bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of the 12 kDa FK506‐binding protein gene
Authors: Somarelli Jason A. , Herrera Rene J.
Published: May 2007

Background information. The FKBPs (FK506‐binding proteins) belong to a ubiquitous family of proteins that are found in a wide range of taxonomic groups. These proteins participate in a variety of pathways, including protein folding, down‐regulation of T‐cell activation and inhibition of cell‐cycle progression.

Results. A cDNA encoding the 12 kDa FKBP gene orthologue (FKBP12) in Bombyx mori was been isolated from both Bm‐5 cultured cells and silk‐gland tissue. Using the FKBP12 cDNA in combination with the B. mori 6× whole‐genome shotgun database, we were able to identify the FKBP12 gene, as well as the positions of its intron—exon junctions.

Conclusions. FKBP12 exon sizes and intronic positions are highly conserved among FKBP12 orthologues in 24 diverse genomes. Comparison of 41 FKBP12 genes revealed several intronic insertion and deletion events throughout evolution. In addition, paralogous FKBP12 isoforms were identified in all 12 vertebrate genomes. Both structural and phylogenetics analyses suggest that the isoforms may be evolving independently, possibly due to the distinct functional roles played by each paralogue.
Dial‐a‐mutant: web‐based knockout collections for model organisms
Authors: Haag Eric S.
Published: May 2007

Although much of eukaryotic cell biology is highly conserved, the most biomedically relevant organisms are often the most difficult or expensive to study. Non‐vertebrate model organisms offer a practical and accessible alternative. Large collections of loss‐of‐function mutants have now been generated in the nematode Caenorhabditis elegans and the angiosperm Arabidopsis thaliana, which can be easily accessed via the Internet. The sites reviewed in the present article include those of the C. elegans Knockout Consortium (http:celeganskoconsortium.omrf.org) and the C. elegans National Bioresource Project of Japan (http:shigen.lab.nig.ac.jpc.elegansindex.jsp), and also the NemaGENETAG project (http:elegans.imbb.forth.grnemagenetag) for the former and T‐DNA Express (http:signal.salk.educgi‐bintdnaexpress) for the latter. These sites allow one to easily identify and request C. elegans strains bearing mutations in approximately half of predicted genes and for essentially every Arabidopsis gene. These tools greatly enhance the ability of non‐specialists to conduct studies of gene function in vivo in these model species.
Recycling endosomes in neuronal membrane traffic
Authors: Schmidt Michael R. , Haucke Volker
Published: May 2007

Neurons are highly polarized cells with axonal and somatodendritic membrane surfaces that spatially separate signal‐sending from signal‐receiving membrane domains. As found in many other cell types, different populations of endosomes are involved in the sorting of synaptic and other membrane cargo in neurons. The exact source of the membrane for neurite extension and process remodelling during neuronal differentiation has remained uncertain, and we do not know exactly how polarized sorting of neuronal membrane proteins is achieved. In the present article, we will provide a brief overview of endosomes and their putative or proven functions in fibroblasts, epithelial cells and neurons. On the basis of insights from non‐neuronal cell types and recent studies on the function of recycling endosomes during synaptic plasticity‐induced membrane remodelling, we postulate a speculative model regarding the role of recycling endosomes in neuronal differentiation.
Laser plasma instability experiments with KrF lasers
Authors: Weaver J. L. , Oh J. , Afeyan B. , Phillips L. , Seely J. , Feldman U. , Brown C. , Karasik M. , Serlin V. , Aglitskiy Y. , Mostovych A. N. , Holland G. , Obenschain S. , Chan L-Y. , Kehne D. , Lehmberg R. H. , Schmitt A. J. , Colombant D. , Velikovich A.
Published: May 2007

Deleterious effects of laser-plasma instability (LPI) may limit the maximum laser irradiation that can be used for inertial confinement fusion. The short wavelength (248nm), large bandwidth, and very uniform illumination available with krypton-fluoride (KrF) lasers should increase the maximum usable intensity by suppressing LPI. The concomitant increase in ablation pressure would allow implosion of low-aspect-ratio pellets to ignition with substantial gain (>20) at much reduced laser energy. The proposed KrF-laser-based Fusion Test Facility (FTF) would exploit this strategy to achieve significant fusion power (150MW) with a rep-rate system that has a per pulse laser energy well below 1 MJ. Measurements of LPI using the Nike KrF laser are presented at and above intensities needed for the FTF (I∼2×1015W∕cm2). The results to date indicate that LPI is indeed suppressed. With overlapped beam intensity above the planar, single beam intensity threshold for the two-plasmon decay instability, no evidence of instability was observed via measurements of 32ωo and 12ωo harmonic emissions.
Influence of charge trapping on electroluminescence from Si-nanocrystal light emitting structure
Authors: Liu Y. , Chen T. P. , Ding L. , Yang M. , Wong J. I. , Ng C. Y. , Yu S. F. , Li Z. X. , Yuen C. , Zhu F. R. , Tan M. C. , Fung S.
Published: May 2007

