bluuebunny/crossref_metadata_2025 huggingface dataset:
Partial purification of heparanase activities in Chinese hamster ovary cells: evidence for multiple intracellular heparanases
Authors: BAME Karen J. , HASSALL Alan , SANDERSON Crystal , VENKATESAN Indumati , SUN Chao
Published: August 2015

Heparanases are mammalian endoglycosidases that cleave heparan sulphate glycosaminoglycans from proteoglycan core proteins and degrade them into shorter chains. The enzymes have been proposed to act in a variety of cellular processes, including proteoglycan catabolism, remodelling of basement membranes and release of heparan sulphate-binding ligands from their extracellular storage sites. Additional functions for heparanases may be to generate short heparan sulphate chains that stabilize or activate other proteins. While heparanase activities have been described in a number of tissues and cell lines, it is not known how many different enzymes are responsible for these activities. Our recent studies characterizing the short glycosaminoglycans produced in Chinese hamster ovary (CHO) cells suggested that multiple heparanases are necessary for the formation of the short heparan sulphate chains [Bame and Robson (1997) J. Biol. Chem. 272, 2245–2251]. We examined whether this is the case by purifying heparanase activity from CHO cell homogenates. Based on their ability to bind ion-exchange resins and their elution from gel-filtration columns, four separate heparanase activities were partially purified. All four activities cleave free glycosaminoglycans over a broad pH range of 3.5–6.0 or 6.5, suggesting that they act in the endosomal/lysosomal pathway. The sizes of the short heparan sulphate chains generated by the partially purified heparanases ranged from 6 to 9 kDa, and for two of the activities the product size is pH-dependent. Three of the four activities degrade proteoglycans as well as the free glycosaminoglycan chain. Interestingly, all four enzymes generate short glycosaminoglycans with a sulphate-rich, modified domain at the non-reducing end of the newly formed chain. Since our previous studies showed that in CHO cells there is also a population of short heparan sulphates with a modified domain at the reducing end of the chain, this suggests that there may be another heparanase in CHO cells that was not purified. Alternatively, our findings suggest that the formation of short heparan sulphate glycosaminoglycans inside CHO cells may be a result of the concerted action of multiple heparanases, and may depend on the proportions of the different enzymes and the environment in which the chains are degraded.
Isolation and characterization of the rat huntingtin promoter
Authors: HOLZMANN Carsten , MÄUELER Winfried , PETERSOHN Dirk , SCHMIDT Thorsten , THIEL Gerald , EPPLEN Jörg T. , RIESS Olaf
Published: August 2015

Huntington's disease (HD) is a neurodegenerative disorder caused by a (CAG)>37 repeat expansion in a novel gene of unknown function. Although the huntingtin gene is expressed in neuronal and non-neuronal tissues, the disease affects nerve cells of selected regional areas of the central nervous system. To gain insight into the regulation of the HD gene we analysed 1348 bp of the rat huntingtin promoter region. This region lacks a TATA and a CAAT box, is rich in GC content and has several consensus sequences for binding sites for SP1, PEA3, Sif and H2A. The stretch between nucleotides -56 and -206 relative to the first ATG is highly conserved between human and rodents and it harbours several potential binding sites for transcription factors. We analysed deletion mutants fused with the chloramphenicol acetyltransferase reporter gene in transfected, HD-expressing neuronal (NS20Y, NG108-15) and non-neuronal Chinese hamster ovary cell lines. Hence these cells should contain the required trans-acting factors necessary for HD gene expression. Partial deletion of the evolutionarily conserved part of the promoter significantly decreases the activity in both neuronal and non-neuronal cells, indicating that the core promoter activity is located between nucleotides -332 and -15. DNase I footprinting and electrophoretic mobility-shift assays were used to define the nucleotide positions and binding affinity of DNA–protein interactions.
Mechanisms and functional features of polarized membrane traffic in epithelial and hepatic cells
Authors: ZEGERS Mirjam M. P. , HOEKSTRA Dick
Published: August 2015

Epithelial cells express plasma-membrane polarity in order to meet functional requirements that are imposed by their interaction with different extracellular environments. Thus apical and basolateral membrane domains are distinguished that are separated by tight junctions in order to maintain the specific lipid and protein composition of each domain. In hepatic cells, the plasma membrane is also polarized, containing a sinusoidal (basolateral) and a bile canalicular (apical)-membrane domain. Relevant to the biogenesis of these domains are issues concerning sorting, (co-)transport and regulation of transport of domain-specific membrane components. In epithelial cells, specific proteins and lipids, destined for the apical membrane, are sorted in the trans-Golgi network (TGN), which involves their sequestration into cholesterol/sphingolipid ‘rafts ’, followed by ‘direct ’ transport to the apical membrane. In hepatic cells, a direct apical transport pathway also exists, as revealed by transport of sphingolipids from TGN to the apical membrane. This is remarkable, since in these cells numerous apical membrane proteins are ‘indirectly ’ sorted, i.e. they are first transferred to the basolateral membrane prior to their subsequent transcytosis to the apical membrane. This raises intriguing questions as to the existence of specific lipid rafts in hepatocytes. As demonstrated in studies with HepG2 cells, it has become evident that, in hepatic cells, apical transport pathways can be regulated by protein kinase activity, which in turn modulates cell polarity. Finally, an important physiological function of hepatic cells is their involvement in intracellular transport and secretion of bile-specific lipids. Mechanisms of these transport processes, including the role of multidrug-resistant proteins in lipid translocation, will be discussed in the context of intracellular vesicular transport. Taken together, hepatic cell systems provide an important asset to studies aimed at elucidating mechanisms of sorting and trafficking of lipids (and proteins) in polarized cells in general.
Oestrogen receptor facilitates the formation of preinitiation complex assembly: involvement of the general transcription factor TFIIB
Authors: SABBAH Michèle , KANG Kwang-Il , TORA Laszlo , REDEUILH Gérard
Published: August 2015

