bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changing nucleosome positions in vivo through modification of the DNA rotational information
Authors: DI MARCOTULLIO Lucia , BUTTINELLI Memmo , COSTANZO Giovanna , DI MAURO Ernesto , NEGRI Rodolfo 
Published: August 2015

The effects of the rotational information of DNA in determining the in vivolocalization of nucleosomal core particles (ncps) have been studied in the Saccharomyces cerevisiae5 S rRNA repeat gene. The distribution of the phased series of flexibility signals present in this DNA has been altered by inserting in its centre a 25 bp tract. The effects of such alteration on the in vivodistribution of the helically phased, alternatively located ncps have been determined relative to a reference 21 bp insertion mutant. The results show that the answers provided in vitroand in vivoby the yeast 5 S rRNA gene sequence to specific modifications of the DNA rotational frame are similar, thus pointing to the relevance of DNA rotational information in vivo.
Thrombin stimulates fibroblast procollagen production via proteolytic activation of protease-activated receptor 1
Authors: CHAMBERS Rachel C. , DABBAGH Karim , McANULTY Robin J. , GRAY Andy J. , BLANC-BRUDE Olivier P. , LAURENT Geoffrey J. 
Published: August 2015

Thrombin is a multifunctional serine protease that has a crucial role in blood coagulation. It is also a potent mesenchymal cell mitogen and chemoattractant and might therefore have an important role in the recruitment and local proliferation of mesenchymal cells at sites of tissue injury. We hypothesized that thrombin might also affect the deposition of connective tissue proteins at these sites by directly stimulating fibroblast procollagen production. To address this hypothesis, the effect of thrombin on procollagen production and gene expression by human foetal lung fibroblasts was assessed over 48 h. Thrombin stimulated procollagen production at concentrations of 1 nM and above, with maximal increases of between 60% and 117% at 10 nM thrombin. These effects of thrombin were, at least in part, due to increased steady-state levels of α1(I) procollagen mRNA. They could furthermore be reproduced with thrombin receptor-activating peptides for the protease-activated receptor 1 (PAR-1) and were completely abolished when thrombin was rendered proteolytically inactive with the specific inhibitors d-Phe-Pro-ArgCH2Cl and hirudin, indicating that thrombin is mediating these effects via the proteolytic activation of PAR-1. These results suggest that thrombin might influence the deposition of connective tissue proteins during normal wound healing and the development of tissue fibrosis by stimulating fibroblast procollagen production.
Targeting and assembly of the oxoglutarate carrier: general principles for biogenesis of carrier proteins of the mitochondrial inner membrane
Authors: PALMISANO Annamaria , ZARA Vincenzo , HÖNLINGER Angelika , VOZZA Angelo , DEKKER Peter J. T. , PFANNER Nikolaus , PALMIERI Ferdinando 
Published: August 2015

We have studied the targeting and assembly of the 2-oxoglutarate carrier (OGC), an integral inner-membrane protein of mitochondria. The precursor of OGC, synthesized without a cleavable presequence, is transported into mitochondria in an ATP- and membrane potential-dependent manner. Import of the mammalian OGC occurs efficiently into both mammalian and yeast mitochondria. Targeting of OGC reveals a clear dependence on the mitochondrial surface receptor Tom70 (the 70 kDa subunit of the translocase of the outer mitochondrial membrane), whereas a cleavable preprotein depends on Tom20 (the 20 kDa subunit), supporting a model of specificity differences of the receptors and the existence of distinct targeting pathways to mitochondria. The assembly of minute amounts of OGC imported in vitro to the dimeric form can be monitored by blue native electrophoresis of digitonin-lysed mitochondria. The assembly of mammalian OGC and fungal ADP/ATP carrier occurs with high efficiency in both mammalian and yeast mitochondria. These findings indicate a dynamic behaviour of the carrier dimers in the mitochondrial inner membrane and suggest a high conservation of the assembly reactions from mammals to fungi.
Identification of the lectin-like receptor for oxidized low-density lipoprotein in human macrophages and its potential role as a scavenger receptor
Authors: YOSHIDA Hiroshi , KONDRATENKO Nonna , GREEN Simone , STEINBERG Daniel , QUEHENBERGER Oswald 
Published: August 2015

