bluuebunny/crossref_metadata_2025 huggingface dataset:
PMA induces stabilization of oncostatin M mRNA in human lymphoma U937 cells
Authors: Bandyopadhyay Sumita , Sengupta Tapas K. , Spicer Eleanor K.
Published: February 2008

OSM (oncostatin M) is a pleiotropic cytokine belonging to the IL (interleukin) 6 family that modulates the growth of some cancer cell lines. We have found that PMA treatment of human U937 lymphoma cells increased the steady-state levels of OSM mRNA. Furthermore, the half-life of OSM mRNA was increased from 2.3 to 6.2 h. Measurement of mRNA/hnRNA (heterogeneous nuclear RNA) ratios in PMA-treated cells suggests further that the increase in OSM mRNA is due to enhanced mRNA stability. Consistent with this, synthetic OSM mRNA transcripts decayed faster in extracts of untreated U937 cells than in extracts of PMA-treated cells. The 3′-untranslated region of OSM mRNA contains a putative ARE (AU-rich element) that may play a role in mRNA stabilization. Addition of the OSM ARE motif to the 3′-end of β-globin mRNA increased its decay rate in vitro. Decay assays with β-globin–AREOSM and β-globin transcripts indicate that PMA induces mRNA stabilization in an ARE-dependent manner. PMA also induces at least five OSM ARE-binding proteins. Supershift assays indicated that HuR is present in PMA-induced OSM mRNA–protein complexes. PMA treatment appears to induce translocation of HuR from the nucleus to the cytoplasm. RNA-decay assays indicated that HuR stabilizes OSM RNA in vitro. Additionally, immunodepletion of HuR from U937 cell extracts led to more rapid decay of OSM transcripts. Collectively, these findings suggest that the ARE plays a role in PMA-induced stabilization of OSM mRNA and that this process involves multiple ARE-binding proteins, including HuR.
The human fibrinolytic system is a target for the staphylococcal metalloprotease aureolysin
Authors: Beaufort Nathalie , Wojciechowski Piotr , Sommerhoff Christian P. , Szmyd Grzegorz , Dubin Grzegorz , Eick Sigrun , Kellermann Josef , Schmitt Manfred , Potempa Jan , Magdolen Viktor
Published: February 2008

The major opportunistic pathogen Staphylococcus aureus utilizes the human fibrinolytic system for invasion and spread via plasmin(ogen) binding and non-proteolytic activation. Because S. aureus secretes several proteases recently proposed as virulence factors, we explored whether these enzymes could add to the activation of the host's fibrinolytic system. Exposure of human pro-urokinase [pro-uPA (where uPA is urokinase-type plasminogen activator)] to conditioned growth media from staphylococcal reference strains results in an EDTA-sensitive conversion of the single-chain zymogen into its two-chain active form, an activity not observed in an aureolysin-deficient strain. Using purified aureolysin, we verified the capacity of this thermolysin-like metalloprotease to activate pro-uPA, with a 2.6×103 M−1·s−1 catalytic efficiency. Moreover, activation also occurs in the presence of human plasma, as well as in conditioned growth media from clinical isolates. Finally, we establish that aureolysin (i) converts plasminogen into angiostatin and mini-plasminogen, the latter retaining its capacity to be activated by uPA and to hydrolyse fibrin, (ii) degrades the plasminogen activator inhibitor-1, and (iii) abrogates the inhibitory activity of α2-antiplasmin. Altogether, we propose that, in parallel with the staphylokinase-dependent activation of plasminogen, aureolysin may contribute significantly to the activation of the fibrinolytic system by S. aureus, and thus may promote bacterial spread and invasion.
A hybrid surface arc discharge ion source to produce ultra pure Ca+2 beams for Ca40(α,γ)Ti44 reaction studies at ISAC/TRIUMF
Authors: Jayamanna K. , Vockenhuber C.
Published: February 2008

ISAC is an accelerator facility primarily dedicated to astrophysical studies. Off-line and online ion sources provide up to 65keV of stable and radioactive beams to the ISAC accelerators. Initial acceleration is done via a constant velocity radio frequency quadrupole that requires 2keV∕u. Then the beam is further accelerated to 1.5MeV∕u at ISAC-I and 6.5MeV∕u at ISAC-II. To study radiative capture reactions relevant for astrophysics, the recoil mass spectrometer DRAGON was built in the experimental area. Ca40(α,γ)Ti44 is identified as one of the key reactions in supernovae to produce Ti44 and is given highest priority. For this experiment, an ultrapure Ca+2 beam was requested from the off-line ion source. Initial tests showed that, when using conventional ion sources, Ar40 and K40 are the impurities that are most difficult to eliminate. In order to overcome this problem, a new concept was needed and the hybrid surface arc discharge ion source was born. The hybrid surface ion source consists of a small surface ionizer and an arc discharge placed in a solenoid field. A very low ratio of Ar40∕Ca40=8×10−5 was achieved with this new source and the experiment was completed successfully. The source is described in detail and its performance is discussed in this article.
Theoretical investigation of electronic excitation energy transfer in bichromophoric assemblies
Authors: Fückel Burkhard , Köhn Andreas , Harding Michael E. , Diezemann Gregor , Hinze Gerald , Basché Thomas , Gauss Jürgen
Published: February 2008