The action of oestrogen hormones is mediated through the oestrogen receptor (ER), a member of a large superfamily of nuclear receptors that function as ligand-activated transcription factors. Sequence-specific transcription factors, including the nuclear receptor superfamily, are thought to interact either directly or indirectly with general transcription factors to regulate transcription. Although numerous studies have focused on the identification of potential co-activators interacting with isolated trans-activation domains of ER, few have investigated the mechanisms by which ER transmits its signal to the basal transcription machinery. We show that ER does not stabilize the binding of the TATA-box binding protein (TBP) of the TFIID complex, or of TFIIB to the promoter, although a stable ER–TBP–TFIIB–promoter complex was detected, suggesting that ER, TBP and TFIIB might interact with each other to form a complex to the promoter. We also demonstrate that ER binds specifically to TFIIB, a key component of the preinitiation complex. Affinity chromatography with immobilized deletion mutants of ER maps a TFIIB interaction region that encompasses the DNA-binding domain. The addition of excess TFIIB to transcription reactions in vitro did not, however, affect the magnitude of transcriptional activation by ER. These results indicate that, in contrast with current models, ER does not activate transcription by increasing the rate of assembly of TFIIB into the transcription complex. An increased concentration of TFIIB was unable, by itself, to overcome the requirement for ER. By using an immobilized promoter-template assay employing nuclear extract from HeLa cells, recombinant human ER increased the stable association of subsequent components of the transcription machinery (TFIIE and TFIIF), in correlation with ER-induced transcription. Our results suggest that ER acts, in an early step, during or immediately after the formation of template-committed complexes containing TFIIB, favouring the recruitment of one or more components of the basic transcription machinery as well as co-activators.
Identification of the separate domains in the hepatic glycogen-targeting subunit of protein phosphatase 1 that interact with phosphorylase a, glycogen and protein phosphatase 1
Authors: ARMSTRONG Christopher G. , DOHERTY Martin J. , COHEN Patricia T. W.
Published: August 2015

Deletion and mutational analyses of the rat liver glycogen-targeting subunit (GL) of protein phosphatase 1 (PP1) have identified three separate domains that are responsible for binding of PP1, glycogen and phosphorylase a. The glycogen-binding domain spans the centre of GL between residues 144 and 231 and appears to be distinct from the glycogen-binding (storage) site of phosphorylase. The regulatory high-affinity binding site for phosphorylase a lies in the 16 amino acids at the C-terminus of GL. The PP1-binding domain is deduced to comprise the -RVXF- motif [Egloff, Johnson, Moorhead, Cohen and Barford (1997) EMBO J. 16, 1876–1887] located at residues 61–64 of GL and preceding lysine residues at positions 56, 57 and 59. A possible approach for increasing glycogen synthesis in certain disorders is discussed.
4-Hydroxy-2(E)-nonenal enantiomers: (S)-selective inactivation of glyceraldehyde-3-phosphate dehydrogenase and detoxification by rat glutathione S-transferase A4-4
Authors: HIRATSUKA Akira , HIROSE Kenichiro , SAITO Hiroshi , WATABE Tadashi
Published: August 2015

The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase was irreversibly and (S)-selectively inactivated by the enantiomers of racemic 4-hydroxy-2(E)-nonenal (HNE), a reactive product released from biomembranes by lipid peroxidation in cells. Rates of the enzyme inactivations were 1.7, 3.0, and 6.0M-1·s-1 for (R)-, racemic and (S)-HNEs respectively. In rat liver cytosol the HNE was detoxified 2.5-fold more (S)-selectively by GSH conjugation and 2.4-fold more (R)-selectively by NADH-dependent reduction mediated by alcohol dehydrogenase (ADH) than the opposite enantiomers. However, in the cytosol the GSH conjugation of (R)-HNE proceeded at a much higher rate than did its ADH-mediated reduction. The minor glutathione S-transferase (GST) isoform, A4-4, in the rat (r) liver had a major role in the cytosolic (S)-selective GSH conjugation. The catalytic efficiency, kcat/Km, of purified rGSTA4-4 was 4-fold higher for (S)-HNE than for (R)-HNE; the Km was 3-fold higher for (R)-HNE than for (S)-HNE. (S)-HNE was preferentially detoxified to (R)-HNE by rGSTA4-4 when racemic HNE was used as a substrate.
Structure and expression of a novel frizzled gene isolated from the developing mouse gut
Authors: MALIK Talat H. , SHIVDASANI Ramesh A.
Published: August 2015