A new receptor for oxidized low-density lipoprotein (LDL), lectin-like oxidized LDL receptor-1 (LOX-1), has recently been cloned from bovine endothelial cells and human lung. A limited tissue-distribution study suggested that the protein was mainly produced by the vascular endothelium. In the present study we demonstrate that LOX-1 is also expressed in macrophages, where it may function as a scavenger receptor. LOX-1 was not detected in undifferentiated THP-1 cells or in freshly isolated human blood monocytes. However, mature human monocyte-derived macrophages and differentiated THP-1 cells showed high levels of LOX-1 transcripts. Consistent with these results, immunofluorescence staining and FACS analysis demonstrated that LOX-1 protein is expressed on the plasma membrane of macrophages. Western-blot analysis of membranes from macrophages (but not those from monocytes) identified a single band, with an apparent molecular mass of about 40 kDa, that displayed oxidized LDL-binding activity. These results suggest that differentiation induces the expression of LOX-1 in macrophages, where it may play a role as a scavenger receptor and/or a receptor for oxidized LDL.
Determinants of catalytic activity with the use of purified I, D and H subunits of the magnesium protoporphyrin IX chelatase from Synechocystis PCC6803
Authors: JENSEN Poul E. , GIBSON Lucien C. D. , HUNTER C. Neil 
Published: August 2015

The I, D and H subunits (ChlI, ChlD and ChlH respectively) of the magnesium protoporphyrin IX chelatase from Synechocystis have been purified to homogeneity as a result of the overexpression of the encoding genes in Escherichia coli and the production of large quantities of histidine-tagged proteins. These subunits have been used in an initial investigation of the biochemical and kinetic properties of the enzyme. The availability of pure ChlI, ChlD and ChlH has allowed us to estimate the relative concentrations of the three protein components required for optimal activity, and to investigate the dependence of chelatase activity on the concentrations of MgCl2, ATP and protoporphyrin IX. It was found that, whereas ChlD and ChlH are likely to be monomeric, ChlI can aggregate in an ATP-dependent manner, changing from a dimeric to an octameric structure. Subunit titration assays suggest an optimal ratio of ChlI, ChlD and ChlH of 2:1:4 respectively. However, the dependence of chelatase activity on increasing concentrations of ChlI and ChlH with respect to ChlD suggests that these two subunits, at least in vitro, behave as substrates in their interaction with ChlD. Mg chelation could not be detected unless the Mg2+ concentration exceeded the ATP concentration, suggesting at least two requirements for Mg2+, one as a component of MgATP2-, the other as the chelated metal. The steady-state kinetic parameters were determined from continuous assays; the Km values for protoporphyrin, MgCl2 and ATP were 1.25 µM, 4.9 mM and 0.49 mM respectively. The rate dependence of Mg2+ was clearly sigmoidal with a Hill coefficient of 3, suggesting positive co-operativity. Initiating the reaction by the addition of one of the substrates in these continuous assays resulted in a significant lag period of at least 10 min before the linear production of Mg protoporphyrin. This lag was significantly decreased by preincubating ChlI and ChlD with ATP and MgCl2, and by mixing it with ChlH that had been preincubated with protoporphyrin IX, ATP and MgCl2. This suggests not only a close MgATP2--dependent interaction between ChlI and ChlD but also an interaction between ChlH and the protoporphyrin substrate that also is stimulated by ATP and MgCl2.
Inactivation of eukaryotic initiation factor 2B in vitro by heat shock
Authors: SCHEPER Gert C. , THOMAS Adri A. M. , WIJK van Roel 
Published: August 2015

Protein synthesis in rat H35 Reuber hepatoma cells is rapidly inhibited on heat shock. At mild heat-shock temperatures the main cause for inhibition is the inactivation of the guanine nucleotide exchange factor eukaryotic initiation factor 2B (eIF2B); under more severe heat-shock conditions the activity of several initiation factors is compromised. eIF2B is required for GDP/GTP exchange on eIF2, which delivers methionyl-tRNA to the 40 S ribosomal subunit. We have tried to elucidate the mechanism underlying the inactivation of eIF2B by assays in vitro. Incubation of cell extracts at 41 °C or higher led to the inactivation of eIF2B. In agreement with observations in cells exposed to mild heat shocks, the thermal inactivation of eIF2B could be ascribed to neither eIF2α phosphorylation nor the induction of another inhibitor. With the use of glycerol gradients we show that eIF2B forms aggregates in heat-treated extracts. Furthermore eIF2B activity is protected against heat shock in thermotolerant cells. Taken together, these results suggest a role for chaperones in the control of eIF2B activity.
Neuropeptide regulation of biosynthesis of the juvenoid, methyl farnesoate, in the edible crab, Cancer pagurus
Authors: WAINWRIGHT Geoffrey , WEBSTER Simon G. , REES Huw H. 
Published: August 2015

