bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental validation of a Richtmyer–Meshkov scaling law over large density ratio and shock strength ranges
Authors: Motl Bradley , Oakley Jason , Ranjan Devesh , Weber Chris , Anderson Mark , Bonazza Riccardo
Published: January 2010

A universal scaling law for the Richtmyer–Meshkov instability is validated with experimental results covering a wide range of density ratios and shock strengths. These results include the first membraneless, gas-phase, interface experiments for A>0.5 and M>1.5. The shock-accelerated, sinusoidal interface experiments are conducted in a vertical shock tube with a large square cross section and cover the experimental parameter space: 0.29<A<0.95, 1.1<M<3, and 3.1×104<Re<1.4×107. Results provide growth-rate data for comparison with computational fluid dynamics simulation codes and verify the nondimensional time and amplitude parameters chosen for scaling are the correct ones. Correct scaling is obtained by including a growth-reduction factor that accounts for diffusion at the interface. Planar imaging techniques are used to diagnose the instability development for a nearly single-mode interface, and results are reported for eight scenarios (including three distinct gas pairs) that span the linear and nonlinear growth regimes. Images from the strongly shocked, high A experiments are the first to provide evidence of bubble-growth suppression due to shock proximity.
Enhanced lateral photovoltaic effect in an improved oxide-metal-semiconductor structure of TiO2/Ti/Si
Authors: Yu Chong Qi , Wang Hui , Xia Yu Xing
Published: January 2010

A greatly enhanced lateral photovoltaic effect (LPE) is achieved in an improved metal-semiconductor (MS) structure of TiO2(1.2 nm)/Ti(6.2 nm)/Si. Compared with the LPE in traditional MS structures of Ti(6.2 nm)/Si and other reported MS structures, this oxide-metal-semiconductor structure presents a much larger sensitivity of lateral photovoltage of 97 mV/mm. We ascribe this to the enhancement of lateral gradient of the density of excess carriers in the structure caused by the increase of surface resistivity.
A density-functional approximation for relativistic kinetic energy
Authors: Becke Axel D.
Published: January 2010

A density-functional approximation for the relativistic kinetic energy of a many-electron system is introduced, depending on the total particle density and the (nonrelativistic) kinetic energy density. The resulting scalar variational orbital equation is similar to Schrödinger’s nonrelativistic equation, but includes relativistic mass-velocity effects to all orders in p. We test the theory by computing relativistic orbitals in the uranium atom and comparing their energies and mean radii with Dirac and zeroth-order regular approximation results.
Irradiation damage in graphene on SiO2 probed by local mobility measurements
Authors: Giannazzo F. , Sonde S. , Raineri V. , Rimini E.
Published: January 2010

Using a method based on scanning capacitance spectroscopy, local measurements of the electron mean free path (l) and mobility (μ) have been carried out on single layers of graphene (SLG) mechanically exfoliated from highly oriented pyrolytic graphite and deposited on SiO2/Si. Lateral inhomogeneity of l and μ was found both on pristine and ion irradiated SLG with different C ion fluences (from 1013 to 1014 cm−2), with an increasing spread in the distribution of l and μ for larger fluences. Before irradiation, the spread was explained by the inhomogeneous distribution of charged impurities on SLG surface and/or at the interface with SiO2. After irradiation, lattice vacancies cause a local reduction of μ in the damaged regions.
Resistive switching characteristics of ZnO thin film grown on stainless steel for flexible nonvolatile memory devices
Authors: Lee Seunghyup , Kim Heejin , Yun Dong-Jin , Rhee Shi-Woo , Yong Kijung
Published: January 2010

This paper reports a resistive switching device of Au/ZnO/stainless steel (SS) and its applicability as a flexible resistive random access memory (ReRAM). The Au/ZnO/SS structure was fabricated by radio frequency sputtering deposition of a ZnO thin film on the SS substrate. The fabricated device showed stable unipolar and bipolar resistive switching behaviors with reliable switching responses over 100 cycles. The device performance was not degraded upon bending, which indicates high potential for flexible ReRAM applications.
Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100)
Authors: Xu Lijun , Mei Donghai , Henkelman Graeme
Published: January 2010

The adaptive kinetic Monte Carlo method was used to calculate the decomposition dynamics of a methanol molecule on Cu(100) at room temperature over a time scale of minutes. Mechanisms of reaction were found using minimum mode following saddle point searches based on forces and energies from density functional theory. Rates of reaction were calculated with harmonic transition state theory. The dynamics followed a pathway from CH3OH, CH3O, CH2O, HCO, and finally to CO. Our calculations confirm that methanol decomposition starts with breaking the O–H bond followed by breaking C–H bonds in the dehydrogenated intermediates until CO is produced. The bridge site on the Cu(100) surface is the active site for scissoring chemical bonds. Reaction intermediates are mobile on the surface which allows them to find this active reaction site. This study illustrates how the adaptive kinetic Monte Carlo method can model the dynamics of surface chemistry from first principles.
Multiscale network model for large protein dynamics
Authors: Jang Hyoseon , Na Sungsoo , Eom Kilho
Published: January 2010

