bluuebunny/crossref_metadata_2025 huggingface dataset:
Coupling landscape water storage and supplemental irrigation to increase productivity and improve environmental stewardship in the U.S. Midwest
Authors: Baker John M. , Griffis Timothy J. , Ochsner Tyson E.
Published: March 2012

Agriculture must increase production for a growing population while simultaneously reducing its environmental impacts. These goals need not be in tension with one another. Here we outline a vision for improving both the productivity and environmental performance of agriculture in the U.S. Midwest, also known as the Corn Belt. Mean annual precipitation has increased throughout the region over the past 50 years, consistent with climate models that attribute the increase to a warming troposphere. Stream gauge data indicate that higher precipitation has been matched or exceeded by higher stream flows, contributing to flooding, soil loss, and excessive nutrient flux to the Gulf of Mexico. We propose increasing landscape hydrologic storage through construction of ponds and restoration of wetlands to retain water for supplemental irrigation while also reducing flood risks. Primary productivity is proportional to transpiration, and analysis shows that in the U.S. Midwest both can be sustainably increased with supplemental irrigation. The proposed strategy should reduce interannual yield variability by limiting losses due to transient drought, while facilitating adoption of cropping systems that “perennialize” the landscape to take advantage of the full potential growing season. When implemented in concert, these practices should reduce the riverine nitrogen export that is a primary cause of hypoxia in the Gulf of Mexico. Erosive sediment losses should also be reduced through the combination of enhanced hydrologic storage and increased vegetative cover. Successful implementation would require watershed‐scale coordination among producers and landowners. An obvious mechanism to encourage this is governmental farm policy.
Observations reveal external driver for Arctic sea‐ice retreat
Authors: Notz Dirk , Marotzke Jochem
Published: March 2012

The very low summer extent of Arctic sea ice that has been observed in recent years is often casually interpreted as an early‐warning sign of anthropogenic global warming. For examining the validity of this claim, previously IPCC model simulations have been used. Here, we focus on the available observational record to examine if this record allows us to identify either internal variability, self‐acceleration, or a specific external forcing as the main driver for the observed sea‐ice retreat. We find that the available observations are sufficient to virtually exclude internal variability and self‐acceleration as an explanation for the observed long‐term trend, clustering, and magnitude of recent sea‐ice minima. Instead, the recent retreat is well described by the superposition of an externally forced linear trend and internal variability. For the externally forced trend, we find a physically plausible strong correlation only with increasing atmospheric CO2concentration. Our results hence show that the observed evolution of Arctic sea‐ice extent is consistent with the claim that virtually certainly the impact of an anthropogenic climate change is observable in Arctic sea ice already today.
Diversion of plasma due to high pressure in the inner magnetosphere during steady magnetospheric convection
Authors: Kissinger J. , McPherron R. L. , Hsu T.‐S. , Angelopoulos V.
Published: March 2012

Steady magnetospheric convection (SMC) events in the Earth's magnetosphere are thought to result from balancing the rate of opening flux through solar wind‐magnetosphere reconnection at the dayside magnetopause to the rate of closing flux through reconnection in the magnetotail. For this to occur, reconnected flux in the tail must return to the dayside to balance the dayside reconnection rate. Using Geotail and THEMIS data over a span of 14 years, we examine the average plasma conditions and fast Earthward flows during SMC intervals and compare them to other types of geomagnetic activity, such as quiet intervals, isolated substorm phases, and the two hours before an SMC (Pre‐SMC intervals). We show that the average total pressure in the inner magnetosphere is higher during SMC events than for other types of activity. This higher pressure region extends to larger radial distances, and causes fast Earthward flows to divert toward the dawn or dusk flanks and continue to the dayside. This pattern is contrasted to substorms, during which flows are directed toward the inner magnetosphere and flux remains there in the “pile‐up region.” We suggest that the SMC pattern of flow deflection carries enough flux from the tail to the dayside to allow for balanced reconnection. Finally, the Pre‐SMC intervals have plasma conditions that are similar to, but slightly weaker than, SMC events. Since most SMCs begin with a substorm, this indicates that preconditioning of the magnetosphere by prior geomagnetic activity is important in setting up the magnetotail for an SMC state.
The hypothalamic genesis of obesity
Authors: Belluscio Daniel Oscar
Published: March 2012

The theories on obesity genesis shifted during the past years from the simple conception of "just overeating" to data supporting the diencephalic origin of the disease. Summarized findings on this issue are displayed.
Steroid-like signalling by interferons: making sense of specific gene activation by cytokines
Authors: Johnson Howard M. , Noon-Song Ezra N. , Kemppainen Kaisa , Ahmed Chulbul M.
Published: March 2012

