bluuebunny/crossref_metadata_2025 huggingface dataset:
Residual dipolar couplings measured in unfolded proteins are sensitive to amino-acid-specific geometries as well as local conformational sampling
Authors: Huang Jie-rong , Gentner Martin , Vajpai Navratna , Grzesiek Stephan , Blackledge Martin
Published: November 2012

Many functional proteins do not have well defined folded structures. In recent years, both experimental and computational approaches have been developed to study the conformational behaviour of this type of protein. It has been shown previously that experimental RDCs (residual dipolar couplings) can be used to study the backbone sampling of disordered proteins in some detail. In these studies, the backbone structure was modelled using a common geometry for all amino acids. In the present paper, we demonstrate that experimental RDCs are also sensitive to the specific geometry of each amino acid as defined by energy-minimized internal co-ordinates. We have modified the FM (flexible-Meccano) algorithm that constructs conformational ensembles on the basis of a statistical coil model, to account for these differences. The modified algorithm inherits the advantages of the FM algorithm to efficiently sample the potential energy landscape for coil conformations. The specific geometries incorporated in the new algorithm result in a better reproduction of experimental RDCs and are generally applicable for further studies to characterize the conformational properties of intrinsically disordered proteins. In addition, the internal-co-ordinate-based algorithm is an order of magnitude more efficient, and facilitates side-chain construction, surface osmolyte simulation, spin-label distribution sampling and proline cis/trans isomer simulation.
Paul S. Hossfeld and His Contribution to Geomorphology
Authors: Twidale C. Rowland
Published: November 2012

The received wisdom was and is that landscapes cannot be more than a few millions of years old. Nevertheless, consideration of local geology and age of sediments in adjacent basins convinced Paul S. Hossfeld that the summit surface of low relief preserved on the northern Mount Lofty Ranges of South Australia resulted from long-continued planation and that it is of Cretaceous age; that is, some 70 million years old. Hossfeld's apparently intuitive suggestion that very old landscapes exist, recorded in his graduate thesis but not further pursued by him, is the earliest known statement of this idea.
Paul Ramdohr in Australia: Contributions to Mineralogy, Mineragraphy, Ore Genesis and Meteoritics Resulting from His Three Visits
Authors: Sutton Pat
Published: November 2012

Paul Ramdohr (1890-1985), celebrated mineralogist, ore-deposit researcher and pioneer of ore microscopy spent three periods in Australia that differed considerably from each other in nature and structure. He was a Principal Research Scientist specializing in microscopy and ore deposits for nine months with the Council for Scientific and Industrial Research in Melbourne in 1948-9. For three months in 1962 he was Visiting Professor of Geology at the University of New South Wales. On holiday in Adelaide and Sydney in December 1970 and January 1971, he negotiated an agreement as a result of which the Mundrabilla II meteorite was shipped to Heidelberg in Germany for slicing and distribution for research purposes. This study summarizes his activities and direct contributions to Australian mineralogy during and as a result of those visits.
Kenneth James Le Couteur 1920 - 2011
Authors: Robson B. A.
Published: November 2012

Kenneth James Le Couteur was born in St Helier, Jersey, on 16 September 1920 and died in Canberra on 18 April 2011. He had a distinguished career as a theoretical physicist in the United Kingdom and in Australia as the Foundation Professor of Theoretical Physics in the Research School of Physical Sciences of the Australian National University. He was internationally recognized for his significant contributions to the statistical model of excited nuclei and the extraction of beams from proton synchrocyclotron accelerators.
Preconceptional omega-3 fatty acid supplementation on a micronutrient-deficient diet improves the reproductive cycle in Wistar rats
Authors: Meher Akshaya P. , Joshi Asmita A. , Joshi Sadhana R.
Published: November 2012

Folic acid and vitamin B12 deficiencies are associated with high reproductive risks ranging from infertility to fetal structural defects. The aim of the present study was to examine the effects of preconceptional omega-3 fatty acid supplementation (eicosapentaenoic acid and docosahexaenoic acid) to a micronutrient-deficient diet on the reproductive cycle in Wistar rats. Female rats were divided into five groups from birth and throughout pregnancy: a control group, a folic acid-deficient (FD) group, a vitamin B12-deficient (BD) group, a folic acid-deficient + omega-3 fatty acid-supplemented (FDO) group and a vitamin B12 deficient + omega-3 fatty acid-supplemented (BDO) group. Dams were killed on gestation Day 20 and their ovaries and mammary glands were dissected out and subjected to histological examination. Maternal micronutrient deficiency (FD and BD groups) resulted in an abnormal oestrous cycle (P < 0.001), whereas omega-3 fatty acid supplementation (FDO and BDO groups) restored the oestrous cycle to normal. There were fewer corpora lutea in the ovaries of FD rats compared with controls. In addition, rats in both the FD and BD groups exhibited an absence of lactating ducts in their mammary glands compared with controls. The findings of the present study indicate, for the first time, that maternal micronutrient deficiency affects the oestrous cycle and morphology of the ovary and mammary glands. Omega-3 fatty acid supplementation ameliorated these effects. This may have implications for infertility and pregnancy outcomes.
Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets
Authors: Davies Douglas R. , Gelinas Amy D. , Zhang Chi , Rohloff John C. , Carter Jeffrey D. , O’Connell Daniel , Waugh Sheela M. , Wolk Steven K. , Mayfield Wesley S. , Burgin Alex B. , Edwards Thomas E. , Stewart Lance J. , Gold Larry , Janjic Nebojsa , Jarvis Thale C.
Published: November 2012

Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.
Integration of nutritional support with paediatric HIV care in developing countries.
Authors: Semba R. D. , Pee S. de , Bloem M. W.
Published: November 2012

Human immunodeficiency virus (HIV) infection and malnutrition remain major causes of morbidity and mortality among children in developing countries. Malnutrition also exacerbates the clinical course of HIV-infected children by further compromising immunity and increasing the severity of opportunistic infections. This review summarizes current scientific knowledge regarding the role of nutrition in the pathophysiology of HIV infection in children and presents the perspective of integrating nutritional interventions with programmes in resource-limited settings to increase survival of HIV-exposed and -infected children. The three major programming areas for identifying and caring for HIV-infected and HIV-exposed children are: (1) prevention of mother-to-child transmission (PMTCT) of HIV, which is the earliest possible detection of HIV-exposure of the child, (2) care for HIV-infected children and (3) treatment of malnourished children, as for many children whose HIV exposure is unknown, malnutrition can be a first sign of HIV infection. Care for HIV-exposed and -infected infants and children requires early diagnosis of HIV exposure and status, especially through PMTCT services, availability of antiretrovirals (ARVs) and nutritional services including growth monitoring, use of specially formulated foods, micronutrient supplementation, vitamin A supplementation, zinc therapy and micronutrient supplementation for the treatment of diarrhoea, use of iodized salt and exclusive breastfeeding according to national guidelines. Given that the scale-up of PMTCT is expected to accelerate in the next several years, basic nutritional interventions should be part of the standard of care of these programmes.
Between-task competition for intentions and actions
Authors: Millington Rebecca S. , Poljac Edita , Yeung Nick
Published: November 2012

People can switch quickly and flexibly from one task to another, but suffer the effects of between-task competition when they do so: After switching, they tend to be distracted by irrelevant stimulus information and hampered by incorrect actions associated with recently performed tasks. This competition results in performance costs of switching, as well as a bias against switching when there is choice over which task to perform, particularly when switching from a difficult task to an easier one. Two experiments investigated the locus of these between-task competition effects in voluntary task switching. Participants switched between an easy location classification and a harder shape classification, making two responses on each trial: the first to register their task choice, the second to perform the chosen task on a subsequently presented stimulus. The results indicated that participants chose to perform the difficult shape task more often than the easier location task, evidence that between-task competition affects intentions that are expressed independently of task-specific actions. The bias was stronger in participants with faster choice speed, suggesting that these influences are relatively automatic. Moreover, even though participants had unlimited time to choose and prepare a task before stimulus presentation, their subsequent performance was nonetheless sensitive to persisting effects of between-task competition. Altogether these results indicate the pervasive influence of between-task competition, which affects both the expression of global task intentions and the production of task-specific actions.
Large magnetoelectric effect and low-loss high relative permittivity in 0–3 CuO/PVDF composite films exhibiting unusual ferromagnetism at room temperature
Authors: Bhadra D , Masud Md G , De S K , Chaudhuri B K
Published: November 2012

Flexible magnetoelectric 0–3 composite films formed with high dielectric (ε
r ∼ 104) CuO microparticles in a polyvinylidene fluoride (PVDF) polymer matrix showed multifunctional properties. The films prepared by the hot-moulding technique exhibit low-loss high relative permittivity (ε
eff ∼ 103) with good ferroelectric behaviour (with P–E loop) at the percolation threshold (f
CuO = f
c ∼ 0.25). Dielectric, ferroelectric, magnetic and direct magnetoelectric properties of the composites depend strongly on the CuO filler concentration (f
CuO). Interesting low field magnetoelectric response appears with about 5% decrease in ferroelectric polarization in the insulating composite (f
CuO = 0.20) along with 7.5% increase in the magnetodielectric coefficient under a magnetic field of 6 kG in the semiconducting percolative composite at room temperature. At this field, a maximum magnetoelectric voltage coefficient of 1.45 mV cm−1 Oe−1 was obtained. Even though the CuO sample is paramagnetic at ambient temperature, this typical composite film exhibits weakly ferromagnetic (with M–H loop) behaviour indicating multiferroic character. Our result represents an important step towards practical device applications using the high dielectric and magnetoelectric effects.
Electroluminescence from n-ZnO : Ga/p-GaN heterojunction light-emitting diodes with different interfacial layers
Authors: Zhang Lichun , Li Qingshan , Shang Liang , Zhang Zhongjun , Huang Ruizhi , Zhao Fengzhou
Published: November 2012

n-ZnO : Ga/p-GaN heterojunction light-emitting diodes with different interfacial layers are fabricated by pulsed laser deposition. All the devices demonstrate nonlinear rectifying behaviour. Due to the formation of Ga2O3 interfacial layers, n-ZnO : Ga/p-GaN exhibits strong ultraviolet emission centred at 382 nm and blue emission centred at 423 nm. Compared with a n-ZnO : Ga/MgO/p-GaN light-emitting diode, the turn-on voltage of n-ZnO : Ga/p-GaN with a Ga2O3 interfacial layer drops down to 7.6 V and the ultraviolet emission intensity is enhanced. Detailed electroluminescence mechanisms influenced by the interfacial layer are discussed using the band diagram of heterojunctions.
Composite metamaterial for ballistic electrons
Authors: Dumitriu A , Dragoman D
Published: November 2012