Protein dynamics is essential for gaining insight into biological functions of proteins. Although protein dynamics is well delineated by molecular model, the molecular model is computationally prohibited for simulating large protein structures. In this work, we provide a multiscale network model (MNM) that allows the efficient computation on low-frequency normal modes related to structural deformation of proteins as well as dynamic behavior of functional sites. Specifically, MNM consists of two regions, one of which is described as a low-resolution structure, while the other is dictated by a high-resolution structure. The high-resolution regions using all alpha carbons of the protein are mainly binding site parts, which play a critical function in molecules, while the low-resolution parts are constructed from a further coarse-grained model (not using all alpha carbons). The feasibility of MNM to observe the cooperative motion of a protein structure was validated. It was shown that the MNM enables us to understand functional motion of proteins with computational efficiency.
Nucleation and growth of C60 nanoparticles from the supersaturated vapor and from the undercooled liquid: A molecular simulation study
Authors: Ngale Kenneth Ndumbe , Desgranges Caroline , Delhommelle Jerome
Published: January 2010

Using molecular simulation, we study the molecular mechanisms underlying the nucleation and growth of C60 nanoparticles from the supersaturated vapor and from the undercooled liquid. We show that in both cases, nucleation proceeds through the formation of small clusters composed of the metastable hexagonal close-packed (HCP) polymorph. This observation differs from the nucleation pathway of simple systems (e.g., modeled by Lennard-Jones potential) in which the nucleation proceeds through the metastable body-centered cubic polymorph. We rationalize this observation in terms of the relative steepness of the repulsion for the different potential models. Finally, we observe two different types of growth leading either to crystallites dominated by the metastable HCP polymorph or to crystallites whose structure is predominantly that of the stable face-centered cubic (FCC) polymorph. This finding is consistent with experiments on the crystallization of C60 from the vapor, which reported the formation of FCC and HCP crystals.
Graphene reveals the Hall-mark of strongly interacting electrons
Authors: Levi Barbara Goss
Published: December 2009

The eagerly anticipated observation of the fractional quantum Hall effect raises hopes of seeing even more exotic behavior.
Gamma-ray telescopes show origins of cosmic rays
Authors: Schwarzschild Bertram
Published: December 2009

The long-held presumption that most cosmic rays are accelerated in supernova remnants has, until now, lacked convincing evidence.
Academic research, DOE facilities are buoyed by recovery act
Authors: Kramer David
Published: December 2009

Nearly a year after passage of the stimulus package, federal agencies are close to committing the entire $18.4 billion provided for basic research. But what happens when funding runs out?
US seeks science ties to salve relations with Muslim world
Authors: Kramer David
Published: December 2009

Agencies move tentatively to implement Obama’s plan, but Iran isn’t invited to the table, and funding is scarce.
The 18th-century battle over lunar motion
Authors: Bodenmann Siegfried
Published: December 2009

In a dispute with more than just scientific import, Alexis Clairaut, Leonhard Euler, and Jean le Rond d’Alembert each employed their own strategies to establish that they were the first to understand a puzzling feature of the Moon’s orbit.
The quantum spin Hall effect and topological insulators
Authors: Qi Xiao-Liang , Zhang Shou-Cheng
Published: December 2009

In topological insulators, spin–orbit coupling and time-reversal symmetry combine to form a novel state of matter predicted to have exotic physical properties.
Bell Labs and the ruby laser
Authors: Nelson Donald F. , Collins Robert J. , Kaiser Wolfgang
Published: December 2009

In 1960 two rival laboratories reported the creation of lasers. Controversy over priority and proper behavior has persisted for half a century. Now three Bell Labs veterans of that confused but exciting summer tell the story as they remember it.
Optical cycling paves the way for laser-cooled molecules
Authors: Miller Johanna
Published: December 2009

Molecules have more degrees of freedom than atoms do, so guiding them into the same few quantum states is a challenge.
Bioartificial matrices for therapeutic vascularization
Authors: Phelps Edward A. , Landázuri Natalia , Thulé Peter M. , Taylor W. Robert , García Andrés J.
Published: January 2010

Therapeutic vascularization remains a significant challenge in regenerative medicine applications. Whether the goal is to induce vascular growth in ischemic tissue or scale up tissue-engineered constructs, the ability to induce the growth of patent, stable vasculature is a critical obstacle. We engineered polyethylene glycol–based bioartificial hydrogel matrices presenting protease-degradable sites, cell-adhesion motifs, and growth factors to induce the growth of vasculature in vivo. Compared to injection of soluble VEGF, these matrices delivered sustained in vivo levels of VEGF over 2 weeks as the matrix degraded. When implanted subcutaneously in rats, degradable constructs containing VEGF and arginine-glycine-aspartic acid tripeptide induced a significant number of vessels to grow into the implant at 2 weeks with increasing vessel density at 4 weeks. The mechanism of enhanced vascularization is likely cell-demanded release of VEGF, as the hydrogels may degrade substantially within 2 weeks. In a mouse model of hind-limb ischemia, delivery of these matrices resulted in significantly increased rate of reperfusion. These results support the application of engineered bioartificial matrices to promote vascularization for directed regenerative therapies.
Stereoelectronic and steric effects in side chains preorganize a protein main chain
Authors: Shoulders Matthew D. , Satyshur Kenneth A. , Forest Katrina T. , Raines Ronald T.
Published: January 2010

Preorganization is shown to endow a protein with extraordinary conformational stability. This preorganization is achieved by installing side-chain substituents that impose stereoelectronic and steric effects that restrict main-chain torsion angles. Replacing proline residues in (ProProGly)
7
collagen strands with 4-fluoroproline and 4-methylproline leads to the most stable known triple helices, having
T

m

values that are increased by > 50 °C. Differential scanning calorimetry data indicate an entropic basis to the hyperstability, as expected from an origin in preorganization. Structural data at a resolution of 1.21 Å reveal a prototypical triple helix with insignificant deviations to its main chain, even though 2/3 of the residues are nonnatural. Thus, preorganization of a main chain by subtle changes to side chains can confer extraordinary conformational stability upon a protein without perturbing its structure.
Yields ofβ-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates formed from OH radical-initiated reactions of 2-methyl-1-alkenes
Authors: Matsunaga Aiko , Ziemann Paul J.
Published: January 2010