We report a study on the influence of charge trapping on electroluminescence (EL) from Si nanocrystal (nc-Si) distributed throughout a 30nm SiO2 thin film synthesized by Si+ implantation into an oxide film thermally grown on a p-type Si substrate. The electron and hole trapping in the nc-Si located near the indium tin oxide gate and the Si substrate, respectively, cause a reduction in the EL intensity. The reduced EL intensity can be recovered after the trapped charges are released. A partial recovery can be easily achieved by the application of a positive gate voltage or thermal annealing at hot temperatures (e.g., 120°C) for a short duration. The present study highlights the impact of charging in the nc-Si on the light emission efficiency and its stability of nc-Si light-emitting devices.
Simple space-time symmetries: Generalizing conformal field theory
Authors: Mack Gerhard , de Riese Mathias
Published: May 2007

We study simple space-time symmetry groups G which act on a space-time manifold M=G∕H which admits a G-invariant global causal structure. We classify pairs (G,M) which share the following additional properties of conformal field theory. (1) The stability subgroup H of o∊M is the identity component of a parabolic subgroup of G, implying factorization H=MAN−, where M generalizes Lorentz transformations, A dilatations, and N− special conformal transformations. (2) Special conformal transformations ξ∊N− act trivially on tangent vectors v∊ToM. The allowed simple Lie groups G are the universal coverings of SU(m,m),SO(2,D),Sp(l,R),SO*(4n), and E7(−25) and H are particular maximal parabolic subgroups. They coincide with the groups of fractional linear transformations of Euclidean Jordan algebras whose use as generalizations of Minkowski space-time was advocated by Günaydin [Mod. Phys. Lett. A 8, 1407 (1993)]. All these groups G admit positive energy representations. It will also be shown that the classical conformal groups SO(2,D) are the only allowed groups which possess an automorphism with properties appropriate for a time reflection.
Off-centered polarization and ferroelectric phase transition in Li-doped ZnO thin films grown by pulsed-laser ablation
Authors: Dhananjay  , Nagaraju J. , Krupanidhi S. B.
Published: May 2007

Li-doped ZnO (Zn1−xLixO, x=0.15) thin films have been grown on platinum-coated silicon substrates via pulsed-laser ablation. The films were grown at fixed substrate temperature of 500 °C and different partial pressure of oxygen (PO2∼100–300 mTorr). The films showed (002) preferred orientation. The doping concentration and built-in potential were estimated from the capacitance-voltage characteristics. In order to investigate the phase transition behavior of the films, dc conductivity and dielectric measurements were conducted. The phase transition temperature was found to be 330 K. The activation energy (dc) has been found to be 0.05 and 0.28 eV in ferroelectric and paraelectric phases, respectively. The Zn0.85Li015O thin films exhibited well-defined polarization hysteresis loop, with a remanent polarization of 0.2 μC∕cm2 and coercive field of 25 kV/cm, at room temperature. The conduction mechanism of the laser ablated Zn0.85Li015O films was analyzed in the light of impedance spectroscopy.
Direct-drive laser target designs for sub-megajoule energies
Authors: Colombant D. G. , Schmitt A. J. , Obenschain S. P. , Zalesak S. T. , Velikovich A. L. , Bates J. W. , Fyfe D. E. , Gardner J. H. , Manheimer W.
Published: May 2007

New direct-drive laser target designs with KrF laser light take advantage of the shorter wavelength to lower the laser energy required for substantial gain (>30×) to sub-MJ level. These low laser-energy pellets are useful in systems that could form an intermediate step towards fusion energy, such as the proposed Fusion Test Facility [S. P. Obenschain et al., Phys. Plasmas 13, 056320 (2006)]. The short wavelength laser should allow higher intensity (and higher pressure) without increasing the risk of laser-plasma instabilities. The higher pressure in turn allows higher velocities to be achieved while keeping the low aspect ratios required for hydrodynamic stability. The canonical laser energy has been chosen to be 500kJ. A target design is presented with various laser pulse shapes and both 1D and 2D simulation results are shown. The sensitivity of these targets to both low-mode and high-mode perturbations is examined. The analysis and simulations in this paper indicate that significant gain (G=57) can be achieved for these targets even in the presence of hydrodynamic instabilities.
Electron surface acceleration on a solid capillary target inner wall irradiated with ultraintense laser pulses
Authors: Nakamura Tatsufumi , Mima Kunioki , Sakagami Hitoshi , Johzaki Tomoyuki
Published: May 2007

When ultraintense laser pulses irradiate solid targets with a large incident angle, quasistatic magnetic and electric fields are induced, which confine electrons along the target surface in an electrostatic and vector potential well. In this case, electrons are resonantly accelerated along the surface by laser electric field inside the potential well. By this surface acceleration process, high energy electrons are effectively generated whose temperature well exceeds the ponderomotive energy. The optimum conditions for realizing surface acceleration and its energy scalings are given. Capillary type targets are shown to have an advantage in utilizing the surface acceleration process by increasing the interaction length.
On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach
Authors: Min Donghong , Liu Yusong , Carbone Irina , Yang Wei
Published: May 2007

As a popular tool in exploring free energy landscapes, the metadynamics method has been widely applied to elucidate various chemical or biochemical processes. As deeply discussed by Laio et al. [J. Phys. Chem. B 109, 6714 (2005)], the size of the updating Gaussian function is pivotal to the free energy convergence toward the target free energy surface. For instance, a greater Gaussian height can facilitate the quick visit of a conformation region of interest; however, it may lead to a larger error of the calculated free energy surface. In contrast, a lower Gaussian height can guarantee a better resolution of the calculated free energy surface; however, it will take longer time for such a simulation to navigate through the defined conformational region. In order to reconcile such confliction, the authors present a method by implementing the Wang-Landau recursion scheme in the metadynamics simulations to adaptively update the height of the unit Gaussian function. As demonstrated in their model studies on both a toy system, and a realistic molecular system treated with the hybrid quantum mechanical and molecular mechanical (QM∕MM) potential, the present approach can quickly result in more decently converged free energy surfaces, compared with the classical metadynamics simulations employing the fixed Gaussian heights.
Role of ambient gas and laser fluence in governing the dynamics of the plasma plumes produced by laser blow off of LiF–C thin film
Authors: Singh R. K. , Kumar Ajai , Patel B. G. , Subramanian K. P.
Published: May 2007

