bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural determination of a 5-O-methyl-deaminated neuraminic acid (Kdn)-containing polysaccharide isolated from Sinorhizobium fredii
Authors: GIL-SERRANO Antonio M. , RODR Miguel A. ÍGUEZ-CARVAJAL , TEJERO-MATEO Pilar , ESPARTERO José L. , THOMAS-OATES Jane , RUIZ-SAINZ José E. , BUEND Ana M. ÍA-CLAVERÍA
Published: August 2015

The structure of a polysaccharide from Sinorhizobium frediiSVQ293, a thiamine auxotrophic mutant of S. fredii HH103, has been determined. This polysaccharide was isolated following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, collision-induced dissociation tandem MS, one-dimensional 1H and 13C NMR and two-dimensional NMR experiments, the structure was shown to consist of the following trisaccharide repeating unit → 2)-α-d-Galp-(1 → 2)-β-d-Ribf-(1 → 9)-α-5-O-Me-Kdnp-(2 →, in which Kdn stands for deaminated neuraminic acid; 25% of the Kdn residues are not methylated. The structure of this polysaccharide is novel and this is the first report of the presence of Kdn in a rhizobial polysaccharide, as well as being the first structure described containing 5-O-Me-Kdn. This Kdn-containing polysaccharide is not present in the wild-type strain HH103, which produces a 3-deoxy-d-manno-2-octulosonic acid (Kdo)-rich polysaccharide. We conclude that it is likely that the appearance of this new Kdn-containing polysaccharide is a consequence of the mutation.
Thyroid hormone regulation of the Na+/glucose cotransporter SGLT1 in Caco-2 cells
Authors: MATOSIN-MATEKALO Miriam , MESONERO José E. , DELEZAY Olivier , POIREE Jean Claude , ILUNDAIN Anunciacion Ana , BROT-LAROCHE Edith
Published: August 2015

The expression of the Na+/glucose cotransporter (SGLT1) in response to thyroid hormone [3,5,3´-tri-iodo-l-thyronine (T3)] was investigated in the enterocytic model cell line Caco-2/TC7. In differentiated cells, T3 treatment induces an average 10-fold increase in glucose consumption as well as a T3 dose-dependent increase in SGLT1 mRNA abundance. Only cells grown on glucose-containing media, but not on the non-metabolizable glucose analogue α-methylglucose (AMG), could respond to T3-treatment. The Vmax parameter of AMG transport was enhanced 6-fold by T3 treatment, whereas the protein abundance of SGLT1 was unchanged. The role of Na+ recycling in the T3-related activation of SGLT1 activity was suggested by both the large increase in Na+/K+ATPase protein abundance and the inhibition, down to control levels, of AMG uptake in ouabain-treated cells. Further investigations aimed at identifying the presence of a second cotransporter that could be expressed erroneously in the colon cancer cell line were unsuccessful: T3-treatment did not modify the sugar-specificity profile of AMG transport and did not induce the expression of SGLT2 as assessed by reverse transcription-PCR. Our results show that T3 can stimulate the SGLT1 cotransport activity in Caco-2 cells. Both transcriptional and translational levels of regulation are involved. Finally, glucose metabolism is required for SGLT1 expression, a result that contrasts with the in vivo situation and may be related to the fetal phenotype of the cells.
Heterologously expressed inner lipoyl domain of dihydrolipoyl acetyltransferase inhibits ATP-dependent inactivation of pyruvate dehydrogenase complex
Authors: JACKSON John C. , VINLUAN Christine C. , DRAGLAND Carol J. , SUNDARARAJAN Vijayayakumar , YAN Bing , GOUNARIDES John S. , NIRMALA Nanguneri R. , TOPIOL Sid , RAMAGE Paul , BLUME John E. , AICHER Thomas D. , BELL Philip A. , MANN William R.
Published: August 2015

The activity of the pyruvate dehydrogenase multienzyme complex (PDC), which catalyses the oxidation of pyruvate to acetyl-CoA within the mitochondrion, is diminished in animal models of diabetes. Studies with purified PDC components have suggested that the kinases responsible for inactivating the decarboxylase catalytic subunits of the complex are most efficient in their regulatory role when they are bound to dihydrolipoyl acetyltransferase (E2) subunits, which form the structural core of the complex. We report that the addition of an exogenous E2 subdomain (inner lipoyl domain) to an intact PDC inhibits ATP-dependent inactivation of the complex. By combining molecular modelling, site-directed mutagenesis and biophysical characterizations, we have also identified two amino acid residues in this subdomain (Ile229 and Phe231) that largely determine the magnitude of this effect.
Transcription of the juvenile hormone esterase gene under the control of both an initiator and AT-rich motif
Authors: JONES Grace , MANCZAK Maria , SCHELLING Douglas , TURNER Helen , JONES Davy
Published: August 2015