Electronic excitation energy transfer (EET) rates in rylene diimide dyads are calculated using second-order approximate coupled-cluster theory and time-dependent density functional theory. We investigate the dependence of the EET rates on the interchromophoric distance and the relative orientation and show that Förster theory works quantitatively only for donor-acceptor separations larger than roughly 5nm. For smaller distances the EET rates are over- or underestimated by Förster theory depending on the respective orientation of the transition dipole moments of the chromophores. In addition to the direct transfer rates we consider bridge-mediated transfer originating from oligophenylene units placed between the chromophores. We find that the polarizability of the bridge significantly enhances the effective interaction. We compare our calculations to single molecule experiments on two types of dyads and find reasonable agreement between theory and experiment.
In situ observation of wet oxidation kinetics on Si(100) via ambient pressure x-ray photoemission spectroscopy
Authors: Rossi Massimiliano , Mun Bongjin S. , Enta Yoshiharu , Fadley Charles S. , Lee Ki-Suk , Kim Sang-Koog , Shin Hyun-Joon , Hussain Zahid , Ross Philip N.
Published: February 2008

The initial stages of wet thermal oxidation of Si(100)−(2×1) have been investigated by in situ ambient pressure x-ray photoemission spectroscopy, including chemical-state resolution via Si 2p core-level spectra. Real-time growth rates of silicon dioxide have been monitored at 100 mTorr of water vapor. This pressure is considerably higher than in any prior study using x-ray photoemission spectroscopy. Substrate temperatures have been varied between 250 and 500 °C. Above a temperature of ∼400 °C, two distinct regimes, a rapid and a quasisaturated one, are identified, and growth rates show a strong temperature dependence which cannot be explained by the conventional Deal-Grove model.
The local environment of Co in B5CHx
Authors: Dowben P. A. , Ignatov A. Yu. , Lui Jing , Skomski Ralph
Published: February 2008

Cobalt-doped boron carbides produced by simultaneous plasma-enhanced chemical vapor deposition of carborane and cobaltocene are investigated. Cobalt does not dope plasma-enhanced chemical vapor deposition grown boron carbides as a random fragment of the cobaltocene source gas. The Co atoms are fivefold boron coordinated (R=2.1Å) and chemically bonded to the icosahedral cages of B10CHx or B9C2Hy. Pairwise Co doping occurs with the cobalt atoms favoring sites about 5.3Å apart. The cobalt strongly hybridizes with the molecular orbitals of the icosahedral cage, and the states in the region of the band gap probably have a strong cobalt weight.
Direct analysis of monomer diffusion times in polyvinyl/acrylamide materials
Authors: Gallego Sergi , Márquez Andrés , Méndez David , Neipp Cristian , Ortuño Manuel , Beléndez Augusto , Fernández Elena , Pascual Inmaculada
Published: February 2008

We propose an alternative, direct method to calculate monomer diffusion times in photopolymer materials. Very long period gratings are recorded in the photopolymer, and the real time variation in diffraction efficiency due to monomer diffusion is then analyzed. In photopolymers, monomer diffusion plays a fundamental role in hologram formation. However, since many interrelated parameters affect hologram formation, the usual techniques do not allow for an independent estimation of monomer diffusion times. The direct method proposed is applied to two polyvinyl based photopolymers with different molecular weights.
Mn substitution effect on the magnetic properties of PrFe1.9 alloy
Authors: Shi Y. G. , Lv L. Y. , Tang S. L. , Yu J. Y. , Wang R. L. , Du Y. W.
Published: February 2008

Polycrystalline magnetostrictive alloys Pr(Fe1−xMnx)1.9 (0⩽x⩽0.2) were synthesized by high-pressure annealing. X-ray diffraction results show that all the samples exhibit cubic Laves phase with MgCu2-type structure. The lattice parameter increases with increasing Mn concentration while the Curie temperature decreases. The saturation magnetization decreases with increasing Mn concentration, which can be understood on the basis of the rigid band model. The magnetizations of the samples with x=0.05 and x=0.1 are easy to get saturated in comparison with that of the sample without Mn, which implies that small amount of substitution Mn for Fe can lower the magnetic anisotropy of the alloy. The saturation magnetostriction decreases monotonously with increasing Mn content, while the magnetostriction of the sample with x=0.1 shows a peak at low magnetic fields.
Determination of the pseudopotential gradient in multiphase lattice Boltzmann models
Authors: Márkus Attila , Házi Gábor
Published: February 2008

Using the multiphase lattice Boltzmann method of Shan and Chen [Phys. Rev. E 47, 1815 (1993)], the intermolecular force is calculated from the gradient of a pseudopotential. The pseudopotential is in quadratic relation with the equation of state of the fluid model. This fact motivated some researchers [P. Yuan and L. Schaefer, Phys. Fluids 18, 042101 (2006); R. S. Qin, Phys. Rev E 73, 066703 (2006)] to introduce new forms for the pseudopotential and to model fluids with some desired equation of state. Using such models the determination of the pseudopotential and its gradient is often ambiguous and lead to numerical instabilities as we demonstrate in this paper. We propose a simple method to solve this problem.
Suppressing the fragmentation of fragile molecules in helium nanodroplets by coembedding with water: Possible role of the electric dipole moment
Authors: Ren Yanfei , Kresin Vitaly V.
Published: February 2008

When fragile molecules such as glycine, polyglycine, alkanes, and alkanethiols are embedded in liquid helium nanodroplets, electron-impact ionization of the beam leads to fragmentation which is as extensive as that of isolated gas-phase molecules. However, it turns out that if a few molecules of water are coembedded with the peptide and alkane chains, their fragmentation is drastically reduced or completely eliminated. On the other hand, the fragmentation of alkanethiols remains unaffected. On the basis of these observations, it is proposed that the fragmentation “buffering” effect may correlate with the magnitude of the impurity’s electric dipole moment, which steers the migration of the ionizing He+ hole in the droplet.
Scaling of the peak magnetic reconnection rate in the inviscid Taylor problem
Authors: Fitzpatrick R.
Published: February 2008