The time- and space-resolved emission profiles of LiI and LiII emission lines from the laser-blow-off plumes of a multilayered LiF–C thin film have been studied using spectroscopic technique. The evolution features were analyzed in different ambient environments ranging from high vacuum to 3mbars of argon pressures and at various fluences of the ablating laser. During the evolution of the plume, a transition region was found to exist between 4 and 6mm. Here, the plume dynamics changed from free expansion to collisional regime, where the plume experienced viscous force of the medium. The enhancement observed in neutral lines, in comparison with ionic lines, is explained in terms of the yield difference in electron impact excitation and ionization processes. Substantial difference in the arrival time distribution of the plume species was observed for LiI and LiII lines at high ambient pressures. Three expansion models are invoked to explain the evolution of the plume in different ambient conditions. The laser fluence was found to control the ratio of ions and neutrals.
Temperature dependence of the Brillouin frequency shift in crystals
Authors: Sonehara Toshiaki , Tatsu Eriko , Saikan Seishiro , Ohno Seigo
Published: May 2007

In order to find a theoretical expression which most faithfully reproduces the temperature dependence of the Brillouin frequency shift in crystals, we have performed stimulated Brillouin spectroscopy in two crystals of TeO2 and PbMoO4 as test crystals by using a high precision Brillouin spectrometer with the frequency resolution of 20 kHz. In general, the temperature dependence of a Brillouin shift in crystals not undergoing phase transitions exhibits a linear negative slope at high temperatures and an asymptotic approach with zero slopes at low temperatures. We have experimentally confirmed that this temperature dependence stems from the temperature change of the elastic constant rather than the thermal changes of the refractive index and the volume expansion coefficient. It has been found that the Lakkad function based on Debye model and the Varshni function based on the Einstein model both reproduce quite well the temperature dependence of the Brillouin frequency shift in crystals.
Magnetocaloric effect and magnetic properties of Tb0.9Sn0.1MnO3
Authors: Fabris F. Wolff , Pekala M. , Drozd V. , Fagnard J-F. , Vanderbemden Ph. , Liu Ru-Shi , Ausloos M.
Published: May 2007

The magnetocaloric effect in magnetic materials is of great interest nowadays. In this article we present an investigation about the magnetic properties near the magnetic transition in a polycrystalline sample of a manganite Tb0.9Sn0.1MnO3. Particularly, we are interested in describing the nature of the magnetic interactions and the magnetocaloric effect in this compound. The temperature dependence of the magnetization was measured to determine the characteristics of the magnetic transition and the magnetic entropy change was calculated from magnetization curves at different temperatures. The magnetic solid is paramagnetic at high temperatures. We observe a dominant antiferromagnetic interaction below Tn=38 K for low applied magnetic fields; the presence of Sn doping in this compound decreases the Néel temperature of the pure TbMnO3 system. A drastic increase in the magnetization as a function of temperature near the magnetic transition suggests a strong magnetocaloric effect. We found a large magnetic entropy change ΔSM(T) of about −4 J/kg K at H=3 T. We believe that the magnetic entropy change is associated with the magnetic transition and we interpret it as due to the coupling between the magnetic field and the spin ordering. This relatively large value and broad temperature interval (about 35 K) of the magnetocaloric effect make the present compound a promising candidate for magnetic refrigerators at low temperatures.
Second harmonic generation in laser magnetized–plasma interaction
Authors: Jha Pallavi , Mishra Rohit K. , Raj Gaurav , Upadhyay Ajay K.
Published: May 2007

When an intense laser pulse interacts with homogeneous plasma embedded in a transverse magnetic field, transverse current density oscillating with frequency twice that of the laser field is set up. This leads to generation of second harmonic radiation with significant conversion efficiency.
Phase locking in backward-wave oscillators with strong end reflections
Authors: Nusinovich G. S. , Sinitsyn O. V. , Rodgers J. , Shkvarunets A. G. , Carmel Y.
Published: May 2007

The theory of phase-locked oscillations in a backward-wave oscillator with strong end reflections is developed. Numerical results demonstrate that the locking bandwidth of such a device phase-locked by a prebunched electron beam can be twice the bandwidth of a resonator formed by a waveguide with strong end reflections. It is also shown that the device can operate with the efficiency exceeding 50% and that, in some cases, it can exhibit a hysteresis in the process of tuning the signal frequency. The applicability of the results obtained to the experiments with the plasma-assisted backward-wave oscillator currently underway at the University of Maryland is discussed.
Terahertz radiation from a wire target irradiated by an ultra-intense laser pulse
Authors: Li Zhi-chao , Zheng Jian
Published: May 2007

