bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of intracellular Ca2+by P2Y1receptors may depend on the developmental stage of cultured rat striatal neurons
Authors: Rubini Patrizia , Pinkwart Christina , Franke Heike , Gerevich Zoltan , Nörenberg Wolfgang , Illes Peter
Published: June 2006

Mixed striatal cell cultures containing neurons and glial cells were grown either in neurobasal medium (NBM) or Dulbecco's modified Eagle's medium (DMEM). Whole‐cell patch‐clamp recordings indicated that, if at all, only a single, low amplitude spike was evoked shortly after starting the injection of a depolarizing current pulse into NBM neurons. In contrast, DMEM neurons fired series of high amplitude action potentials, without apparent spike frequency adaptation. The possible reason for the observed action potential failure in NBM neurons was a low density of Na+channels per unit of membrane surface area. However, both in NBM and DMEM neurons, ATP did not induce inward current responses via P2X receptor‐channels, although GABAAandN‐methyl‐D‐aspartate (NMDA) receptor‐channels could be activated by muscimol and NMDA, respectively. Ca2+imaging experiments by means of the Fura‐2 method were utilized to measure intracellular Ca2+([Ca2+]i) in neurons and glial cells. NBM, but not DMEM neurons responded to ATP with [Ca2+]itransients; glial cells grown in either culture medium were equally sensitive to ATP. ATP caused an increase of [Ca2+]iby a mechanism only partly dependent on external Ca2+; the residual ATP effect was blocked by cyclopiazonic acid (CPA) and was therefore due to the release of Ca2+from its intracellular pools. The receptor involved was characterized by P2 receptor antagonists (PPADS, MRS 2179, AR‐C69931MX) and was found to belong to the P2Y1subtype. CPA caused an early [Ca2+]iresponse due to release from intracellular storage sites, followed by a late [Ca2+]iresponse due to the influx of this cation from the extracellular space, probably triggered by the opening of store‐operated channels (SOCs) in the plasma membrane. It is concluded that in partial analogy with the effect of CPA, ATP releases [Ca2+]ivia the Gq/phospholipase C/inositoltrisphosphate (IP3) pathway, thereby opening SOCs. It is hypothesized that this effect of ATP may have an important role for the proliferation and migration of striatal neuronal progenitors. J. Cell. Physiol. 209: 81–93, 2006. © 2006 Wiley‐Liss, Inc.
Boundary element‐free method for fracture analysis of 2‐D anisotropic piezoelectric solids
Authors: Liew K. M. , Sun Yuzhou , Kitipornchai S.
Published: June 2006

This paper considers a 2‐D fracture analysis of anisotropic piezoelectric solids by a boundary element‐free method. A traction boundary integral equation (BIE) that only involves the singular terms of order 1/r is first derived using integration by parts. New variables, namely, the tangential derivative of the extended displacement (the extended displacement density) for the general boundary and the tangential derivative of the extended crack opening displacement (the extended displacement dislocation density), are introduced to the equation so that solution to curved crack problems is possible. This resulted equation can be directly applied to general boundary and crack surface, and no separate treatments are necessary for the upper and lower surfaces of the crack. The extended displacement dislocation densities on the crack surface are expressed as the product of the characteristic terms and unknown weight functions, and the unknown weight functions are modelled using the moving least‐squares (MLS) approximation. The numerical scheme of the boundary element‐free method is established, and an effective numerical procedure is adopted to evaluate the singular integrals. The extended ‘stress intensity factors’ (SIFs) are computed for some selected example problems that contain straight or curved cracks, and good numerical results are obtained. Copyright © 2006 John Wiley & Sons, Ltd.
Fast reactions of arylnitrenium ions with amino acids and proteins: a laser flash photolysis study
Authors: Thomas Selina I. , Falvey Daniel E.
Published: June 2006

Laser flash photolysis was used to examine the reaction of N‐methyl‐N‐(4‐biphenylyl)nitrenium ion with various amino acids and proteins in aqueous media. This nitrenium ion was found to react rapidly (>108 M−1 s−1) with tryptophan, tyrosine, methionine and cysteine, more slowly (107–108 M−1 s−1) with lysine, histidine, and arginine. Rapid reaction was also seen with several representative proteins including bovine serum albumin, lysozyme, and chymotrypsin. These results suggest that reaction with proteins is likely to be a significant pathway in the reactions of nitrenium ions generated in vivo. Copyright © 2006 John Wiley & Sons, Ltd.
Structural and functional evolution of transthyretin and transthyretin‐like proteins
Authors: Hennebry Sarah C. , Wright Hannah M. , Likic Vladimir A. , Richardson Samantha J.
Published: June 2006

Transthyretin (TTR) is a tetrameric protein involved in the distribution of thyroid hormones in vertebrates. The amino acid sequence of TTR is highly conserved across vertebrates. Hypothetical TTR‐like proteins (TLPs) were inferred from the identification of genes in nonvertebrate species. Here, we identified five motifs defining TLPs and three motifs defining both TTRs and TLPs. These motifs were mapped onto structurally conserved and functionally important regions of TTRs. These motifs were used to build hidden Markov models for accurate identification of TLPs in other organisms. TLPs were divided into three main groups based on their N‐terminal regions. Most TLPs are cytosolic, but in plants and slime mold, we predict they are peroxisomal. We verified that the TLPs from enterobacteria were periplasmic. We demonstrated that TLP genes are expressed in a bacterium (E. coli), an invertebrate animal (C. elegans), and a plant (A. thaliana). These TLPs have similar subunit molecular weights to TTRs, are tetramers, and are predicted to have similar three‐dimensional (3D) structures to TTRs, but do not bind thyroid hormones or similar ligands. We suggest that like TTRs, the N‐terminal and C‐terminal regions of TLPs are integral in defining the function of TLPs in nonvertebrate species and that the TLP gene duplicated in primitive vertebrates to produce the TTR gene. TLP/TTR has retained its overall structure, but changed function and localization during evolution in bacteria, invertebrates, plants, and vertebrates. Proteins 2006. © 2006 Wiley‐Liss, Inc.
An analysis for a cross‐over cohort study with an application to the study of triggers of Menière's disease
Authors: Salim Agus , Becker Niels G. , Möller Jette , Hessén‐Söderman Anne‐Charlotte
Published: June 2006