A dispute regarding the scaling of the peak magnetic reconnection rate in the inviscid Taylor problem for ka⪡1 is resolved.
Star-configured carbazole as an efficient near-ultraviolet emitter and hole-transporting material for organic light-emitting devices
Authors: Xiang Hai-Feng , Xu Zong-Xiang , Roy V. A. L. , Che Chi-Ming , Lai P. T. , Zeng Peng-Ju , Niu Fang-Fang , Liu Ya-Wei , Tang Wei-Qun , He Cai-Jie , Niu Han-Ben
Published: February 2008

A novel organic material, 9-methyl-1,3,6,8-tetraphenyl-carbazole (MTPC-Me), for use in organic electroluminescent devices has been developed. This star-configured carbazole gives a strong near-ultraviolet (n-UV) emission (λmax=389nm) with a high emission quantum efficiency of 47% and a narrow full width half maximum of 40nm. Two types of high-performance organic light-emitting devices were obtained using MTPC-Me as a n-UV emitter and hole-transporting material with maximum external quantum efficiency, brightness, and turn-on voltage of 1.2%, 1040cd∕m2, and 3.5V for the former and 1.1%, 18000cd∕m2, and 2.4V for the latter, respectively.
Ultrafast crystallization and thermal stability of In–Ge doped eutectic Sb70Te30 phase change material
Authors: Lee Mei Ling , Miao Xiang Shui , Ting Lee Hou , Shi Lu Ping
Published: February 2008

Effect of In and Ge doping in the form of In2Ge8Sb85Te5 on optical and thermal properties of eutectic Sb70Te30 alloys was investigated. Crystalline structure of In2Ge8Sb85Te5 phase change material consists of a mixture of phases. Thermal analysis shows higher crystallization temperature and activation energy for crystallization. Isothermal reflectivity-time measurement shows a growth-dominated crystallization mechanism. Ultrafast crystallization speed of 30ns is realized upon irradiation by blue laser beam. The use of ultrafast and thermally stable In2Ge8Sb85Te5 phase change material as mask layer in aperture-type super-resolution near-field phase change disk is realized to increase the carrier-to-noise ratio and thermal stability.
Dielectric properties of MgO-doped compositionally graded multilayer barium strontium titanate films
Authors: Cole M. W. , Ngo E. , Hirsch S. , Okatan M. B. , Alpay S. P.
Published: February 2008

We have grown 5mol% MgO-doped multilayered Ba1−xSrxTiO3 (BST) films having a nominal thickness of 220nm with compositions of each layer as BST60/40, BST75/25, and BST90/10 (upgraded). We also fabricated undoped upgraded BST and uniform BST60/40 films for comparison. Results show that Mg-doping improves dielectric loss (tanδ=0.008) and yields better surface roughness (∼3.1nm) compared to undoped upgraded BST. Mg-doped films displayed excellent temperature stability with temperature coefficient of capacitances of −0.94 and 1.14ppt∕°C from 20to90°C and 20to−10°C, respectively. Mg doping resulted in a moderate dielectric tunability (29%) compared to undoped BST (65.5%) at 444kV∕cm.
The enhanced signal of subgap centers in tip-probing photoabsorption spectroscopy with an assist of a subsidiary light
Authors: Naruse Nobuyasu , Mera Yutaka , Nakamura Yoshiaki , Ichikawa Masakazu , Maeda Koji
Published: February 2008

We found that photoabsorption spectra (PASs) of a n-type Si exhibit a pronounced sub-bandgap peak when the sample was probed by a scanning tunneling microscope tip in a recently introduced scheme of Fourier transform (FT) spectroscopy. The peak, not observable in the conventional scheme of lock-in detection, emerged when, simulating the multiplex light illumination in the FT scheme, the sample was illuminated with a suprabandgap light in addition to the spectroscopic subgap lights. We concluded that this peculiar phenomenon is due to the optical neutralization of ionized donors by the subgap light which reduces, rather than increases, the surface photovoltage induced by the subsidiary suprabandgap lights. The use of such a subsidiary light in addition to spectroscopic lights will serve to enhance the sensitivity for tip-probing PAS detection of sub-bandgap centers.
Biexciton binding energy in parabolic quantum-well wires
Authors: Zhang Hong , Shen Man , Liu Jian-Jun
Published: February 2008

The problem of a biexciton confined in parabolic GaAs quantum-well wires in the presence of a perpendicular magnetic field is discussed. We apply an analytical one-dimensional formula for the effective interaction potential between the confined charge carriers to study the binding energies of a biexciton, which results in a numerical “exactly” solvable model. The ratio of the binding energy of a biexciton to that of an exciton for a range of confinement lengths (l<ad) is found from 0.183 to 0.313. Magnetic field dependence of the biexciton binding energy is also investigated and it is found that the influence is stronger when the confinement length is larger.
Linewidth enhancement factor of terahertz quantum cascade lasers
Authors: Green Richard P. , Xu Ji-Hua , Mahler Lukas , Tredicucci Alessandro , Beltram Fabio , Giuliani Guido , Beere Harvey E. , Ritchie David A.
Published: February 2008