We show that a periodic structure can act as a composite metamaterial for ballistic electrons, allowing charge carrier propagation in energy regions in which the wavenumber is imaginary in both layers that compose the structure. We also calculate the phase and traversal times through this composite metamaterial and compare their energy dependence. Our results allow a generalization of the class of nanostructures similar to metamaterials with negative refractive index in optics.
Mean absorption coefficient of H2O–air–MgCl2/CaCl2/NaCl thermal plasmas
Authors: Hannachi R , Cressault Y , Salem D , Teulet Ph , Béji L , Lakhdar Z Ben
Published: November 2012

Under the local thermodynamic equilibrium hypothesis, the mean absorption coefficients (MACs) were calculated for H2O–air–MgCl2/CaCl2/NaCl thermal plasmas in a temperature range from 300 to 30 000 K and at atmospheric pressure. The MACs were computed under the hypothesis of isothermal plasmas which allows a good description of the radiation absorbed in cold regions. In this study, we took into account the absorption radiation resulting from the atomic continuum, molecular continuum, atomic lines and some molecular bands. Free–free transitions (bremsstrahlung) and free–bound (electron–ion recombination and electron attachment) or bound–free transitions in terms of absorption were considered for the calculation of atomic continuum. For bound–bound transitions, natural, resonance, van der Waals, Stark and Doppler effects were taken into account for the line broadenings while the escape factors were used to treat the self-absorption of the resonance lines. Molecular continuum was considered for the main molecules (H2, O2, N2, OH, NO, H2O, N2O, NO2, O3, NO3 and N2O5) whereas we studied only diatomic systems O2, N2, NO and

for the absorption of molecular bands. The influence of the proportion of MgCl2, CaCl2 or NaCl in a water–air mixture was analysed as the effect of the strong self-absorbed resonance lines of the alkaline salts (Ca, Ca+, Na, Na+, Mg, Mg+, Cl and Cl+). Our results show that a low concentration of alkaline salts (less than 1% in molar proportions) in the plasma increased the MACs at low temperatures (T < 10 000 K) due to the resonance lines mainly localized in the near-UV and visible spectral regions in opposition to hydrogen, oxygen or nitrogen species for which 90% of them exist in ultraviolet. In addition to the atomic and molecular continuum, the absorption radiation of molecular bands is important at low temperatures.
Model of a low-pressure radio-frequency inductive discharge in Ar/O2 used for plasma spray deposition
Authors: Lazzaroni C , Baba K , Nikravech M , Chabert P
Published: November 2012

A global (volume-averaged) model of a low-pressure radio-frequency (RF) inductive discharge used for nanostructured zinc oxide thin film deposition, the so-called spray-plasma device, is proposed. The plasma reactor is fed with an admixture of argon and oxygen and the pressure is typically several tens of mTorr. In the first step of the modelling, the injector and the substrate holder are not taken into account, and therefore zinc-containing species are not considered. The global model is based on the numerical integration of the particle balance equations and the electronic power balance equation. The model is first run until the steady state is reached to determine the equilibrium discharge parameters that are the species densities and the electron temperature. A parametric study is carried out varying the gas pressure, the RF power and the O2 fraction in the reactor. A parameter of great importance for the deposition process is the flux of the reactive species on the substrate holder and the model allows a fast exploration of this parameter. For continuous plasmas, the ratio of the reactive species flux to the total positive ion flux can be controlled varying the three basic parameters cited before (pressure, power and dilution). In the last part of the paper, we also investigate pulsed plasmas and the effect of the duty cycle variations on the neutral/ion flux ratio.
A new kind of electro-active polymer composite composed of silicone elastomer and polyethylene glycol
Authors: Liu Haoliang , Zhang Liqun , Yang Dan , Ning Nanying , Yu Yingchun , Yao Lu , Yan Bingyue , Tian Ming
Published: November 2012