The binding of transcription factors to the core promoter of the juvenile hormone esterase gene was functionally characterized using both a cell-free in vitrotranscription functional assay and a cell transfection assay. A core JHE promoter (-61 to +28 bp relative to transcription start site) supported faithful transcription from the in vivo transcription start site. The nuclear extracts from the Sf9 insect cell line that provided transcription from that template also bound to that template as a probe in gel-mobility shift assays. Deletion or transversion of the initiator-binding motif (-1 to +4 bp) abolished detectable transcription either in vitro or in transfected cells. An AT-rich motif (ATATAT; -28 to -23 bp) serves another transcription factor-binding site. Mutation of the AT-rich motif to a canonical TATA-box preserved transcription, while either its deletion or complete transversion abolished or significantly reduced detectable transcriptional activity. These results indicate that, under these conditions, the functional operation of this core promoter approaches that of a composite promoter in which both the TATA- and initiator-binding protein complexes are necessary, even for basal transcription. On the other hand, these debilitating mutations to either the TATA box or initiator motif did not prevent the ability of the corresponding gel-shift competitive probes to compete with the wild-type promoter for binding by the transcription factors. Even a double transversion of both the AT-rich motif and the initiator-binding motif was able to competitively displace the protein complex that bound to the labelled wild-type probe. These data strongly indicate the presence of (an) additional core-promoter-associated transcription factor(s) (that is not the ‘downstream element ’) that contact(s) the AT-binding complex and/or initiator-binding factor with sufficient avidity to remove them from binding to the competing wild-type promoter sequence.
Polyunsaturated fatty acid enrichment enhances endothelial cell-induced low-density-lipoprotein peroxidation
Authors: MAZIÈRE Cécile , DANTIN Françoise , CONTE Marie-Alix , DEGONVILLE James , ALI Dany , DUBOIS Françoise , MAZIÈRE Jean-Claude
Published: August 2015

Oxidative modification of low-density lipoprotein (LDL) is an important feature in the initiation and progression of atherosclerosis. LDL modification by endothelial cells was studied after supplementation of the cells with oleic acid and polyunsaturated fatty acids (PUFA) of the n-6 and n-3 series. In terms of the lipid peroxidation product [thiobarbituric acid reactive substances (TBARS)] content and diene level of the LDL particle, oleic acid had no significant effect, and linoleic acid was poorly effective. Gamma linolenic acid (C18:3, n-6) and arachidonic acid (C20:4, n-6) increased by about 1.6–1.9-fold the cell-mediated LDL modification. PUFA from the n-3 series, alpha linolenic acid (C18:3, n-3), eicosapentaenoic acid (C20:5, n-3) and docosahexaenoic acid (C22:6, n-3), induced a less marked effect (1.3–1.6-fold increase). The relative electrophoretic mobility of the LDL particle and its degradation by macrophages were enhanced in parallel. Concomitantly, PUFA stimulated superoxide anion secretion by endothelial cells. The intracellular TBARS content was also increased by PUFA. Comparison of PUFA from the two series indicates a good correlation between LDL oxidative modification, superoxide anion secretion and intracellular lipid peroxidation. The lipophilic antioxidant vitamin E decreased the basal as well as the PUFA-stimulated LDL peroxidation. These results indicate that PUFAs with a high degree of unsaturation of the n-6 and n-3 series could accelerate cell-mediated LDL peroxidation and thus aggravate the atherosclerotic process.
Two HNF-1 binding sites govern the glucose repression of the human sucrase-isomaltase promoter
Authors: RODOLOSSE Annie , CARRIERE Véronique , ROUSSET Monique , LACASA Michel
Published: August 2015

We have previously shown, using the Caco-2 clone PF11, that glucose represses transcription of the human sucrase-isomaltase (SI) gene and that the -370/+30 fragment of the SI gene conferred glucose-regulated expression on a heterologous gene. Different fragments beginning at the already characterized SI footprint (SIF) 1 (-53/-37), SIFR (-153/-129) or SIF3 (-176/-156) elements [Wu, Chen, Forslund and Traber (1994) J. Biol. Chem. 269, 17080–17085] were tested, in comparison with the -370/+30 fragment, for their capacity to inhibit reporter gene expression under high-glucose (25 mM) conditions. Unlike SIF1 and SIFR, the addition of the HNF (hepatocyte nuclear factor)-1-binding element SIF3 to the promoter fragment was required for repression under high-glucose conditions. This effect was enhanced when the SI promoter was extended to position -370, indicating that the -370/-176 region contains elements that may co-operate with SIF3 to increase the metabolic control of the SI promoter. We have characterized an additional HNF-1-binding site near to and upstream from SIF3; SIF4. By mutagenesis of the three HNF-1-binding elements we show that the two distal HNF-1-recognition sites are the most important for the glucose regulation of the SI gene. Moreover, this glucose regulation was abolished in PF11 cells overexpressing vHNF-1C (variant HNF, an isoform of the HNF-1 family). We thus propose that the differential binding of HNF-1-family proteins to their DNA targets on the SI promoter constitutes the molecular mechanism that controls the glucose regulation of the SI gene transcription.
cAMP-response-element-binding-protein-binding protein (CBP) and p300 are transcriptional co-activators of early growth response factor-1 (Egr-1)
Authors: SILVERMAN Eric S. , DU Jing , WILLIAMS Amy J. , WADGAONKAR Raj , DRAZEN Jeffrey M. , COLLINS Tucker
Published: August 2015