The Wnt/APC (adenomatous polyposis coli)/β-catenin pathway plays a central role in the pathogenesis of colorectal cancer and probably also in normal development of the gastrointestinal tract. Frizzled proteins function as cell-surface receptors for the Wnt family of extracellular ligands. Many components of the Wnt signalling pathway are expressed widely, and determinants of tissue-specific functions are poorly understood. A better understanding of how Wnt signalling regulates tissue-specific development and gut epithelial homoeostasis requires characterization of the many components of this signalling pathway. We therefore wished to identify frizzled genes with limited tissue distribution of expression and isolated Mfz10, a novel member of the mouse family of frizzled genes, from the developing fetal gut. Highest levels of Mfz10 mRNA are detected throughout late embryonic development, in the brain, heart, lung and digestive tract. In adult mice Mfz10 mRNA is detected at highest levels in the heart, brain and lung. Expression in the adult gastrointestinal tract is much weaker, with higher levels in foregut derivatives (oesophagus and stomach) compared with regions derived from the fetal midgut and hindgut; particularly strong mRNA expression is observed in the squamous epithelium of the oesophagus. The amino acid sequence of Mfz10 is nearly identical to that of human FzE2 (also known as FzD2). Interestingly, mRNA levels of human FzD2 are reported to be up-regulated in oesophageal squamous cell carcinomas. These findings suggest a likely role for Mfz10 in the developing and adult foregut.
Regulation of cyclin-dependent kinase (Cdk) 2 Thr-160 phosphorylation and activity by mitogen-activated protein kinase in late G1 phase
Authors: CHIARIELLO Mario , GOMEZ Eliana , GUTKIND J. Silvio
Published: August 2015

Mitogen-activated protein (MAP) kinases, p42MAPK and p44MAPK, are central components of growth-promoting signalling pathways. However, how stimulation of MAP kinases culminates in cell-cycle progression is still poorly understood. Here we show that mitogenic stimulation of NIH 3T3 cells causes a sustained activation of MAP kinases, which lasts until cells begin progressing through the G1/S boundary. Furthermore, we observed that disruption of the MAP-kinase pathway with a selective MEK (MAP kinase/extracellular-signal-regulated protein kinase kinase) inhibitor, PD98059, prevents the activation of cyclin-dependent kinase (Cdk) 2 and DNA synthesis, even when added during late G1 phase, once the known mechanisms by which MAP kinase controls G1 progression, accumulation of G1 cyclins and degradation of Cdk inhibitors have already taken place. Moreover, we provide evidence indicating that MAP kinases control Cdk2 Thr-160 activating phosphorylation and function, possibly by regulating the activity of a Cdk-activating kinase, thus promoting the re-initiation of DNA synthesis. These findings suggest the existence of a novel mechanism whereby signal-transducing pathways converging on MAP kinases can affect the cell-cycle machinery and, ultimately, participate in cell-growth control.
Evaluation of the role of proline residues flanking the RGD motif of dendroaspin, an inhibitior of platelet aggregation and cell adhesion
Authors: LU Xinjie , SUN Yingqing , SHANG Dazhuang , WATTAM Beth , EGGLEZOU Sofia , HUGHES Tracy , HYDE Eva , SCULLY Mike , KAKKAR Vijay
Published: August 2015

The effect of a panel of proline mutants of dendroaspin, an inhibitor of platelet aggregation and cell adhesion, including A42-dendroaspin, A47-dendroaspin, A49-dendroaspin, A42,47-dendroaspin and A47,49-dendroaspin, was investigated using platelet-aggregation and cell-adhesion assays. Here we show that a single alanine-for-proline substitution did not affect potency when measured as the ability either to inhibit platelet aggregation induced by ADP (IC50 ≈ 170nM) or to block transfected A375-SM cell adhesion to fibrinogen in the presence of Mn2+ as compared with wild-type dendroaspin. By comparison, double proline substitution with alanines significantly reduced the potency in both assays by approx. 5–8-fold. These observations, therefore, suggest that proline residues flanking the RGD motif in dendroaspin and other RGD-containing venom proteins, e.g. disintegrins, may contribute to maintaining a favourable conformation for the solvent-exposed RGD site for its recognition by integrin receptors.
Cloning, expression and localization of human BM88 shows that it maps to chromosome 11p15.5, a region implicated in Beckwith–Wiedemann syndrome and tumorigenesis
Authors: GAITANOU Maria , BUANNE Pasquale , PAPPA Christina , GEORGOPOULOU Niki , MAMALAKI Avgi , TIRONE Felice , MATSAS Rebecca
Published: August 2015

Porcine BM88 is a neuron-specific protein that enhances neuroblastoma cell differentiation in vitro and may be involved in neuronal differentiation in vivo. Here we report the identification, by Western blotting, of homologous proteins in human and mouse brain and the isolation of their respective cDNAs. Several human and mouse clones were identified in the EST database using porcine BM88 cDNA as a query. A human and a mouse EST clone were chosen for sequencing and were found both to predict a protein of 149 amino acids, with 79.9% reciprocal identity, and 76.4% and 70.7% identities to the porcine protein, respectively. This indicated that the clones corresponded to the human and mouse BM88homologues. In vitro expression in a cell-free system as well as transient expression in COS7 cells yielded polypeptide products that were recognized by anti-BM88 antibodies and were identical in size to the native BM88 protein. Northern-blot analysis showed a wide distribution of the gene in human brain whereas immunohistochemistry on human brain sections demonstrated that the expression of BM88 is confined to neurons. The initial mapping assignment of human BM88 to chromosome 11p15.5, a region implicated in Beckwith–Wiedemann syndrome and tumorigenesis, was retrieved from the UniGene database maintained at the National Centre for Biotechnology Information (NCBI, Bethesda, MD, U.S.A.). We confirmed this localization by performing fluorescence in situ hybridization on BM88-positive cosmid clones isolated from a human genomic library. These results suggest that BM88 may be a candidate gene for genetic disorders associated with alterations at 11p15.5.