In this work, a new kind of electro-active polymer composite composed of silicone and polyethylene glycol (PEG) was prepared by solution blending. Two types of PEG with average molecular weights of 600(PEG600) and 1500(PEG1500) were first blended with liquid silicone (DC3481) separately. Then, the dielectric, electrical, mechanical and electromechanical properties of pure silicone and the silicone/PEG composites were investigated. The silicone/PEG600 composite shows an increased dielectric constant and a decreased Young's modulus, resulting in an improved figure of merit (FOM) and an actuation strain of 11.5% at 40 V µm−1, which is 64% higher than pure silicone. This indicates that the actuation properties of silicone are largely improved by the addition of PEG600. However, for the silicone/PEG1500 composite, a much higher dielectric constant and an increased modulus due to its semi-crystalline structure are obtained, which lead to a decreased FOM and a smaller actuation strain than that of pure silicone. In addition, a comparison between theoretical strain and the corresponding experiment value was made. And the results indicate that not only the FOM, but the dielectric loss and mechanical loss play an important role in the actuation properties.
Atomistic simulation for the size-dependent melting behaviour of vanadium nanowires
Authors: Yang Xiyuan , Hu Wangyu , Liu Fusheng , Li Yan
Published: November 2012

Molecular dynamics and the modified analytical embedded atom potential are employed to study the size effect of a V nanowire (NW) on the melting behaviour. It is found that the melting temperature of the NW and its latent heat of fusion are much lower than those of the bulk, and depend strongly on the size. The calculated self-diffusion coefficient indicates that the premelting phenomenon first occurs at the surface and then spreads inwards with increasing temperature. The activation energy Q of the shell decreases as the reciprocal of the diameter increases. The lower activation energy indicates that premelting and melting can take place more easily. Finally, some representative snapshots on the temperature dependence of the cross-section atomic structure reveal that the melting mechanism of a large-sized NW is quite different from that of a small-sized one. For large-sized NWs (>4.0 nm), the surface plays a dominant role in the melting process, which is made up of two stages, i.e. gradual premelting and rapid melting. For small-sized NWs (<3.0 nm), the melting results mainly from the anharmonic effect of crystal lattice vibration, and the surface melting is barely noticeable. When the diameter size of the NWs ranges from 3.0 to 4.0 nm, both foregoing factors have an influence on the melting behaviour, which indicates that the critical diameter of the NW with a different melting mechanism is about 3.0 nm.
Electronegative plasma equilibria with spatially varying ionization
Authors: Kawamura E , Lichtenberg A J , Lieberman M A
Published: November 2012

Electronegative inductive discharges in higher pressure ranges typically exhibit strongly localized ionization near the coil structure, with decay of the electron temperature and ionization into the central discharge region. We use a two-dimensional (2D) fluid code with a chlorine feedstock gas to determine the spatial profiles of the particle densities and electron temperature in a cylindrical transformer-coupled plasma device excited by a stove-top coil on top of the plasma chamber. To compare with one-dimensional (1D) analytical models, the 2D results are area-averaged over the radius. The area-averaged ionization frequency ν
iz is found to decay exponentially away from the coils, allowing the ansatz of an exponentially decaying axial variation for ν
iz to be used in a 1D numerical model. The 1D model captures the main features of the axial variations of the area-averaged 2D fluid simulation, indicating that the main diffusion mechanisms act along the axial direction. A simple analytical global discharge model is also developed, accounting for the asymmetric density and ionization profiles. The global model gives the scalings of the ion densities and electron temperature with power and pressure. The 1D and global models are compared with the 2D fluid simulations, showing reasonable agreement.
Nylon-sputtered nanoparticles: fabrication and basic properties
Authors: Polonskyi O , Kylián O , Solař P , Artemenko A , Kousal J , Slavínská D , Choukourov A , Biederman H
Published: November 2012

Nylon-sputtered nanoparticles were prepared using a simple gas aggregation cluster source based on a planar magnetron (Haberland type) and equipped with a nylon target. Plasma polymer particles originated in an aggregation chamber and travelled to a main (deposition) chamber with a gas flow through an orifice. The deposited nanoparticles were observed to have a cauliflower-like structure. The nanoparticles were found to be nitrogen-rich with N/C ratio close to 0.5. An increase in rf power from 60 to 100 W resulted in a decrease in mean particle size from 210 to 168 nm whereas an increase in their residence time in the cluster source from 0.7 to 4.6 s resulted in an increase in the size from 73 to 231 nm.
Inadequacy of the Mott–Schottky equation in strongly pinned double Schottky barriers with no deep donors
Authors: Schipani F , Aldao C M , Ponce M A
Published: November 2012

The capacitive behaviour of an intergranular double Schottky barrier in a polycrystalline semiconductor was evaluated. We found that the widely applied version of the Mott–Schottky equation can lead to significant errors. Even though we considered strong Fermi level pinning at the interface and no deep levels, the Mott–Schottky equation can be inadequate leading to huge errors due to voltage splitting at double Schottky barriers. Experiments carried out on ZnO varistors corroborated the main trends of our analysis.
Effect of Ti addition on the structural, mechanical and damping properties of magnetron sputtered Ni–Mn–Sn ferromagnetic shape memory alloy thin films
Authors: Choudhary Nitin , Kaur Davinder
Published: November 2012

Titanium (Ti) co-sputtered Ni50.4Mn34.7Sn14.9 films deposited by magnetron sputtering onto Si(1 0 0) substrates at 823 K were investigated. X-ray diffraction profiles revealed the formation of highly (2 2 0)-oriented Ni–Mn–Sn–Ti austenite phase with significant decrease in grain size with increasing Ti power. Hardness (H), elastic modulus (E
r), damping (tan δ), figure of merit (FOM) and coefficient of restitution (e) of the films were evaluated using nanoindentation tests. A significant improvement in the hardness (10.5 GPa) and toughness