Egr-1 (early-growth response factor-1) is a sequence-specific transcription factor that plays a regulatory role in the expression of many genes important for cell growth, development and the pathogenesis of disease. The transcriptional co-activators CBP (cAMP-response-element-binding-protein-binding protein) and p300 interact with sequence-specific transcription factors as well as components of the basal transcription machinery to facilitate RNA polymerase II recruitment and transcriptional initiation. Here we demonstrate a unique way in which Egr-1 physically and functionally interacts with CBP/p300 to modulate gene transcription. CBP/p300 potentiated Egr-1 mediated expression of 5-lipoxygenase (5-LO) promoter–reporter constructs, and the degree of trans-activation was proportional to the number of Egr-1 consensus binding sites present in wild-type and naturally occurring mutants of the 5-LO promoter. The N- and C-terminal domains of CBP interact with the transcriptional activation domain of Egr-1, as demonstrated by a mammalian two-hybrid assay. Direct protein–protein interactions between CBP/p300 and Egr-1 were demonstrated by glutathione S-transferase fusion-protein binding and co-immunoprecipitation/Western-blot studies. These data suggest that CBP and p300 act as transcriptional co-activators for Egr-1-mediated gene expression and that variations between individuals in such co-activation could serve as a genetic basis for variability in gene expression.
Cloning of an intracellular protein that binds selectively to mitogenic acidic fibroblast growth factor
Authors: KOLPAKOVA Elona , WIĘDŁOCHA Antoni , STENMARK Harald , KLINGENBERG Olav , FALNES Pål Ø. , OLSNES Sjur
Published: August 2015

In addition to its extracellular action, there is evidence that acidic fibroblast growth factor (aFGF) acts inside cells. To identify intracellular proteins interacting with aFGF, we screened a HeLa cell library in the yeast two-hybrid system using pLex-aFGF as a bait. A clone binding to aFGF, but not to the non-mitogenic mutant aFGF-K132E, was isolated and characterized. The insert contained an open reading frame corresponding to a novel protein of 42 kDa. The protein, termed aFGF intracellular binding protein (FIBP), is mainly hydrophilic and does not contain an N-terminal signal sequence. In vitro-translated FIBP bound specifically to a fusion protein of maltose-binding protein and aFGF. FIBP became post-translationally associated with microsomes added to the cell-free protein synthesizing system, and the membrane-associated protein bound aFGF with high efficiency. Immunoblots and fluorescence microscopy demonstrated that the protein is present in nuclei and, to a lesser extent, associated with mitochondria and other cytoplasmic membranes. The possibility is discussed that FIBP may be involved in the mitogenic action of aFGF.

The nucleotide sequences described in this paper have been submitted to GeneBank database under accession numbers AF010187 (human FIBP) and AF010188 (simian FIBP).
Furin and proprotein convertase 7 (PC7)/lymphoma PC endogenously expressed in rat liver can be resolved into distinct post-Golgi compartments
Authors: WOUTERS Sandrine , LERUTH Michèle , DECROLY Etienne , VANDENBRANDEN Michel , CREEMERS John W. M. , LOO De Jan-Willem H. P. van , RUYSSCHAERT Jean-Marie , COURTOY Pierre J.
Published: August 2015

The intracellular compartmentalization in rat liver of the membrane-associated convertases furin and proprotein convertase 7 (PC7)/lymphoma PC (LPC) was investigated by analytical subcellular fractionation. In control animals, both enzymes were found to localize in fractions depleted of endoplasmic reticulum, cis-Golgi and lysosomal markers, but to co-distribute with the Golgi marker galactosyltransferase and the trans-Golgi network (TGN) marker TGN38. After overloading Golgi-derived vesicles with very-low-density lipoproteins (VLDL) by feeding rats with ethanol, the distribution of PC7/LPC was shifted markedly towards lower densities, in contrast with those of furin and the TGN marker. This provides support for the TGN localization of endogenously expressed furin and indicates that, at steady state, a considerable proportion of PC7/LPC may be associated with vesicles derived from the TGN.
Studies of the regulation of the mouse carboxyl ester lipase gene in mammary gland
Authors: KANNIUS-JANSON Marie , LIDBERG Ulf , HULTÉN Kåre , GRITLI-LINDE Amel , BJURSELL Gunnar , NILSSON Jeanette
Published: August 2015

The lactating mammary gland and pancreas of mouse constitute the main tissues for synthesis and secretion of a bile-salt-stimulated lipase called carboxyl ester lipase (CEL). In this paper we have analysed the endogenous CEL gene expression in mammary gland. It is shown that the gene is expressed at day 14 of pregnancy, which is synchronous with that of the whey acidic protein (WAP) gene. Even though the CEL and WAP genes are induced at the same time during mammary gland differentiation, their regulation is different with respect to dependence on lactogenic hormones. The high induction of the WAP gene expression due to the activation of signal transducer and activator of transcription (STAT)5 by prolactin has not been observed for the CEL gene, even though it has been demonstrated that both STAT5 isoforms interact with one of the γ-interferon activation sequence sites in the promoter of the CEL gene. Hence we have demonstrated that the prolactin/STAT5 signal is not involved in a general and significant activation of ‘milk genes ’. Instead of a direct effect of the lactogenic hormones, the up-regulation of the CEL gene is correlated with an increase in the number of differentiated epithelial cells. Furthermore, promoter studies using the mammary-gland-derived cell line, HC11, show that a major positive element in the CEL gene promoter interacts with a member(s) of the CCAAT-binding transcription factor/nuclear factor 1 family, binding to a palindromic site. Binding of this factor(s) is important for the tissue-specific activation of the CEL gene in the mammary gland, because no activation by this factor(s) was seen in cells of pancreatic origin.
Occurrence of paradoxical or sustained control by an enzyme when overexpressed: necessary conditions and experimental evidence with regard to hepatic glucokinase
Authors: DE ATAURI Pedro , ACERENZA Luis , KHOLODENKO Boris N. , DE LA IGLESIA Núria , GUINOVART Joan J. , AGIUS Loranne , CASCANTE Marta
Published: August 2015

