ROGER A. , LIAO LI
Published: November 2007

Abstract:  Predicting protein–protein interactions has become a key step of reverse‐engineering biological networks to better understand cellular functions. The experimental methods in determining protein–protein interactions are time‐consuming and costly, which has motivated vigorous development of computational approaches for predicting protein–protein interactions. A set of recently developed bioinformatics methods utilizes coevolutionary information of the interacting partners (e.g., as exhibited in the form of correlations between distance matrices, where, for each protein, a matrix stores the pairwise distances between the protein and its orthologs in a group of reference genomes). We proposed a novel method to account for the intra‐matrix correlations in improving predictive accuracy. The distance matrices for a pair of proteins are transformed and concatenated into a phylogenetic vector. A least‐squares support vector machine is trained and tested on pairs of proteins, represented as phylogenetic vectors, whose interactions are known. The intra‐matrix correlations are accounted for by introducing a weighted linear kernel, which determines the dot product of two phylogenetic vectors. The performance, measured as receiver operator characteristic (ROC) score in cross‐validation experiments, shows significant improvement of our method (ROC score 0.928) over that obtained by Pearson correlations (0.659).
Data Requirements of Reverse‐Engineering Algorithms
Authors: JUST WINFRIED
Published: November 2007

Abstract:  Data Sets used in reverse engineering of biochemical networks contain usually relatively few high‐dimensional data points, which makes the problem in general vastly underdetermined. It is therefore important to estimate the probability that a given algorithm will return a model of acceptable quality when run on a data set of small size but high dimension. We propose a mathematical framework for investigating such questions. We then demonstrate that without assuming any prior biological knowledge, in general no theoretical distinction between the performance of different algorithms can be made. We also give an example of how expected algorithm performance can in principle be altered by utilizing certain features of the data collection protocol. We conclude with some examples of theorems that were proven within the proposed framework.
Benchmarking of Dynamic Bayesian Networks Inferred from Stochastic Time‐Series Data
Authors: DAVID LAWRENCE A. , WIGGINS CHRIS H.
Published: November 2007

Abstract: We seek to quantify the failure and success of dynamic Bayesian networks (DBNs), a popular tool for reverse‐engineering networks from time‐series data. In particular, we focus on data generated by continuous time processes (e.g., genetic expression) and sampled at discrete times. To facilitate analysis and interpretation, we employ a “minimal model” to generate arbitrary abundances of stochastic data from networks of known topologies, which are then sub‐sampled and in some cases interpolated. We find that DBNs perform relatively poorly when given data sets comparable to those used for genetic network inference. Interpolation does not appear to improve inference success. Finally, we contrast the performance of DBNs with results from linear regression on our synthetic data.
Alternative Pathway Approach for Automating Analysis and Validation of Cell Perturbation Networks and Design of Perturbation Experiments
Authors: GONG YUNCHEN , ZHANG ZHAOLEI
Published: November 2007

Abstract:  Cell perturbation data are a very important resource to analyze and reconstruct cell‐signaling networks. To facilitate the utilization of this type of data and enable large‐scale and automated network reconstruction effort, we have already developed a data structure for storing cell perturbation results and deducing perturbation networks (CellFrame). For automating network analysis, we here propose a computational method called the “alternative pathway approach” (ALPA) in this work. This method can validate the signaling networks with conditional perturbation data extracted from published experiments, and can suggest additional tests to improve the network. It searches the alternative pathway space between all pairs of nodes, constructs pathnets (set of pathways between two nodes) and validates the network edges using conditional perturbation. For pathnets without conditional data, experiments with the fewest number of perturbations or the most parsimonious are designed. For pathnets without experimentally derived
or detected pair‐wise interactions, ALPA can predict the potential effects or propose additional pathways to expand the existing network. We have tested the ALPA method on the TNFα‐MAPK signaling cascade; the reconstructed network is consistent with the consensus model. We also used the ALPA algorithm to analyze a yeast gene perturbation network, using the data from the Rosetta compendium of expression profiles, which demonstrates that it can be also used for large‐scale analysis. We compared the performance of the ALPA approach with Boolean and Bayesian network algorithms for their efficiency and accuracy, respectively, in network construction.
Reverse Engineering of Dynamic Networks
Authors: STIGLER B. , JARRAH A. , STILLMAN M. , LAUBENBACHER R.
Published: November 2007