When an ultra-intense laser pulse impacts the tip of a wire whose other end is grounded, a strong return current can be driven along the wire because some energetic electrons generated in ultra-intense laser matter interaction can escape from the target and an electric field builds up. The wire then behaves like a current-carrying antenna that can emit electromagnetic radiations. If the duration of the driving pulse is several tens of femtoseconds, the radiation spectrum reaches a maximum at terahertz region, and the radiation power per solid angle could be as high as 109W∕rad.
Structural and optical properties of the three-dimensional CdS nanocone arrays on the self-assembled Cd∕CdS core-shell microspheres
Authors: Zhou Qingtao , Chen Yiqing , Kong Weihai , Su Yong , Peng Bo , Jia Chong , Zhang Xinhua , Yin Song , Li Sen
Published: May 2007

The authors report on an approach to homoepitaxial growth of the three-dimensional CdS nanocone arrays, in which the Cd∕CdS core-shell sphere is designed to serve as a template. The alternation of the wurtzite (WZ) and zinc blende (ZB) phases along the growth direction of the nanocones is observed in the as-synthesized CdS nanocones. The WZ/ZB admixtures exhibit the features of a quantum well, which causes the two peaks centered at 506 and 503nm in the room-temperature photoluminescence spectrum.
Integrated ZnO nanotips on GaN light emitting diodes for enhanced emission efficiency
Authors: Zhong J. , Chen H. , Saraf G. , Lu Y. , Choi C. K. , Song J. J. , Mackie D. M. , Shen H.
Published: May 2007

Enhancement of light extraction from an integrated ZnO nanotips/GaN light emitting diode (LED) is demonstrated. The device is composed of a GaN LED with a Ga-doped ZnO (GZO) transparent conductive layer and ZnO nanotips grown on GZO for light extraction. The light output power of a ZnO nanotips/GZO/GaN LED exhibits 1.7 times enhancement, in comparison with a conventional Ni∕Au p-metal LED. The higher emission efficiency is attributed to the enhanced light transmission and scattering in the ZnO∕GaN multilayer.
Nanoimprint mold fabrication and replication by room-temperature conformal chemical vapor deposition
Authors: Murphy Patrick F. , Morton Keith J. , Fu Zengli , Chou Stephen Y.
Published: May 2007

The authors present a technique for the replication of molds for nanoimprint lithography (NIL) without solvents or etching. A thin hard amorphous silicon film is deposited onto imprinted or self-assembled polymer nanostructures by room-temperature conformal plasma-enhanced chemical vapor deposition. After attachment to another substrate and separation from the polymer original, the thin hard film forms a NIL mold that is the inverse of the polymer original. Using this technology, the authors demonstrate the replication of a 200nm pitch grating mold and sub-50-nm features over wafer-scale areas without introducing additional line edge roughness associated with conventional replication methods.
Difference between bending and stretching moduli of single-walled carbon nanotubes that are modeled as an elastic tube
Authors: DiBiasio Christopher M. , Cullinan Michael A. , Culpepper Martin L.
Published: May 2007

The authors show that an elastic tube model of a (5,5) carbon nanotube predicts stretching and bending moduli that differ by 19%. This is due to (1) differing energy storage mechanisms in each mode and (2) the inability of the tube model to capture these effects. Conventional tube models assume a common energy storage mechanism in stretching and bending. They show that energy is stored primarily through bond stretching/rotation and bond torsion/van der Waals interactions in stretching and bending, respectively. This knowledge underscores the need to use different moduli to predict stretching, bending, and combined bending and stretching when using the tube model.
Varieties of Glocalisation: The International Economic Strategies of Amsterdam, Manchester, and Zurich Compared
Authors: van der Heiden Nico , Terhorst Pieter
Published: May 2007

Our aim in this paper is to explain the international strategies of cities by focusing on market conditions. Drawing on a critique of the glocalisation thesis we show that the design of these strategies can plausibly be explained by the specific characteristics of urban capitalism found in the different cities. Whereas the international strategy of Manchester must be seen as a response to problems of postindustrial restrictions, the importance of the logistic sector in Dutch capitalism strongly shapes Amsterdam's strategy. In Zurich, though, it is argued that the city was already very well prepared for the transformation towards a post-Fordist regime, and so did not need any strategy at all. We conclude that varieties of glocalisation trajectories are a major factor driving and shaping the characteristics of international urban strategies.
Stochastic fluctuations in metabolic pathways
Authors: Levine Erel , Hwa Terence
Published: May 2007

Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of downstream targets in a network. Here, we develop an analytic framework to investigate the phenomenon of noise correlation in molecular networks. Specifically, we focus on the metabolic network, which is highly interlinked, and noise properties may constrain its structure and function. Motivated by the analogy between the dynamics of a linear metabolic pathway and that of the exactly soluble linear queuing network or, alternatively, a mass transfer system, we derive a plethora of results concerning fluctuations in the abundance of intermediate metabolites in various common motifs of the metabolic network. For all but one case examined, we find the steady-state fluctuation in different nodes of the pathways to be effectively uncorrelated. Consequently, fluctuations in enzyme levels only affect local properties and do not propagate elsewhere into metabolic networks, and intermediate metabolites can be freely shared by different reactions. Our approach may be applicable to study metabolic networks with more complex topologies or protein signaling networks that are governed by similar biochemical reactions. Possible implications for bioinformatic analysis of metabolomic data are discussed.
Holocene morphogenesis of Alexander the Great's isthmus at Tyre in Lebanon
Authors: Marriner Nick , Morhange Christophe , Meulé Samuel
Published: May 2007