The linewidth enhancement factor (LEF) of terahertz quantum cascade lasers is measured using an optical feedback self-mixing technique. As expected, a much lower LEF is found than is common for interband lasers, but instead of the predicted value of zero, the LEF depends on the laser conditions and can be as high as 0.5. The measured value tends to increase with increasing current. Cross absorption within the laser active region is suggested as a possible cause for the nonzero LEF observed.
Role of charge-transfer states of Cr3+ in creation and annihilation of light-induced polarons in LiNbO3:Cr3+, MgO crystals
Authors: Kobyakov S. , Suchocki A. , Arizmendi L. , Jaque F.
Published: February 2008

It is shown that Cr impurity takes a crucial role in the process of creation of hole O− and electron NbNb4+ polarons by the UV light in LiNbO3:Cr crystal codoped with MgO above threshold concentration. Thermal stability of both types of polarons shows that they are created and they annihilate simultaneously with each other in such crystals.
Magneto-optical isolator with silicon waveguides fabricated by direct bonding
Authors: Shoji Yuya , Mizumoto Tetsuya , Yokoi Hideki , Hsieh I-Wei , Osgood Richard M.
Published: February 2008

A magneto-optical isolator is demonstrated for use with a Si waveguide. The isolator is based on a Mach–Zehnder interferometer employing a nonreciprocal phase shift and is fabricated by bonding a magneto-optic garnet CeY2Fe5O12 (Ce:YIG) directly onto the Si waveguide. The surface-activated bonding is based on oxygen-plasma exposure in a high-vacuum chamber. The nonreciprocal phase shift is observed by applying an external magnetic field. An isolation ratio of 21dB is obtained at a wavelength of 1559nm.
Fluoride removal from aqueous solution by Ca-pretreated macrophyte biomass
Authors: Miretzky Patricia , Muñoz Carolina , Carrillo-Chávez Alejandro
Published: February 2008

Environmental context. Fluoride concentrations in drinking water above 1.5 mg L–1 may be detrimental to human health. Many methods have been developed for removing excessive fluoride from drinking water. The use of an aquatic macrophyte biomass (Eleocharis acicularis) pretreated with Ca2+, a low-cost natural material, could be a technique for rural populations in developing countries that cannot afford treated or bottled water for daily consumption.
Abstract. The use of an aquatic macrophyte biomass (Eleocharis acicularis) pretreated with Ca2+ as a low-cost natural material for the removal of fluoride from aqueous solution was studied. Batch experiments were carried out to determine fluoride sorption capacity and the efficiency of the sorption process under different pH, initial F– and macrophyte biomass doses. The experimental data showed good fitting to Langmuir and Freundlich isotherm models. The maximum F adsorption capacity was 0.110 mmol g–1 with an efficiency of 64.5% (pH 6.0; 5.0 g L–1 Ca-pretreated biomass). The binding of Ca2+ to the biomass increased the removal efficiency over 100%. The F– removal kinetics were rapid, less than 30 min, and best described by the pseudo-second order rate model. The rate constant, the initial sorption rate and the equilibrium sorption capacity were determined. These results may be useful for deprived rural population water supply schemes in Mexico and in other developing countries.
On the evolutionary significance and metal-binding characteristics of a monolobal transferrin fromCiona intestinalis
Authors: Tinoco Arthur D. , Peterson Cynthia W. , Lucchese Baldo , Doyle Robert P. , Valentine Ann M.
Published: February 2008

Transferrins are a family of proteins that bind and transport Fe(III). Modern transferrins are typically bilobal and are believed to have evolved from an ancient gene duplication of a monolobal form. A novel monolobal transferrin, nicatransferrin (nicaTf), was identified in the primitive ascidian speciesCiona intestinalisthat possesses the characteristic features of the proposed ancestral Tf protein. In this work, nicaTf was expressed inPichia pastoris. Extensive solution studies were performed on nicaTf, including UV-vis, fluorescence, CD, EPR and NMR spectroscopies, and electrospray time-of-flight mass spectrometry. The expressed protein is nonglycosylated, unlike the protein isolated from the organism. This property does not affect its ability to bind Fe(III). However, Fe(III)-bound nicaTf displays important spectral differences from other Fe(III)-bound transferrins, which are likely the consequence of differences in metal coordination. Coordination differences could also account for the weaker affinity of nicaTf for Fe(III) (log K = 18.5) compared with bilobal human serum transferrin (HsTf) (log K = 22.5 and 21.4). The Fe–nicaTf complex is not labile, as indicated by slow metal removal kinetics by the high-affinity chelator tiron at pH 7.4. The protein alternatively binds up to one equivalent of Ti(IV) or V(V), which suggests that it may transport nonferric metals. These solution studies provide insight into the structure and function of the primitive monolobal transferrin ofC. intestinalisfor comparison with higher order bilobal transferrins. They suggest that a major advantage for the evolution of modern transferrins, dominantly of bilobal form, is stronger Fe(III) affinity because of cooperativity.
Regulation of excitability and plasticity by endocannabinoids and PKA in developing hippocampus
Authors: Yasuda Hiroki , Huang Yan , Tsumoto Tadaharu
Published: February 2008