Abstract:  We consider the problem of reverse‐engineering dynamic models of biochemical networks from experimental data using polynomial dynamic systems. In earlier work, we developed an algorithm to identify minimal wiring diagrams, that is, directed graphs that represent the causal relationships between network variables. Here we extend this algorithm to identify a most likely dynamic model from the set of all possible dynamic models that fit the data over a fixed wiring diagram. To illustrate its performance, the method is applied to simulated time‐course data from a published gene regulatory network in the fruitfly Drosophila melanogaster.
Dispensing errors in community pharmacy: frequency, clinical significance and potential impact of authentication at the point of dispensing
Authors: Franklin Bryony Dean , O'Grady Kara
Published: November 2007

Objective

Our aims were to explore the nature of dispensing errors in community pharmacy, and investigate the potential impact of authentication at the point of dispensing using barcodes or radio-frequency identification tags. Objectives were to develop a dispensing error definition for use in the community setting, to describe the incidence, types and clinical significance of dispensing errors in UK community pharmacies and to assess the likely impact of authentication at the point of dispensing.

Setting

Eleven UK community pharmacies.

Method

A definition of a dispensing error was developed using the Delphi technique. A research pharmacist checked dispensed items awaiting collection and compared them against the original prescription to identify dispensing errors. An expert panel assessed the potential clinical significance of the errors identified. We then predicted the likely impact of three different systems of authentication at the point of dispensing: (a) stand-alone; (b) linked to patient medication records (PMR); and (c) linked to electronic transfer of prescriptions (ETP).

Key findings

We found a content error in 49 (1.7%) of 2859 dispensed items, and a labelling error in 46 (1.6%). The majority (67%) were of minor clinical significance. We estimated that a stand-alone system would prevent about one in five content errors and very few labelling errors, a PMR-linked system would prevent one-quarter of content errors and one-third of labelling errors, and an ETP-linked system would prevent nearly half of content and labelling errors. While none of the three systems would have prevented the one serious error identified, 22–60% of moderate errors could have been prevented, depending on the system used.

Conclusion

Content errors were identified in 1.7% of dispensed items, and labelling errors in 1.6%. Authentication at the point of dispensing could prevent a significant proportion of these, particularly if the system were linked to PMR or ETP. An experimental study is now needed.
A descriptive study of anxiolytic and hypnotic prescribing according to age and sex
Authors: Kairuz Therése E , Truter Ilse
Published: November 2007

Objective

Benzodiazepines are primarily indicated for the treatment of anxiety states and as hypnotics. Their inappropriate use often relates to duration and manner of use. Few studies have attempted to assess the prevalence of benzodiazepine prescribing in South Africa. The primary aim of the study was to examine the prevalence of sedative/hypnotic prescribing according to patient age and sex in a primary care setting. Setting South African private healthcare patients.

Method

An exposure cohort drug utilisation study was conducted. Prescription data were obtained from a South African private medical aid administrator. Descriptive statistics were used in the data analysis.

Key findings

Prescription records (n = 27 080) of 8084 patients in 2004 who were prescribed one or more benzodiazepines were retrospectively analysed. The average age of patients receiving benzodiazepines was 43.17 years (standard deviation (SD) 14.42 years). Benzodiazepine prescribing was more common in females (55.64% of patients were female). There was an increase in prescriptions per patient with increasing age, peaking at an older age among females. Diazepam (13.36%), zopiclone (13.19%) and oxazepam (12.03%) were the most frequently prescribed active ingredients. The majority of benzodiazepine hypnotics were prescribed in quantities of up to 14 units (tablets or capsules), while the benzodiazepine-related drugs zolpidem and zopiclone were prescribed in quantities of up to 30 units. Anxiolytics were often prescribed in quantities of 20 to 30 units.

Conclusion

Anxiolytics were prescribed in greater quantities than hypnotics. An increase in anxiolytic/hypnotic prescriptions and quantities of tablets/capsules occurred with increasing age. The trends and differences that were detected in the prescribing of benzodiazepines warrant further investigation in larger patient populations, especially with respect to the choice of agent, duration of treatment and patient age.