Sequence data for the human and mouse BM88 cDNAs have been deposited in the EMBL/GenBank Nucleotide Sequence Databases under accession numbers AF235030 and AF243130, respectively.
Inhibitory effects of acidic phospholipids on the binding of origin-recognition complex to origin DNA
Authors: LEE Jong-Ryul , MAKISE Masaki , TAKENAKA Hitomi , TAKAHASHI Naoko , YAMAGUCHI Yoshihiro , TSUCHIYA Tomofusa , MIZUSHIMA Tohru
Published: August 2015

Origin-recognition complex (ORC), a candidate initiator of chromosomal DNA replication in eukaryotes, shares certain biochemical characteristics with DnaA, the initiator of chromosomal DNA replication in prokaryotes. These similarities include origin-specific DNA binding, ATP binding and ATPase activity. DnaA interacts with acidic phospholipids, such as cardiolipin, and its activity is regulated by these phospholipids. In this study, we examined whether Saccharomyces cerevisiae ORC also interacts with phospholipids. Among the various phospholipids tested, ORC was found to bind specifically to cardiolipin. This binding was inhibited by excess concentrations of salts but unaffected by ATP, adenosine 5′-[γ-thio]triphosphate or the origin DNA. Cardiolipin weakly inhibited the ATP-binding activity of ORC, whereas it strongly inhibited ORC binding to origin DNA. Acidic phospholipids other than cardiolipin (phosphatidylglycerol and phosphatidylinositol) weakly inhibited ORC binding to origin DNA. Furthermore, total phospholipids extracted from yeast nuclear membranes inhibited ORC binding to origin DNA. We consider that phospholipids may modulate initiation of DNA replication in eukaryotes in a similar manner to that found in prokaryotes.
Identification of an initiator-like element essential for the expression of the tissue inhibitor of metalloproteinases-4 (Timp-4) gene
Authors: YOUNG David A. , PHILLIPS Blaine W. , LUNDY Caroline , NUTTALL Robert K. , HOGAN Aileen , SCHULTZ Gilbert A. , LECO Kevin J. , CLARK Ian M. , EDWARDS Dylan R.
Published: August 2015

We have used real-time quantitative reverse transcriptase PCR (TaqMan®) to quantify the expression of the four tissue inhibitor of metalloproteinases (Timp) genes in mouse tissues during development and in the adult. Among the four Timp genes, Timp-4 shows the most restricted pattern of expression, with highest RNA levels in brain, heart and testes. These data indicate that in the brain, Timp-4 transcripts are temporally regulated during development, becoming more abundant than those of the other Timps after birth. Cloning of the Timp-4 gene confirmed a five-exon organization resembling that of Timp-2 and Timp-3, and like all Timps, Timp-4 is located within an intron of a synapsin gene. Ribonuclease protection analysis and 5′-rapid amplification of cDNA ends PCR identified multiple transcription starts for Timp-4 from brain and heart mRNA. The promoter region of Timp-4 was functional in transient transfection analysis in mouse C3H10T1/2 fibroblasts, where it directed basal expression that was non-inducible by serum. The TATA-less promoter contains consensus motifs for Sp1 and an inverted CCAAT box upstream of an initiator-like element that is in close proximity to a transcription start site. Mutation of the CCAAT box caused a 2-fold increase in reporter expression. More significantly, mutation of the Sp1 motif or initiator-like element almost completely abolished reporter expression. This first functional characterization of the Timp-4 promoter shows it to be distinct from other members of the Timp family and provides insights into potential mechanisms controlling the tight spatio-temporal expression pattern of the gene.
Regulated intramembrane proteolysis: from the endoplasmic reticulum to the nucleus
Authors: Rawson Robert B
Published: August 2015

Regulated intramembrane proteolysis (Rip) is an ancient and widespread process by which cells transmit information from one compartment (the endoplasmic reticulum) to another (the nucleus). Two separate cleavages that are carried out by two separate proteases are required for Rip. The first protease cleaves its protein substrate within an extracytoplasmic domain; the second cleaves it within a membrane-spanning domain, releasing a functionally active fragment of the target protein. In eukaryotes, examples of Rip can be divided into two classes, according to the proteases that are involved and the orientation of the substrates with the membrane. Class 1 Rip involves type 1 transmembrane proteins and requires presenilin for cleavage within a membrane-spanning domain. In Class 2 Rip, the highly hydrophobic metalloprotease, site-2 protease, is required for cleavage within a membrane-spanning domain and substrates are type 2 transmembrane proteins. Both classes of Rip are implicated in diseases that are important in modern societies, such as hyperlipidaemias (via the sterol regulatory element binding protein pathway) and Alzheimer's disease (via processing of the amyloid precursor protein.)
Nitric oxide and reactive oxygen species in vascular injury
Authors: Rubbo Homero , Tarpey Margaret , Freeman Bruce A.
Published: August 2015