Yields ofβ-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates, in particles formed from OH radical-initiated reactions of C9-C152-methyl-1-alkenes in the presence of NOxwere measured by using a thermal desorption particle beam mass spectrometer coupled to a high-performance liquid chromatograph with a UV-visible (UV-vis) detector. Yields ofβ-hydroxynitrates and dihydroxynitrates increased with carbon number primarily due to enhanced gas-to-particle partitioning before reaching plateaus at ≈C14-C15, where the compounds were essentially entirely in the particle phase. Plateau yields ofβ-hydroxynitrates, dihydroxynitrates, and trihydroxynitrates were 0.183 ± 0.005, 0.045 ± 0.005, and 0.034 ± 0.005, and, after normalization for OH radical addition to the C = C double bond, were 0.225 ± 0.007, 0.055 ± 0.006, and 0.042 ± 0.006. The fractions of 1-hydroxy and 2-hydroxyβ-hydroxynitrate isomers were 0.90/0.10. Yields measured here and in our previous study of reactions of linear internal alkenes and linear 1-alkenes indicate that, for these alkene classes, the relative branching ratios for forming tertiary, secondary, and primaryβ-hydroxyalkyl radicals by OH radical addition to the C = C double bond are 4.3/1.9/1.0, and the branching ratios for formingβ-hydroxynitrates from reactions of tertiary, secondary, and primaryβ-hydroxyperoxy radicals with NO are 0.25, 0.15, and 0.12. The effects of H2O vapor and NH3on yields were also explored.
Reactive intermediates revealed in secondary organic aerosol formation from isoprene
Authors: Surratt Jason D. , Chan Arthur W. H. , Eddingsaas Nathan C. , Chan ManNin , Loza Christine L. , Kwan Alan J. , Hersey Scott P. , Flagan Richard C. , Wennberg Paul O. , Seinfeld John H.
Published: January 2010

Isoprene is a significant source of atmospheric organic aerosol; however, the oxidation pathways that lead to secondary organic aerosol (SOA) have remained elusive. Here, we identify the role of two key reactive intermediates, epoxydiols of isoprene (IEPOX = 
β
-IEPOX + 
δ
-IEPOX) and methacryloylperoxynitrate (MPAN), which are formed during isoprene oxidation under low- and high-NO

x

conditions, respectively. Isoprene low-NO

x

SOA is enhanced in the presence of acidified sulfate seed aerosol (mass yield 28.6%) over that in the presence of neutral aerosol (mass yield 1.3%). Increased uptake of IEPOX by acid-catalyzed particle-phase reactions is shown to explain this enhancement. Under high-NO

x

conditions, isoprene SOA formation occurs through oxidation of its second-generation product, MPAN. The similarity of the composition of SOA formed from the photooxidation of MPAN to that formed from isoprene and methacrolein demonstrates the role of MPAN in the formation of isoprene high-NO

x

SOA. Reactions of IEPOX and MPAN in the presence of anthropogenic pollutants (i.e., acidic aerosol produced from the oxidation of SO
2
and NO
2
, respectively) could be a substantial source of “missing urban SOA” not included in current atmospheric models.
Protein refolding by pH-triggered chaperone binding and release
Authors: Tapley Timothy L. , Franzmann Titus M. , Chakraborty Sumita , Jakob Ursula , Bardwell James C. A.
Published: January 2010

Molecular chaperones are typically either adenosine triphosphate (ATP) dependent or rely heavily on their ATP-dependent chaperone counterparts in order to promote protein folding. This presents a challenge to chaperones that are localized to ATP-deficient cellular compartments. Here we describe a mechanism by which the pH-regulated acid stress chaperone HdeA is capable of independently facilitating the refolding of acid-denatured proteins in the bacterial periplasm, which lacks both ATP and ATP-dependent chaperone machines. Our results are consistent with a model in which HdeA stably binds substrates at low pH, thereby preventing their irreversible aggregation. pH neutralization subsequently triggers the slow release of substrate proteins from HdeA, keeping the concentration of aggregation-sensitive intermediates below the threshold where they begin to aggregate. This provides a straightforward and ATP-independent mechanism that allows HdeA to facilitate protein refolding. Unlike previously characterized chaperones, HdeA appears to facilitate protein folding by using a single substrate binding-release cycle. This cycle is entirely regulated by the external environment and is therefore energy-neutral for the bacteria.
Cavity opto-mechanics using an optically levitated nanosphere
Authors: Chang D. E. , Regal C. A. , Papp S. B. , Wilson D. J. , Ye J. , Painter O. , Kimble H. J. , Zoller P.
Published: January 2010

Recently, remarkable advances have been made in coupling a number of high-Q modes of nano-mechanical systems to high-finesse optical cavities, with the goal of reaching regimes in which quantum behavior can be observed and leveraged toward new applications. To reach this regime, the coupling between these systems and their thermal environments must be minimized. Here we propose a novel approach to this problem, in which optically levitating a nano-mechanical system can greatly reduce its thermal contact, while simultaneously eliminating dissipation arising from clamping. Through the long coherence times allowed, this approach potentially opens the door to ground-state cooling and coherent manipulation of a single mesoscopic mechanical system or entanglement generation between spatially separate systems, even in room-temperature environments. As an example, we show that these goals should be achievable when the mechanical mode consists of the center-of-mass motion of a levitated nanosphere.
Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism
Authors: Gu Meigang , Rice Charles M.
Published: January 2010