When studying the effect of a transient exposure on the risk of a rare illness, for time and cost effectiveness it is desirable to follow a cohort of individuals who are ‘prone’ to the illness over an observation period. In this paper, we present a method of analysis for data arising from such a study. The proposed method can be used to estimate the relative risk of an exposure triggering the illness and the distribution of the time delay from exposure to the onset of illness. The model is extended to include covariate effects and to the situation where there are two types of exposure. For the two types of exposures situation, a model to handle a possible synergism of the exposures is proposed. Finally, the method is applied to study the potential triggers of attacks of Menière's disease. Copyright © 2006 John Wiley & Sons, Ltd.
Conditioning on the propensity score can result in biased estimation of common measures of treatment effect: a Monte Carlo study
Authors: Austin Peter C. , Grootendorst Paul , Normand Sharon‐Lise T. , Anderson Geoffrey M.
Published: June 2006

Propensity score methods are increasingly being used to estimate causal treatment effects in the medical literature. Conditioning on the propensity score results in unbiased estimation of the expected difference in observed responses to two treatments. The degree to which conditioning on the propensity score introduces bias into the estimation of the conditional odds ratio or conditional hazard ratio, which are frequently used as measures of treatment effect in observational studies, has not been extensively studied. We conducted Monte Carlo simulations to determine the degree to which propensity score matching, stratification on the quintiles of the propensity score, and covariate adjustment using the propensity score result in biased estimation of conditional odds ratios, hazard ratios, and rate ratios. We found that conditioning on the propensity score resulted in biased estimation of the true conditional odds ratio and the true conditional hazard ratio. In all scenarios examined, treatment effects were biased towards the null treatment effect. However, conditioning on the propensity score did not result in biased estimation of the true conditional rate ratio. In contrast, conventional regression methods allowed unbiased estimation of the true conditional treatment effect when all variables associated with the outcome were included in the regression model. The observed bias in propensity score methods is due to the fact that regression models allow one to estimate conditional treatment effects, whereas propensity score methods allow one to estimate marginal treatment effects. In several settings with non‐linear treatment effects, marginal and conditional treatment effects do not coincide. Copyright © 2006 John Wiley & Sons, Ltd.
Lipid imbalance in the neurological disorder, Niemann‐Pick C disease
Authors: Vance Jean E.
Published: June 2006

Niemann‐Pick C (NPC) disease is a progressive neurological disorder in which cholesterol, gangliosides and bis‐monoacylglycerol phosphate accumulate in late endosomes/lysosomes. This disease is caused by mutations in either the NPC1 or NPC2 gene. NPC1 and NPC2 are involved in egress of lipids, particularly cholesterol, from late endosomes/lysosomes but the precise functions of these proteins are not clear. An important question regarding the function of NPC proteins is: why do mutations in these ubiquitously expressed proteins have such dire consequences in the brain? This review summarizes the roles of NPC proteins in lipid homeostasis particularly in the central nervous system.
Late onset cerebellar degeneration in a middle-aged cat
Authors: Negrin Arianna , Bernardini Marco , Baumgärtner Wolfgang , Castagnaro Massimo
Published: June 2006

Cerebellar degeneration (abiotrophy) (CD) is a spontaneous and accelerated degeneration of one or several mature cerebellar neuronal cell populations and has been described in many domestic animals, especially in dogs, with numerous breed-related cases. In cats, CD is mentioned as a rare sporadic entity. Late onset CDs are exceptionally uncommon and only two cases are reported in young adults, both aged 18 months. This report describes clinical and pathological findings of a late onset feline CD in a 9-year-old male Persian cat. The cat was presented with a history of progressive ataxia lasting 2 years. Neurological examination revealed severe neurological deficits such as generalised and severe ataxia, hypermetria in all four limbs, and bilateral absence of menace response. The lesion was diffusely localised in cerebellum. On gross pathology, the cerebellum appeared of normal size and shape and kidneys were characterised by mild hyperaemia. Histologically, lesions were limited to the cerebellum and kidneys. In the cerebellum, all cerebellar folia of both hemispheres and the vermis were affected. Changes were characterised by severe and diffuse loss of Purkinje cells, loss of cellularity in the granular layer, mild astrogliosis associated with moderate hypertrophy of Bergmann's glia. Immunohistochemistry for feline parvovirus antigen revealed a negative result. Renal lesions consisted of chronic fibrosis associated with chronic interstitial nephritis. CD is a rare disease and occurs commonly in puppies or young animals, who are clinically normal at birth and usually develop neurological signs within a few weeks or months after birth. This report represents the first case of CD in a middle-aged cat.
Remote sensing observations of ocean physical and biological properties in the region of the Southern Ocean Iron Experiment (SOFeX)
Authors: Moore J. Keith , Doney Scott C.
Published: June 2006