The activity-dependent strengthening and weakening of synaptic transmission are hypothesized to be the basis of not only memory and learning but also the refinement of neural circuits during development. Here we report that, in the developing CA1 area of the hippocampus, endocannabinoid (eCB)-mediated heterosynaptic long-term depression (LTD) of glutamatergic excitatory synaptic transmission is associated with PKA-mediated homosynaptic long-term potentiation (LTP). This form of LTD was dominant at postnatal days 2–10 (P2–P10), attenuated during development, and finally disappeared in the mature hippocampus. Heterosynaptic LTD of excitatory postsynaptic currents in the developing hippocampus was expressed presynaptically, spread to neighboring neurons, and was mediated by eCBs. Heterosynaptic LTD of field excitatory postsynaptic potentials was associated with a decrease in fiber volley amplitude with a similar time course. Depression of fiber volleys was blocked by K
+
channel blockers, suggesting the involvement of the decrease in presynaptic excitability in heterosynaptic LTD. In the P2–P5 hippocampus, eCBs also attenuate LTP and fiber volleys in homosynaptic pathways and help to prevent too much excitability in the neonatal hippocampus where the GABAergic system is poorly developed and even excitatory. In the hippocampus older than P6 (P > 6), however, LTP is protected from eCB-mediated depression by PKA activated at presynaptic sites by high-frequency stimulation, serving to highlight PKA-mediated LTP by weakening inactive synapses even in adjacent cells. Thus, eCBs and PKA make synapses plastic without changing excitability homeostasis in the developing hippocampus.
Natural selection and cultural rates of change
Authors: Rogers Deborah S. , Ehrlich Paul R.
Published: February 2008

It has been claimed that a meaningful theory of cultural evolution is not possible because human beliefs and behaviors do not follow predictable patterns. However, theoretical models of cultural transmission and observations of the development of societies suggest that patterns in cultural evolution do occur. Here, we analyze whether two sets of related cultural traits, one tested against the environment and the other not, evolve at different rates in the same populations. Using functional and symbolic design features for Polynesian canoes, we show that natural selection apparently slows the evolution of functional structures, whereas symbolic designs differentiate more rapidly. This finding indicates that cultural change, like genetic evolution, can follow theoretically derived patterns.
Antisera induced by infusions of autologous Ad-CD154-leukemia B cells identify ROR1 as an oncofetal antigen and receptor for Wnt5a
Authors: Fukuda Tetsuya , Chen Liguang , Endo Tomoyuki , Tang Li , Lu Desheng , Castro Januario E. , Widhopf George F. , Rassenti Laura Z. , Cantwell Mark J. , Prussak Charles E. , Carson Dennis A. , Kipps Thomas J.
Published: February 2008

We examined the sera of six patients before and after i.v. infusions of autologous chronic lymphocytic leukemia (CLL) cells transducedex vivowith an adenovirus encoding CD154 (Ad-CD154). Five patients made high-titer antibodies against adenovirus and three made IgG reactive with a leukemia-associated surface antigen, which we identified as ROR1. Anti-ROR1 antibodies were not detected in the sera of untreated patients. We generated anti-ROR1 mAbs and found they reacted specifically with the CLL cells of all patients, but not with nonleukemic leukocytes, a wide variety of normal adult tissues, or blood mononuclear cells, including CD5+B cells of healthy adults. ROR1 could bind Wnt5a, which induced activation of NF-κB when coexpressed withROR1in HEK293 cells and enhanced the survival of CLL cellsin vitro, an effect that could be neutralized by posttreatment anti-ROR1 antisera. We conclude that patients with CLL can break immune tolerance to ROR1, which is an oncofetal surface antigen and survival-signaling receptor in this neoplastic disease.
Allelic mutant series reveal distinct functions for
Arabidopsis
cycloartenol synthase 1 in cell viability and plastid biogenesis
Authors: Babiychuk Elena , Bouvier-Navé Pierrette , Compagnon Vincent , Suzuki Masashi , Muranaka Toshiya , Van Montagu Marc , Kushnir Sergei , Schaller Hubert
Published: February 2008

Sterols have multiple functions in all eukaryotes. In plants, sterol biosynthesis is initiated by the enzymatic conversion of 2,3-oxidosqualene to cycloartenol. This reaction is catalyzed by cycloartenol synthase 1 (CAS1), which belongs to a family of 13 2,3-oxidosqualene cyclases in
Arabidopsis thaliana
. To understand the full scope of sterol biological functions in plants, we characterized allelic series of
cas1
mutations. Plants carrying the weak mutant allele
cas1–1
were viable but developed albino inflorescence shoots because of photooxidation of plastids in stems that contained low amounts of carotenoids and chlorophylls. Consistent with the CAS1 catalyzed reaction, mutant tissues accumulated 2,3-oxidosqualene. This triterpenoid precursor did not increase at the expense of the pathway end products. Two strong mutations,
cas1–2
and
cas1–3
, were not transmissible through the male gametes, suggesting a role for CAS1 in male gametophyte function. To validate these findings, we analyzed a conditional
CRE/loxP
recombination-dependent
cas1–2
mutant allele. The albino phenotype of growing leaf tissues was a typical defect observed shortly after the
CRE/loxP
-induced onset of
CAS1
loss of function. In the induced
cas1–2
seedlings, terminal phenotypes included arrest of meristematic activity, followed by necrotic death. Mutant tissues accumulated 2,3-oxidosqualene and contained low amounts of sterols. The vital role of sterols in membrane functioning most probably explains the requirement of CAS1 for plant cell viability. The observed impact of
cas1
mutations on a chloroplastic function implies a previously unrecognized role of sterols or triterpenoid metabolites in plastid biogenesis.
Discovery of a lysophospholipid acyltransferase family essential for membrane asymmetry and diversity
Authors: Hishikawa Daisuke , Shindou Hideo , Kobayashi Saori , Nakanishi Hiroki , Taguchi Ryo , Shimizu Takao
Published: February 2008