It is widely assumed that the control coefficient of an enzyme on pathway flux decreases as the concentration of enzyme increases. However, it has been shown [Kholodenko and Brown (1996) Biochem. J. 314, 753–760] that enzymes with sigmoidal kinetics can maintain or even gain control with an increase in enzyme activity or concentration. This has been described as ‘paradoxical control’. Here we formulate the general requirements for allosteric enzyme kinetics to display this behaviour. We show that a necessary condition is that the Hill coefficient of the enzyme should increase with an increase in substrate concentration or decrease with an increase in product concentration. We also describe the necessary and sufficient requirements for the occurrence of paradoxical control in terms of the flux control coefficients and the derivatives of the elasticities. The derived expression shows that the higher the control coefficient of an allosteric enzyme, the more likely it is that the pathway will display this behaviour. Control of pathway flux is generally shared between a large number of enzymes and therefore the likelihood of observing sustained or increased control is low, even if the kinetic parameters are in the most favourable range to generate the phenomenon. We show that hepatic glucokinase, which has a very high flux control coefficient and displays sigmoidal behaviour within the hepatocyte in situ as a result of interaction with a regulatory protein, displays sustained or increased control over an extended range of enzyme concentrations when the regulatory protein is overexpressed.
Apoptosis: bombarding the mitochondria
Authors: Parone Philippe , Priault Muriel , James Dominic , Nothwehr Steven F , Martinou Jean-Claude
Published: August 2015

Mitochondria play a central role in apoptosis triggered by many stimuli. They integrate death signals through Bcl-2 family members and co-ordinate caspase activation through the release of apoptogenic factors that are normally sequestered in the mitochondrial intermembrane space. The release of these proteins is the result of the outer mitochondrial membrane becoming permeable. In addition, mitochondria can initiate apoptosis through the production of reactive oxygen species.
Systems analysis of MAPK signal transduction
Authors: Blüthgen Nils , Legewie Stefan
Published: August 2015

For more than a decade, the MAPK (mitogen-activated protein kinase) cascade has been studied using mathematical modelling and quantitative experimentation [1]. The MAPK cascade relays the presence of extracellular stimuli such as growth hormones to the nucleus and controls the expression of hundreds of genes. MAPKs control major cell fate decisions such as proliferation, differentiation and apoptosis, mainly by inducing alterations in gene expression. In this chapter, we discuss how systems biology analysis provides insights into the functioning of this cascade. We show how this pathway assists the cell in responding properly to extracellular cues by filtering out sub-threshold stimuli, while efficiently transmitting physiologically relevant inputs. Several different receptors signal through the MAPK pathway even though they elicit opposite biological responses, thus raising the question of how specificity is achieved in MAPK signalling. Experimental studies revealed that specific biological responses are encoded by quantitative aspects of the MAPK signal such as amplitude or duration. We discuss mechanisms that enable the pathway to generate quantitatively different signals, and also explain how different signals are interpreted by the downstream gene expression machinery.
Alzheimer's disease: dysfunction of a signalling pathway mediated by the amyloid precursor protein?
Authors: Neve Rachael L. , McPhie Donna L. , Chen Yuzhi
Published: August 2015

All individuals with Alzheimer's disease (AD) experience a progressive loss of cognitive function, resulting from a neurodegenerative process characterized by the deposition of ϐ-amyloid (Aϐ) in plaques and in the cerebrovasculature, and by the formation of neurofibrillary tangles in neurons. The cause of the neuronal death is unknown but it is thought to be linked in some way to the ϐ-amyloid precursor protein (APP), which is the source of the Aϐ that accumulates in the AD brain. There are two pieces of supporting data for this: first, APP is overexpressed in Down's syndrome, which leads to AD-like neuropathology by the age of 40 in virtually all affected individuals; secondly, specific point mutations in APP cause some forms of familial AD. Our laboratory has focused on a specific aspect of APP and its connection with the neuronal destruction seen in AD. We have hypothesized that AD results from a progressive dysfunction of APP. In addition, on the basis of recent data generated by our laboratory and others, we propose that in the normal brain a percentage of APP is present as an integral protein of the plasma membrane that mediates the transduction of extracellular signals into the cell via its Aϐ-containing C-terminal tail. In AD, accumulation of abnormal levels of the C-terminus in the neuron disturbs this signal-transduction function of APP, causing disorders in the cell-cycle machinery and consequent apoptosis. Here, we discuss the key findings that support this hypothesis, and discuss its therapeutic implications for AD.
Self-perpetuating changes in Sup35 protein conformation as a mechanism of heredity in yeast
Authors: Serio Tricia R. , Cashikar Anil G. , Kowal Anthony S. , Sawicki George J. , Lindquist Susan L.
Published: August 2015