Satellite remote sensing estimates of surface chlorophyll, temperature, wind speed, and sea ice cover are examined in the region of the Southern Ocean Iron Experiment (SOFeX). Our objectives are to place SOFeX into a regional context and highlight regional mesoscale spatial and monthly temporal variability. SOFeX fertilized two patches with iron, one south of the Antarctic Polar Front (PF) and one north of the PF but south of the Subantarctic Front (SAF). Satellite‐observable phytoplankton blooms developed in both patches. The spring sea ice retreat near the south patch site was delayed in the 2001–2002 season, in turn delaying the naturally occurring, modest spring bloom in this region. Ambient surface chlorophyll concentrations for the area surrounding the southern patch during January 2002 are low (mean 0.26 mg/m3) compared with climatological January values (0.42 mg/m3). Regions east and west at similar latitudes exhibited higher mean chlorophyll concentrations (0.79 and 0.74 mg/m3, respectively). These modest phytoplankton blooms were likely stimulated by melting sea ice via changes in the light‐mixing regime and release of iron and were smaller in magnitude than the iron‐induced bloom within the SOFeX southern patch (>3 mg/m3). Iron inputs from melting ice may drive much of the natural spatial and temporal variability within the seasonal ice zone. Mean chlorophyll concentrations surrounding the SOFeX northern patch site were similar to climatological values during the SOFeX season. The northern patch was stretched into a long, thin filament along the southern boundary of the SAF, likely increasing the mixing/dilution rate with surrounding waters.
Global trends (1996–2003) of total column precipitable water observed by Global Ozone Monitoring Experiment (GOME) on ERS‐2 and their relation to near‐surface temperature
Authors: Wagner T. , Beirle S. , Grzegorski M. , Platt U.
Published: June 2006

We have analyzed global trends of total column precipitable water from measurements of the Global Ozone Monitoring Experiment (GOME) on the European Research Satellite (ERS‐2) for the period January 1996 to June 2003. In contrast to other satellite retrieval methods of total column precipitable water, our analysis does not rely on a priori assumptions or additional information; thus it is particularly well suited to trend studies. The chosen wavelength range in the red spectral region ensures similar sensitivity for observations over land and ocean and thus a consistent global picture. To minimize the influence of clouds on the water vapor trends, we selected observations under mainly clear‐sky conditions. The temporal evolution of the monthly or yearly averaged total column precipitable water, especially in the tropics, is highly correlated to that of the near‐surface temperature, indicating that the global atmospheric humidity is mainly driven by Clausius‐Clapeyron's principle. The magnitude of the dependence on near‐surface temperature indicates a strong water vapor feedback. The spatial patterns of the water vapor trends show both positive and negative signs. Especially over the oceans, trend patterns very similar to those of near‐surface temperature are found. In contrast, over Northern Hemispheric continents the trend patterns are much less correlated, and even opposite trends for water vapor and the near‐surface temperatures are found. During the period 1996–2002 the globally and yearly averaged total column precipitable water increased by 2.8 ± 0.8% (excluding the ENSO period).
Stratospheric and mesospheric HOx: Results from Aura MLS and FIRS‐2
Authors: Canty T. , Pickett H. M. , Salawitch R. J. , Jucks K. W. , Traub W. A. , Waters J. W.
Published: June 2006

Observations of OH and HO2 from Aura MLS for four seasons and diurnal profiles from the FIRS‐2 balloon instrument for Fall 2004 are compared with photochemical model simulations testing three sets of kinetics parameters. MLS and FIRS‐2 OH profiles, between 25–60 km, are lower than model results using standard kinetics. Use of a faster, previously published rate constant for O+OH leads to better agreement with MLS and FIRS‐2 profiles of OH. A 20% increase in the rate of HO2+OH and the faster rate for O+OH results in improved overall agreement with observations of OH, HO2, HOx, and HO2/OH. Since the MLS and FIRS‐2 observations of HOx are reasonably well described by these models, they are therefore not consistent with the previously reported HOx dilemma. However, all models considered here result in calculated odd oxygen loss exceeding production, consistent with the long standing ozone deficit problem.
Replacement of the positively charged Walker A lysine residue with a hydrophobic leucine residue and conformational alterations caused by this mutation in MRP1 impair ATP binding and hydrolysis
Authors: Buyse Frederic , Hou Yue-xian , Vigano Catherine , Zhao Qing , Ruysschaert Jean-Marie , Chang Xiu-bao
Published: June 2006

MRP1 (multidrug resistance protein 1) couples ATP binding/hydrolysis at its two non-equivalent NBDs (nucleotide-binding domains) with solute transport. Some of the NBD1 mutants, such as W653C, decreased affinity for ATP at the mutated site, but increased the rate of ATP-dependent solute transport. In contrast, other NBD1 mutants, such as K684L, had decreased ATP binding and rate of solute transport. We now report that mutations of the Walker A lysine residue, K684L and K1333L, significantly alter the tertiary structure of the protein. Due to elimination of the positively charged group and conformational alterations, the K684L mutation greatly decreases the affinity for ATP at the mutated NBD1 and affects ATP binding at the unmutated NBD2. Although K684L-mutated NBD1 can bind ATP at higher concentrations, the bound nucleotide at that site is not efficiently hydrolysed. All these alterations result in decreased ATP-dependent solute transport to approx. 40% of the wild-type. In contrast, the K1333L mutation affects ATP binding and hydrolysis at the mutated NBD2 only, leading to decreased ATP-dependent solute transport to approx. 11% of the wild-type. Consistent with their relative transport activities, the amount of vincristine accumulated in cells is in the order of K1333L≥CFTR (cystic fibrosis transmembrane conductance regulator)>K684L⋙wild-type MRP1. Although these mutants retain partial solute transport activities, the cells expressing them are not multidrug-resistant owing to inefficient export of the anticancer drugs by these mutants. This indicates that even partial inhibition of transport activity of MRP1 can reverse the multidrug resistance caused by this drug transporter.
A Pak- and Pix-dependent branch of the SDF-1α signalling pathway mediates T cell chemotaxis across restrictive barriers
Authors: Volinsky Natalia , Gantman Anna , Yablonski Deborah
Published: June 2006