All organisms consist of cells that are enclosed by a cell membrane containing bipolar lipids and proteins. Glycerophospholipids are important not only as structural and functional components of cellular membrane but also as precursors of various lipid mediators. Polyunsaturated fatty acids comprising arachidonic acid or eicosapentaenoic acid are located at
sn
-2 position, but not at
sn
-1 position of glycerophospholipids in an asymmetrical manner. In addition to the asymmetry, the membrane diversity is important for membrane fluidity and curvature. To explain the asymmetrical distribution of fatty acids, the rapid turnover of
sn
-2 position was proposed in 1958 by Lands [Lands WE (1958) Metabolism of glycerolipides: A comparison of lecithin and triglyceride synthesis.
J Biol Chem
231:883–888]. However, the molecular mechanisms and biological significance of the asymmetry remained unknown. Here, we describe a putative enzyme superfamily consisting mainly of three gene families, which catalyzes the transfer of acyl-CoAs to lysophospholipids to produce different classes of phospholipids. Among them, we characterized three important enzymes with different substrate specificities and tissue distributions; one, termed lysophosphatidylcholine acyltransferase-3 (a mammalian homologue of
Drosophila nessy
critical for embryogenesis), prefers arachidonoyl-CoA, and the other two enzymes incorporate oleoyl-CoAs to lysophosphatidylethanolamine and lysophosphatidylserine. Thus, we propose that the membrane diversity is produced by the concerted and overlapped reactions with multiple enzymes that recognize both the polar head group of glycerophospholipids and various acyl-CoAs. Our findings constitute a critical milestone for our understanding about how membrane diversity and asymmetry are established and their biological significance.
Elevated globotriaosylsphingosine is a hallmark of Fabry disease
Authors: Aerts Johannes M. , Groener Johanna E. , Kuiper Sijmen , Donker-Koopman Wilma E. , Strijland Anneke , Ottenhoff Roelof , van Roomen Cindy , Mirzaian Mina , Wijburg Frits A. , Linthorst Gabor E. , Vedder Anouk C. , Rombach Saskia M. , Cox-Brinkman Josanne , Somerharju Pentti , Boot Rolf G. , Hollak Carla E. , Brady Roscoe O. , Poorthuis Ben J.
Published: February 2008

Fabry disease is an X-linked lysosomal storage disease caused by deficiency of α-galactosidase A that affects males and shows disease expression in heterozygotes. The characteristic progressive renal insufficiency, cardiac involvement, and neuropathology usually are ascribed to globotriaosylceramide accumulation in the endothelium. However, no direct correlation exists between lipid storage and clinical manifestations, and treatment of patients with recombinant enzymes does not reverse several key signs despite clearance of lipid from the endothelium. We therefore investigated the possibility that globotriaosylceramide metabolites are a missing link in the pathogenesis. We report that deacylated globotriaosylceramide, globotriaosylsphingosine, and a minor additional metabolite are dramatically increased in plasma of classically affected male Fabry patients and plasma and tissues of Fabry mice. Plasma globotriaosylceramide levels are reduced by therapy. We show that globotriaosylsphingosine is an inhibitor of α-galactosidase A activity. Furthermore, exposure of smooth muscle cells, but not fibroblasts, to globotriaosylsphingosine at concentrations observed in plasma of patients promotes proliferation. The increased intima-media thickness in Fabry patients therefore may be related to the presence of this metabolite. Our findings suggest that measurement of circulating globotriaosylsphingosine will be useful to monitor Fabry disease and may contribute to a better understanding of the disorder.
Retinoic acid deficiency alters second heart field formation
Authors: Ryckebusch Lucile , Wang Zengxin , Bertrand Nicolas , Lin Song-Chang , Chi Xuan , Schwartz Robert , Zaffran Stéphane , Niederreither Karen
Published: February 2008

Retinoic acid (RA), the active derivative of vitamin A, has been implicated in various steps of cardiovascular development. The retinaldehyde dehydrogenase 2 (RALDH2) enzyme catalyzes the second oxidative step in RA biosynthesis and its loss of function creates a severe embryonic RA deficiency.
Raldh2
−/−
knockout embryos fail to undergo heart looping and have impaired atrial and sinus venosus development. To understand the mechanism(s) producing these changes, we examined the contribution of the second heart field (SHF) to pharyngeal mesoderm, atria, and outflow tract in
Raldh2
−/−
embryos. RA deficiency alters SHF gene expression in two ways. First,
Raldh2
−/−
embryos exhibited a posterior expansion of anterior markers of the SHF, including
Tbx1
,
Fgf8
, and the
Mlc1v-nlacZ-24
/
Fgf10
reporter transgene as well as of
Islet1
. This occurred at early somite stages, when cardiac defects became irreversible in an avian vitamin A-deficiency model, indicating that endogenous RA is required to restrict the SHF posteriorly. Explant studies showed that this expanded progenitor population cannot differentiate properly. Second, RA up-regulated cardiac
Bmp
expression levels at the looping stage. The contribution of the SHF to both inflow and outflow poles was perturbed under RA deficiency, creating a disorganization of the heart tube. We also investigated genetic cross-talk between Nkx2.5 and RA signaling by generating double mutant mice. Strikingly,
Nkx2.5
deficiency was able to rescue molecular defects in the posterior region of the
Raldh2
−/−
mutant heart, in a gene dosage-dependent manner.
Inhibition of proinflammatory and innate immune signaling pathways by a cytomegalovirus RIP1-interacting protein
Authors: Mack Claudia , Sickmann Albert , Lembo David , Brune Wolfram
Published: February 2008