Nitric oxide (.NO), a free radical species produced by several mammalian cell types, plays a role in regulation of vascular, neurological and immunological signal transduction and function. The role of .NO in cytotoxic events is acquiring increased significance. The high rate of production and broad distribution of sites of production of .NO, combined with its facile direct and indirect reactions with metalloproteins, thiols and various oxygen radical species, assures that .NO will play a central role in regulating vascular, physiological and cellular homoeostasis, as well as critical intravascular free radical and oxidant reactions. At the same time, there are contradictions as to whether .NO mediates or limits free-radical-mediated tissue injury, and uncertainty regarding its mechanisms of action. .NO has been portrayed as a pathogenic mediator during ischaemia-reperfusion, and inflammatory and septic tissue injury. In contrast, cell-, metal- and oxidant-induced lipoprotein oxidation events, as well as hepatic, cerebrovascular, pulmonary and myocardial inflammatory and ischaemia-reperfusion injury studies, show convincingly that stimulation of endogenous .NO production or exogenous administration of .NO-donating molecules can serve a protective role by inhibition of often oxidant-related mechanisms. The final outcome of toxic versus tissue-protective reactions of .NO will depend on several factors, including sites and relative concentrations of individual reactive species and their diffusion distances. The following sections address these issues and conclude with a proposal as to how .NO serves as a central regulator of oxidant reactions and diverse free radical-related disease processes.
Meprin proteolytic complexes at the cell surface and in extracellular spaces
Authors: Villa James P. , Bertenshaw Greg P. , Bylander John E. , Bond Judith S.
Published: August 2015

Meprins are metalloproteinases of the astacin family and metzincin superfamily that are composed of evolutionarily related α and ϐ subunits, which exist as homo- and hetero-oligomeric complexes. These complexes are abundant at the brush border membranes of kidney proximal tubule cells and epithelial cells of the intestine, and are also expressed in certain leucocytes and cancer cells. Meprins cleave bioactive peptides such as gastrin, cholecystokinin and parathyroid hormone, cytokines such as osteopontin and monocyte chemotactic peptide-1, as well as proteins such as gelatin, collagen IV, fibronectin and casein. Database predictions and initial data indicate that meprins are also capable of shedding proteins, including itself, from the cell surface. Membrane-bound meprin subunits are composed of dimeric meprin ϐ subunits or tetrameric hetero-oligomeric αϐ complexes of approx. 200-400 kDa, and can be activated at the cell surface; secreted forms of homo-oligomeric meprin α are zymogens that form high-molecular-mass complexes of 1-6 MDa. These are among the largest extracellular proteases identified thus far. The latent (self-associating) homo-oligomeric complexes can move through extracellular spaces in a non-destructive manner, and deliver a concentrated form of the metalloproteinase to sites that have activating proteases, such as sites of inflammation, infection or cancerous growth. Meprins provide examples of novel ways of concentrating proteolytic activity at the cell surface and in the extracellular milieu, which may be critical to proteolytic function.
Antioxidant and cytoprotective responses to redox stress
Authors: Mathers Joanne , Fraser Jennifer A. , McMahon Michael , Saunders Robert D. C. , Hayes John D. , McLellan Lesley I.
Published: August 2015

Aerobic cells produce reactive oxygen species as a consequence of normal cellular metabolism, and an array of antioxidant systems are in place to maintain the redox balance. When the redox equilibrium of the cell is upset by pro-oxidant environmental stimuli, adaptive responses to the redox stress take place, which can result in up-regulation of antioxidant proteins and detoxification enzymes. Over the past few years, it has become apparent that members of the CNC (cap 'n' collar)-basic leucine zipper family of transcription factors are principal mediators of defensive responses to redox stress. In mammals, the CNC family members nuclear factor-erythroid 2 p45-related factors 1 and 2 (Nrf1 and Nrf2) have been shown to be involved in the transcriptional up-regulation of cytoprotective genes including those encoding glutamate cysteine ligase, NAD(P)H:quinone oxidoreductase, glutathione S-transferases and aldo-keto reductases. An evolutionarily conserved system exists in Caenorhabditis elegans, and it is possible that Drosophila melanogaster may also utilize CNC transcription factors to induce antioxidant genes in response to pro-oxidant chemicals. The advent of microarray and proteomic technologies has advanced our understanding of the gene batteries regulated by oxidative insult, but has highlighted the complexity of gene regulation by environmental factors. This review focuses on the antioxidant response to environmental stress, and the impact that microarrays and proteomics have made in this field.
The role of microtubules in transport between the endoplasmic reticulum and Golgi apparatus in mammalian cells.
Authors: Palmer Krysten J. , Watson Peter , Stephens David J.
Published: August 2015

The organization of intracellular compartments and the transfer of components between them are central to the correct functioning of mammalian cells. Proteins and lipids are transferred between compartments by the formation, movement and subsequent specific fusion of transport intermediates. These vesicles and membrane clusters must be coupled to the cytoskeleton and to motor proteins that drive motility. Anterograde ER (endoplasmic reticulum)-to-Golgi transport, and the converse step of retrograde traffic from the Golgi to the ER, are now known to involve coupling of membranes to the microtubule cytoskeleton. Here we shall discuss our current understanding of the mechanisms that link membrane traffic in the early secretory pathway to the microtubule cytoskeleton in mammalian cells. Recent data have also provided molecular detail of functional co-ordination of motor proteins to specify directionality, as well as mechanisms for regulating motor activity by protein phosphorylation.
Membrane traffic to and from lysosomes.
Authors: Luzio J. Paul , Pryor Paul R. , Gray Sally R. , Gratian Matthew J. , Piper Robert C. , Bright Nicholas A.
Published: August 2015