Pak (p21-activated kinase) serine/threonine kinases have been shown to mediate directional sensing of chemokine gradients. We hypothesized that Pak may also mediate chemokine-induced shape changes, to facilitate leucocyte chemotaxis through restrictive barriers, such as the extracellular matrix. A potent inhibitor, Paki, was characterized and used to probe the role of Pak-family kinases in SDF-1α (stromal-cell derived factor-1α/CXCL12)-induced chemotaxis in a T cell model. Paki potently inhibited SDF-1α-induced Pak activation by a bivalent mechanism, as indicated by its complete inactivation upon point mutation of two binding sites, but partial inactivation upon mutation of either site alone. Importantly, Paki was not toxic to cells over the time frame of our experiments, since it did not substantially affect cell surface expression of CXCR4 (CXC chemokine receptor 4) or integrins, cell cycle progression, or a number of ligand-induced responses. Paki produced dose-dependent inhibition of SDF-1α-induced migration through rigid filters bearing small pores; but unexpectedly, did not substantially affect the magnitude or kinetics of chemotaxis through filters bearing larger pores. SDF-1α-induced Pak activation was partly dependent on PIX (Pak-interactive exchange factor); correspondingly, an allele of β-PIX that cannot bind Pak inhibited SDF-1α-induced chemotaxis through small, but not large pores. By contrast, other key players in chemotaxis: Gi, PI3K (phosphoinositide 3-kinase), and the Rho-family G-proteins, Rac and Cdc42 (cell division cycle 42), were required for SDF-1α-induced migration regardless of the barrier pore-size. These studies have revealed a distinct branch of the SDF-1α signalling pathway, in which the Rac/Cdc42 effector, Pak, and its partner, PIX, specifically regulate the cellular events required for chemokine-induced migration through restrictive barriers.
Proteomic analysis of altered protein expression in skeletal muscle of rats in a hypermetabolic state induced by burn sepsis
Authors: Duan Xunbao , Berthiaume François , Yarmush David , Yarmush Martin L.
Published: June 2006

mRNA profiling has been extensively used to study muscle wasting. mRNA level changes may not reflect that of proteins, especially in catabolic muscle where there is decreased synthesis and increased degradation. As sepsis is often associated with burn injury, and burn superimposed by sepsis has been shown to result in significant loss of lean tissues, we characterized changes in the skeletal-muscle proteome of rats subjected to a cutaneous burn covering 20% of the total body surface area, followed 2 days later by sepsis induced by CLP (caecal ligation and puncture). EDL (extensor digitorum longus) muscles were dissected from Burn-CLP animals (n=4) and controls (sham-burned and sham-CLP-treated, n=4). Burn-CLP injury resulted in a rapid loss of EDL weight, increased ubiquitin-conjugated proteins and increased protein carbonyl groups. EDL protein profiles were obtained by two-dimensional gel electrophoresis using two immobilized pH gradient strips with overlapping pH range covering a pH 3–8 range. Seventeen spots were significantly altered in the Burn-CLP compared with the control group, representing 15 different proteins identified by peptide mass fingerprinting. The identities of three proteins including transferrin were further confirmed by liquid chromatography–tandem MS. The significant changes in transferrin and HSP27 (heat-shock protein 27) were verified by Western-blot analysis. HSP60, HSP27 and HSPβ6 were down-regulated, along with HSP70, as detected by Western blotting. Six metabolic enzymes related to energy production were also down-regulated. A simultaneous decrease in chaperone proteins and metabolic enzymes could decrease protein synthesis. Furthermore, decreased HSPs could increase oxidative damage, thus accelerating protein degradation. Using cultured C2C12 myotubes, we showed that H2O2-induced protein degradation in vitro could be partially attenuated by prior heat-shock treatment, consistent with a protective role of HSP70 and/or other HSPs against proteolysis.
Probing the substrate specificity of the dengue virus type 2 NS3 serine protease by using internally quenched fluorescent peptides
Authors: Niyomrattanakit Pornwaratt , Yahorava Sviatlana , Mutule Ilze , Mutulis Felikss , Petrovska Ramona , Prusis Peteris , Katzenmeier Gerd , Wikberg Jarl E. S.
Published: June 2006