Many cytokines, hormones and growth factors use the JAK (Janus kinase)/STAT (signal transducer and activator of transcription) pathway for cell signalling and specific gene activation. In the classical model, ligand is said to interact solely with the receptor extracellular domain, which triggers JAK activation of STATs at the receptor cytoplasmic domain. Activated STATs are then said to carry out nuclear events of specific gene activation. Given the limited number of STATs (seven) and the activation of the same STATs by cytokines with different functions, the mechanism of the specificity of their signalling is not obvious. Focusing on IFNγ (interferon γ), we have shown that ligand, receptor and activated JAKs are involved in nuclear events that are associated with specific gene activation, where the receptor subunit IFNGR1 (IFNγ receptor 1) functions as a transcription/co-transcription factor and the JAKs are involved in key epigenetic events. RTKs (receptor tyrosine kinases) such as EGFR [EGF (epidermal growth factor) receptor] and FGFR [FGF (fibroblast growth factor) receptor] also undergo nuclear translocation in association with their respective ligands. EGFR and FGFR, like IFNGR1, have been shown to function as transcription/co-transcription factors. The RTKs also regulate other kinases that have epigenetic effects. Our IFNγ model, as well as the RTKs EGFR and FGFR, have similarities to that of steroid receptor signalling. These systems consist of ligand–receptor–co-activator complexes at the genes that they activate. The co-activators consist of transcription factors and kinases, of which the latter play an important role in the associated epigenetics. It is our view that signalling by cytokines such as IFNγ is but a variation of specific gene activation by steroid hormones.
Effects of a glucokinase activator on hepatic intermediary metabolism: study with 13C-isotopomer-based metabolomics
Authors: Nissim Itzhak , Horyn Oksana , Nissim Ilana , Daikhin Yevgeny , Wehrli Suzanne L. , Yudkoff Marc , Matschinsky Franz M.
Published: March 2012

GKAs (glucokinase activators) are promising agents for the therapy of Type 2 diabetes, but little is known about their effects on hepatic intermediary metabolism. We monitored the fate of 13C-labelled glucose in both a liver perfusion system and isolated hepatocytes. MS and NMR spectroscopy were deployed to measure isotopic enrichment. The results demonstrate that the stimulation of glycolysis by GKA led to numerous changes in hepatic metabolism: (i) augmented flux through the TCA (tricarboxylic acid) cycle, as evidenced by greater incorporation of 13C into the cycle (anaplerosis) and increased generation of 13C isotopomers of citrate, glutamate and aspartate (cataplerosis); (ii) lowering of hepatic [Pi] and elevated [ATP], denoting greater phosphorylation potential and energy state; (iii) stimulation of glycogen synthesis from glucose, but inhibition of glycogen synthesis from 3-carbon precursors; (iv) increased synthesis of N-acetylglutamate and consequently augmented ureagenesis; (v) increased synthesis of glutamine, alanine, serine and glycine; and (vi) increased production and outflow of lactate. The present study provides a deeper insight into the hepatic actions of GKAs and uncovers the potential benefits and risks of GKA for treatment of diabetes. GKA improved hepatic bioenergetics, ureagenesis and glycogenesis, but decreased gluconeogenesis with a potential risk of lactic acidosis and fatty liver.
Analysis of eddy current losses in cylindrical linear oscillatory actuator with Halbach permanent magnet array mover
Authors: Ko Kyoung-Jin , Choi Ji-Hwan , Jang Seok-Myeong , Choi Jang-Young
Published: March 2012

This paper describes calculations and comparisons of eddy current losses in a cylindrical linear oscillatory actuator with a Halbach array permanent magnet mover for different voltage source waveforms. Using the magnetic vector potential and a two-dimensional cylindrical coordinate system, the paper presents an analytical procedure and obtains solutions for the eddy current losses using the Poynting theorem. To verify the proposed method, the eddy current losses obtained from the analytical solutions are compared with the results of a non-linear finite element method. Moreover, this paper shows that the eddy current losses are more significant when the actuator is driven by a square voltage waveform than when it is driven by a sinusoidal voltage waveform.
Improved conductivity of aluminum-doped ZnO: The effect of hydrogen diffusion from a hydrogenated amorphous silicon capping layer
Authors: Ponomarev M. V. , Sharma K. , Verheijen M. A. , van de Sanden M. C. M. , Creatore M.
Published: March 2012

Plasma-deposited aluminum-doped ZnO (ZnO:Al) demonstrated a resistivity gradient as function of the film thickness, extending up to about 600 nm. This gradient decreased sharply when the ZnO:Al was capped by a hydrogenated amorphous silicon layer (a-Si:H) and subsequently treated according to the solid phase crystallization (SPC) procedure at 600 °C. The resistivity reduced from 1.2 · 10−1 to 2.6 · 10−3 Ω · cm for a film thickness of 130 nm, while for thicker films the decrease in resistivity was less pronounced, i.e., a factor of 2 for a film thickness of 810 nm. While the carrier concentration was not affected, the mobility significantly increased from 7 to 30 cm2/V · s for the thick ZnO:Al layers. This increase was ascribed to the passivation of grain boundary defects by hydrogen, which diffused from the a-Si:H toward the ZnO:Al during the SPC procedure. The passivation effect was more pronounced in thinner ZnO:Al layers, characterized by a smaller grain size, due to the presence of large grain boundaries. For thicker films with grain sizes up to 200–300 nm the mobility became progressively less affected by the presence of grain boundaries. Therefore, the hydrogen-induced improvement in conductivity was less significant for the thick ZnO:Al films.
A tuneable ultra-compact high-power, ultra-short pulsed, bright gamma-ray source based on bremsstrahlung radiation from laser-plasma accelerated electrons
Authors: Cipiccia S. , Wiggins S. M. , Shanks R. P. , Islam M. R. , Vieux G. , Issac R. C. , Brunetti E. , Ersfeld B. , Welsh G. H. , Anania M. P. , Maneuski D. , Lemos N. R. C. , Bendoyro R. A. , Rajeev P. P. , Foster P. , Bourgeois N. , Ibbotson T. P. A. , Walker P. A. , Shea V. O. , Dias J. M. , Jaroszynski D. A.
Published: March 2012