In the late endocytic pathway, it has been proposed that endocytosed macromolecules are delivered to a proteolytic environment by 'kiss-and-run' events or direct fusion between late endosomes and lysosomes. To test whether the fusion hypothesis accounts for delivery to lysosomes in living cells, we have used confocal microscopy to examine content mixing between lysosomes loaded with rhodamine-dextran and endosomes subsequently loaded with Oregon-Green-dextran. Both kissing and explosive fusion events were recorded. Data from cell-free content-mixing assays have suggested that fusion is initiated by tethering, which leads to formation of a trans-SNARE (soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor) protein complex and then release of lumenal Ca2+, followed by membrane bilayer fusion. We have shown that the R-SNARE (arginine-containing SNARE) protein VAMP (vesicle-associated membrane protein) 7 is necessary for heterotypic fusion between late endosomes and lysosomes, whereas a different R-SNARE, VAMP 8 is required for homotypic fusion of late endosomes. After fusion of lysosomes with late endosomes, lysosomes are re-formed from the resultant hybrid organelles, a process requiring condensation of content and the removal/recycling of some membrane proteins.
Investigations of the modular structure of bacterial promoters
Authors: Miroslavova Nora S. , Busby Stephen J.W.
Published: August 2015

Bacterial RNA polymerase holoenzyme carries different determinants that contact different promoter DNA sequence elements. These contacts are essential for the recognition of promoters prior to transcript initiation. Here, we have investigated how active promoters can be built from different combinations of elements. Our results show that the contribution of different contacts to promoter activity is critically dependent on the overall promoter context, and that certain combinations of contacts can hinder transcription initiation.
MOZ fusion proteins in acute myeloid leukaemia
Authors: Troke Philip J.F. , Kindle Karin B. , Collins Hilary M. , Heery David M.
Published: August 2015

MOZ (monocytic leukaemia zinc finger protein; also known as ZNF220 or MYST3) is a member of the MYST family of protein acetyltransferases. Chromosomal translocations involving the MOZ gene are associated with AML (acute myeloid leukaemia), suggesting that it has a role in haematopoiesis. Recurrent reciprocal translocations fuse the MOZ gene [or the gene encoding MORF (MOZ-related factor); also known as MYST4] to genes encoding the nuclear receptor co-activators CBP [CREB (cAMP response element-binding protein)-binding protein], p300 or the p160 protein TIF2 (transcription intermediary factor 2). The resulting fusion proteins can transform haematopoietic progenitors in vitro, and induce myeloproliferative disease in mice. Recent insights into the molecular mechanisms underlying these effects indicate that MOZ fusion proteins interfere with the activities of transcription factors such as nuclear receptors, p53 and Runx proteins. Our studies suggest that subverting the function of cellular CBP and p300 proteins may play a key role in this process. Here we review the recent progress in understanding the role of MOZ fusion proteins in the aetiology of AML.
Flower colour and visitation rates of Costus arabicus support the ‘bee avoidance’ hypothesis for red‐reflecting hummingbird‐pollinated flowers
Authors: Bergamo Pedro J. , Rech André R. , Brito Vinícius L. G. , Sazima Marlies
Published: August 2015

Floral colour mediates plant–pollinator interactions by often signalling floral resources. In this sense, hummingbird‐pollinated flowers are frequently red‐coloured, and there are two tentative hypotheses to explain this pattern: 1. hummingbirds are attracted to red due its easier detection and 2. bees are sensorially excluded from red flowers. The second hypothesis is based on bees’ red colour blindness, which lead them to be less frequent and less important than hummingbirds as pollinators of red‐reflecting flowers.

Here, we untangled the role of different flower traits mediating plant–pollinator interactions and empirically tested the above hypotheses. We chose Costus arabicus due to its synchronopatric white‐ and pink‐flowered individuals and its bee and hummingbird pollination system. Although pink flowers are not totally achromatic as pure red ones, they show an achromaticity degree that could drive bee exclusion. Specifically, we tested whether differences on red reflectance work attracting hummingbirds or excluding bees and the consequent implications for the plant's reproduction.

Flower colour morphs of C. arabicus do differ neither in morphology nor in nectar sugar content. Moreover, white and pink flowers can be discriminated by the bees’ and hummingbirds’ colour vision system. Both groups are able to discriminate the red colour variation morph on the flower petals, the white flowers being more easily detected by bees and the pink flowers by hummingbirds. Bees preferentially visited the white flowers, whereas hummingbirds visited both colours at the same rate – both patterns corroborating the second hypothesis.

Pollen loads deposited on stigmas did not differ between flower colour morphs, indicating that bees and hummingbirds play a similar role in the overall pollen deposition. However, bees are more likely to self‐pollinate than hummingbirds. Self‐pollination limits C. arabicus reproduction, and red‐reflecting flowers may be better pollinated by discouraging bee visitation. Therefore, the intraspecific colour variation is driving flowers to show colour‐related different levels of generalization.