The NS3 (dengue virus non-structural protein 3) serine protease of dengue virus is an essential component for virus maturation, thus representing an attractive target for the development of antiviral drugs directed at the inhibition of polyprotein processing. In the present study, we have investigated determinants of substrate specificity of the dengue virus NS3 protease by using internally quenched fluorogenic peptides containing Abz (o-aminobenzoic acid; synonymous to anthranilic acid) and 3-nitrotyrosine (nY) representing both native and chimaeric polyprotein cleavage site sequences. By using this combinatorial approach, we were able to describe the substrate preferences and determinants of specificity for the dengue virus NS2B(H)–NS3pro protease. Kinetic parameters (kcat/Km) for the hydrolysis of peptide substrates with systematic truncations at the prime and non-prime side revealed a length preference for peptides spanning the P4–P3′ residues, and the peptide Abz-RRRRSAGnY-amide based on the dengue virus capsid protein processing site was discovered as a novel and efficient substrate of the NS3 protease (kcat/Km=11087 M−1·s−1). Thus, while having confirmed the exclusive preference of the NS3 protease for basic residues at the P1 and P2 positions, we have also shown that the presence of basic amino acids at the P3 and P4 positions is a major specificity-determining feature of the dengue virus NS3 protease. Investigation of the substrate peptide Abz-KKQRAGVLnY-amide based on the NS2B/NS3 polyprotein cleavage site demonstrated an unexpected high degree of cleavage efficiency. Chimaeric peptides with combinations of prime and non-prime sequences spanning the P4–P4′ positions of all five native polyprotein cleavage sites revealed a preponderant effect of non-prime side residues on the Km values, whereas variations at the prime side sequences had higher impact on kcat.
Interaction between Tiam1 and the Arp2/3 complex links activation of Rac to actin polymerization
Authors: ten Klooster Jean Paul , Evers Eva E. , Janssen Lennert , Machesky Laura M. , Michiels Frits , Hordijk Peter , Collard John G.
Published: June 2006

The Rac-specific GEF (guanine-nucleotide exchange factor) Tiam1 (T-lymphoma invasion and metastasis 1) regulates migration, cell–matrix and cell–cell adhesion by modulating the actin cytoskeleton through the GTPase, Rac1. Using yeast two-hybrid screening and biochemical assays, we found that Tiam1 interacts with the p21-Arc [Arp (actin-related protein) complex] subunit of the Arp2/3 complex. Association occurred through the N-terminal pleckstrin homology domain and the adjacent coiled-coil region of Tiam1. As a result, Tiam1 co-localizes with the Arp2/3 complex at sites of actin polymerization, such as epithelial cell–cell contacts and membrane ruffles. Deletion of the p21-Arc-binding domain in Tiam1 impairs its subcellular localization and capacity to activate Rac1, suggesting that binding to the Arp2/3 complex is important for the function of Tiam1. Indeed, blocking Arp2/3 activation with a WASP (Wiskott–Aldrich syndrome protein) inhibitor leads to subcellular relocalization of Tiam1 and decreased Rac activation. Conversely, functionally active Tiam1, but not a GEF-deficient mutant, promotes activation of the Arp2/3 complex and its association with cytoskeletal components, indicating that Tiam1 and Arp2/3 are mutually dependent for their correct localization and signalling. Our data suggests a model in which the Arp2/3 complex acts as a scaffold to localize Tiam1, and thereby Rac activity, which are both required for activation of the Arp2/3 complex and further Arp2/3 recruitment. This ‘self-amplifying’ signalling module involving Tiam1, Rac and the Arp2/3 complex could thus drive actin polymerization at specific sites in cells that are required for dynamic morphological changes.
TYK2 activity promotes ligand-induced IFNAR1 proteolysis
Authors: Marijanovic Zrinka , Ragimbeau Josiane , Kumar K. G. Suresh , Fuchs Serge Y. , Pellegrini Sandra
Published: June 2006

The type I IFNR (interferon receptor) is a heterodimer composed of two transmembrane chains, IFNAR1 (interferon-α receptor 1 subunit) and IFNAR2, which are associated with the tyrosine kinases Tyk2 and Jak1 (Janus kinase 1) respectively. Ligand-induced down-regulation of the type I IFNR is a major mechanism of negative regulation of cellular signalling and involves the internalization and lysosomal degradation of IFNAR1. IFNα promotes the phosphorylation of IFNAR1 on Ser535, followed by recruitment of the E3 ubiquitin ligase, β-TrCP2 (β-transducin repeats-containing protein 2), ubiquitination of IFNAR1 and proteolysis. The non-catalytic role of Tyk2 in sustaining the steady-state IFNAR1 level at the plasma membrane is well documented; however, little is known about the function of Tyk2 in the steps that precede and succeed serine phosphorylation and ubiquitination of IFNAR1 in response to ligand binding. In the present study, we show that catalytic activation of Tyk2 is not essential for IFNAR1 internalization, but is required for ligand-induced IFNAR1 serine phosphorylation, ubiquitination and efficient lysosomal proteolysis.
How plants tell the time
Authors: Gardner Michael J. , Hubbard Katharine E. , Hotta Carlos T. , Dodd Antony N. , Webb Alex A. R.
Published: June 2006

Plants, like all eukaryotes and most prokaryotes, have evolved sophisticated mechanisms for anticipating predictable environmental changes that arise due to the rotation of the Earth on its axis. These mechanisms are collectively termed the circadian clock. Many aspects of plant physiology, metabolism and development are under circadian control and a large proportion of the transcriptome exhibits circadian regulation. In the present review, we describe the advances in determining the molecular nature of the circadian oscillator and propose an architecture of several interlocking negative-feedback loops. The adaptive advantages of circadian control, with particular reference to the regulation of metabolism, are also considered. We review the evidence for the presence of multiple circadian oscillator types located in within individual cells and in different tissues.
The BMAL1 C terminus regulates the circadian transcription feedback loop
Authors: Kiyohara Yota B. , Tagao Sayaka , Tamanini Filippo , Morita Akira , Sugisawa Yukiko , Yasuda Maya , Yamanaka Iori , Ueda Hiroki R. , van der Horst Gijsbertus T. J. , Kondo Takao , Yagita Kazuhiro
Published: June 2006