A virally encoded superfamily-2 (SF2) helicase (NS3h) is essential for the replication of hepatitis C virus, a leading cause of liver disease worldwide. Efforts to elucidate the function of NS3h and to develop inhibitors against it, however, have been hampered by limited understanding of its molecular mechanism. Here we show x-ray crystal structures for a set of NS3h complexes, including ground-state and transition-state ternary complexes captured with ATP mimics (ADP·BeF
3
and

). These structures provide, for the first time, three conformational snapshots demonstrating the molecular basis of action for a SF2 helicase. Upon nucleotide binding, overall domain rotation along with structural transitions in motif V and the bound DNA leads to the release of one base from the substrate base-stacking row and the loss of several interactions between NS3h and the 3′ DNA segment. As nucleotide hydrolysis proceeds into the transition state, stretching of a “spring” helix and another overall conformational change couples rearrangement of the (d)NTPase active site to additional hydrogen-bonding between NS3h and DNA. Together with biochemistry, these results demonstrate a “ratchet” mechanism involved in the unidirectional translocation and define the step size of NS3h as one base per nucleotide hydrolysis cycle. These findings suggest feasible strategies for developing specific inhibitors to block the action of this attractive, yet largely unexplored drug target.
Requirement for deoxycytidine kinase in T and B lymphocyte development
Authors: Toy Gerald , Austin Wayne R. , Liao Hsiang-I , Cheng Donghui , Singh Arun , Campbell Dean O. , Ishikawa Tomo-o , Lehmann Lynn W. , Satyamurthy Nagichettiar , Phelps Michael E. , Herschman Harvey R. , Czernin Johannes , Witte Owen N. , Radu Caius G.
Published: January 2010

Deoxycytidine kinase (dCK) is a rate-limiting enzyme in deoxyribonucleoside salvage, a metabolic pathway that recycles products of DNA degradation. dCK phosphorylates and therefore activates nucleoside analog prodrugs frequently used in cancer, autoimmunity, and viral infections. In contrast to its well established therapeutic relevance, the biological function of dCK remains enigmatic. Highest levels of dCK expression are found in thymus and bone marrow, indicating a possible role in lymphopoiesis. To test this hypothesis we generated and analyzed dCK knockout (KO) mice. dCK inactivation selectively and profoundly affected T and B cell development. A 90-fold decrease in thymic cellularity was observed in the dCK KO mice relative to wild-type littermates. Lymphocyte numbers in the dCK KO mice were 5- to 13-fold below normal values. The severe impact of dCK inactivation on lymphopoiesis was unexpected given that nucleoside salvage has been thought to play a limited, "fine-tuning" role in regulating deoxyribonucleotide triphosphate pools produced by the de novo pathway. The dCK KO phenotype challenges this view and indicates that, in contrast to the great majority of other somatic cells, normal lymphocyte development critically requires the deoxyribonucleoside salvage pathway.
50 years of fusion research and the road to fusion energy
Authors: Kikuchi M.
Published: December 2009

The full text of this editorial is available in the PDF.
Tokamak foundation in USSR/Russia 1950–1990
Authors: Smirnov V.P.
Published: December 2009

In the USSR, nuclear fusion research began in 1950 with the work of I.E. Tamm, A.D. Sakharov and colleagues. They formulated the principles of magnetic confinement of high temperature plasmas, that would allow the development of a thermonuclear reactor. Following this, experimental research on plasma initiation and heating in toroidal systems began in 1951 at the Kurchatov Institute. From the very first devices with vessels made of glass, porcelain or metal with insulating inserts, work progressed to the operation of the first tokamak, T-1, in 1958. More machines followed and the first international collaboration in nuclear fusion, on the T-3 tokamak, established the tokamak as a promising option for magnetic confinement. Experiments continued and specialized machines were developed to test separately improvements to the tokamak concept needed for the production of energy. At the same time, research into plasma physics and tokamak theory was being undertaken which provides the basis for modern theoretical work. Since then, the tokamak concept has been refined by a world-wide effort and today we look forward to the successful operation of ITER.
Magnetic fusion development for global warming suppression
Authors: Li Jiangang , Zhang Jie , Duan Xuru
Published: December 2009

Energy shortage and environmental pollution are two critical issues for human beings in the 21st century. There is an urgent need for new sustainable energy to meet the fast growing demand for clean energy. Fusion is one of the few options which may be able to satisfy the requirement for large scale sustainable energy generation and global warming suppression and therefore must be developed as quickly as possible. Fusion research has been carried out for the past 50 years. It is too long to wait for another 50 years to generate electricity by fusion. A much more aggressive approach should be taken with international collaboration towards the early use of fusion energy to meet the urgent needs for energy and global warming suppression.
A new model of home‐based telemonitored cardiac rehabilitation in patients with heart failure: effectiveness, quality of life, and adherence
Authors: Piotrowicz Ewa , Baranowski Rafał , Bilinska Maria , Stepnowska Monika , Piotrowska Malgorzata , Wójcik Anna , Korewicki Jerzy , Chojnowska Lidia , Malek Lukasz A. , Klopotowski Mariusz , Piotrowski Walerian , Piotrowicz Ryszard
Published: December 2009

Aims

Despite proven benefits of cardiac rehabilitation (CR), currently proposed CR models are not acceptable for many heart failure (HF) patients. The purpose of this study was to evaluate a new model of home‐based telemonitored cardiac rehabilitation (HTCR) using walking training compared with an outpatient‐based standard cardiac rehabilitation (SCR) using interval training on a cycle ergometer.