In 332 B.C., Alexander the Great constructed an ≈1,000-m-long causeway to seize the offshore island of Tyre. The logistics behind this engineering feat have long troubled archaeologists. Using the Holocene sedimentary record, we demonstrate that Alexander's engineers cleverly exploited a shallow proto-tombolo, or sublittoral sand spit, to breach the offshore city's defensive impregnability. We elucidate a three-phase geomorphological model for the spit's evolution. Settled since the Bronze Age, the area's geological record manifests a long history of natural and anthropogenic forcings. (
i
) Leeward of the island breakwater, the maximum flooding surface (e.g., drowning of the subaerial land surfaces by seawater) is dated ≈8000 B.P. Fine-grained sediments and brackish and marine-lagoonal faunas translate shallow, low-energy water bodies at this time. Shelter was afforded by Tyre's elongated sandstone reefs, which acted as a 6-km natural breakwater. (
ii
) By 6000 B.P., sea-level rise had reduced the dimensions of the island from 6 to 4 km. The leeward wave shadow generated by this island, allied with high sediment supply after 3000 B.P., culminated in a natural wave-dominated proto-tombolo within 1–2 m of mean sea level by the time of Alexander the Great (4th century B.C.). (
iii
) After 332 B.C., construction of Alexander's causeway entrained a complete anthropogenic metamorphosis of the Tyrian coastal system.
Parasites alter community structure
Authors: Wood Chelsea L. , Byers James E. , Cottingham Kathryn L. , Altman Irit , Donahue Megan J. , Blakeslee April M. H.
Published: May 2007

Parasites often play an important role in modifying the physiology and behavior of their hosts and may, consequently, mediate the influence hosts have on other components of an ecological community. Along the northern Atlantic coast of North America, the dominant herbivorous snail
Littorina littorea
structures rocky intertidal communities through strong grazing pressure and is frequently parasitized by the digenean trematode
Cryptocotyle lingua
. We hypothesized that the effects of parasitism on host physiology would induce behavioral changes in
L. littorea
, which in turn would modulate
L. littorea
's influence on intertidal community composition. Specifically, we hypothesized that
C. lingua
infection would alter the grazing rate of
L. littorea
and, consequently, macroalgal communities would develop differently in the presence of infected versus uninfected snails. Our results show that uninfected snails consumed 40% more ephemeral macroalgal biomass than infected snails in the laboratory, probably because the digestive system of infected snails is compromised by
C. lingua
infection. In the field, this weaker grazing by infected snails resulted in significantly greater expansion of ephemeral macroalgal cover relative to grazing by uninfected snails. By decreasing the per-capita grazing rate of the dominant herbivore,
C. lingua
indirectly affects the composition of the macroalgal community and may in turn affect other species that depend on macroalgae for resources or habitat structure. In light of the abundance of parasites across systems, we suggest that, through trait-mediated indirect effects, parasites may be a common determinant of structure in ecological communities.
The helix–turn–helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain
Authors: Religa Tomasz L. , Johnson Christopher M. , Vu Dung M. , Brewer Scott H. , Dyer R. Brian , Fersht Alan R.
Published: May 2007

Helices 2 and 3 of Engrailed homeodomain (EnHD) form a helix–turn–helix (HTH) motif. This common motif is believed not to fold independently, which is the characteristic feature of a motif rather than a domain. But we found that the EnHD HTH motif is monomeric and folded in solution, having essentially the same structure as in full-length protein. It had a sigmoidal thermal denaturation transition. Both native backbone and local tertiary interactions were formed concurrently at 4 × 10
5
s
−1
at 25°C, monitored by IR and fluorescence T-jump kinetics, respectively, the same rate constant as for the fast phase in the folding of EnHD. The HTH motif, thus, is an ultrafast-folding, natural protein domain. Its independent stability and appropriate folding kinetics account for the stepwise folding of EnHD, satisfy fully the criteria for an on-pathway intermediate, and explain the changes in mechanism of folding across the homeodomain family. Experiments on mutated and engineered fragments of the parent protein with different probes allowed the assignment of the observed kinetic phases to specific events to show that EnHD is not an example of one-state downhill folding.
Effects of Iron Deficiency on Iron Binding and Internalization into Acidic Vacuoles in Dunaliella salina
Authors: Paz Yakov , Shimoni Eyal , Weiss Meira , Pick Uri
Published: May 2007

Uptake of iron in the halotolerant alga Dunaliella salina is mediated by a transferrin-like protein (TTf), which binds and internalizes Fe3+ ions. Recently, we found that iron deficiency induces a large enhancement of iron binding, which is associated with accumulation of three other plasma membrane proteins that associate with TTf. In this study, we characterized the kinetic properties of iron binding and internalization and identified the site of iron internalization. Iron deficiency induces a 4-fold increase in Fe binding, but only 50% enhancement in the rate of iron uptake and also increases the affinity for iron and bicarbonate, a coligand for iron binding. These results indicate that iron deprivation leads to accumulation and modification of iron-binding sites. Iron uptake in iron-sufficient cells is preceded by an apparent time lag, resulting from prebound iron, which can be eliminated by unloading iron-binding sites. Iron is tightly bound to surface-exposed sites and hardly exchanges with medium iron. All bound iron is subsequently internalized. Accumulation of iron inhibits further iron binding and internalization. The vacuolar inhibitor bafilomycin inhibits iron uptake and internalization. Internalized iron was localized by electron microscopy within vacuolar structures that were identified as acidic vacuoles. Iron internalization is accompanied by endocytosis of surface proteins into these acidic vacuoles. A novel kinetic mechanism for iron uptake is proposed, which includes two pools of bound/compartmentalized iron separated by a rate-limiting internalization stage. The major parameter that is modulated by iron deficiency is the iron-binding capacity. We propose that excessive iron binding in iron-deficient cells serves as a temporary reservoir for iron that is subsequently internalized. This mechanism is particularly suitable for organisms that are exposed to large fluctuations in iron availability.
The Senescence-Induced Staygreen Protein Regulates Chlorophyll Degradation
Authors: Park So-Yon , Yu Jae-Woong , Park Jong-Sung , Li Jinjie , Yoo Soo-Cheul , Lee Na-Yeoun , Lee Sang-Kyu , Jeong Seok-Won , Seo Hak Soo , Koh Hee-Jong , Jeon Jong-Seong , Park Youn-Il , Paek Nam-Chon
Published: May 2007