Recently, a novel mode of inheritance has been described in the yeast Saccharomyces cerevisiae. The mechanism is based on the prion hypothesis, which posits that self-perpetuating changes in the conformation of single protein, PrP, underlie the severe neurodegeneration associated with the transmissible spongiform enchephalopathies in mammals. In yeast, two prions, [URE3] and [PSI+], have been identified, but these factors confer unique phenotypes rather than disease to the organism. In each case, the prion-associated phenotype has been linked to alternative conformations of the Ure2 and Sup35 proteins. Remarkably, Ure2 and Sup35 proteins existing in the alternative conformations have the unique capacity to transmit this physical state to the newly synthesized protein in vivo. Thus, a mechanism exists to ensure replication of the conformational information that underlies protein-only inheritance. We have characterized the mechanism by which Sup35 conformational information is replicated in vitro. The assembly of amyloid fibres by a region of Sup35 encompassing the N-terminal 254 amino acids faithfully recapitulates the in vivo propagation of [PSI+]. Mutations that alter [PSI+] inheritance in vivo change the kinetics of amyloid assembly in vitro in a complementary fashion, and lysates from [PSI+] cells, but not [psi-] cells, accelerate assembly in vitro. Using this system we propose a mechanism by which the alternative conformation of Sup35 is adopted by an unstructured oilgomeric intermediate at the time of assembly.
New I-type lectins of the CD 33-related siglec subgroup identified through genomics
Authors: Crocker Paul R. , Zhang Jiquan
Published: August 2015

Siglecs are sialic-acid-binding proteins of the Ig superfamily that are involved in cell–cell interactions and signalling. In recent years, several novel siglecs that are highly related to CD33/Siglec-2 have been identified through genomics and functional screens. In addition to their distinct sialic-acid-binding properties, most of these novel siglecs bear tyrosine-based signalling motifs that are typically found in inhibitory receptors of the immune system. The restricted expression patterns of CD33-related siglecs in the haemopoietic and immune systems suggests that they are involved in regulating leucocyte activation during inflammatory and immune responses.
Cytokine synergy, collagenases and cartilage collagen breakdown
Authors: Cawston Tim E. , Milner Jenny M. , Catterall Jon B. , Rowan Andrew D.
Published: August 2015

We have investigated proteinases that degrade cartilage collagen. We show that pro-inflammatory cytokines act synergistically with oncastatin M to promote cartilage collagen resorption by the up-regulation and activation of matrix metalloproteinases (MMPs). The precise mechanisms are not known, but involve the up-regulation of c-fos, which binds to MMP promoters at a proximal activator protein-1 (AP-1) site. This markedly up-regulates transcription and leads to higher levels of active MMP proteins.
Regulation of the clathrin-coated vesicle cycle by reversible phosphorylation.
Authors: Flett Alexander , Semerdjieva Sophia , Jackson Antony P. , Smythe Elizabeth
Published: August 2015

Reversible phosphorylation has long been an attractive mechanism to control cycles of coat assembly and disassembly during clathrin-mediated endocytosis. Many of the coat proteins are phosphorylated in vivo and in vitro. Our work has focused on the role of phosphorylation of the $#x03BC;2 subunit of AP-2 (adaptor protein 2), which appears to be necessary for efficient cargo recruitment. Studies to probe the regulation of $#x03BC;2 phosphorylation demonstrated that clathrin is a specific activator of the $#x03BC;2 kinase, and, in permeabilized cells, cargo sequestration, driven by exogenously added clathrin, results in elevated levels of $#x03BC;2 phosphorylation. Furthermore, phosphorylated $#x03BC;2 is mainly associated with assembled clathrin in vivo and its steady-state level is strongly reduced in cells depleted of clathrin heavy chain. Our results imply a central role for clathrin in the regulation of cargo selection via modulation of phospho-$#x03BC;2 levels. This is therefore a novel regulatory role for clathrin that is independent of its structural role and that provides elegant spatial control of AP-2 and cargo interactions, ensuring that AP-2 is only activated at the correct cellular location and in the correct functional context. Ongoing studies are exploring further the roles of reversible phosphorylation in the coated vesicle cycle.
Aggregation and fibrillization of prions in lipid membranes.
Authors: Kazlauskaite Jurate , Pinheiro Teresa J. T.
Published: August 2015

A key molecular event in prion diseases is the conversion of PrP (prion protein) from its normal cellular form (PrPc) into the disease-specific form (PrPSc). The transition from PrPc to PrPSc involves a major conformational change, resulting in amorphous aggregates and/or fibrillar amyloid deposits. Here, we review several lines of evidence implicating membranes in the conversion of PrP, and summarize recent results from our own work on the role of lipid membranes in conformational transitions of prion proteins. By establishing new correlations between in vivo biological findings with in vitro biophysical results, we propose a role for lipid rafts in prion conversion, which takes into account the structural heterogeneity of PrP in different lipid environments.
Nucleosome dynamics
Authors: Stockdale Chris , Bruno Michael , Ferreira Helder , Garcia-Wilson Elisa , Wiechens Nicola , Engeholm Maik , Flaus Andrew , Owen-Hughes Tom
Published: August 2015

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.
The p53 response during DNA damage: impact of transcriptional cofactors
Authors: Coutts Amanda S. , La Thangue Nicholas
Published: August 2015