The circadian clock is driven by cell-autonomous transcription/translation feedback loops. The BMAL1 transcription factor is an indispensable component of the positive arm of this molecular oscillator in mammals. Here, we present a molecular genetic screening assay for mutant circadian clock proteins that is based on real-time circadian rhythm monitoring in cultured fibroblasts. By using this assay, we identified a domain in the extreme C terminus of BMAL1 that plays an essential role in the rhythmic control of E-box-mediated circadian transcription. Remarkably, the last 43 aa of BMAL1 are required for transcriptional activation, as well as for association with the circadian transcriptional repressor CRYPTOCHROME 1 (CRY1), depending on the coexistence of CLOCK protein. C-terminally truncated BMAL1 mutant proteins still associate with mPER2 (another protein of the negative feedback loop), suggesting that an additional repression mechanism may converge on the N terminus. Taken together, these results suggest that the C-terminal region of BMAL1 is involved in determining the balance between circadian transcriptional activation and suppression.
Regulation of nitrogenase by 2-oxoglutarate-reversible, direct binding of a PII-like nitrogen sensor protein to dinitrogenase
Authors: Dodsworth Jeremy A. , Leigh John A.
Published: June 2006

Posttranslational regulation of nitrogenase, or switch-off, in the methanogenic archaeon
Methanococcus maripaludis
requires both
nifI
1
and
nifI
2
, which encode members of the PII family of nitrogen-regulatory proteins. Previous work demonstrated that nitrogenase activity in cell extracts was inhibited in the presence of NifI
1
and NifI
2
, and that 2-oxoglutarate (2OG), a potential signal of nitrogen limitation, relieved this inhibition. To further explore the role of the NifI proteins in switch-off, we found proteins that interact with NifI
1
and NifI
2
and determined whether 2OG affected these interactions. Anaerobic purification of His-tagged NifI
2
resulted in copurification of NifI
1
and the dinitrogenase subunits NifD and NifK, and 2OG or a deletion mutation affecting the T-loop of NifI
2
prevented copurification of dinitrogenase but did not affect copurification of NifI
1
. Similar results were obtained with His-tagged NifI
1
. Gel-filtration chromatography demonstrated an interaction between purified NifI
1,2
and dinitrogenase that was inhibited by 2OG. The NifI proteins themselves formed a complex of ≈85 kDa, which appeared to further oligomerize in the presence of 2OG. NifI
1,2
inhibited activity of purified nitrogenase when present in a 1:1 molar ratio to dinitrogenase, and 2OG fully relieved this inhibition. These results suggest a model for switch-off of nitrogenase activity, where direct interaction of a NifI
1,2
complex with dinitrogenase causes inhibition, which is relieved by 2OG. The presence of
nifI
1
and
nifI
2
in the
nif
operons of all nitrogen-fixing Archaea and some anaerobic Bacteria suggests that this mode of nitrogenase regulation may operate in a wide variety of diazotrophs.
Robust estimation of the false discovery rate
Authors: Pounds Stan , Cheng Cheng
Published: June 2006

Motivation: Presently available methods that use p-values to estimate or control the false discovery rate (FDR) implicitly assume that p-values are continuously distributed and based on two-sided tests. Therefore, it is difficult to reliably estimate the FDR when p-values are discrete or based on one-sided tests.

Results: A simple and robust method to estimate the FDR is proposed. The proposed method does not rely on implicit assumptions that tests are two-sided or yield continuously distributed p-values. The proposed method is proven to be conservative and have desirable large-sample properties. In addition, the proposed method was among the best performers across a series of ‘real data simulations’ comparing the performance of five currently available methods.

Availability: Libraries of S-plus and R routines to implement the method are freely available from

Contact:  stanley.pounds@stjude.org

Supplementary information: Supplementary data are avilable at Bioinformatics online.
The World Is Watching: Polaroid and South Africa
Authors: Morgan Eric J.
Published: June 2006

This article examines the Polaroid Corporation’s “experiment” in South Africa during the 1970s, which began after African American workers pressured the company to pull its operations out of South Africa in protest of the white minority government’s apartheid policies. It argues that Polaroid’s initiatives, little studied until now, led other American companies to question their presence in South Africa and inspired both student divestment movements at Harvard and other colleges and universities and the efforts of Leon Sullivan, whose 1977 “Sullivan Principles” urged American companies to treat their workers in South Africa as they would treat their counterparts in the United States in an effort to battle racism and apartheid. Despite Polaroid’s efforts, engagement with South Africa and apartheid proved futile, which initiated a larger movement to completely disengage from South Africa.
Psychophysics of sweet and fat perception in obesity: problems, solutions and new perspectives
Authors: Bartoshuk Linda M , Duffy Valerie B , Hayes John E , Moskowitz Howard R , Snyder Derek J
Published: June 2006