(0.040) was observed in the Ni51.0Mn28.2Sn11.0Ti9.7 nanocomposite film as compared with pure Ni50.4Mn34.7Sn14.9films. An impact model, which incorporates material behaviour, is presented that predicts the experimentally observed material quantities, including energy dissipation metrics such as the coefficient of restitution e with high accuracy. The highest damping factor (tan δ = 0.061), high FOM (0.79) with low coefficient of restitution (e = 0.28) quantifies excellent energy dissipation capacity in the Ni51.0Mn28.2Sn11.0Ti9.7 nanocomposite. Temperature dependence of magnetization (M–T) curves showed an increase in martensitic transformation temperatures with increasing Ti content. The Ni–Mn–Sn–Ti composite films exhibit ferromagnetic behaviour at room temperature.
Vibrational and rotational CARS measurements of nitrogen in afterglow of streamer discharge in atmospheric pressure fuel/air mixtures
Authors: Pendleton S J , Montello A , Carter C , Lempert W , Gundersen M A
Published: November 2012

The use of nonequilibrium plasma generated by nanosecond discharges to ignite fuel/air mixtures, known as transient plasma ignition (TPI), has been shown to effectively reduce ignition delay and improve engine performance relative to spark ignition for combustion engines. While this method is potentially useful for many engine applications, at present the underlying physics are poorly understood. This work uses coherent anti-Stokes Raman spectroscopy (CARS) to measure the rotational and vibrational excitation of nitrogen molecules in the discharge afterglow in a variety of fuel/air mixtures outside the limits of combustion in order to elucidate the thermal behaviour of TPI. The time evolution of relative populations of vibrationally excited states of nitrogen in the electronic ground state are reported for each gas mixture; it is shown that generation of these vibrationally excited states is inefficient during the discharge in air but that generation occurs at a high rate roughly 5 µs following the discharge; with the addition of fuels vibrationally excited states are observed during the discharge but an increase in population is still seen at 5 µs. Possible mechanisms for this behaviour are discussed. In addition, rotational temperature increases of at least 500 K are reported for all gas mixtures. The effect of this temperature increase on ignition, reaction rates, and thermal energy pathways are discussed.
The Circadian Clock-Associated Small GTPase LIGHT INSENSITIVE PERIOD1 Suppresses Light-Controlled Endoreplication and Affects Tolerance to Salt Stress in Arabidopsis
Authors: Terecskei Kata , Tóth Réka , Gyula Péter , Kevei Éva , Bindics János , Coupland George , Nagy Ferenc , Kozma-Bognár László
Published: November 2012

Circadian clocks are biochemical timers regulating many physiological and molecular processes according to the day/night cycle. The small GTPase LIGHT INSENSITIVE PERIOD1 (LIP1) is a circadian clock-associated protein that regulates light input to the clock. In the absence of LIP1, the effect of light on free-running period length is much reduced. Here, we show that in addition to suppressing red and blue light-mediated photomorphogenesis, LIP1 is also required for light-controlled inhibition of endoreplication and tolerance to salt stress in Arabidopsis (Arabidopsis thaliana). We demonstrate that in the processes of endoreplication and photomorphogenesis, LIP1 acts downstream of the red and blue light photoreceptors phytochrome B and cryptochromes. Manipulation of the subcellular distribution of LIP1 revealed that the circadian function of LIP1 requires nuclear localization of the protein. Our data collectively suggest that LIP1 influences several signaling cascades and that its role in the entrainment of the circadian clock is independent from the other pleiotropic effects. Since these functions of LIP1 are important for the early stages of development or under conditions normally experienced by germinating seedlings, we suggest that LIP1 is a regulator of seedling establishment.
Identification and Origin of N-Linked β-d-N-Acetylglucosamine Monosaccharide Modifications on Arabidopsis Proteins
Authors: Kim Young-Cheon , Jahren Neal , Stone Matthew D. , Udeshi Namrata D. , Markowski Todd W. , Witthuhn Bruce A. , Shabanowitz Jeffrey , Hunt Donald F. , Olszewski Neil E.
Published: November 2012