TNFα is an important cytokine in antimicrobial immunity and inflammation. The receptor-interacting protein RIP1 is an essential component of the TNF receptor 1 signaling pathway that mediates the activation of NF-κB, MAPKs, and programmed cell death. It also transduces signals derived from Toll-like receptors and intracellular sensors of DNA damage and double-stranded RNA. Here, we show that the murine CMV M45 protein binds to RIP1 and inhibits TNFα-induced activation of NF-κB, p38 MAPK, and caspase-independent cell death. M45 also inhibited NF-κB activation upon stimulation of Toll-like receptor 3 and ubiquitination of RIP1, which is required for NF-κB activation. Hence, M45 functions as a viral inhibitor of RIP1-mediated signaling. The results presented here reveal a mechanism of viral immune subversion and demonstrate how a viral protein can simultaneously block proinflammatory and innate immune signaling pathways by interacting with a central mediator molecule.
Diary of a Tv Station
Authors: Muchnik Viktor , Hercules Olia
Published: February 2008

Viktor Muchnik explains the secret of running one of Russia’s most respected regional channels: from reporting a putsch to surviving a takeover
Rab8 Regulates Basolateral Secretory, But Not Recycling, Traffic at the Recycling Endosome
Authors: Henry Lauren , Sheff David R.
Published: February 2008

Rab8 is a monomeric GTPase that regulates the delivery of newly synthesized proteins to the basolateral surface in polarized epithelial cells. Recent publications have demonstrated that basolateral proteins interacting with the μ1-B clathrin adapter subunit pass through the recycling endosome (RE) en route from the TGN to the plasma membrane. Because Rab8 interacts with these basolateral proteins, these findings raise the question of whether Rab8 acts before, at, or after the RE. We find that Rab8 overexpression during the formation of polarity in MDCK cells, disrupts polarization of the cell, explaining how Rab8 mutants can disrupt basolateral endocytic and secretory traffic. However, once cells are polarized, Rab8 mutants cause mis-sorting of newly synthesized basolateral proteins such as VSV-G to the apical surface, but do not cause mis-sorting of membrane proteins already at the cell surface or in the endocytic recycling pathway. Enzymatic ablation of the RE also prevents traffic from the TGN from reaching the RE and similarly results in mis-sorting of newly synthesized VSV-G. We conclude that Rab8 regulates biosynthetic traffic through REs to the plasma membrane, but not trafficking of endocytic cargo through the RE. The data are consistent with a model in which Rab8 functions in regulating the delivery of TGN-derived cargo to REs.
p204 Protein Overcomes the Inhibition of Core Binding Factor α-1–mediated Osteogenic Differentiation by Id Helix-Loop-Helix Proteins
Authors: Luan Yi , Yu Xiu-Ping , Yang Ning , Frenkel Sally , Chen Lin , Liu Chuan-ju
Published: February 2008

Id proteins play important roles in osteogenic differentiation; however, the molecular mechanism remains unknown. In this study, we established that inhibitor of differentiation (Id) proteins, including Id1, Id2, and Id3, associate with core binding factor α-1 (Cbfa1) to cause diminished transcription of the alkaline phosphatase (ALP) and osteocalcin (OCL) gene, leading to less ALP activity and osteocalcin (OCL) production. Id acts by inhibiting the sequence-specific binding of Cbfa1 to DNA and by decreasing the expression of Cbfa1 in cells undergoing osteogenic differentiation. p204, an interferon-inducible protein that interacts with both Cbfa1 and Id2, overcame the Id2-mediated inhibition of Cbfa1-induced ALP activity and OCL production. We show that 1) p204 disturbed the binding of Id2 to Cbfa1 and enabled Cbfa1 to bind to the promoters of its target genes and 2) that p204 promoted the translocation from nucleus to the cytoplasm and accelerated the degradation of Id2 by ubiquitin–proteasome pathway during osteogenesis. Nucleus export signal (NES) of p204 is required for the p204-enhanced cytoplasmic translocation and degradation of Id2, because a p204 mutant lacking NES lost these activities. Together, Cbfa1, p204, and Id proteins form a regulatory circuit and act in concert to regulate osteoblast differentiation.
mDia2 Induces the Actin Scaffold for the Contractile Ring and Stabilizes Its Position during Cytokinesis in NIH 3T3 Cells
Authors: Watanabe Sadanori , Ando Yoshikazu , Yasuda Shingo , Hosoya Hiroshi , Watanabe Naoki , Ishizaki Toshimasa , Narumiya Shuh
Published: February 2008

mDia proteins are mammalian homologues of Drosophila diaphanous and belong to the formin family proteins that catalyze actin nucleation and polymerization. Although formin family proteins of nonmammalian species such as Drosophila diaphanous are essential in cytokinesis, whether and how mDia proteins function in cytokinesis remain unknown. Here we depleted each of the three mDia isoforms in NIH 3T3 cells by RNA interference and examined this issue. Depletion of mDia2 selectively increased the number of binucleate cells, which was corrected by coexpression of RNAi-resistant full-length mDia2. mDia2 accumulates in the cleavage furrow during anaphase to telophase, and concentrates in the midbody at the end of cytokinesis. Depletion of mDia2 induced contraction at aberrant sites of dividing cells, where contractile ring components such as RhoA, myosin, anillin, and phosphorylated ERM accumulated. Treatment with blebbistatin suppressed abnormal contraction, corrected localization of the above components, and revealed that the amount of F-actin at the equatorial region during anaphase/telophase was significantly decreased with mDia2 RNAi. These results demonstrate that mDia2 is essential in mammalian cell cytokinesis and that mDia2-induced F-actin forms a scaffold for the contractile ring and maintains its position in the middle of a dividing cell.
Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs
Authors: Jacob Juby , Jentsch Marcel , Kostka Dennis , Bentink Stefan , Spang Rainer
Published: February 2008

Motivation: Molecular diagnostics aims at classifying diseases into clinically relevant sub-entities based on molecular characteristics. Typically, the entities are split into subgroups, which might contain several variants yielding a hierarchical model of the disease. Recent years have introduced a plethora of new molecular screening technologies to molecular diagnostics. As a result molecular profiles of patients became complex and the classification task more difficult.