Methods and results

The study included 152 HF patients (aged 58.1 ± 10.2 years, NYHA class II and III, ejection fraction ≤40%) who were randomized to HTCR (n = 77) or SCR (n = 75). All patients underwent 8 weeks of CR. Both groups were comparable in terms of demographic and clinical characteristics and medical therapy. The effectiveness of CR was assessed by changes in NYHA class, peak oxygen consumption, 6‐min walking test distance, and SF‐36 score. Cardiac rehabilitation resulted in a significant improvement of all parameters in both groups. All patients in the HTCR group completed the 8 weeks of CR, whereas 15 patients in the SCR group (20%) discontinued CR.

Conclusion

In patients with HF, HTCR is equally as effective as SCR and provides a similar improvement in quality of life. Adherence to CR seems to be better for HTCR. Home‐based telemonitored cardiac rehabilitation may be a useful alternative form of CR in patients with HF.
Clinical trials update from the Heart Failure Society of America Meeting 2009: FAST, IMPROVE‐HF, COACH galectin‐3 substudy, HF‐ACTION nuclear substudy, DAD‐HF, and MARVEL‐1
Authors: Lainscak Mitja , Coletta Alison P. , Sherwi Nasser , Cleland John G.F.
Published: December 2009

This article presents findings and a commentary on late‐breaking trials presented during the meeting of the Heart Failure Society of America in September 2009. Unpublished reports should be considered as preliminary, since analyses may change in the final publication. The FAST trial showed somewhat better performance of intrathoracic impedance for prediction of deterioration in patients with heart failure (HF) when compared with daily weighing. The IMPROVE‐HF study reported the benefits of education on the management of patients with systolic HF. Galectin‐3 appeared a useful method for improving risk stratification of patients with chronic HF in a substudy of the COACH trial. A nuclear substudy of the HF‐ACTION trial failed to demonstrate that resting myocardial perfusion imaging, a measure of myocardial scar and viability, was clinically useful. A small randomized controlled trial (DAD‐HF) suggested that the use of low‐dose dopamine in patients with acutely decompensated HF was associated with less deterioration in renal function and less hypokalaemia. The MARVEL‐1 trial raises further concerns about the safety of myoblast transplantation in ischaemic HF.
Endogeneity in Probit Response Models
Authors: Freedman David A. , Sekhon Jasjeet S.
Published: January 2010

We look at conventional methods for removing endogeneity bias in regression models, including the linear model and the probit model. It is known that the usual Heckman two-step procedure should not be used in the probit model: from a theoretical perspective, it is unsatisfactory, and likelihood methods are superior. However, serious numerical problems occur when standard software packages try to maximize the biprobit likelihood function, even if the number of covariates is small. We draw conclusions for statistical practice. Finally, we prove the conditions under which parameters in the model are identifiable. The conditions for identification are delicate; we believe these results are new.
Phytohabitans suffuscus gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae isolated from plant roots
Authors: Inahashi Yuki , Matsumoto Atsuko , Danbara Hirofumi , Ōmura Satoshi , Takahashi Yōko
Published: December 2009

An actinomycete strain, K07-0523T, was isolated from the roots of an orchid collected in Okinawa prefecture, Japan. 16S rRNA gene sequence analysis indicated that the new strain belonged to the familyMicromonosporaceaeand the similarity values between strain K07-0523Tand the type species of 24 genera in the familyMicromonosporaceaewere 93.3–97.7 %. Strain K07-0523Tcontainedd-glutamic acid, glycine,d-alanine,meso-diaminopimelic acid, hydroxydiaminopimelic acid andl-lysine in the cell wall. The major menaquinones were MK-9(H6), MK-10(H4) and MK-10(H6). Galactose, glucose, mannose, ribose and xylose were present in the whole-cell sugars. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were anteiso-C17 : 0, iso-C17 : 0, iso-C16 : 0and iso-C15 : 0. Phosphatidylethanolamine was detected as the major phospholipid and corresponded to phospholipid type II. The G+C content of the genomic DNA was 73 mol%. On the basis of phylogenetic and chemotaxonomic data, the new strain represents a member of a new genus and novel species, namelyPhytohabitans suffuscusgen. nov., sp. nov., in the familyMicromonosporaceae. The type strain of the type species is K07-0523T(=DSM 45306T=NBRC 105367T).
Social modulation of learning in rats
Authors: Knapska Ewelina , Mikosz Marta , Werka Tomasz , Maren Stephen
Published: December 2009

It is well known that emotions participate in the regulation of social behaviors and that the emotion displayed by a conspecific influences the behavior of other animals. In its simplest form, empathy can be characterized as the capacity to be affected by and/or share the emotional state of another. However, to date, relatively little is known about the mechanisms by which animals that are not in direct danger share emotions. In the present study, we used a model of between-subject transfer of fear to characterize the social interaction during which fear is transmitted, as well as the behavioral effects of socially transmitted fear. We found that (1) during social interaction with a recently fear-conditioned partner, observers and demonstrators exhibit social exploratory behaviors rather than aggressive behaviors; (2) learning and memory in a shock-motivated shuttle avoidance task are facilitated in rats that underwent a social interaction with a partner that had been fear conditioned; and (3) a brief social interaction with a recently fear-conditioned partner immediately before fear conditioning increases conditioned freezing measured on the next day. The observed effects were not due to a stress-induced increase in pain sensitivity or analgesia. Collectively, these data suggest that a brief social interaction with a cage mate that has undergone an aversive learning experience promotes aversive learning in an otherwise naïve animal. We argue that socially transferred fear is an adaptation that promotes defensive behavior to potentially dangerous situations in the environment.
AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
Authors: de Oliveira Dal'Molin Cristiana Gomes , Quek Lake-Ee , Palfreyman Robin William , Brumbley Stevens Michael , Nielsen Lars Keld
Published: January 2010