The neuropeptide mandibular organ (MO)-inhibiting hormone (MO-IH), synthesized and secreted from the X-organ-sinus-gland complex of the eyestalk, regulates the biosynthesis of the putative crustacean juvenile hormone, methyl farnesoate (MF). Using radiolabelled acetate as a precursor for isoprenoid biosynthesis, farnesoic acid (FA), farnesol, farnesal, MF and geranyl geraniol were detected in MOs cultured for 24 h. Treatment of MOs with extract of sinus gland inhibited the final step of biosynthesis of MF, catalysed by FA O-methyltransferase. Additionally, treatment of MOs with purified MO-IH exhibited a dose-dependent inhibition of this final step of MF synthesis. The extent of this inhibition was dependent on the ovary stage of the MO-donor animal, being maximal in MOs from animals in the early stages of ovarian development. Assay of FA O-methyltransferase activity, using [3H]FA in the presence of S-adenosyl-l-methionine, demonstrated that the enzyme was located in the cytosolic fraction of MOs and was inhibited by incubation of MOs with MO-IH prior to preparation of subcellular fractions. For cytosolic preparations taken from vitellogenic animals, both Vmax and Km were appreciably lower than for those taken from non-vitellogenic animals. Conversely, eyestalk ablation of early-vitellogenic animals, which removes the source of MO-IH in vivo, resulted in enhancement of the cytosolic FA O-methyltransferase activity. Although both Vmax and Km show an appreciable increase upon eyestalk ablation, the increased enzyme activity is probably reflected by the fact that Vmax/Km (an approximate indication of kcat) has increased 5-fold. The combined evidence demonstrates that MO-IH inhibits FA O-methyltransferase, the enzyme which catalyses the final step of MF biosynthesis in MOs.
Voltammetric studies of the reactions of iron–sulphur clusters ([3Fe-4S] or [M3Fe-4S]) formed in Pyrococcus furiosus ferredoxin
Authors: FAWCETT Sarah E. J. , DAVIS David , BRETON Jacques L. , THOMSON Andrew J. , ARMSTRONG Fraser A. 
Published: August 2015

Reactions of the [3Fe-4S] cluster and various metallated [M3Fe-4S] adducts co-ordinated in the ferredoxin from the hyperthermophile Pyrococcus furiosus have been studied by protein-film voltammetry, bulk-solution voltammetry, solution kinetics and magnetic CD (MCD). The [3Fe-4S] cluster exhibits two couples, [3Fe-4S]+/0 and [3Fe-4S]0/2-. Film voltammetry is possible over a wide pH range (2–8), revealing that the [3Fe-4S]+/0 couple shows a complex pH dependence with pKred1 = 2.8, pKox = 4.9 and pKred2 = 6.7. From MCD, pKred1 corresponds with protonation of [3Fe-4S]0 to give a spectroscopically distinct species, as reported for ferredoxins from Azotobacterand Sulfolobus. The status of the disulphide/disulphydryl entity makes no significant difference to the data (given for the -S-S- form). Formation of the hyper-reduced [3Fe-4S]2- state is observed, requiring 3H+ for the overall 3e- reduction of [3Fe-4S]+, the change therefore being electroneutral. By comparison with the ferredoxin from Desulfovibrio africanus, uptake of Fe(II) and other M(II) by [3Fe-4S]0 to give [M3Fe-4S] clusters is slow (t1/2 &gt; 10 min at room temperature, slower still if the protein is adsorbed on the electrode), whereas reaction with Tl(I) to produce [Tl3Fe-4S] is very rapid (t1/2 ≪ 1 s), suggesting that co-ordination of Tl does not require reorganization of the protein structure. Rates of formation of [3Fe-4S] from [M3Fe-4S] adducts increase sharply at high potentials, showing that metal release involves a labile ‘super-oxidized ’ [M3Fe-4S]3+ state.
Purification and biochemical characterization of a poly(ADP-ribose) polymerase-like enzyme from the thermophilic archaeon Sulfolobus solfataricus
Authors: FARAONE-MENNELLA Maria Rosaria , GAMBACORTA Agata , NICOLAUS Barbara , FARINA Benedetta 
Published: August 2015