The laser driven plasma wakefield accelerator is a very compact source of high energy electrons. When the quasi-monoenergetic beam from these accelerators passes through dense material, high energy bremsstrahlung photons are emitted in a collimated beam with high flux. We show how a source based on this emission process can produce more than 109 photons per pulse with a mean energy of 10 MeV. We present experimental results that show the feasibility of this method of producing high energy photons and compare the experimental results with GEANT4 Montecarlo simulations, which also give the scaling required to evaluate its suitability as method to produce radioisotopes via photo-nuclear reactions or for imaging applications.
Spin-polarized itinerant electrons in Co-based Heusler compounds investigated by magnetic Compton scattering
Authors: Mizusaki S. , Ohnishi T. , Ozawa T. C. , Noro Y. , Itou M. , Sakurai Y. , Nagata Y.
Published: March 2012

The spin-polarized electron momentum density distributions (magnetic Compton profiles) of Co2YAl (Y = Ti, V, Cr, and Fe) Heusler compounds have been measured using a magnetic Compton scattering technique. The experimental magnetic Compton profiles have been decomposed into the itinerant electron and localized 3d electron contributions. The decomposition shows that the number of spin-polarized itinerant electrons is proportional to that of spin-polarized localized 3d electrons, indicating that the strength of indirect exchange interaction is dominated by the localized 3d magnetic moment. This finding suggests that the spin-polarized itinerant part in the magnetic Compton profile is used as a scale that can measure the strength of the sp-d interaction.
Asymmetric stochasticity of magnetization reversal dynamics in exchange-biased IrMn/CoFe Film
Authors: Lee Hun-Sung , Ryu Kwang-Su , You Chun-Yeol , Jeon Kun-Rok , Yang See-Hun , Parkin Stuart S. P. , Shin Sung-Chul
Published: March 2012

In this study, we investigated the stochastic nature of domain reversal dynamics in exchange-biased IrMn/CoFe film using a time-resolved Kerr microscope. Interestingly, the statistical distributions of the magnetization half-reversal times for both forward and backward applied fields show that the magnetization reversal dynamics is much more stochastic for the backward branch, where an applied field is parallel to the exchange-bias field direction. The enhanced stochasticity is ascribed to the large degree of magnetic disorder during backward reversal, which induces discrete and random Barkhausen jumps, whereas the forward branch reversal is dominated by a thermally activated depinning process caused by a single potential barrier. This result can be explained by the asymmetry of the magnetic disorder between both branches of a hysteresis loop.
First-principles study of interstitial diffusion of oxygen in nickel chromium binary alloy
Authors: Jin Kim Jong , Hun Shin Sang , Ang Jung Ju , Joon Choi Kyung , Hyun Kim Ji
Published: March 2012

The first-principles calculations of the diffusion processes of oxygen in pure Ni and Ni-Cr binary alloy are conducted to understand the oxidation behavior of nickel base alloys. The cohesive energy, insertion energy of atomic oxygen, and vacancy formation energy in nickel are calculated and compared with experimental data. The activation energies of oxygen are also calculated. The results show agreement with previous work for the oxygen diffusion in pure nickel. However, the calculated activation energy for the diffusion of oxygen in Ni-Cr binary alloy showed lower values than that in nickel because of the limitations of the current calculation model.
Electronic excitations in long polyenes revisited
Authors: Schmidt Maximilian , Tavan Paul
Published: March 2012

We apply the valence shell model OM2 [W. Weber and W. Thiel, Theor. Chem. Acc. 103, 495, (2000)10.1007/s002149900083] combined with multireference configuration interaction (MRCI) to compute the vertical excitation energies and transition dipole moments of the low-energy singlet excitations in the polyenes with 4 ⩽ N ⩽ 22π-electrons. We find that the OM2/MRCI descriptions closely resemble those of Pariser-Parr-Pople (PPP) π-electron models [P. Tavan and K. Schulten, Phys. Rev. B 36, 4337, (1987)], if equivalent MRCI procedures and regularly alternating model geometries are used. OM2/MRCI optimized geometries are shown to entail improved descriptions particularly for smaller polyenes (N ⩽ 12), for which sizeable deviations from the regular model geometries are found. With configuration interaction active spaces covering also the σ- in addition to the π-electrons, OM2/MRCI excitation energies turn out to become smaller by at most 0.35 eV for the ionic and 0.15 eV for the covalent excitations. The particle-hole (ph) symmetry, which in Pariser-Parr-Pople models arises from the zero-differential overlap approximation, is demonstrated to be only weakly broken in OM2 such that the oscillator strengths of the covalent \documentclass[12pt]{minimal}\begin{document}${\rm 1B_u^-}$\end{document}1Bu− states, which artificially vanish in ph-symmetric models, are predicted to be very small. According to OM2/MRCI and experimental data the \documentclass[12pt]{minimal}\begin{document}${\rm 1B_u^-}$\end{document}1Bu− state is the third excited singlet state for N < 12 and becomes the second for N ⩾ 14. By comparisons with results of other theoretical approaches and experimental evidence we argue that deficiencies of the particular MRCI method employed by us, which show up in a poor size consistency of the covalent excitations for N > 12, are caused by its restriction to at most doubly excited references.
Generating an inhomogeneous stress field as a technique to study cell mechanoresponse
Authors: Raz-Ben Aroush D. , Barlam D. , Daniel Wagner H.
Published: March 2012