Loss of green color in leaves results from chlorophyll (Chl) degradation in chloroplasts, but little is known about how Chl catabolism is regulated throughout leaf development. Using the staygreen (sgr) mutant in rice (Oryza sativa), which maintains greenness during leaf senescence, we identified Sgr, a senescence-associated gene encoding a novel chloroplast protein. Transgenic rice overexpressing Sgr produces yellowish-brown leaves, and Arabidopsis thaliana pheophorbide a oxygenase–impaired mutants exhibiting a stay-green phenotype during dark-induced senescence have reduced expression of Sgr homologs, indicating that Sgr regulates Chl degradation at the transcriptional level. We show that the leaf stay-greenness of the sgr mutant is associated with a failure in the destabilization of the light-harvesting chlorophyll binding protein (LHCP) complexes of the thylakoid membranes, which is a prerequisite event for the degradation of Chls and LHCPs during senescence. Transient overexpression of Sgr in Nicotiana benthamiana and an in vivo pull-down assay show that Sgr interacts with LHCPII, indicating that the Sgr-LHCPII complexes are formed in the thylakoid membranes. Thus, we propose that in senescing leaves, Sgr regulates Chl degradation by inducing LHCPII disassembly through direct interaction, leading to the degradation of Chls and Chl-free LHCPII by catabolic enzymes and proteases, respectively.
Components of theArabidopsismRNA Decapping Complex Are Required for Early Seedling Development
Authors: Goeres David C. , Van Norman Jaimie M. , Zhang Weiping , Fauver Nellie A. , Spencer Mary Lou , Sieburth Leslie E.
Published: May 2007

To understand the mechanisms controlling vein patterning in Arabidopsis thaliana, we analyzed two phenotypically similar mutants, varicose (vcs) and trident (tdt). We had previously identified VCS, and recently, human VCS was shown to function in mRNA decapping. Here, we report that TDT encodes the mRNA-decapping enzyme. VCS and TDT function together in small cytoplasmic foci that appear to be processing bodies. To understand the developmental requirements for mRNA decapping, we characterized the vcs and tdt phenotypes. These mutants were small and chlorotic, with severe defects in shoot apical meristem formation and cotyledon vein patterning. Many capped mRNAs accumulated in tdt and vcs mutants, but surprisingly, some mRNAs were specifically depleted. In addition, loss of decapping arrested the decay of some mRNAs, while others showed either modest or no decay defects, suggesting that mRNAs may show specificity for particular decay pathways (3′ to 5′ and 5′ to 3′). Furthermore, the severe block to postembryonic development in vcs and tdt and the accompanying accumulation of embryonic mRNAs indicate that decapping is important for the embryo-to-seedling developmental transition.
TomatoBRASSINOSTEROID INSENSITIVE1Is Required for Systemin-Induced Root Elongation inSolanum pimpinellifoliumbut Is Not Essential for Wound Signaling
Authors: Holton Nicholas , Caño-Delgado Ana , Harrison Kate , Montoya Teresa , Chory Joanne , Bishop Gerard J.
Published: May 2007

The tomato Leu-rich repeat receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1) has been implicated in both peptide (systemin) and steroid (brassinosteroid [BR]) hormone perception. In an attempt to dissect these signaling pathways, we show that transgenic expression of BRI1 can restore the dwarf phenotype of the tomato curl3 (cu3) mutation. Confirmation that BRI1 is involved in BR signaling is highlighted by the lack of BR binding to microsomal fractions made from cu3 mutants and the restoration of BR responsiveness following transformation with BRI1. In addition, wound and systemin responses in the cu3 mutants are functional, as assayed by proteinase inhibitor gene induction and rapid alkalinization of culture medium. However, we observed BRI1-dependent root elongation in response to systemin in Solanum pimpinellifolium. In addition, ethylene perception is required for normal systemin responses in roots. These data taken together suggest that cu3 is not defective in systemin-induced wound signaling and that systemin perception can occur via a non-BRI1 mechanism.
Canonical Signal Recognition Particle Components Can Be Bypassed for Posttranslational Protein Targeting in Chloroplasts
Authors: Tzvetkova-Chevolleau Tzvetelina , Hutin Claire , Noël Laurent D. , Goforth Robyn , Carde Jean-Pierre , Caffarri Stephano , Sinning Irmgard , Groves Matthew , Teulon Jean-Marie , Hoffman Neil E. , Henry Ralph , Havaux Michel , Nussaume Laurent
Published: May 2007