A poly(ADP-ribose) polymerase-like enzyme, detected in a crude homogenate from Sulfolobus solfataricus by means of activity and immunoblot analyses, was purified to electrophoretic homogeneity by a rapid procedure including two sequential affinity chromatographies, on NAD+-agarose and DNA-Sepharose. The latter column selected specifically the poly(ADP-ribosyl)ating enzyme with a 17% recovery of enzymic activity and a purification of more than 15000-fold. The molecular mass (54–55 kDa) assessed by SDS/PAGE and immunoblot was definitely lower than that determined for the corresponding eukaryotic protein. The enzyme was proved to be thermophilic, with a temperature optimum of approx. 80 °C, and thermostable, with a half-life of 204 min at 80 °C, in good agreement with the requirements of a thermozyme. It displayed a Km towards NAD+ of 154±50 µM; in the pH range 6.5–10.0 the activity values were similar, not showing a real optimum pH. The enzyme was able to bind homologous DNA, as evidenced by the ethidium bromide displacement assay. The product of the ADP-ribosylating reaction co-migrated with the short oligomers of ADP-ribose (less than 6 residues) from a eukaryotic source. Reverse-phase HPLC analysis of the products, after digestion with phosphodiesterase I, gave an elution profile reproducing that obtained by the enzymic digestion of the rat testis poly(ADP-ribose). These results strongly suggest that the activities of the purified enzyme include the elongation step.
CCAAT/enhancer binding protein regulates the promoter activity of the rat GLUT2 glucose transporter gene in liver cells
Authors: KIM Jae-woo , AHN Yong-ho 
Published: August 2015

The liver-specific expression of the GLUT2 glucose transporter gene is suppressed in cultured hepatoma cell lines as well as in hepatocytes in primary culture. To understand the underlying mechanism involved in this process, we analysed the rat GLUT2 promoter region. A DNase I footprinting assay with rat liver nuclear extract revealed eight protected regions within a -500 bp region of the GLUT2 promoter (sites A to H). Three of these sites (B, F and H) were occupied by transcription factors that are considerably enriched in liver cells compared with spleen or kidney. The proteins binding to these sites were investigated by a combination of DNase I footprinting assay and electrophoretic mobility-shift assay with the addition of specific oligonucleotide competitors and specific antibody against known transcription factors. As a result it was revealed that hepatocyte nuclear factor 3 binds to site B (-120 to -70), and CCAAT/enhancer binding protein α (C/EBPα) and C/EBPβ bind to site F (-375 to -356) and site H (-500 to -471). The binding of C/EBP to sites F and H was markedly decreased within 4 h when liver cells were subjected to primary culture, suggesting that C/EBP might be responsible for the decreased expression of GLUT2 in this process. In contrast, Western blot analysis revealed that C/EBPα began to decrease after 1 h of hepatocyte culture, and C/EBPβ was not changed significantly throughout the culture period, suggesting that C/EBP could be regulated at the transcriptional level as well as the post-translational level when hepatocytes were put in culture. To confirm the role of C/EBP in the regulation of GLUT2 promoter activity, sites F and H were ligated to a chloramphenicol acetyltransferase (CAT) reporter gene and co-transfected with a C/EBP expression vector into HepG2 cells. The co-expression of C/EBPα and C/EBPβ resulted in 9.1-fold and 3.8-fold increases of CAT activities in the site F-CAT and site H-CAT constructs respectively. These results indicate that C/EBPα and C/EBPβ regulate the promoter activity of the GLUT2 gene and might be responsible for the down-regulation of the GLUT2 gene when hepatocytes are subjected to primary culture.
Intestinal trefoil factor binds to intestinal epithelial cells and induces nitric oxide production: priming and enhancing effects of mucin
Authors: TAN Xiao-Di , LIU Qian-Ping , HSUEH Wei , CHEN Yi-Hua , CHANG Hong , GONZALEZ-CRUSSI Frank 
Published: August 2015

Intestinal trefoil factor (ITF or TFF3), NO and epithelium-associated mucin have important roles in sustaining mucosal integrity in the gastrointestinal tract. In the present study we examined ITF-binding molecules on IEC-18 cells (an intestinal epithelial cell line) with the use of flow cytometry and localized these molecules on the cell surface by confocal microscopy. Furthermore, we studied the interaction of mucin and ITF and their co-operative effect on NO production by the epithelium. Stimulation of cells with mucin (5 mg/ml) for 90 min resulted in a 5-fold increase in ITF binding. Treatment of IEC-18 cells with actinomycin D or cycloheximide attenuated mucin-enhanced ITF binding. Ligand blot analysis confirmed the induction of ITF-binding protein in IEC-18 cells by mucin. These results indicate that transcriptional and translational mechanisms are involved in the effect of mucin. Treatment with ITF overnight resulted in a low level of nitrite production by the cells, a 5-fold increase over control, in a concentration-dependent manner. ITF-induced NO production was attenuated by 1400W, a selective type II nitric oxide synthase (NOS2) inhibitor. By immunoblotting we found that NOS2 was up-regulated by ITF treatment. Priming IEC-18 cells with mucin for 90 min enhanced the effect of ITF on NO production, suggesting that the up-regulation of ITF-binding molecules by mucin might be physiologically relevant. Taken together, these observations indicate (1) that ITF-binding molecules that are up-regulated by mucin exist on the intestinal epithelial surface, and (2) that ITF modulates epithelial NO production via the NOS2 pathway, which is enhanced by mucin.
Association of polo-like kinase with α-, β- and γ-tubulins in a stable complex
Authors: FENG Yang , HODGE David R. , PALMIERI Giuseppe , CHASE Dan L. , LONGO Dan L. , FERRIS Douglas K. 
Published: August 2015