Psychophysical comparisons seem to show that obese individuals experience normal sweet and fat sensations, they like sweetness the same or less, but like fat more than the non-obese do. These psychophysical comparisons have been made using scales (visual analogue or category) that assume intensity labels (e.g.extremely) which denote the same absolute perceived intensity to all. In reality, the perceived intensities denoted by labels vary because they depend on experiences with the substances to be judged. This variation makes comparisons invalid. Valid comparisons can be made by asking the subjects to rate their sensory/hedonic experiences in contexts that are not related to the specific experiences of interest. Using this methodology, we present the evidence that the sensory and hedonic properties of sweet and fat vary with body mass index. The obese live in different orosensory and orohedonic worlds than do the non-obese; the obese experience reduced sweetness, which probably intensifies fat sensations, and the obese like both sweet and fat more than the non-obese do. Genetic variation as well as taste pathology contribute to these results. These psychophysical advances will impact experimental as well as clinical studies of obesity and other eating disorders.
Hyperphagia and obesity in OLETF rats lacking CCK-1 receptors
Authors: Moran Timothy H , Bi Sheng
Published: June 2006

The brain–gut peptide cholecystokinin (CCK) inhibits food intake following peripheral or site directed central administration. Peripheral exogenous CCK inhibits food intake by reducing the size and duration of a meal. Antagonist studies have demonstrated that the actions of the exogenous peptide mimic those of endogenous CCK. Antagonist administration results in increased meal size and meal duration. The feeding inhibitory actions of CCK are mediated through interactions with CCK-1 receptors. The recent identification of the Otsuka–Long–Evans–Tokushima Fatty (OLETF) rat as a spontaneous CCK-1 receptor knockout model has allowed a more comprehensive evaluation of the feeding actions of CCK. OLETF rats become obese and develop non-insulin dependent diabetes mellitus (NIDDM). Consistent with the absence of CCK-1 receptors, OLETF rats do not respond to exogenous CCK. OLETF rats are hyperphagic and their increased food intake is characterized by a large increase in meal size with a decrease in meal frequency that is not sufficient to compensate for the meal size increase. Deficits in meal size control are evident in OLETF rats as young as 2 days of age. OLETF obesity is secondary to the increased food intake. Pair feeding to amounts consumed by intact control rats normalizes body weight, body fat and elevated insulin and glucose levels. Hypothalamic arcuate nucleus peptide mRNA expression in OLETF rats is appropriate to their obesity and is normalized by pair feeding. In contrast, pair fed and young pre-obese OLETF rats have greatly elevated dorsomedial hypothalamic (DMH) neuropeptide Y (NPY) mRNA expression. Elevated DMH NPY in OLETF rats appears to be a consequence of the absence of CCK-1 receptors. In intact rats NPY and CCK-1 receptors colocalize to neurons within the compact subregion of the DMH and local CCK administration reduces food intake and decreases DMH NPY mRNA expression. We have proposed that the absence of DMH CCK-1 receptors significantly contributes to the OLETF's inability to compensate for their meal size control deficit leading to their overall hyperphagia. Access to a running wheel and the resulting exercise normalizes food intake and body weight in OLETF rats. When given access to running wheels for 6 weeks shortly after weaning, OLETF rats do not gain weight to the same degree as sedentary OLETF rats and do not develop NIDDM. Exercise also prevents elevated levels of DMH NPY mRNA expression, suggesting that exercise exerts an alternative, non-CCK mediated, control on DMH NPY. The OLETF rat is a valuable model for characterizing actions of CCK in energy balance and has provided novel insights into interactions between exercise and food intake.
Women and Money: Lessons from Senegal
Authors: Guérin Isabelle
Published: June 2006

This article examines the complexity and diversity of women's informal financial practices using data from surveys conducted in Senegal. It suggests that these practices are at the centre of a constant dialectic between short‐term and long‐term horizons, between the requirements of daily survival and the demands of community solidarity, and between personal aspirations and collective constraints. These practices also clearly illustrate a desire among the women in Senegal to impose a form of financial self‐discipline, and to create situations that will oblige them to earn income. The socio‐economic diversity among these entrepreneurs is also underscored. Informal financial arrangements are both a product and producer of gender inequalities and inequalities among women, as reflected in the research. This has direct policy implications, especially for microfinance products. If they are to be effective, microfinance services must develop beyond a standard, one‐size fits all model and become more innovative and adaptable to the diverse demands of women. They must be combined with complementary measures that challenge the systemic causes of inequality. Microfinance programmes should draw on informal financial arrangements while challenging their tendency to perpetuate inequality.
A statistical model predicting high hepatocyte proliferation index and the risk of developing hepatocellular carcinoma in patients with hepatitis C virus‐related cirrhosis
Authors: AZZAROLI F. , COLECCHI A. , LODATO F. , TRERÈ D. , BACCHI REGGIANI M. L. , FESTI D. , PRATI G. M. , ACCOGLI E. , CASANOVA S. , DERENZINI M. , RODA E. , MAZZELLA G.
Published: June 2006

Background

Incidence of hepatocellular carcinoma in hepatitis C virus‐related cirrhosis is 4% per year. Although cost‐effective, current screening could be improved.

Aim

To develop a statistical model including non‐invasive parameters able to identify patients at high risk of developing hepatocellular carcinoma.

Methods

One hundred and fifty‐eight patients (73F:85M) with compensated chronic hepatitis C virus liver disease underwent evaluation, including argyrophilic nucleolar organizer regions proliferation index, and were followed up for 56.18 ± 1.44 months.