Many plant proteins are modified with N-linked oligosaccharides at asparagine-X-serine/threonine sites during transit through the endoplasmic reticulum and the Golgi. We have identified a number of Arabidopsis (Arabidopsis thaliana) proteins with modifications consisting of an N-linked N-acetyl-d-glucosamine monosaccharide (N-GlcNAc). Electron transfer dissociation mass spectrometry analysis of peptides bearing this modification mapped the modification to asparagine-X-serine/threonine sites on proteins that are predicted to transit through the endoplasmic reticulum and Golgi. A mass labeling method was developed and used to study N-GlcNAc modification of two thioglucoside glucohydrolases (myrosinases), TGG1 and TGG2 (for thioglucoside glucohydrolase). These myrosinases are also modified with high-mannose (Man)-type glycans. We found that N-GlcNAc and high-Man-type glycans can occur at the same site. It has been hypothesized that N-GlcNAc modifications are generated when endo-β-N-acetylglucosaminidase (ENGase) cleaves N-linked glycans. We examined the effects of mutations affecting the two known Arabidopsis ENGases on N-GlcNAc modification of myrosinase and found that modification of TGG2 was greatly reduced in one of the single mutants and absent in the double mutant. Surprisingly, N-GlcNAc modification of TGG1 was not affected in any of the mutants. These data support the hypothesis that ENGases hydrolyze high-Man glycans to produce some of the N-GlcNAc modifications but also suggest that some N-GlcNAc modifications are generated by another mechanism. Since N-GlcNAc modification was detected at only one site on each myrosinase, the production of the N-GlcNAc modification may be regulated.
Structure–activity correlations of variant forms of the B pentamer ofEscherichia colitype II heat-labile enterotoxin LT-IIb with Toll-like receptor 2 binding
Authors: Cody Vivian , Pace Jim , Nawar Hesham F. , King-Lyons Natalie , Liang Shuang , Connell Terry D. , Hajishengallis George
Published: November 2012

The pentameric B subunit of the type II heat-labile enterotoxin ofEscherichia coli(LT-IIb-B5) is a potent signaling molecule capable of modulating innate immune responses. It has previously been shown that LT-IIb-B5, but not the LT-IIb-B5Ser74Asp variant [LT-IIb-B5(S74D)], activates Toll-like receptor (TLR2) signaling in macrophages. Consistent with this, the LT-IIb-B5(S74D) variant failed to bind TLR2, in contrast to LT-IIb-B5and the LT-IIb-B5Thr13Ile [LT-IIb-B5(T13I)] and LT-IIb-B5Ser74Ala [LT-IIb-B5(S74A)] variants, which displayed the highest binding activity to TLR2. Crystal structures of the Ser74Asp, Ser74Ala and Thr13Ile variants of LT-IIb-B5have been determined to 1.90, 1.40 and 1.90 Å resolution, respectively. The structural data for the Ser74Asp variant reveal that the carboxylate side chain points into the pore, thereby reducing the pore size compared with that of the wild-type or the Ser74Ala variant B pentamer. On the basis of these crystallographic data, the reduced TLR2-binding affinity of the LT-IIb-B5(S74D) variant may be the result of the pore of the pentamer being closed. On the other hand, the explanation for the enhanced TLR2-binding activity of the LT-IIb-B5(S74A) variant is more complex as its activity is greater than that of the wild-type B pentamer, which also has an open pore as the Ser74 side chain points away from the pore opening. Data for the LT-IIb-B5(T13I) variant show that four of the five variant side chains point to the outside surface of the pentamer and one residue points inside. These data are consistent with the lack of binding of the LT-IIb-B5(T13I) variant to GD1a ganglioside.
Substrate channels revealed in the trimericLactobacillus reuteribacterial microcompartment shell protein PduB
Authors: Pang Allan , Liang Mingzhi , Prentice Michael B. , Pickersgill Richard W.
Published: November 2012

Lactobacillus reuterimetabolizes two similar three-carbon molecules, 1,2-propanediol and glycerol, within closed polyhedral subcellular bacterial organelles called bacterial microcompartments (metabolosomes). The outer shell of the propanediol-utilization (Pdu) metabolosome is composed of hundreds of mainly hexagonal protein complexes made from six types of protein subunits that share similar domain structures. The structure of the bacterial microcompartment protein PduB has a tandem structural repeat within the subunit and assembles into a trimer with pseudo-hexagonal symmetry. This trimeric structure forms sheets in the crystal lattice and is able to fit within a polymeric sheet of the major shell component PduA to assemble a facet of the polyhedron. There are three pores within the trimer and these are formed between the tandem repeats within the subunits. The structure shows that each of these pores contains three glycerol molecules that interact with conserved residues, strongly suggesting that these subunit pores channel glycerol substrate into the metabolosome. In addition to the observation of glycerol occupying the subunit channels, the presence of glycerol on the molecular threefold symmetry axis suggests a role in locking closed the central region.
Structural studies of human insulin cocrystallized with phenol or resorcinolviapowder diffraction
Authors: Karavassili Fotini , Giannopoulou Anastasia E. , Kotsiliti Eleni , Knight Lisa , Norrman Mathias , Schluckebier Gerd , Drube Lene , Fitch Andrew N. , Wright Jonathan P. , Margiolaki Irene
Published: November 2012

The effects of the ligands phenol and resorcinol on the crystallization of human insulin have been investigated as a function of pH. Powder diffraction data were used to characterize several distinct polymorphic forms. A previously unknown polymorph with monoclinic symmetry (P21) was identified for both types of ligand with similar characteristics [the unit-cell parameters for the insulin–resorcinol complex werea= 114.0228 (8),b= 335.43 (3),c= 49.211 (6) Å, β = 101.531 (8)°].
Nearest-cell: a fast and easy tool for locating crystal matches in the PDB
Authors: Ramraj V. , Evans G. , Diprose J. M. , Esnouf R. M.
Published: November 2012