Genome-scale metabolic network models have been successfully used to describe metabolism in a variety of microbial organisms as well as specific mammalian cell types and organelles. This systems-based framework enables the exploration of global phenotypic effects of gene knockouts, gene insertion, and up-regulation of gene expression. We have developed a genome-scale metabolic network model (AraGEM) covering primary metabolism for a compartmentalized plant cell based on the Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a comprehensive literature-based, genome-scale metabolic reconstruction that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association entries, and 1,567 unique reactions compartmentalized into the cytoplasm, mitochondrion, plastid, peroxisome, and vacuole. The curation process identified 75 essential reactions with respective enzyme associations not assigned to any particular gene in the Kyoto Encyclopedia of Genes and Genomes or AraCyc. With the addition of these reactions, AraGEM describes a functional primary metabolism of Arabidopsis. The reconstructed network was transformed into an in silico metabolic flux model of plant metabolism and validated through the simulation of plant metabolic functions inferred from the literature. Using efficient resource utilization as the optimality criterion, AraGEM predicted the classical photorespiratory cycle as well as known key differences between redox metabolism in photosynthetic and nonphotosynthetic plant cells. AraGEM is a viable framework for in silico functional analysis and can be used to derive new, nontrivial hypotheses for exploring plant metabolism.
TheRON1/FRY1/SAL1Gene Is Required for Leaf Morphogenesis and Venation Patterning in Arabidopsis
Authors: Robles Pedro , Fleury Delphine , Candela Héctor , Cnops Gerda , Alonso-Peral María Magdalena , Anami Sylvester , Falcone Andrea , Caldana Camila , Willmitzer Lothar , Ponce María Rosa , Van Lijsebettens Mieke , Micol José Luis
Published: January 2010

To identify genes involved in vascular patterning in Arabidopsis (Arabidopsis thaliana), we screened for abnormal venation patterns in a large collection of leaf shape mutants isolated in our laboratory. The rotunda1-1 (ron1-1) mutant, initially isolated because of its rounded leaves, exhibited an open venation pattern, which resulted from an increased number of free-ending veins. We positionally cloned the RON1 gene and found it to be identical to FRY1/SAL1, which encodes an enzyme with inositol polyphosphate 1-phosphatase and 3′ (2′),5′-bisphosphate nucleotidase activities and has not, to our knowledge, previously been related to venation patterning. The ron1-1 mutant and mutants affected in auxin homeostasis share perturbations in venation patterning, lateral root formation, root hair length, shoot branching, and apical dominance. These similarities prompted us to monitor the auxin response using a DR5-GUS auxin-responsive reporter transgene, the expression levels of which were increased in roots and reduced in leaves in the ron1-1 background. To gain insight into the function of RON1/FRY1/SAL1 during vascular development, we generated double mutants for genes involved in vein patterning and found that ron1 synergistically interacts with auxin resistant1 and hemivenata-1 but not with cotyledon vascular pattern1 (cvp1) and cvp2. These results suggest a role for inositol metabolism in the regulation of auxin responses. Microarray analysis of gene expression revealed that several hundred genes are misexpressed in ron1-1, which may explain the pleiotropic phenotype of this mutant. Metabolomic profiling of the ron1-1 mutant revealed changes in the levels of 38 metabolites, including myoinositol and indole-3-acetonitrile, a precursor of auxin.
WOX4 Promotes Procambial Development
Authors: Ji Jiabing , Strable Josh , Shimizu Rena , Koenig Daniel , Sinha Neelima , Scanlon Michael J.
Published: January 2010

Plant shoot organs arise from initial cells that are recruited from meristematic tissues. Previous studies have shown that members of the WUSCHEL-related HOMEOBOX (WOX) gene family function to organize various initial cell populations during plant development. The function of the WOX4 gene is previously undescribed in any plant species. Comparative analyses of WOX4 transcription and function are presented in Arabidopsis (Arabidopsis thaliana), a simple-leafed plant with collateral vasculature, and in tomato (Solanum lycopersicum), a dissected-leafed species with bicollateral venation. WOX4 is transcribed in the developing vascular bundles of root and shoot lateral organs in both Arabidopsis and tomato. RNA interference-induced down-regulation of WOX4 in Arabidopsis generated small plants whose vascular bundles accumulated undifferentiated ground tissue and exhibited severe reductions in differentiated xylem and phloem. In situ hybridization analyses of Atwox4-RNA interference plants revealed delayed and reduced expression of both the phloem developmental marker ALTERED PHLOEM1 and HOMEOBOX GENE8, a marker of the vascular procambium. Overexpression of SlWOX4 correlated with overproliferation of xylem and phloem in transgenic tomato seedlings. The cumulative data suggest that the conserved WOX4 function is to promote differentiation and/or maintenance of the vascular procambium, the initial cells of the developing vasculature.
ZmPIN1-Mediated Auxin Transport Is Related to Cellular Differentiation during Maize Embryogenesis and Endosperm Development
Authors: Forestan Cristian , Meda Silvia , Varotto Serena
Published: January 2010