Over the last decade, it has been shown that cells can sense and respond to mechanical perturbations in their underlying substrate (or extra-cellular matrix, ECM). However, the effect of an inhomogeneous stress on cell response has been scarcely studied, mainly due to technical difficulty to create a well-controlled stress (or strain) state in the ECM, even though stress gradients are of critical importance in—and likely induce—wound healing, for example, through local cell growth and tissue formation. Here, we present a technique which can be easily used to study the response behavior of cells to a well-defined inhomogeneous stress field.
Analysis of the reverse leakage current in AlGaN/GaN Schottky barrier diodes treated with fluorine plasma
Authors: Jin Ha Woo , Chhajed Sameer , Jae Oh Seung , Hwang Sunyong , Kyu Kim Jong , Lee Jae-Hoon , Kim Ki-Se
Published: March 2012

The carrier transport mechanism of CF4 plasma-treated AlGaN/GaN Schottky barrier diodes (SBDs) under reverse bias is investigated. The reverse leakage current is reduced by ∼2 orders of magnitude after the CF4 plasma treatment, but increases exponentially with increasing temperature, indicating that a thermally activated transport mechanism is involved. Based on the activation energy estimated from temperature-dependent current-voltage characteristics and the emission barrier height extracted from Frenkel-Poole emission model, it is suggested that the dominant carrier transport mechanism in the CF4 plasma treated SBDs is the Frenkel-Poole emission from fluorine-related deep-level states into the continuum states of dislocations.
Ti-electrode effects of NiO based resistive switching memory with Ni insertion layer
Authors: Ryu Seung Wook , Ahn Young Bae , Kim Hyeong Joon , Nishi Yoshio
Published: March 2012

Effects of Ti top electrode on unipolar resistive switching characteristics are investigated for NiO based resistive switching memory with Ni-inserting layer, compared with those for Pt-electrode. Current-voltage curves for forming process are almost identical for Ti-Ni-NiO-Pt and Pt-Ni-NiO-Pt structure, which may suggest that Ti does not chemically react with NiO. However, I-V curves for reset and set operation with Ti top electrode show improved resistive switching behaviors, such as reduction of reset current and less variation of both high and low resistance states. In order to understand the mechanism for improved resistive switching properties, electro-thermal simulation is performed, which shows that improvement in resistive switching characteristics is ascribed to reduced heat flow through top electrode resulting from lower thermal conductivity of Ti as compared to Pt.
Two-photon-pumped optical gain in dye-polymer composite materials
Authors: Li Wei , Zhang Chunfeng , Chen Qi , Wang Xiaoyong , Xiao Min
Published: March 2012

Optical gain with two-photon pumping has been quantitatively characterized in the energy-transfer-coupled dye-polymer composite materials. Using femtosecond transient absorption spectroscopy, we observed frequency up-converted optical amplification in the dye-doped polymer films. Net optical gain coefficient in the polymer films with optimized doping is evaluated to be about 25 cm−1 by the variable-stripe-length measurements, which induces spectral narrowing of emission with linewidth changing from 42 nm to 9 nm. The intrinsic mechanisms for the optical gain in such composite system have been assigned to the amplified spontaneous emission and superfluorescence at relatively low and high excitation regimes, respectively.
Effect of in-situ oxygen on the electronic properties of graphene grown by carbon molecular beam epitaxy
Authors: Park Jeongho , Mitchel W. C. , Elhamri Said , Back Tyson C.
Published: March 2012

We report that graphene grown by molecular beam epitaxy from solid carbon (CMBE) on (0001) SiC in the presence of unintentional oxygen exhibits a small bandgap on the order of tens of meV. The presence of bandgaps is confirmed by temperature dependent Hall effect and resistivity measurements. X-ray photoelectron spectroscopy (XPS) measurements suggest that oxygen incorporates into the SiC substrate in the form of O-Si-C and not into the graphene as graphene oxide or some other species. The effect is independent of the carrier type of the graphene. Temperature dependent transport measurements show the presence of hopping conduction in the resistivity and a concurrent disappearance of the Hall voltage. Interactions between the graphene layers and the oxidized substrate are believed to be responsible for the bandgap.
High optical sensitivity to ambient conditions of uncapped InGaAs surface quantum dots
Authors: Milla M. J. , Ulloa J. M. , Guzmán A.
Published: March 2012

The influence of the environment on the optical properties of self-assembled In0.5Ga0.5As surface quantum dots is studied as a function of different ambient conditions for sensing applications. Their room temperature photoluminescence (PL) quenches under vacuum and decreases strongly under dry O2 or N2 environments. Nevertheless, they have a strong signal at 1.55 μm in air or in a wet atmosphere. The presence of water molecules in the environment improves the PL intensity likely due to its polar character and therefore its easier adsorption by the surface dangling bonds, leading to a suppression of the non-radiative recombination centers.
Electroluminescence from strained germanium membranes and implications for an efficient Si-compatible laser
Authors: Nam Donguk , Sukhdeo David , Cheng Szu-Lin , Roy Arunanshu , Chih-Yao Huang Kevin , Brongersma Mark , Nishi Yoshio , Saraswat Krishna
Published: March 2012

We demonstrate room-temperature electroluminescence (EL) from light-emitting diodes (LEDs) on highly strained germanium (Ge) membranes. An external stressor technique was employed to introduce a 0.76% bi-axial tensile strain in the active region of a vertical PN junction. Electrical measurements show an on-off ratio increase of one order of magnitude in membrane LEDs compared to bulk. The EL spectrum from the 0.76% strained Ge LED shows a 100 nm redshift of the center wavelength because of the strain-induced direct band gap reduction. Finally, using tight-binding and finite-difference time domain simulations, we discuss the implications for highly efficient Ge lasers.
First principle electronic, structural, elastic, and optical properties of strontium titanate
Authors: Ekuma Chinedu E. , Jarrell Mark , Moreno Juana , Bagayoko Diola
Published: March 2012