Our results support the ‘bee avoidance’ rather than the ‘hummingbird preference’ hypothesis. Sensory exclusion of bees seems to be the pressure for red‐reflecting flowers evolution, driving specialization in hummingbird‐pollinated flowers due to the costs of bee pollination on plant reproduction.
Palate Shape and Depth: A Shape‐Matching and Machine Learning Method for Estimating Ancestry from Human Skeletal Remains
Authors: Maier Christopher A. , Zhang Kang , Manhein Mary H. , Li Xin
Published: August 2015

In the past, assessing ancestry relied on the naked eye and observer experience; however, replicability has become an important aspect of such analysis through the application of metric techniques. This study examines palate shape and assesses ancestry quantitatively using a 3D digitizer and shape‐matching and machine learning methods. Palate curves and depths were recorded, processed, and tested for 376 individuals. Palate shape was an accurate indicator of ancestry in 58% of cases. Cluster analysis revealed that the parabolic, hyperbolic, and elliptical shapes are discrete from one another. Preliminary results indicate that palate depth in Hispanic individuals is greatest. Palate shape appears to be a useful indicator of ancestry, particularly when assessed by a computer. However, these data suggest that palate shape is not useful for assessing ancestry in Hispanic individuals. Although ancestry may be determined from palate shape, the use of multiple features is recommended and more reliable.
Mining for Murder‐Suicide: An Approach to Identifying Cases of Murder‐Suicide in the National Violent Death Reporting System Restricted Access Database
Authors: McNally Matthew R. , Patton Christina L. , Fremouw William J.
Published: August 2015

The National Violent Death Reporting System (NVDRS) is a United States Centers for Disease Control and Prevention (CDC) database of violent deaths from 2003 to the present. TheNVDRScollects information from 32 states on several types of violent deaths, including suicides, homicides, homicides followed by suicides, and deaths resulting from child maltreatment or intimate partner violence, as well as legal intervention and accidental firearm deaths. Despite the availability of data from police narratives, medical examiner reports, and other sources, reliably finding the cases of murder‐suicide in theNVDRShas proven problematic due to the lack of a unique code for murder‐suicide incidents and outdated descriptions of case‐finding procedures from previous researchers. By providing a description of the methods used to access to theNVDRSand coding procedures used to decipher these data, the authors seek to assist future researchers in correctly identifying cases of murder‐suicide deaths while avoiding false positives.
Detection of Traces of Ovalbumin and Casein in White and Red Wines by Quantitative Western Blotting
Authors: Meyer Philippe , Zanetti Simone
Published: August 2015

Fining of wine with agents containing cow's milk or hen's egg white is a common and traditional procedure. In light of increasing food allergies all over the world, the presence of fining residues has been subject of intense debate. Switzerland does not make exception, and since 2009 the Federal Department of Home Affairs has modified its food regulations stating that the labels must show if traces of fining agents are present. Nevertheless, the application of this regulation is not based on an official analytical method. In this study we show that immunoblotting is an efficient technique to detect and quantify ovalbumin and casein residues in bottled wine. We showed that final filtration is an essential step to remove finings in red wine, and that overfining of white wine may result in fining residues in finished products. Finally, for the first time in Switzerland, 22 samples were taken by food safety inspectors and officially analyzed for the regional food control authority of the Canton of Vaud. These samples were allergen free, but a larger study is currently planned in collaboration with other regional authorities of Switzerland to complete these results and make a complete picture of the Swiss wine production.
Pathway Analysis for RNA-Seq Data Using a Score-Based Approach
Authors: Zhou Yi-Hui
Published: August 2015

A variety of pathway/gene-set approaches have been proposed to provide evidence of higher-level biological phenomena in the association of expression with experimental condition or clinical outcome. Among these approaches, it has been repeatedly shown that resampling methods are far preferable to approaches that implicitly assume independence of genes. However, few approaches have been optimized for the specific characteristics of RNA-Seq transcription data, in which mapped tags produce discrete counts with varying library sizes, and with potential outliers or skewness patterns that violate parametric assumptions. We describe transformations to RNA-Seq data to improve power for linear associations with outcome and flexibly handle normalization factors. Using these transformations or alternate transformations, we apply recently developed null approximations to quadratic form statistics for both self-contained and competitive pathway testing. The approach provides a convenient integrated platform for RNA-Seq pathway testing. We demonstrate that the approach provides appropriate type I error control without actual permutation and is powerful under many settings in comparison to competing approaches. Pathway analysis of data from a study of F344 vs. HIV1Tg rats, and of sex differences in lymphoblastoid cell lines from humans, strongly supports the biological interpretability of the findings.
Editorial: Evidence‐guided interventions and optimising outcomes in routine clinical care of children and young people's mental health
Authors: Sayal Kapil
Published: August 2015

This Editorial reflects on several articles in this issue of the journal that focus on evidence‐based interventions in routine clinical care. In particular, it highlights the approaches advocated in the review by Bearman & Weisz into overcoming barriers to the implementation of research findings into routine clinical care: conceptually unified treatments that acknowledge the overlap and comorbidity between presenting problems; modular approaches to co‐ordinate and combine treatment approaches to improve the fit for young people presenting with multiple problems; and approaches to monitoring and feedback of progress and outcomes to aid clinical review and decision‐making. Issues of access, stigma and measurement of meaningful outcomes in routine clinical practice are also considered.
An Image Degradation Model for Depth‐augmented Image Editing
Authors: Hennessey James W. , Mitra Niloy J.
Published: August 2015