To study the influence of PINFORMED1 (PIN1)-mediated auxin transport during embryogenesis and endosperm development in monocots, the expression pattern of the three identified ZmPIN1 genes was determined at the transcript level. Localization of the corresponding proteins was also analyzed during maize (Zea mays) kernel development. An anti-indole-3-acetic acid (IAA) monoclonal antibody was used to visualize IAA distribution and correlate the direction of auxin active transport, mediated by ZmPIN1 proteins, with the actual amount of auxin present in maize kernels at different developmental stages. ZmPIN1 genes are expressed in the endosperm soon after double fertilization occurs; however, unlike other tissues, the ZmPIN1 proteins were never polarly localized in the plasma membrane of endosperm cells. ZmPIN1 transcripts and proteins also colocalize in developing embryos, and the ZmPIN1 proteins are polarly localized in the embryo cell plasma membrane from the first developmental stages, indicating the existence of ZmPIN1-mediated auxin fluxes. Auxin distribution visualization indicates that the aleurone, the basal endosperm transfer layer, and the embryo-surrounding region accumulate free auxin, which also has a maximum in the kernel maternal chalaza. During embryogenesis, polar auxin transport always correlates with the differentiation of embryo tissues and the definition of the embryo organs. On the basis of these reports and of the observations on tissue differentiation and IAA distribution in defective endosperm-B18 mutant and in N-1-naphthylphthalamic acid-treated kernels, a model for ZmPIN1-mediated transport of auxin and the related auxin fluxes during maize kernel development is proposed. Common features between this model and the model previously proposed for Arabidopsis (Arabidopsis thaliana) are discussed.
Identification and Functional Characterization of Monofunctionalent-Copalyl Diphosphate andent-Kaurene Synthases in White Spruce Reveal Different Patterns for Diterpene Synthase Evolution for Primary and Secondary Metabolism in Gymnosperms
Authors: Keeling Christopher I. , Dullat Harpreet K. , Yuen Mack , Ralph Steven G. , Jancsik Sharon , Bohlmann Jörg
Published: January 2010

The biosynthesis of the tetracyclic diterpene ent-kaurene is a critical step in the general (primary) metabolism of gibberellin hormones. ent-Kaurene is formed by a two-step cyclization of geranylgeranyl diphosphate via the intermediate ent-copalyl diphosphate. In a lower land plant, the moss Physcomitrella patens, a single bifunctional diterpene synthase (diTPS) catalyzes both steps. In contrast, in angiosperms, the two consecutive cyclizations are catalyzed by two distinct monofunctional enzymes, ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS). The enzyme, or enzymes, responsible for ent-kaurene biosynthesis in gymnosperms has been elusive. However, several bifunctional diTPS of specialized (secondary) metabolism have previously been characterized in gymnosperms, and all known diTPSs for resin acid biosynthesis in conifers are bifunctional. To further understand the evolution of ent-kaurene biosynthesis as well as the evolution of general and specialized diterpenoid metabolisms in gymnosperms, we set out to determine whether conifers use a single bifunctional diTPS or two monofunctional diTPSs in the ent-kaurene pathway. Using a combination of expressed sequence tag, full-length cDNA, genomic DNA, and targeted bacterial artificial chromosome sequencing, we identified two candidate CPS and KS genes from white spruce (Picea glauca) and their orthologs in Sitka spruce (Picea sitchensis). Functional characterization of the recombinant enzymes established that ent-kaurene biosynthesis in white spruce is catalyzed by two monofunctional diTPSs, PgCPS and PgKS. Comparative analysis of gene structures and enzyme functions highlights the molecular evolution of these diTPSs as conserved between gymnosperms and angiosperms. In contrast, diTPSs for specialized metabolism have evolved differently in angiosperms and gymnosperms.
A Gain-of-Function Mutation ofArabidopsisLipid Transfer Protein 5 Disturbs Pollen Tube Tip Growth and Fertilization
Authors: Chae Keun , Kieslich Chris A. , Morikis Dimitrios , Kim Seung-Chul , Lord Elizabeth M.
Published: January 2010

During compatible pollination of the angiosperms, pollen tubes grow in the pistil transmitting tract (TT) and are guided to the ovule for fertilization. Lily (Lilium longiflorum) stigma/style Cys-rich adhesin (SCA), a plant lipid transfer protein (LTP), is a small, secreted peptide involved in pollen tube adhesion-mediated guidance. Here, we used a reverse genetic approach to study biological roles of Arabidopsis thaliana LTP5, a SCA-like LTP. The T-DNA insertional gain-of-function mutant plant for LTP5 (ltp5-1) exhibited ballooned pollen tubes, delayed pollen tube growth, and decreased numbers of fertilized eggs. Our reciprocal cross-pollination study revealed that ltp5-1 results in both male and female partial sterility. RT-PCR and β-glucuronidase analyses showed that LTP5 is present in pollen and the pistil TT in low levels. Pollen-targeted overexpression of either ltp5-1 or wild-type LTP5 resulted in defects in polar tip growth of pollen tubes and thereby decreased seed set, suggesting that mutant ltp5-1 acts as a dominant-active form of wild-type LTP5 in pollen tube growth. The ltp5-1 protein has additional hydrophobic C-terminal sequences, compared with LTP5. In our structural homology/molecular dynamics modeling, Tyr-91 in ltp5-1, replacing Val-91 in LTP5, was predicted to interact with Arg-45 and Tyr-81, which are known to interact with a lipid ligand in maize (Zea mays) LTP. Thus, Arabidopsis LTP5 plays a significant role in reproduction.
Does long‐term use of unstable dentures weaken jaw muscles?
Authors: CALOSS R. , AL‐ARAB M. , FINN R. A. , LONERGAN O. , THROCKMORTON G. S.
Published: December 2009