We report self-consistent ab-initio electronic, structural, elastic, and optical properties of cubic SrTiO3 perovskite. Our non-relativistic calculations employed a generalized gradient approximation (GGA) potential and the linear combination of atomic orbitals (LCAO) formalism. The distinctive feature of our computations stem from solving self-consistently the system of equations describing the GGA, using the Bagayoko-Zhao-Williams (BZW) method. Our results are in agreement with experimental ones where the later are available. In particular, our theoretical, indirect band gap of 3.24 eV, at the experimental lattice constant of 3.91 Å, is in excellent agreement with experiment. Our predicted, equilibrium lattice constant is 3.92 Å, with a corresponding indirect band gap of 3.21 eV and bulk modulus of 183 GPa.
Copper Modulation of Amyloid Beta 42 Interactions with Model Membranes
Authors: Weber Daniel K. , Gehman John D. , Separovic Frances , Sani Marc-Antoine
Published: March 2012

Growing evidence supports that interactions of the amyloid-β peptide Aβ(1–42) with neuronal cell membranes and copper are involved in Alzheimer’s disease pathogenesis. We report using solid-state NMR that the peptide significantly perturbed the phosphate and upper acyl chain region of bilayers comprising brain total lipid extract to cause domain segregation. Deep headgroup perturbations were also realized for palmitoyloleoylphospatidylcholine–cholesterol model systems; however, incorporating 10 % palmitoyloleoylphosphatidylserine or the ganglioside GM1 resulted in a more peripheral interaction. Cu2+ at a 1 : 7 molar ratio to peptide caused deeper penetration into model systems, but partially attenuated interactions with brain total lipid extract. Thioflavin T assay showed that bilayers affected amyloid formation in a mode dependant on lipid content, and was further modulated by addition of Cu2+. Our data support that ternary interactions between Cu2+, lipids and Aβ(1–42) may have significance in Alzheimer’s disease, and challenge the validity of model bilayers as substitutes for natural systems.
A New and Efficient Procedure for Friedländer Synthesis of Quinolines in Low Melting Tartaric Acid-Urea Mixtures
Authors: Ma Fei-Ping , Cheng Gui-Tian , He Zhi-Guo , Zhang Zhan-Hui
Published: March 2012

A general, efficient and green method for the synthesis of quinoline derivatives via the Friedländer heteroannulation reaction of 2-aminoaryl ketones and α-methylene ketones has been developed, employing low melting mixtures of L-(+)-tartaric acid and urea derivatives as an inexpensive, non-toxic, easily biodegradable reaction medium. The melt acts as both the reaction medium and catalyst, furnishing quinolines in high to excellent yields.
Seed-bank and seedling dynamics in Hyparrhenia hirta are influenced by herbicide application and mowing management
Authors: Chejara V. K. , Kristiansen P. , Sindel B. M. , Whalley R. D. B. , Nadolny C.
Published: March 2012

Hyparrhenia hirta (L.) Stapf (Coolatai grass) is a summer-active, C4 perennial tussock grass, native to southern Africa and the Mediterranean region, which has invaded areas of native flora in Australia in recent decades. Understanding its seed and seedling dynamics and how various management treatments (e.g. mowing, herbicide and no management) affect these may assist in identifying the conditions and management strategies required to limit its invasion. The population dynamics of H. hirta have not been comprehensively studied previously. A 2-year field experiment (December 2005–December 2007) was conducted to determine the seed-bank size, pattern of seedling emergence and survival of H. hirta seedlings at three sites in northern New South Wales, Australia, under three treatments: unmanaged (control), mowing and herbicide treatments. The density of H. hirta seeds in the soil at each experimental site under different treatments was measured in December 2005 at the start of the experiment, in December 2006 before the application of the second round of treatments and again at the end of the experiment in December 2007. Hyparrhenia hirta seedlings were assessed at monthly intervals in permanent quadrats (0.5 × 0.5 m) to determine seedling emergence and survival. Seedling emergence occurred on many occasions during the 2-year period of the experiment in each treatment and at all sites but the main seedling flushes were observed from mid summer to early autumn. In 2007, at all sites, seedling emergence declined by more than 90% on the mowing and herbicide treatments compared with the control treatment. Seedling survival was greater in the mowing and herbicide treatments than in the control treatment. The seedling cohorts emerging in winter had a lower survival. This study showed that H. hirta infestations have a large viable seed-bank (~3000 m–2), dependent on the level of infestation and climatic conditions, but that the seed-bank declines rapidly when seed addition is prevented. Some form of direct control of established H. hirta plants in combination with providing appropriate grazing management to encourage competition between grasses will assist in the control of H. hirta.
Drosophila
Mgr, a Prefoldin subunit cooperating with von Hippel Lindau to regulate tubulin stability
Authors: Delgehyr Nathalie , Wieland Uta , Rangone Hélène , Pinson Xavier , Mao Guojie , Dzhindzhev Nikola S. , McLean Doris , Riparbelli Maria G. , Llamazares Salud , Callaini Giuliano , Gonzalez Cayetano , Glover David M.
Published: March 2012