The chloroplast signal recognition particle (cpSRP) and its receptor (cpFtsY) target proteins both cotranslationally and posttranslationally to the thylakoids. This dual function enables cpSRP to utilize its posttranslational activities for targeting a family of nucleus-encoded light-harvesting chlorophyll binding proteins (LHCPs), the most abundant membrane proteins in plants. Previous in vitro experiments indicated an absolute requirement for all cpSRP pathway soluble components. In agreement, a cpFtsY mutant in Arabidopsis thaliana exhibits a severe chlorotic phenotype resulting from a massive loss of LHCPs. Surprisingly, a double mutant, cpftsy cpsrp54, recovers to a great extent from the chlorotic cpftsy phenotype. This establishes that in plants, a new alternative pathway exists that can bypass cpSRP posttranslational targeting activities. Using a mutant form of cpSRP43 that is unable to assemble with cpSRP54, we complemented the cpSRP43-deficient mutant and found that this subunit is required for the alternative pathway. Along with the ability of cpSRP43 alone to bind the ALBINO3 translocase required for LHCP integration, our results indicate that cpSRP43 has developed features to function independently of cpSRP54/cpFtsY in targeting LHCPs to the thylakoid membranes.
Carbon dynamics in a model grassland with functionally different soil communities
Authors: BRADFORD M. A. , TORDOFF G. M. , BLACK H. I. J. , COOK R. , EGGERS T. , GARNETT M. H. , GRAYSTON S. J. , HUTCHESON K. A. , INESON P. , NEWINGTON J. E. , OSTLE N. , SLEEP D. , STOTT A. , JONES T. HEFIN
Published: May 2007

Impacts of environmental changes on carbon cycling in terrestrial ecosystems are typically correlated with shifts in the composition, biomass and activity of soil faunal communities. Given the role of soil fauna in decomposition, shifts in soil faunal communities may further modify the carbon dynamics of a perturbed system.

To test this possibility, we manipulated soil community composition in model grassland ecosystems and used a13CO2‐tracer to follow the assimilation, retention and pathways of recent, photosynthetically fixed carbon. The community treatments formed a nested hierarchy of functional complexity: (1) microbiota only; (2) microbiota and mesofauna; (3) microbiota, mesofauna and macrofauna.

These treatments significantly affected the rate of decline in13C‐label respiration rate and the amount of13C‐label retained by the communities: while the rate of decline in13C‐label respiration rate was greatest in the microbiota treatment, the treatment with both micro‐ and mesofauna retained less13C‐label than either the more functionally complex or simple treatments. The presence of macrofauna altered the utilization of13C‐label by Collembola and Enchytraeidae: they decreased the mass of13C‐label utilized by Collembola and increased that utilized by Enchytraeidae.

Our results suggest that soil community composition may play a key role in regulating the dynamics of recent, photosynthetically fixed carbon.
Carbon dioxide uptake, water relations and drought survival for Dudleya saxosa, the ‘rock live‐forever’, growing in small soil volumes
Authors: NOBEL P. S. , ZUTTA B. R.
Published: May 2007

Although many plants grow in rock crevices and other regions of small soil volume, including over 20 000 epiphytic and hemi‐epiphytic species, analyses of the actual soil volume occupied, the water availability in that soil, the water‐storage capacity in the shoots and underground organs, and the photosynthetic pathway utilized have rarely been combined.

Dudleya saxosa (M.F. Jones) Britton and Rose (Crassulaceae), growing in the Sonoran Desert, has very shallow roots that occupied soil volumes averaging only 43 × 10−6 m3 per medium‐sized plant. This volume of soil can hold about the same amount of water (10 g) as can be stored in the leaves, corm and roots combined (11 g), but at a sufficiently high water potential for transfer to the plant for less than 1 week after a substantial rainfall.

About 80% of the net carbon dioxide uptake by D. saxosa over a 24‐h period occurred during the daytime (C3) under wet conditions, the daily total decreasing by 34% and the pattern shifting to nocturnal net CO2 uptake (CAM) after 46 days’ drought. Seventy‐seven days’ drought eliminated its daily net CO2 uptake.

Stomatal frequency was only 67 mm−2 on the adaxial (upper) surface and twofold lower on the abaxial surface. The cuticle was thick, 34 µm for the adaxial surface. Leaves had 24 mesophyll cell layers, leading to a high mesophyll cell surface area per unit leaf area of 142.

The three leaf anatomical features plus utilization of CAM increased net CO2 uptake per unit of water transpired, and helped D. saxosa thrive in a small soil volume, with the underground corm being a major supplier of water to the succulent leaves during 2.5 months of drought. The maximum water‐holding capacity of the soil explored by the roots closely matched the maximum water‐holding capacity of the plant, reflecting the conservative strategy used by D. saxosa in a stressful semi‐arid environment.
Cytokine‐mediated control of lipopolysaccharide‐induced activation of small intestinal epithelial cells
Authors: Lotz Michael , König Till , Ménard Sandrine , Gütle Dominique , Bogdan Christian , Hornef Mathias W.
Published: May 2007