Defects in the DNA damage response pathways can lead to tumour development. The tumour suppressor p53 is a key player in the DNA damage response, and the precise regulation of p53 is critical for the suppression of tumorigenesis. DNA damage induces the activity of p53, via damage sensors such as ATM (ataxia telangiectasia mutated) and ATR (ataxia telangiectasia-related), which leads to the transcriptional regulation of a variety of genes involved in cell cycle control and apoptosis. p53 is therefore tightly controlled, and its activity is regulated at a multiplicity of levels. An increasing array of cofactors are now known to influence p53 activity. Here we will discuss several of the cofactors that impact on p53 activity, specifically those involved in the function of the two novel p53 cofactors JMY (junction-mediating and regulatory protein) and Strap (serine/threonine-kinase-receptor-associated protein).
The IP3 receptor/Ca2+ channel and its cellular function
Authors: Mikoshiba Katsuhiko
Published: August 2015

The IP3R [IP3 (inositol 1,4,5-trisphosphate) receptor] is responsible for Ca2+ release from the ER (endoplasmic reticulum). We have been working extensively on the P400 protein, which is deficient in Purkinje-neuron-degenerating mutant mice. We have discovered that P400 is an IP3R and we have determined the primary sequence. Purified IP3R, when incorporated into a lipid bilayer, works as a Ca2+ release channel and overexpression of IP3R shows enhanced IP3 binding and channel activity. Addition of an antibody blocks Ca2+ oscillations indicating that IP3R1 works as a Ca2+ oscillator. Studies on the role of IP3R during development show that IP3R is involved in fertilization and is essential for determination of dorso-ventral axis formation. We found that IP3R is involved in neuronal plasticity. A double homozygous mutant of IP3R2 (IP3R type 2) and IP3R3 (IP3R type 3) shows a deficit of saliva secretion and gastric juice secretion suggesting that IP3Rs are essential for exocrine secretion. IP3R has various unique properties: cryo-EM (electron microscopy) studies show that IP3R contains multiple cavities; IP3R allosterically and dynamically changes its form reversibly (square form–windmill form); IP3R is functional even though it is fragmented by proteases into several pieces; the ER forms a meshwork but also forms vesicular ER and moves along microtubules using a kinesin motor; X ray analysis of the crystal structure of the IP3 binding core consists of an N-terminal β-trefoil domain and a C-terminal α-helical domain. We have discovered ERp44 as a redox sensor in the ER which binds to the luminal part of IP3R1 and regulates its activity. We have also found the role of IP3 is not only to release Ca2+ but also to release IRBIT which binds to the IP3 binding core of IP3R.
Effects of competition on the sleep patterns of elite rugby union players
Authors: Shearer David A. , Jones Rhys M. , Kilduff Liam P. , Cook Christian J.
Published: August 2015

No published research has assessed sleep patterns of elite rugby union players following match‐play. The present study examined sleep patterns of professional rugby union players, prior and post‐match‐play, to assess the influence of competition. Twenty‐eight male rugby union players (24.4 ± 2.9 years, 103.9 ± 12.2 kg) competed in one of four competitive home matches. Player's sleep behaviours were monitored continuously using an Actiwatch® from two days before the match, until three days post‐match. Repeated measures of analysis of variance (ANOVA) showed significant differences across the time points measured for time to bed (F = 26.425, η2
= 0.495, p <. 001), get up time (F = 21.175, η2 = 0.440, p < .001), time spent in bed (F = 10.669, η2 = 0.283, p < .001), time asleep (F = 8.752, η2 = 0.245, p < .001) and percentage of time moving (F = 4.602, η2 = 0.146 p < .05). Most notable, post hocs revealed a significant increase for time in bed the night before the match (p < .01; 95% CI = 0 : 10–1 : 28 h; 9.7 ± 13.5%) compared with the reference night sleep. Furthermore, time asleep significantly decreased post‐match (p < .05; 95% CI = −0:03 to −1:59 h; −19.5 ± 19.8%) compared to two nights pre‐match. Across all time points, sleep latency and efficiency for most players were considered abnormal compared to that expected in normal populations. The results demonstrate that sleep that is deprived post‐match may have detrimental effects on the recovery process.
Recovery Rates of Human Fetal Skeletal Remains Using Varying Mesh Sizes
Authors: Pokines James T. , De La Paz Jade S.
Published: August 2015

Human fetal skeletal elements of different gestational ages were screened with multiple mesh sizes (6.4 mm [1/4 inch], 3.2 mm [1/8 inch], 2.0 mm, and 1.0 mm) to determine their recovery rates. All remains were previously macerated, and no significantly damaged elements were used. The 6.4 mm mesh allowed a large loss of elements (63.2% overall), including diagnostic elements, while no diagnostic elements were lost when the 1 mm mesh (0.2%) was used. When using the 3.2 mm mesh, 16.2% of the bones were lost, including some diagnostic elements (primarily tooth crowns), while 7.5% were lost using the 2.0 mm mesh. The authors recommend that the potential loss of information incurred when utilizing larger mesh sizes be taken into consideration when planning recovery methods where fetal remains may be encountered and that a minimum of 1.0 mm mesh be utilized in recovery contexts known to include fetal remains.
LeSSS: Learned Shared Semantic Spaces for Relating Multi‐Modal Representations of 3D Shapes
Authors: Herzog Robert , Mewes Daniel , Wand Michael , Guibas Leonidas , Seidel Hans‐Peter
Published: August 2015