Mutations in
Drosophila merry-go-round (mgr)
have been known for over two decades to lead to circular mitotic figures and loss of meiotic spindle integrity. However, the identity of its gene product has remained undiscovered. We now show that
mgr
encodes the Prefoldin subunit counterpart of human von Hippel Lindau binding-protein 1. Depletion of Mgr from cultured cells also leads to formation of monopolar and abnormal spindles and centrosome loss. These phenotypes are associated with reductions of tubulin levels in both
mgr
flies and
mgr
RNAi-treated cultured cells. Moreover,
mgr
spindle defects can be phenocopied by depleting β-tubulin, suggesting Mgr function is required for tubulin stability. Instability of β-tubulin in the
mgr
larval brain is less pronounced than in either
mgr
testes or in cultured cells. However, expression of transgenic β-tubulin in the larval brain leads to increased tubulin instability, indicating that Prefoldin might only be required when tubulins are synthesized at high levels. Mgr interacts with
Drosophila
von Hippel Lindau protein (Vhl). Both proteins interact with unpolymerized tubulins, suggesting they cooperate in regulating tubulin functions. Accordingly, codepletion of Vhl with Mgr gives partial rescue of tubulin instability, monopolar spindle formation, and loss of centrosomes, leading us to propose a requirement for Vhl to promote degradation of incorrectly folded tubulin in the absence of functional Prefoldin. Thus, Vhl may play a pivotal role: promoting microtubule stabilization when tubulins are correctly folded by Prefoldin and tubulin destruction when they are not.
Ectodysplasin regulates hormone-independent mammary ductal morphogenesis via NF-κB
Authors: Voutilainen Maria , Lindfors Päivi H. , Lefebvre Sylvie , Ahtiainen Laura , Fliniaux Ingrid , Rysti Elisa , Murtoniemi Marja , Schneider Pascal , Schmidt-Ullrich Ruth , Mikkola Marja L.
Published: March 2012

Ductal growth of the mammary gland occurs in two distinct stages. The first round of branching morphogenesis occurs during embryogenesis, and the second round commences at the onset of puberty. Currently, relatively little is known about the genetic networks that control the initial phases of ductal expansion, which, unlike pubertal development, proceeds independent of hormonal input in female mice. Here we identify NF-κB downstream of the TNF-like ligand ectodysplasin (Eda) as a unique regulator of embryonic and prepubertal ductal morphogenesis. Loss of Eda, or inhibition of NF-κB, led to smaller ductal trees with fewer branches. On the other hand, overexpression of Eda caused a dramatic NF-κB–dependent phenotype in both female and male mice characterized by precocious and highly increased ductal growth and branching that correlated with enhanced cell proliferation. We have identified several putative transcriptional target genes of Eda/NF-κB, including
PTHrP
,
Wnt10a
, and
Wnt10b
, as well as Egf family ligands a
mphiregulin
and
epigen
. We developed a mammary bud culture system that allowed us to manipulate mammary development ex vivo and found that recombinant PTHrP, Wnt3A, and Egf family ligands stimulate embryonic branching morphogenesis, suggesting that these pathways may cooperatively mediate the effects of Eda.
Phosphorylation-regulated axonal dependent transport of syntaxin 1 is mediated by a Kinesin-1 adapter
Authors: Chua John Jia En , Butkevich Eugenia , Worseck Josephine M. , Kittelmann Maike , Grønborg Mads , Behrmann Elmar , Stelzl Ulrich , Pavlos Nathan J. , Lalowski Maciej M. , Eimer Stefan , Wanker Erich E. , Klopfenstein Dieter Robert , Jahn Reinhard
Published: March 2012

Presynaptic nerve terminals are formed from preassembled vesicles that are delivered to the prospective synapse by kinesin-mediated axonal transport. However, precisely how the various cargoes are linked to the motor proteins remains unclear. Here, we report a transport complex linking syntaxin 1a (Stx) and Munc18, two proteins functioning in synaptic vesicle exocytosis at the presynaptic plasma membrane, to the motor protein Kinesin-1 via the kinesin adaptor FEZ1. Mutation of the FEZ1 ortholog UNC-76 in
Caenorhabditis elegans
causes defects in the axonal transport of Stx. We also show that binding of FEZ1 to Kinesin-1 and Munc18 is regulated by phosphorylation, with a conserved site (serine 58) being essential for binding. When expressed in
C. elegans
, wild-type but not phosphorylation-deficient FEZ1 (S58A) restored axonal transport of Stx. We conclude that FEZ1 operates as a kinesin adaptor for the transport of Stx, with cargo loading and unloading being regulated by protein kinases.
Histone H3R17me2a mark recruits human RNA Polymerase-Associated Factor 1 Complex to activate transcription
Authors: Wu Jiacai , Xu Wei
Published: March 2012

The histone coactivator-associated arginine methyltransferase 1 (CARM1) is a coactivator for a number of transcription factors, including nuclear receptors. Although CARM1 and its asymmetrically deposited dimethylation at histone H3 arginine 17 (H3R17me2a) are associated with transcription activation, the mechanism by which CARM1 activates transcription remains unclear. Using an unbiased biochemical approach, we discovered that the transcription elongation-associated PAF1 complex (PAF1c) directly interacts with H3R17me2a. PAF1c binds to histone H3 tails harboring dimethylation at R17 in CARM1-methylated histone octamers. Knockdown of either PAF1c subunits or CARM1 affected transcription of CARM1-regulated, estrogen-responsive genes. Furthermore, either CARM1 knockdown or CARM1 enzyme-deficient mutant knockin resulted in decreased H3R17me2a accompanied by the reduction of PAF1c occupancy at the proximal promoter estrogen-responsive elements. In contrast, PAF1c knockdown elicited no effects on H3R17me2a but reduced the H3K4me3 level at estrogen-responsive elements. These observations suggest that, apart from PAF1c's established roles in directing histone modifications, PAF1c acts as an arginine methyl histone effector that is recruited to promoters and activates a subset of genes, including targets of estrogen signaling.
Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop
Authors: Eicher Thomas , Cha Hi-jea , Seeger Markus A. , Brandstätter Lorenz , El-Delik Jasmin , Bohnert Jürgen A. , Kern Winfried V. , Verrey François , Grütter Markus G. , Diederichs Kay , Pos Klaas M.
Published: March 2012