Results

Fifty‐six patients had chronic hepatitis without cirrhosis and low argyrophilic nucleolar organizer regions proliferation index (≤25%), 65 had hepatitis C virus‐related cirrhosis and low argyrophilic nucleolar organizer regions proliferation index and 37 had hepatitis C virus‐related cirrhosis and high argyrophilic nucleolar organizer regions proliferation index (>25%). Groups were similar for gender and viral genotype distribution. None of the patients with chronic hepatitis without cirrhosis developed hepatocellular carcinoma, compared with 6.1% of low argyrophilic nucleolar organizer regions proliferation index and 30.6% of high argyrophilic nucleolar organizer regions proliferation index (P = 0.002). By multivariable logistic regression analysis, the following parameters were independently associated with hepatocellular carcinoma development and used for the development of the statistical model: platelets (OR 0.98), γ‐globulins (OR 0.111), alanine aminotransferase/aspartate aminotransferase ratio (OR 0.07), serum ferritin (OR 1.0) and ultrasonographyc pattern (coarse OR 2.9, coarse nodular OR 10.12). The statistical model properly allocated 95.9% of patients with low argyrophilic nucleolar organizer regions proliferation index and 72.2% of patients with high argyrophilic nucleolar organizer regions proliferation index.

Conclusions

The model, to be validated in large prospective studies, may help tailoring screening according to the risk of hepatocellular carcinoma development.
Systematic review: the use of serology to exclude or diagnose coeliac disease (a comparison of the endomysial and tissue transglutaminase antibody tests)
Authors: LEWIS N. R. , SCOTT B. B.
Published: June 2006

Background

With the appreciation of the high prevalence of coeliac disease there is increasing use of serology in screening asymptomatic people and testing those with suggestive features.

Aim

To compare the sensitivities and specificities of the endomysial antibody and the tissue transglutaminase antibody tests.

Methods

Using electronic databases a search was made for relevant papers using the terms tissue transglutaminase and endomysial antibody.

Results

Both the endomysial antibody and tissue transglutaminase antibody have very high sensitivities (93% for both) and specificities (>99% and >98% respectively) for the diagnosis of typical coeliac disease with villous atrophy. Human recombinant tissue transglutaminase performs much better than guinea pig tissue transglutaminase. Review of studies comparing endomysial antibody with human recombinant tissue transglutaminase antibody shows that endomysial antibody more often has a higher specificity and human recombinant tissue transglutaminase antibody more often has a higher sensitivity.

Conclusion

The human recombinant tissue transglutaminase antibody is the preferred test for screening asymptomatic people and for excluding coeliac disease in symptomatic individuals with a low pretest probability (i.e. <25%) for coeliac disease. Furthermore, it has a number of practical and financial advantages. If the pretest probability is >25%, biopsy is preferred as the post‐test probability of coeliac disease with a negative test is still >2%.
Inhibition of oxidative stress and cytokine activity by curcumin in amelioration of endotoxin-induced experimental hepatoxicity in rodents
Authors: Kaur G , Tirkey N , Bharrhan S , Chanana V , Rishi P , Chopra K
Published: June 2006

The present study is aimed at investigating the effect of curcumin (CMN) in salvaging endotoxin-induced hepatic dysfunction and oxidative stress in the liver of rodents. Hepatotoxicity was induced by administering lipopolysaccharide (LPS) in a single dose of 1 mg/kg intraperitoneally to the animals, which were being treated with CMN daily for 7 days. Liver enzymes serum alanine aminotransferase (ALT), serum aspartate aminotransferase (AST) and alkaline phosphatase (ALP), total bilirubin and total protein were estimated in serum. Oxidative stress in liver tissue homogenates was estimated by measuring thiobarbituric acid reactive substances (TBARS), glutathione (GSH) content and superoxide dismutase (SOD) activity. Serum and tissue nitrite was estimated using Greiss reagent and served as an indicator of NO production. A separate set of experiments was performed to estimate the effect of CMN on cytokine levels in mouse serum after LPS challenge. LPS induced a marked hepatic dysfunction evident by rise in serum levels of ALT, AST, ALP and total bilirubin (P < 0·05). TBARS levels were significantly increased, whereas GSH and SOD levels decreased in the liver homogenates of LPS-challenged rats. CMN administration attenuated these effects of LPS successfully. Further CMN treatment also regressed various structural changes induced by LPS in the livers of rats and decreased the levels of tumour necrosis factor-α and interleukin-6 in mouse plasma. In conclusion, these findings suggest that CMN attenuates LPS-induced hepatotoxicity possibly by preventing cytotoxic effects of NO, oxygen free radicals and cytokines.
Cognitive performance in Rett syndrome girls: a pilot study using eyetracking technology
Authors: Baptista P. M. , Mercadante M. T. , Macedo E. C. , Schwartzman J. S.
Published: June 2006

Background  Rett syndrome (RS) is a pervasive developmental disorder with cognitive and neuromotor impairments (including loss of handiness and loss of communicative skills).

Objective  To verify whether girls with RS use their gaze intentionally, by observing their performance in three cognitive tasks: (1) verbal instruction condition (look at picture X), (2) recognition and matching of pictures (look at the one that is the same), and (3) categorization of pictures (look at the one that is similar).

Method  Seven girls diagnosed with RS according to DSM‐IV criteria were studied. Eyegaze® technology was used to record the girls’ eye movements’ responses to visual stimulation.

Results  The comparison of fixation time on the alternatives revealed a higher percentage (62.4%) of correct alternatives (χ2 = 76.31; P = 0.000). Of the seven children assessed, only one did not present predominance of fixations on the correct alternatives in any one of the tasks. One did well in all tasks. Six responded correctly to all verbal instructions.

Conclusion  The rate of correct answers suggests that there is measurable and intentional gaze in RS girls and it can be used as a path to explore their cognitive performance.