In this paper, we propose a new method for structuring multi‐modal representations of shapes according to semantic relations. We learn a metric that links semantically similar objects represented in different modalities. First, 3D‐shapes are associated with textual labels by learning how textual attributes are related to the observed geometry. Correlations between similar labels are captured by simultaneously embedding labels and shape descriptors into a common latent space in which an inner product corresponds to similarity. The mapping is learned robustly by optimizing a rank‐based loss function under a sparseness prior for the spectrum of the matrix of all classifiers. Second, we extend this framework towards relating multi‐modal representations of the geometric objects. The key idea is that weak cues from shared human labels are sufficient to obtain a consistent embedding of related objects even though their representations are not directly comparable. We evaluate our method against common base‐line approaches, investigate the influence of different geometric descriptors, and demonstrate a prototypical multi‐modal browser that relates 3D‐objects with text, photographs, and 2D line sketches.
Adenosine monophosphate is not superior to histamine for bronchial provocation test for assessment of asthma control and symptoms
Authors: Wu Fan , Guan Wei‐Jie , Gao Yi , An Jia‐Ying , Xie Yan‐Qing , Liu Wen‐Ting , Yu Xin‐Xin , Zheng Jin‐Ping
Published: August 2015

Background

Adenosine monophosphate (AMP) may reflect airway inflammation and hyperresponsiveness, but relationship between AMP and histamine (His, a conventional stimulus) bronchial provocation test (BPT) in asthma is not fully elucidated.

Objectives

To compare both BPTs and determine their utility in reflecting changes of asthmatic symptoms.

Methods

BPTs were performed in a cross‐over fashion, at 2–4 day intervals. Cumulative doses eliciting 20% FEV1fall (PD20FEV1), diagnostic performance and adverse events (AEs) were compared. Patients with PD20FEV1 lower than geometric mean were defined as responders, otherwise poor responders. Patients with uncontrolled and partly controlled asthma, who maintained their original inhaled corticosteroids therapy, underwent reassessment of airway responsiveness and asthmatic symptoms 3 and 6 months after.

Results

Nineteen uncontrolled, 22 partly controlled and 19 controlled asthmatic patients and 24 healthy subjects were recruited. Lower PD20FEV1 geometric means were associated with poorer asthma control in His‐BPT (0.424 μmol vs 1.684 μmol vs 3.757 μmol), but not AMP‐BPT (11.810 μmol vs 7.781 μmol vs 10.220 μmol). Both BPTs yielded similar overall diagnostic performance in asthma (area under curve: 0.842 in AMP‐BPT vs 0.850 in His‐BPT). AEs, including wheezing and tachypnea, were similar and mild. Ten patients with uncontrolled and 10 partly controlled asthma were followed‐up. At months 3 and 6, we documented an increase in PD20FEV1‐AMP and PD20FEV1‐His, which did not correlate with reduction asthmatic symptom scores. This overall applied in responders and poor responders of AMP‐BPT and His‐BPT.

Conclusion

Despite higher screening capacity of well‐controlled asthma, AMP‐BPT confers similar diagnostic performance and safety with His‐BPT. AMP‐BPT might not preferentially reflect changes asthmatic symptoms.
Adaptive Tactical Pricing in Multi‐Agent Supply Chain Markets Using Economic Regimes
Authors: Hogenboom Alexander , Ketter Wolfgang , van Dalen Jan , Kaymak Uzay , Collins John , Gupta Alok
Published: August 2015

In today's complex and dynamic supply chain markets, information systems are essential for effective supply chain management. Complex decision making processes on strategic, tactical, and operational levels require substantial timely support in order to contribute to organizations' agility. Consequently, there is a need for sophisticated dynamic product pricing mechanisms that can adapt quickly to changing market conditions and competitors' strategies. We propose a two‐layered machine learning approach to compute tactical pricing decisions in real time. The first layer estimates prevailing economic conditions—economic regimes—identifying and predicting current and future market conditions. In the second layer, we train a neural network for each regime to estimate price distributions in real time using available information. The neural networks compute offer acceptance probabilities from a tactical perspective to meet desired sales quotas. We validate our approach in the trading agent competition for supply chain management. When competing against the world's leading agents, the performance of our system significantly improves compared to using only economic regimes to predict prices. Profits increase significantly even though the prices and sales volume do not change significantly. Instead, tactical pricing results in a more efficient sales strategy by reducing both finished goods and components inventory costs.
The quest for patterns in dyskinetic cerebral palsy
Authors: Himmelmann Kate
Published: August 2015

This commentary is on the original article by Monbaliu et al. on pages 138–144 of this issue.
Metabolic reprogramming of the tumour microenvironment
Authors: Xing Yazhi , Zhao Shimin , Zhou Binhua P. , Mi Jun
Published: August 2015

Tumour cells, stromal cells and the stroma comprise the tumour microenvironment. The metabolism of both tumour cells and several types of tumour stromal cells, such as cancer‐associated fibroblasts and tumour‐associated macrophages, is reprogrammed. Current studies have found that stromal cells promote tumour progression and metastasis, through not only the paracrine secretion of cytokines or chemokines, but also intermediate metabolites. Here, we summarize the latest insights into the mechanism of metabolic reprogramming in cancer cells, cancer‐associated fibroblasts and tumour‐associated macrophages, and their potential roles in tumour progression and metastasis.
A global, remote sensing‐based characterization of terrestrial habitat heterogeneity for biodiversity and ecosystem modelling
Authors: Tuanmu Mao‐Ning , Jetz Walter
Published: August 2015

Aim

Habitat heterogeneity has long been recognized as a key landscape characteristic determining biodiversity patterns. However, a lack of standardized, large‐scale, high‐resolution and temporally updatable heterogeneity information based on direct observations has limited our understanding of this connection and its effective use for biodiversity conservation. To address this, we develop here remote sensing‐based metrics to characterize global habitat heterogeneity at 1‐km resolution and assess their value for biodiversity modelling.