AcrAB-TolC is the major efflux protein complex in
Escherichia coli
extruding a vast variety of antimicrobial agents from the cell. The inner membrane component AcrB is a homotrimer, and it has been postulated that the monomers cycle consecutively through three conformational stages designated loose (L), tight (T), and open (O) in a concerted fashion. Binding of drugs has been shown at a periplasmic deep binding pocket in the T conformation. The initial drug-binding step and transport toward this drug-binding site has been elusive thus far. Here we report high resolution structures (1.9–2.25 Å) of AcrB/designed ankyrin repeat protein (DARPin) complexes with bound minocycline or doxorubicin. In the AcrB/doxorubicin cocrystal structure, binding of three doxorubicin molecules is apparent, with one doxorubicin molecule bound in the deep binding pocket of the T monomer and two doxorubicin molecules in a stacked sandwich arrangement in an access pocket at the lateral periplasmic cleft of the L monomer. This access pocket is separated from the deep binding pocket apparent in the T monomer by a switch-loop. The localization and conformational flexibility of this loop seems to be important for large substrates, because a G616N AcrB variant deficient in macrolide transport exhibits an altered conformation within this loop region. Transport seems to be a stepwise process of initial drug uptake in the access pocket of the L monomer and subsequent accommodation of the drug in the deep binding pocket during the L to T transition to the internal deep binding pocket of the T monomer.
Evidence for a Peierls phase-transition in a three-dimensional multiple charge-density waves solid
Authors: Mansart Barbara , Cottet Mathieu J. G. , Penfold Thomas J. , Dugdale Stephen B. , Tediosi Riccardo , Chergui Majed , Carbone Fabrizio
Published: March 2012

The effect of dimensionality on materials properties has become strikingly evident with the recent discovery of graphene. Charge ordering phenomena can be induced in one dimension by periodic distortions of a material’s crystal structure, termed Peierls ordering transition. Charge-density waves can also be induced in solids by strong coulomb repulsion between carriers, and at the extreme limit, Wigner predicted that crystallization itself can be induced in an electrons gas in free space close to the absolute zero of temperature. Similar phenomena are observed also in higher dimensions, but the microscopic description of the corresponding phase transition is often controversial, and remains an open field of research for fundamental physics. Here, we photoinduce the melting of the charge ordering in a complex three-dimensional solid and monitor the consequent charge redistribution by probing the optical response over a broad spectral range with ultrashort laser pulses. Although the photoinduced electronic temperature far exceeds the critical value, the charge-density wave is preserved until the lattice is sufficiently distorted to induce the phase transition. Combining this result with ab initio electronic structure calculations, we identified the Peierls origin of multiple charge-density waves in a three-dimensional system for the first time.
Nonprocessive [2 + 2]e
-
off-loading reductase domains from mycobacterial nonribosomal peptide synthetases
Authors: Chhabra Arush , Haque Asfarul S. , Pal Ravi Kant , Goyal Aneesh , Rai Rajkishore , Joshi Seema , Panjikar Santosh , Pasha Santosh , Sankaranarayanan Rajan , Gokhale Rajesh S.
Published: March 2012

In mycobacteria, polyketide synthases and nonribosomal peptide synthetases (NRPSs) produce complex lipidic metabolites by using a thio-template mechanism of catalysis. In this study, we demonstrate that off-loading reductase (R) domain of mycobacterial NRPSs performs two consecutive [2 + 2]e
-
reductions to release thioester-bound lipopeptides as corresponding alcohols, using a nonprocessive mechanism of catalysis. The first crystal structure of an R domain from
Mycobacterium tuberculosis
NRPS provides strong support to this mechanistic model and suggests that the displacement of intermediate would be required for cofactor recycling. We show that 4e
-
reductases produce alcohols through a committed aldehyde intermediate, and the reduction of this intermediate is at least 10 times more efficient than the thioester-substrate. Structural and biochemical studies also provide evidence for the conformational changes associated with the reductive cycle. Further, we show that the large substrate-binding pocket with a hydrophobic platform accounts for the remarkable substrate promiscuity of these domains. Our studies present an elegant example of the recruitment of a canonical short-chain dehydrogenase/reductase family member as an off-loading domain in the context of assembly-line enzymology.
Loss of DNA methylation affects the recombination landscape in
Arabidopsis
Authors: Mirouze Marie , Lieberman-Lazarovich Michal , Aversano Riccardo , Bucher Etienne , Nicolet Joël , Reinders Jon , Paszkowski Jerzy
Published: March 2012