Results: We present a novel tool for detecting hierarchical structure in binary datasets. We aim for identifying molecular characteristics, which are stochastically implying other characteristics. The final hierarchical structure is encoded in a directed transitive graph where nodes represent molecular characteristics and a directed edge from a node A to a node B denotes that almost all cases with characteristic B also display characteristic A. Naturally, these graphs need to be transitive. In the core of our modeling approach lies the problem of calculating good transitive approximations of given directed but not necessarily transitive graphs. By good transitive approximation we understand transitive graphs, which differ from the reference graph in only a small number of edges. It is known that the problem of finding optimal transitive approximation is NP-complete. Here we develop an efficient heuristic for generating good transitive approximations. We evaluate the computational efficiency of the algorithm in simulations, and demonstrate its use in the context of a large genome-wide study on mature aggressive lymphomas.

Availability: The software used in our analysis is freely available from http://compdiag.uni-regensburg.de/software/transApproxs.shtml

Contact:  Juby.Jacob@klinik.uni-regensburg.de, Rainer.Spang@klinik.uni-regensburg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics
Authors: Kwon Yung-Keun , Cho Kwang-Hyun
Published: February 2008

Motivation: It has been widely reported that biological networks are robust against perturbations such as mutations. On the contrary, it has also been known that biological networks are often fragile against unexpected mutations. There is a growing interest in these intriguing observations and the underlying design principle that causes such robust but fragile characteristics of biological networks. For relatively small networks, a feedback loop has been considered as an important motif for realizing the robustness. It is still, however, not clear how a number of coupled feedback loops actually affect the robustness of large complex biological networks. In particular, the relationship between fragility and feedback loops has not yet been investigated till now.

Results: Through extensive computational experiments, we found that networks with a larger number of positive feedback loops and a smaller number of negative feedback loops are likely to be more robust against perturbations. Moreover, we found that the nodes of a robust network subject to perturbations are mostly involved with a smaller number of feedback loops compared with the other nodes not usually subject to perturbations. This topological characteristic eventually makes the robust network fragile against unexpected mutations at the nodes not previously exposed to perturbations.

Contact:  ckh@kaist.ac.kr

Supplementary information: Supplementary data are available at Bioinformatics online.
Increasing the nonlinear character of microbubble oscillations at low acoustic pressures
Authors: Stride E , Pancholi K , Edirisinghe M.J , Samarasinghe S
Published: February 2008

The nonlinear response of gas bubbles to acoustic excitation is an important phenomenon in both the biomedical and engineering sciences. In medical ultrasound imaging, for example, microbubbles are used as contrast agents on account of their ability to scatter ultrasound nonlinearly. Increasing the degree of nonlinearity, however, normally requires an increase in the amplitude of excitation, which may also result in violent behaviour such as inertial cavitation and bubble fragmentation. These effects may be highly undesirable, particularly in biomedical applications, and the aim of this work was to investigate alternative means of enhancing nonlinear behaviour. In this preliminary report, it is shown through theoretical simulation and experimental verification that depositing nanoparticles on the surface of a bubble increases the nonlinear character of its response significantly at low excitation amplitudes. This is due to the fact that close packing of the nanoparticles restricts bubble compression.
Differences in virulence attributes between cytolethal distending toxin positive and negative Campylobacter jejuni strains
Authors: Jain Deepika , Prasad Kashi Nath , Sinha Sushmita , Husain Nuzhat
Published: February 2008

Campylobacter jejuni is a common gastrointestinal bacterial pathogen. Although cytolethal distending toxin (CDT) is proposed to be an important virulence determinant of this pathogen, how CDT+ and CDT− strains differ in their biological properties remains largely unknown. The virulence properties of CDT+ and CDT− strains were studied on HeLa cells and in the suckling mouse model. Presence of the cdtB gene in Campylobacter species was determined by PCR. Five each of CDT+ and CDT−
C. jejuni strains were subjected to adherence, invasion and cytotoxicity assay on the HeLa cell line. Bacterial culture supernatants with and without CDT activity were inoculated intragastrically into 2-day-old suckling mice. The mice were sacrificed within 48 h. Histopathological examination of stomach, jejunum, ileum and colon was performed by haematoxylin/eosin staining. cdtB was detected in 88 % and 14 % of C. jejuni and Campylobacter coli strains, respectively. CDT+
C. jejuni strains adhered to and invaded HeLa cells in significantly higher numbers than CDT− strains [CDT+ vs CDT−, adherence 2.7×104±3.5×104 vs 2.7×102±1.9×102; invasion 1.0×103±1.3×103 vs1.4×101±3.1×101; P<0.01]. Culture supernatants of all CDT+ strains demonstrated CDT activity on HeLa cells. Mice inoculated with supernatant containing CDT activity had moderate to severe pathology in different parts of their gastrointestinal tract, with the colon being the major target. Mice inoculated with supernatant lacking CDT activity showed no significant pathology in the gastrointestinal tract. The results demonstrate that CDT+
C. jejuni strains adhere to and invade epithelial cells more efficiently than CDT− strains. CDT is responsible for intestinal pathology and the colon is the major target.