Location

Global.

Methods

We develop 14 heterogeneity metrics (available athttp://www.earthenv.org) based on the textural features of the enhanced vegetation index (EVI) imagery from the Moderate Resolution Imaging Spectroradiometer (MODIS), and closely examine a complementary core set of six of these metrics. We evaluate their ability to provide fine‐grain habitat heterogeneity by comparing the heterogeneity information captured by them with that measured by 30‐m Landsat‐based land‐cover data. Using spatial autoregressive models, we then compare their utility with that of more conventional metrics (derived from topography or categorical land‐cover data) for modelling the species richness of bird communities across the conterminousUnitedStates based onBreedingBirdSurvey data.

Results

The newly derived metrics capture different aspects of habitat heterogeneity and provide fine‐grain information for locations deemed homogeneous by traditional land‐cover classifications at both continental and global extents. Most of them strongly exceed conventional heterogeneity variables in capturing the spatial variation in bird species richness, withHomogeneity emerging as the strongest predictor.

Main conclusions

This study develops and validates the performance of readily usable metrics of textural measures capturing fine‐grain habitat heterogeneity. The presented metrics outperform conventional measures in capturing detailed spatial variation in habitats and in predicting key biodiversity patterns. They provide a rigorous and comparable basis for understanding heterogeneity–diversity relationships, and offer a powerful tool for monitoring and understanding the responses of biodiversity and ecosystems to the changing environment.
Looking Philosophical: Stuff, Stereotypes, and Self‐Presentation
Authors: Olberding Amy
Published: August 2015

Self‐presentation is a complex phenomenon through which individuals present themselves in performance of social roles. The success of such performances rests not just on how well a performer fulfills expectations regarding the role she would play, but on whether observers find her convincing. I focus on how self‐presentation entails making use of material environment and objects: One may “dress for the part” and employ props that suit a desired role. However, regardless of dress or props, one can nonetheless fail to “look the part” owing to expectations informed by biases patterned along commonplace social stereotypes. Using the social role of philosopher as my example, I analyze how the stereotype attached to this role carries implications for how demographically under‐represented philosophers may self‐present, specifically with regard to dress and decoration. I look, in particular, to the alienation from one's material environment that may follow on the frustration of self‐presentation through bias. One pernicious effect of bias, I argue, is the power it has to deform and distort its target's relation to her physical setting and objects. Where comfort and ease in one's material environment can be a significant ethico‐aesthetic good, bias can inhibit access to, and enjoyment of, this good.
Analysis of limb segments length and body proportion of southern Chinese children and adolescents
Authors: Zhu Min , Jiao Yan‐Hua , Xiong Feng , Xie Fang , Guo Shu‐Juan , Cun Yue‐Shuang
Published: August 2015

Aim

This cross‐sectional study was designed to characterize by age the ratios of limb segments length to height and extremities–trunk ratio and body proportions of southern Chinese children.

Methods

Data were collected from students (n = 4715) from five school, aged 6–17 years, in the city of Chongqing. Their standing height, sitting height, arm span, forearm length, upper arm length, leg length, lower leg length, and ratios of extremities to trunk length were determined.

Results

Sitting height, forearm length, upper arm length, arm span, and lower leg length were highly correlated with standing height (r > 0.9; P < 0.05). The ratio of extremities to trunk increased till about 13 years of age for both genders.

Conclusions

The length of extremities and their ratio to sitting height reflect regular changes of growth in Chinese children as their age, and limb segments length is highly correlated with height.
Exposure assessment of epidermal growth factor to various tissues in mice after intravenous and subcutaneous administration
Authors: Lee Jong Bong , Shin Beomsoo , Lee Sang Ho , Lee Bong Yong , Kim Tae Hwan , Kim Min Gi , Yoo Sun Dong
Published: August 2015

Objectives

This study was conducted to examine the tissue distribution of human recombinant epidermal growth factor (EGF) after multiple intravenous and subcutaneous injections in mice.

Methods

Male BALB/c mice were divided into (1) EGF 1 mg/kg intravenous dose, (2) EGF 5 mg/kg intravenous dose, (3) drug-free intravenous control, (4) EGF 1 mg/kg subcutaneous dose, (5) EGF 5 mg/kg subcutaneous dose and (6) drug-free subcutaneous control groups. EGF and drug-free dosing solutions were injected by intravenous and subcutaneous injections once a day for 3 days. EGF concentrations in serum and tissues of kidney, liver, lung, small intestine and tongue were determined by ELISA.

Key findings

As the intravenous and subcutaneous doses were increased from 1 to 5 mg/kg, serum Cmax and area under the concentration–time curve (AUC) values were increased dose-proportionally. In lung, tongue and small intestine, increases in AUC were dose-proportional after intravenous injections, but greater than dose-proportional after subcutaneous injections. The fold-increases in Cmax and AUC values were lowest in liver and highest in kidney.

Conclusion

Based on Cmax and AUC data, the systemic exposure achieved by subcutaneous injections was comparable with that achieved by intravenous injections.