Cytokines with anti‐inflammatory properties have been implicated in the prevention of inappropriate immune activation by commensal bacteria in the intestinal tract. Here, we analysed receptor expression, cellular signalling, and the inhibitory activity of interleukin (IL)‐4, ‐10, ‐11, and ‐13 as well as of transforming growth factor‐β on lipopolysaccharide‐mediated small intestinal epithelial cell activation. Only IL‐4 and IL‐13 had a significant inhibitory effect on chemokine secretion and nitric oxide (NO) production in differentiated and polarized cells. Reverse transcription–polymerase chain reaction of primary intestinal epithelial cells obtained by laser‐microdissection confirmed expression of the type II IL‐4 receptor consisting of the IL‐4 receptor α and the IL‐13 receptor α1. Also, IL‐4 or IL‐13 led to rapid signal transducer and activator of transcription 6 phosphorylation, diminished inducible NO synthase expression, and enhanced the antagonistic arginase 1 activity. In conclusion, cytokines such as IL‐4 and IL‐13 affect intestinal epithelial cells and exhibit a modulating activity on Toll‐like receptor‐4‐mediated epithelial cell activation.
Effectiveness of two nickel‐titanium rotary instruments and a hand file for removing gutta‐percha in severely curved root canals during retreatment: an ex vivo study
Authors: Gergi R. , Sabbagh C.
Published: May 2007

Aim  To evaluate ex vivo the effectiveness of hand files, ProTaper and R‐Endo rotary instruments when removing gutta‐percha from curved root canals.

Methodology  Ninety severely curved teeth were divided into three groups. The root canals were accessed, prepared and filled with vertically condensed gutta‐percha and sealer. Removal of gutta‐percha was performed with the following devices and techniques: Hedström files (Vereinigte Dentalwerke, Munich, Germany), ProTaper (Dentsply Maillefer, Ballaigues, Switzerland) and R‐Endo (Micro‐Mega, Besançon, France). All techniques were used with the solvent eucalyptol. The amount of filling material debris remaining on root canal walls was assessed radiographically from two directions: mesio‐distal and bucco‐lingual. The images were digitized and analysed with autocad 2000 software. Total canal area, area of the cervical, middle and apical thirds, and area of remaining filling material from both directions were outlined by two different operators and calculated. Statistical analysis of remaining filling material within each third of the canals was performed by the Kruskal–Wallis test.

Results  Comparisons of the percentages of remaining filling material in the entire canal did not reveal any significant differences between the methods of removal. However, the canal third was of relevance in all groups; the apical third had the most remaining filling material compared with the middle and cervical thirds (P = 0.0012).

Conclusion  All instruments left filling material inside the root canal. ProTaper and R‐Endo rotary instruments were inadequate for the complete removal of filling material from the root canal system.
Fatigue testing of a NiTi rotary instrument. Part 2: fractographic analysis
Authors: Cheung G. S. P. , Darvell B. W.
Published: May 2007

Aim  To examine the topographic features of the fracture surface of a NiTi instrument after fatigue failure, and to correlate the measurements of some features with the cyclic load.

Methodology  A total of 212 ProFile rotary instruments were subjected to a rotational‐bending test at various curvatures until broken. The fracture surface of all fragments was examined by SEM to identify the crack origins. The crack radius, i.e. extent of the fatigue‐crack growth towards the centroid of the cross‐section, was also measured, and correlated with the strain amplitude for each instrument.

Results  All fracture surfaces revealed the presence of one or more crack origins, a region occupied by microscopic striations, and an area with microscopic dimples. The number of specimens showing multiple crack origins was significantly greater in the group fatigued under water than in air (P < 0.05). A linear relationship between the reciprocal of the square root of the crack radius and the strain amplitude was discernible (P < 0.001), the slopes of which were not significantly different for instruments fatigued in air and water.

Conclusions  The fractographic appearance of NiTi engine‐files that had failed because of fatigue is typical of that for other metals. The fatigue behaviour of NiTi instruments is adversely affected by water, not only for the low‐cycle fatigue life, but also the number of crack origins. There appears to be a critical extent of crack propagation for various strain amplitudes leading to final rupture (akin to the Griffith's criterion for brittle materials).
Comparison of root canal preparation with two rotary NiTi instruments: ProFile .04 and GT Rotary
Authors: Rödig T. , Hülsmann M. , Kahlmeier C.
Published: May 2007

Aim  To compare root canal preparation using ProFile .04 and GT Rotary nickel–titanium instruments (both Dentsply Maillefer, Ballaigues, Switzerland).

Methodology  Fifty extracted mandibular molars with mesial root canal curvatures between 20 and 40° were randomly divided into two groups and embedded in a muffle system. All root canals were prepared to size 45 using ProFile .04 or GT rotary instruments. The following parameters were evaluated: straightening of root canal curvature, postoperative root canal cross‐section, cleaning ability, safety issues and working time.

Results  Both NiTi systems maintained curvature well; the mean degree of straightening was <1°. The majority of the root canals prepared with ProFile .04 (80.8%) and GT (84.0%) postoperatively showed a round or oval cross‐section. For debris, ProFile .04 and GT rotary achieved 67.1% and 71.6% scores of 1 and 2, respectively. Concerning the coronal region statistical analysis showed a better result for GT than for ProFile .04. For the middle and apical thirds of the root canals, results did not differ significantly. None of the two systems completely removed smear layer. Ten procedural incidents occurred with ProFile .04 compared with five with GT. Mean working time was shorter for ProFile .04 (131.8 s) than for GT (143.7 s); the difference was not significant.

Conclusions  Both systems respected original root canal curvature well and were safe to use. Smear layer removal was not satisfactory with either systems.