Summary  Although it is well known that conventional denture wearers have lower maximum bite forces than dentate subjects, no previous studies have compared the strength of the jaw muscles between these two groups. This study compared maximum bite forces, electromyographic (EMG) activity and estimated jaw muscle strength among three groups: (i) 17 edentulous subjects using newly acquired implant‐retained overdentures (seven men, 10 women; mean age 60·3 ± 13·0 years); (ii) 10 age‐matched, fully dentate subjects (five men, five women; mean age 57·9 ± 11·0 years); and (iii) 39 young, fully dentate subjects (19 men, 20 women; mean age 24·4 ± 3·5 years). Electromyographic activity was recorded from subjects’ bilateral superficial masseter and anterior temporalis muscles while they generated maximum voluntary bite forces at the right central incisor, right first premolar and right first molar positions. Jaw muscle strength was estimated as the ratio of average EMG activity for all four muscles to the maximum bite force. At all three bite positions, edentulous subjects produced maximum bite forces that were less than half that of dentate subjects. Edentulous subjects also produced significantly less EMG activity and had significantly lower estimated jaw muscle strength. Our results suggest that weakened jaw muscles are one factor contributing to lower maximum bite forces among users of conventional dentures.
Panel reactive HLA antibodies, soluble CD30 levels, and acute rejection six months following renal transplant
Authors: Domingues Elizabeth M.F.L. , Matuck Teresa , Graciano Miguel L. , Souza Edison , Rioja Suzimar , Falci Mônica C. , Monteiro de Carvalho Deise B. , Porto Luís Cristóvão
Published: December 2009

Domingues EMFL, Matuck T, Graciano ML, Souza E, Rioja S, Falci MC, Monteiro de Carvalho DB, Porto LC. Panel reactive HLA antibodies, soluble CD30 levels, and acute rejection six months following renal transplant.  Clin Transplant 2010: 24: 821–829. © 2009 John Wiley & Sons A/S.

Abstract:  Background:  Specific anti‐human leukocyte antigen antibodies (HLA) in the post‐transplant period may be present with acute rejection episodes (ARE), and high soluble CD30 (sCD30) serum levels may be a risk factor for ARE and graft loss.

Methods:  HLA cross‐matching, panel reactive antibodies (PRA), and sCD30 levels were determined prior to transplantation in 72 patients. Soluble CD30 levels and PRA were re‐assessed at day 7, 14, 21, and 28, and monthly up to the sixth.

Results:  Twenty‐four subjects had a positive PRA and 17 experienced ARE. Nine of 17 ARE subjects demonstrated positive PRA and 16 had HLA mismatches. Positive PRA was more frequent in ARE subjects (p = 0.03). Eight subjects with ARE had donor‐specific antibodies (DSA) in serum samples pre‐transplantation, two subjects developed DSA. Three subjects without ARE had positive PRA only in post‐transplantation samples. Soluble CD30 levels were higher in pre‐transplant samples and ARE subjects than non‐ARE subjects (p = 0.03). Post‐transplant sCD30 levels were elevated in subjects who experienced rejection and were significantly higher at seven d (p = 0.0004) and six months (p = 0.03).

Conclusions:  Higher sCD30 levels following transplant were associated with ARE. Elevated sCD30 levels may represent a risk factor for acute rejection.
Randomized trial of early corticosteroid reduction vs. regular‐dose corticosteroid maintenance in combination with tacrolimus and mycophenolate mofetil in living donor kidney transplant recipients: the Brazilian CORRETA trial
Authors: Garcia Valter D. , Carvalho Deise B.M. , Gonçalves Renato T. , Cavalcanti Ruy L. , Campos Henry H. , Abbud‐Filho Mário , Lobao‐Neto Abner A.
Published: December 2009

Garcia VD, Carvalho DBM, Gonçalves RT, Cavalcanti RL, Campos HH, Abbud‐Filho M, Lobao‐Neto AA. Randomized trial of early corticosteroid reduction vs. regular‐dose corticosteroid maintenance in combination with tacrolimus and mycophenolate mofetil in living donor kidney transplant recipients: the Brazilian CORRETA trial. Clin Transplant 2010: 24: E109–E115. © 2009 John Wiley & Sons A/S.

Abstract:  This multicenter, randomized trial aimed to compare the safety and efficacy of an early reduction in corticosteroid dose vs. long‐term maintenance in Brazilian patients on an immunosuppressive regimen based on tacrolimus and mycophenolate mofetil (MMF). In the control arm, prednisone was progressively reduced from days 8 to 90 and then kept for 12 months. In the experimental arm, prednisone was given for 12 months at the dose of 5 mg every other day. Endpoints were the composite occurrence of death, graft loss, or Banff III acute rejection, and safety. A total of 83 patients were enrolled, and 77 were analyzed for efficacy safety. One death occurred in each group. There were no cases of graft loss and one case of grade 3 acute rejection in the early reduction arm. There was no difference in the rate of the composite primary endpoint between both arms (p = 0.215), and there were no significant differences between both arms in terms of adverse events. Except for higher incidence of hypertriglyceridemia levels among patients in the regular‐dose arm, there were no significant differences between both arms in terms of adverse events. The results of this trial suggest that early reduction of corticosteroid can be feasible and safe within a timeframe of 12 months in patients receiving tacrolimus and MMF.