The polo-like kinase (Plk) family has been shown to have an important role in the regulation of the cell-division cycle, especially in organization of the spindle structure, in species from fungi to humans. Recent reports have demonstrated that in mammalian cells Plk is associated with components of the anaphase-promoting complex and a peptidyl-prolyl isomerase, Pin1. To characterize a putative Plk-containing complex, we fractionated mitotic cell lysates on a gel-filtration column. The Plk complex was eluted from the column at molecular sizes ranging from 669 to 2500 kDa in the presence of detergent and high concentrations of salt. Specific associations of Plk with α-, β- and γ-tubulins in both interphase and mitotic cells were shown by reciprocal immunoprecipitations and immunoblottings and were independent of the microtubule polymerization state, whereas binding assays in vitro indicated that Plk interacts with α- and β-tubulins directly. In addition, mitotic Plk was able to phosphorylate associated tubulins in vitro. Finally, we show that the kinase domain of the Plk molecule is both required and sufficient for its binding to tubulins in vivo. The specific interaction between Plk and tubulins might provide a molecular basis for the physiological functions of Plk in regulating the cell cycle, particularly in establishing the normal bipolar spindle.
Active-site characterization of Candida boidinii formate dehydrogenase
Authors: LABROU Nikolaos E. , RIGDEN Daniel J. 
Published: August 2015

NAD+-dependent formate dehydrogenase (FDH) from Candida boidinii was cloned and expressed to a high level in Escherichia coli (20% of soluble E. coli protein). Molecular modelling studies were used to create a three-dimensional model of C. boidinii FDH, based on a known structure of the Pseudomonas sp. 101 enzyme. This model was used for investigating the catalytic mechanism by site-directed mutagenesis. Eleven forms of C. boidinii FDH were characterized by steady-state kinetic analysis: the wild type as well as 10 mutants involving single (Phe-69–Ala, Asn-119–His, Ile-175–Ala, Gln-197–Leu, Arg-258–Ala, Gln-287–Glu and His-311–Gln) and double amino acid substitutions (Asn-119–His/His-311–Gln, Gln-287–Glu/His-311–Gln and Gln-287–Glu/Pro-288–Thr). The kinetic results of the mutant enzymes provide the first experimental support that hydrophobic patches, formed by Phe-69 and Ile-175, destabilize substrates and stabilize products. Also, the key role of Arg-258 in stabilization of the negative charge on the migrating hydride was established. Asn-119, besides being an anchor group for formate, also may comprise one of the hinge regions around which the two domains shift on binding of NAD+. The more unexpected results, obtained for the His-311–Gln and Gln-287–Glu/His-311–Gln mutants, combined with molecular modelling, suggest that steric as well as electrostatic properties of His-311 are important for enzyme function. An important structural role has also been attributed to cis-Pro-288. This residue may provide the key residues Gln-287 and His-311 with the proper orientation for productive binding of formate.
The FDH nucleotide sequence has been submitted to the EMBL Nucleotide Sequence Database under the accession no. AJ011046.
Push–pull mode digital control for LLC series resonant dc‐to‐dc converters
Authors: Pidaparthy Syam K. , Jang Jinhaeng , Choi Byungcho 
Published: August 2015

This study presents the design and performance evaluation of the digital control adapted to an LLC series resonant dc‐to‐dc converter operating with wide input and load variations. The proposed control design correctly incorporates the wide‐varying power stage dynamics and variable small‐signal gain of a digitally controlled oscillator, thereby offering satisfactory converter performance for all the operational conditions. The proposed digital controller adopts the push–pull mode control scheme, which executes the control action two times in one switching period, to minimise the time delay and enhance the performance. Using a 150 W experimental converter, the performance of the proposed push–pull mode digital control is demonstrated in comparison with that of the conventional complementary mode digital control, which performs the control action only once in one switching period.