When embarking upon X-ray diffraction data collection from a potentially novel macromolecular crystal form, it can be useful to ascertain whether the measured data reflect a crystal form that is already recorded in the Protein Data Bank and, if so, whether it is part of a large family of related structures. Providing such information to crystallographers conveniently and quickly, as soon as the first images have been recorded and the unit cell characterized at an X-ray beamline, has the potential to save time and effort as well as pointing to possible search models for molecular replacement. Given an input unit cell, and optionally a space group,Nearest-cellrapidly scans the Protein Data Bank and retrieves near-matches.
In situreaction furnace for real-time XRD studies
Authors: Riello Pietro , Lausi Andrea , Macleod Jennifer , Plaisier Jasper Rikkert , Zerauschek Giulio , Fornasiero Paolo
Published: November 2012

The new furnace at the Materials Characterization by X-ray Diffraction beamline at Elettra has been designed for powder diffraction measurements at high temperature (up to 1373 K at the present state). Around the measurement region the geometry of the radiative heating element assures a negligible temperature gradient along the capillary and can accommodate either powder samples in capillary or small flat samples. A double capillary holder allows flow-through of gas in the inner sample capillary while the outer one serves as the reaction chamber. The furnace is coupled to a translating curved imaging-plate detector, allowing the collection of diffraction patterns up to 2θ ≃ 130°.
A preliminary design of a knot undulator
Authors: Xi Fuchun , Shi Tan , Fan Qingyan , Prestemon Soren , Wan Weishi , An Zhenghua , Qiao S.
Published: November 2012

The magnetic field configuration of the previously proposed knot undulator [Qiaoet al.(2009).Rev. Sci. Instrum.80, 085108] is realised in the design of a hybridized elliptically polarized undulator, which is presented. Although the details of the field distribution are not the same as those in the theoretical proposal, it is demonstrated that the practical knot undulator could work perfectly. In order to understand the minor discrepancies of the two, mathematical formulae of the synchrotron radiation are derived based on the Fourier transform of the magnetic field. From the results of calculations by simulation program, the discrepancies could be well interpreted by the corresponding formulae. The results show the importance of optimization of the end sections of the knot undulator to suppress the on-axis heat load. Furthermore, a study of the impact of the undulator on beam dynamics of the storage ring was conducted using the Shanghai Synchrotron Radiation Facility as an example and the results show that the knot undulator has little effect on the beam.
Measurements of spatial variations in response of ionization chambers
Authors: Miller William E. B. , Kastengren Alan L.
Published: November 2012

Measurements of the spatial variations in the response of three ionization chamber (IC) designs were tested as a function of chamber bias voltage, incident X-ray flux and fill gas. Two components of spatial variation are seen. When the ionization chambers are near saturation, spatial variations exist that are tied to the chamber geometry. While the response of some chambers is relatively flat, others show significant variation across the IC. These variations appear to be inherent in the response of each IC at saturation. When the chamber is far from saturation, large spatial variations in response are present when N2is used as a fill gas, but not when ambient air is used as a fill gas. These appear to be tied to space charge effects.
Does the leaf economic spectrum hold within local species pools across varying environmental conditions?
Authors: Wright Justin P. , Sutton‐Grier Ariana
Published: November 2012

Understanding patterns of trait variation across environmental variability is necessary for development of ecological predictions. The leaf economic spectrum (LES) has demonstrated global trade‐offs in leaf traits, but it is unclear whether such patterns are robust in local communities exposed to varying environments.

We conducted separate greenhouse experiments to examine the effects of varying water‐table depth and nitrogen availability on leaf‐level trait values among a suite of co‐occurring wetland species. We then assessed the effects of species‐specific trait value responses on relationships predicted by LES and whether species responded similarly to variations in water‐table depth and nitrogen availability.

We found that both water‐table depth and nitrogen availability had significant species by treatment interactions for specific leaf area, leaf nitrogen and photosynthetic rates, indicating species‐specific responses to environmental variability. The responses of individual traits to different treatment levels were relatively consistent across species, but multivariate responses were more variable.

We found that apart from significant relationships between specific leaf area and photosynthetic rate under some treatments, there was little support for the relationships predicted by the LES.

These results suggest that, before trait‐based ecology will be able to make progress towards using plant traits to predict responses of communities and ecosystems to changes in environmental drivers, considerable attention needs to be paid to the processes that control intraspecific trait variation.
The peptide chain release factor methyltransferase PrmC is essential for pathogenicity and environmental adaptation of Pseudomonas aeruginosaPA14
Authors: Pustelny Christian , Brouwer Stephan , Müsken Mathias , Bielecka Agata , Dötsch Andreas , Nimtz Manfred , Häussler Susanne
Published: November 2012