During sexual reproduction, one-half of the genetic material is deposited in gametes, and a complete set of chromosomes is restored upon fertilization. Reduction of the genetic information before gametogenesis occurs in meiosis, when cross-overs (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it was postulated that DNA hypermethylation is inhibitory to COs. Here, when analyzing meiotic recombination in mutant plants with hypomethylated DNA, we observed unexpected and counterintuitive effects of DNA methylation losses on CO distribution. Recombination was further promoted in the hypomethylated chromosome arms while it was inhibited in heterochromatic regions encompassing pericentromeric DNA. Importantly, the total number of COs was not affected, implying that loss of DNA methylation led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influence recombination—whether directly
in cis
or indirectly
in trans
by changing expression of genes encoding recombination components—we analyzed CO distribution in wild-type lines with randomly scattered and well-mapped hypomethylated chromosomal segments. The results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination
in cis
. Because DNA methylation exhibits significant variation even within a single species, our results imply that it may influence the evolution of plant genomes through the control of meiotic recombination.
PIM1
gene cooperates with human
BCL6
gene to promote the development of lymphomas
Authors: Baron Beverly W. , Anastasi John , Hyjek Elizabeth M. , Bies Juraj , Reddy Poluru L. , Dong Jingfang , Joseph Loren , Thirman Michael J. , Wroblewski Kristen , Wolff Linda , Baron Joseph M.
Published: March 2012

Diffuse large B-cell lymphomas in humans are associated with chromosomal rearrangements (∼40%) and/or mutations disrupting autoregulation (∼16%) involving the
BCL6
gene. Studies of lymphoma development in humans and mouse models have indicated that lymphomagenesis evolves through the accumulation of multiple genetic alterations. Based on our prior studies, which indicated that carcinogen-induced DNA mutations enhance the incidence of lymphomas in our mouse model expressing a human
BCL6
transgene, we hypothesized that mutated genes are likely to play an important cooperative role in
BCL6
-associated lymphoma development. We used retroviral insertional mutagenesis in an effort to identify which genes cooperate with
BCL6
in lymphomagenesis in our
BCL6
transgenic mice. We identified
PIM1
as the most frequently recurring cooperating gene in our murine BCL6-associated lymphomas (T- and B-cell types), and we observed elevated levels of PIM1 mRNA and protein expression in these neoplasms. Further, immunohistochemical staining, which was performed in 20 randomly selected BCL6-positive human B- and T-cell lymphomas, revealed concurrent expression of BCL6 and PIM1 in these neoplasms. As
PIM1
encodes a serine/threonine kinase, PIM1 kinase inhibition may be a promising therapy for BCL6/PIM1-positive human lymphomas.
Corticotropin-releasing factor receptor-dependent effects of repeated stress on tau phosphorylation, solubility, and aggregation
Authors: Rissman Robert A. , Staup Michael A. , Lee Allyson Roe , Justice Nicholas J. , Rice Kenner C. , Vale Wylie , Sawchenko Paul E.
Published: March 2012

Exposure and/or sensitivity to stress have been implicated as conferring risk for development of Alzheimer's disease (AD). Although the basis for such a link remains unclear, we previously reported differential involvement of corticotropin-releasing factor receptor (CRFR) 1 and 2 in acute stress-induced tau phosphorylation (tau-P) and solubility in the hippocampus. Here we examined the role of CRFRs in tau-P induced by repeated stress and the structural manifestations of altered tau solubility. Robust tau-P responses were seen in WT and CRFR2 null mice exposed to repeated stress, which were sustained at even 24 h after the final stress exposure. A portion of phosphorylated tau in these mice was sequestered in detergent-soluble cellular fractions. In contrast, CRFR1 and CRFR double-KO mice did not exhibit repeated stress-induced alterations in tau-P or solubility. Similarly, treatment with CRFR1 antagonist attenuated repeated stress-induced tau-P. Using histochemical approaches in a transgenic CRFR1 reporter mouse line, we found substantial overlap between hippocampal CRFR1 expression and cells positive for phosphorylated tau after exposure to repeated stress. Ultrastructural analysis of negatively stained extracts from WT and CRFR2 null mice identified globular aggregates that displayed positive immunogold labeling for tau-P, as well as conformational changes in tau (MC1) seen in early AD. Given that repeated stress exposure results in chronic increases in hippocampal tau-P and its sequestration in an insoluble (and potentially prepathogenic) form, our data may define a link between stress and an AD-related pathogenic mechanism.
Potential and challenges in making physic nut (
Jatropha curcas
L.) a viable biofuel crop: the Brazilian perspective.
Authors: Durães F. O. M. , Laviola B. G. , Alves A. A.
Published: March 2012

Fossil-derived fuels currently supply 86% of the world's energy, even though it represents a finite resource. With the aim of reducing the fossil fuels dependency, alternative sources of energy have been pursued in recent years. In view of the urgent need to develop new technologies that may enable environmentally friendly forms of energy to become widespread, biofuels in general and biodiesel in particular are receiving considerable attention throughout the world and especially in Brazil. Given the high quality of its oil, which meets the rapeseed quality standard and can be easily converted into biodiesel, and because of its wide adaptability, physic nut has been considered a potential crop to serve as feedstock for biodiesel production. Popular claims, e.g. enhanced drought tolerance, low nutrient requirements, pest and disease resistance, have also helped to increase the expectations of the crop, even though most of these claims are yet to be supported by scientific evidence. However, the fact is that besides its advantageous characteristics, physic nut cultivation is challenging as it is a quasi-undomesticated species. In that context, this review seeks to demonstrate the physic nut potential as a biofuel crop, highlighting, however, the challenges to its wide adoption as a fuel crop. Despite facing enormous challenges (as detailed below), our cautiously optimistic vision is that a substantial and focused research programme may make physic nut a viable feedstock for biodiesel production. We detail the Brazilian research initiative that is addressing many of these challenges.