Images remain the most popular medium to capture our surroundings. Although significant advances have been made in developing image editing tools, the key challenge is to intelligently account for missing depth information. The growing popularity of depth images offers a new avenue to revisit image editing tasks. In this work, we investigate how even coarse depth information can be exploited to address some of the fundamental challenges in image editing namely producing correct perspective, handling occlusion, and obtaining segmentation. To this end, we propose a novel image degradation model that predicts how well an image edit can be performed in presence of coarse depth information. Technically, we create proxy geometry to summarize available depth information, and use it to predict occlusions and ordering between image patches, complete occluded regions, and anticipate image‐level changes under camera movement. We evaluate the proposed image degradation model in the context of parallax photography from single depth images.
Risks and benefits in treatment of mediastinal abscess by endobronchial ultrasound‐guided transbronchial needle aspiration
Authors: Tian Lei , Krimsky William S. , Wu Qingchen , Sun Jiayuan
Published: August 2015

Introduction: Mediastinal abscess is a fatal condition, treatment of mediastinal abscess is with antibiotics and sometimes surgery for debridement and drainage. Endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) is a safe assessment and candidate treatment method of mediastinal lesions.

Objectives: This study aimed to HYPERLINK “javascript:void(0);” discuss risks and benefits in treatment of mediastinal abscess by EBUS‐TBNA.

Methods: We noticed a 56‐year‐old man with developed bilateral pneumonia and sepsis after puncture of mediastinal abscess by EBUS‐TBNA. The patient was successfully treated with a combination of systemic anti‐infection treatment and intracavitary administration of antibiotics, antifungal and repeated drainage and lavage via EBUS‐TBNA, in 1 year follow‐up without recurrence.

Results: This study indicated infection spread risk of mediastinal abscess after EBUS‐TBNA, and mediastinal abscess was successfully cured by combination of systemic anti‐infection and local intervention through EBUS‐TBNA.

Conclusion: EBUS‐TBNA is a potential effective minimally invasive treatment for mediastinal abscess, and it is necessary to be aware of clinical complications after puncture of mediastinal infectious lesions by EBUS‐TBNA.
Principles of cooperation across systems: from human sharing to multicellularity and cancer
Authors: Aktipis Athena
Published: August 2015

From cells to societies, several general principles arise again and again that facilitate cooperation and suppress conflict. In this study, I describe three general principles of cooperation and how they operate across systems including human sharing, cooperation in animal and insect societies and the massively large‐scale cooperation that occurs in our multicellular bodies. The first principle is that of Walk Away: that cooperation is enhanced when individuals can leave uncooperative partners. The second principle is that resource sharing is often based on the need of the recipient (i.e., need‐based transfers) rather than on strict account‐keeping. And the last principle is that effective scaling up of cooperation requires increasingly sophisticated and costly cheater suppression mechanisms. By comparing how these principles operate across systems, we can better understand the constraints on cooperation. This can facilitate the discovery of novel ways to enhance cooperation and suppress cheating in its many forms, from social exploitation to cancer.
Extended Sex: An Account of Sex for a More Just Society
Authors: Ayala Saray , Vasilyeva Nadya
Published: August 2015

We propose an externalist understanding of sex that builds upon extended and distributed approaches to cognition, and contributes to building a more just, diversity‐sensitive society. Current sex categorization practices according to the female/male dichotomy are not only inaccurate and incoherent (attributing nonreproductive properties to differences in vaguely defined reproductive roles), but they also ground moral and political pressures that harm and oppress people. We argue that a new understanding of sex is due, an understanding that would acknowledge the variability and, most important, the flexibility of sex properties, as well as the moral and political meaning of sex categorization. We propose an externalist account of sex, elaborating on extended and distributed approaches to cognition that capitalize on the natural capacity of organisms to couple with environmental resources. We introduce the notion of extended sex, and argue that properties relevant for sex categorization are neither exclusively internal to the individual skin, nor fixed. Finally, we spell out the potential of extended sex to support an active defense of diversity and an intervention against sex‐based discrimination.
A software tool for tomographic axial superresolution in STED microscopy
Authors: KOHO S. , DEGUCHI T. , HÄNNINEN P. E.
Published: August 2015

A method for generating three‐dimensional tomograms from multiple three‐dimensional axial projections in STimulated Emission Depletion (STED) superresolution microscopy is introduced. Our STED< method, based on the use of a micromirror placed on top of a standard microscopic sample, is used to record a three‐dimensional projection at an oblique angle in relation to the main optical axis. Combining the STED< projection with the regular STED image into a single view by tomographic reconstruction, is shown to result in a tomogram with three‐to‐four‐fold improved apparent axial resolution. Registration of the different projections is based on the use of a mutual‐information histogram similarity metric. Fusion of the projections into a single view is based on Richardson‐Lucy iterative deconvolution algorithm, modified to work with multiple projections. Our tomographic reconstruction method is demonstrated to work with real biological STED superresolution images, including a data set with a limited signal‐to‐noise ratio (SNR); the reconstruction software (SuperTomo) and its source code will be released under BSD open‐source license.