Pseudomonas aeruginosa pathogenicity and its capability to adapt to multiple environments are dependent on the production of diverse virulence factors, controlled by the sophisticated quorum sensing (QS) network of P. aeruginosa. To better understand the molecular mechanisms that underlie this adaptation we searched for novel key regulators of virulence factor production by screening a PA14 transposon mutant library for potential candidates acting downstream of the unique 2‐alkyl‐4‐quinolone (AQ) QS system of P. aeruginosa. We focused the work on a protein named HemK with high homology to PrmC of Escherichia coli displaying a similar enzymatic activity (therefore also referred to as PrmC). In this study, we demonstrate that PrmC is an S‐adenosyl‐l‐methionine (AdoMet)‐dependent methyltransferase of peptide chain release factors (RFs) essential for the expression of several virulence factors, such as pyocyanin, rhamnolipids and the type III‐secreted toxin ExoT. Furthermore, the PA14_prmC mutant strain is unable to grow under anoxic conditions and has a significantly reduced pathogenicity in the infection model Galleria mellonella. Along with transcriptomic and proteomic analyses, the presented data indicate that the methylation of RFs in P. aeruginosa seems to have a global effect on cellular processes related to the virulence of this nosocomial pathogen.
Inconsistencies in clinical guidelines for obstetric anaesthesia for Caesarean section
Authors: WINTHER L. P. , MITCHELL A. U. , MØLLER A. M.
Published: November 2012

Background

Anaesthetists need evidence‐based clinical guidelines, also in obstetric anaesthesia. We compared the Danish, English, American, and German national guidelines for anaesthesia for Caesarean section. We focused on assessing the quality of guideline development and evaluation of the guidelines' content.

Methods

We compared the four countries' guideline developmental quality by using the Appraisal of Guidelines for Research and Evaluation (AGREE) instrument, an international tool for development and assessment of guidelines. The clinically important content of these countries' guidelines was compared.

Results

We found differences in the quality of guideline development in the four countries. The German guidelines scored very low in the AGREE analysis, and the Danish national guideline scored low in the AGREE analysis. The American and British guideline both achieved high scores in the AGREE analysis. We found differences in the content of the four countries' guidelines. The Danish, American, and British guidelines were comprehensive but with some variation in the content.

Conclusion

Development of national guidelines might benefit from following standardised regulations, such as those used in the AGREE tool. Content of guidelines is not standardised. Recommendations for the content of guidelines might contribute to standardising clinical guidelines.
Psychopathological long‐term outcome of schizophrenia – a review
Authors: Lang F. U. , Kösters M. , Lang S. , Becker T. , Jäger M.
Published: November 2012

Objective

In the past, the comparability of empirical studies that examined the course and outcome of schizophrenia was limited by their use of different diagnostic systems. Focussing on the psychopathological long‐term outcome, the present article aims to review follow‐up studies that used modern operationalized diagnostic criteria for schizophrenia (DSM‐III, DSM‐III‐R, DSM‐IV and ICD‐10).

Method

We searched MEDLINE, the Cochrane Central Register of Controlled Trials, EMBASE, PsycINFO and PSYNDEX for relevant studies up to the year 2011. Twenty‐one studies were included in the final analysis.

Results

The long‐term outcome of schizophrenia was heterogeneous and included full remissions as well as severe chronic states. Schizophrenia, however, showed a considerably more unfavourable outcome than other diagnostic groups such as schizoaffective or affective disorders. Psychopathological symptoms remained relatively stable in the course of illness. Several predictors for a poor outcome were identified, such as male gender or pronounced negative symptoms.

Conclusion

Recent studies using modern diagnostic systems largely confirm the results of earlier studies. Current diagnostic criteria for schizophrenia identify a heterogeneous sample of patients. The influence of therapeutic interventions on long‐term outcome remains unclear.
The mediating role of alcohol‐related memory associations on the relation between perceived parental drinking and the onset of adolescents' alcohol use
Authors: Van Der Vorst Haske , Krank Marvin , Engels Rutger C. M. E. , Pieters Sara , Burk William Jay , Mares Suzanne H. W.
Published: November 2012

Aims

The aim of the current study was to examine the mediating role of alcohol‐related memory associations in the relation between perceived parental drinking and the onset of adolescents' alcohol use. Gender and grade were also included in the analyses.

Design

We tested a mediation model within a structural path modelling framework using longitudinal data (two waves).

Setting and Participants

The sample consisted of 608 Canadian adolescents (42.9% boys), who did not have any alcohol experiences at the first measurement. The adolescents were recruited from all grades 7–9 classes in a large school district in western Canada.

Measurements

Alcohol‐related memory associations were tested with the Word Association Test. We used adolescent self‐reports of alcohol use and parental drinking.

Findings

Results clearly showed a mediation effect of alcohol‐related memory associations [estimate = 0.023, 95% confidence interval (CI): 0.002–0.044). That is, parental drinking as perceived by the adolescent was related positively to alcohol‐related memory associations, which in turn predicted adolescents' alcohol use a year later. Gender and grade were related to alcohol‐related memory associations. That is, boys and adolescents of higher grades had more memory associations.

Conclusions

Children appear to form memory associations related to alcohol before they ever drink alcohol themselves, and these associations appear to mediate the link between their perceptions of their parents' drinking and their own initial alcohol use.