bluuebunny/crossref_metadata_2025 huggingface dataset:
Field Emission Properties of ZnO Single Crystal Microtubes
Authors: Cheng Jiping , Zhang Yunjin , Guo Ruyan
Published: February 2009

Field emission properties of ZnO single-crystal microtubes were investigated in this work. The turn-on voltages for the as-grown and postannealed ZnO microtube samples were 5.6 and 6.4 V/μm, respectively. The emission current density was 11 mA/cm2 at an applied field of 20 V/μm for the as grown ZnO microtube and 12.5 mA/cm2 at an applied field of 13 V/μm for the postannealed ZnO microtube. Due to the relatively large tip area (in comparison with ZnO nanomaterials) of the ZnO microtubes, the intrinsic field emission enhancement factor β of the ZnO microtube was comparatively low (estimated to be around 6.5). However, the experimental β values were quite high (418 for the as-grown ZnO microtube and 1466 for the postannealed ZnO microtube), indicating strong field emission characteristics of the ZnO microtubes.
Two-beam magnetron injection guns for coaxial gyrotron with two electron beams
Authors: Fu Wenjie , Yan Yang , Yuan Xuesong , Liu Shenggang
Published: February 2009

To verify the concept of a coaxial gyrotron with two electron beams (CGTB), an electron gun with two beams is needed. In this paper, two types of two-beam magnetron injection guns are proposed: a normal two-beam magnetron injection gun and a coaxial two-beam magnetron injection gun. The design models and space charge limiting current are given. The simulation results show that both types of guns could fulfill the requirement for a CGTB. Comparisons between the two types of injection guns are discussed.
Turbulent parametric surface waves
Authors: Snouck Daniel , Westra Mark-Tiele , van de Water Willem
Published: February 2009

We study disordered capillary waves on the surface of a vertically oscillated fluid layer and try to establish their relation with weak wave turbulence. We measure the surface gradient in space and time and argue that gradient spectra are better suited for comparison to the predictions of weak wave turbulence theory than spectra of the surface elevation. Because the gradient is a vector quantity, we must distinguish longitudinal and transverse spectra. However, they prove to be related trivially through isotropy. From the measured wavenumber-frequency spectrum it appears that the dispersion relation is only satisfied approximately. In the wavenumber direction the spectral features are strongly broadened due to spatial disorder. This disagrees with weak wave turbulence theory where exact satisfaction of the dispersion relation is pivotal. We find approximate algebraic frequency and wavenumber spectra but with exponents that are different from those predicted by weak wave turbulence theory. However, other findings, such as the broadening of harmonics proportional to their frequency and the emergence of Gaussian statistics at selected wavenumber bands, point to weak wave turbulence.
Slow photoelectron velocity-map imaging spectroscopy of C2N−, C4N−, and C6N−
Authors: Garand Etienne , Yacovitch Tara I. , Neumark Daniel M.
Published: February 2009

High resolution photoelectron spectra of C2N−, C4N−, and C6N− anions are reported, obtained using slow electron velocity-map imaging. The spectra show well resolved transitions to the X̃ Π2 neutral ground state of all three species and to the ã Σ4− excited state of C2N and C4N. This study yields the adiabatic electron affinity of C2N, C4N, and C6N, the spin-orbit splitting in the X̃ Π2 state of each radical, and the term energy of the ã Σ4− state in C2N and C4N. Relatively little vibrational activity is observed, indicating small geometry changes upon photodetachment. This result, plus the observation of transitions to neutral quartet states, indicates that the C2nN− (n=1–3) anions all have linear Σ3− ground states.
Quantitative analytical model for magnetic reconnection in Hall magnetohydrodynamics
Authors: Simakov Andrei N. , Chacón L.
Published: February 2009

Magnetic reconnection is of fundamental importance for laboratory and naturally occurring plasmas. Reconnection usually develops on time scales which are much shorter than those associated with classical collisional dissipation processes, and which are not fully understood. While such dissipation-independent (or “fast”) reconnection rates have been observed in particle and Hall magnetohydrodynamics (MHD) simulations and predicted analytically in electron MHD, a quantitative analytical theory of fast reconnection valid for arbitrary ion inertial lengths di has been lacking. Here we propose such a theory without a guide field. The theory describes two-dimensional magnetic field diffusion regions, provides expressions for the reconnection rates, and derives a formal criterion for fast reconnection in terms of dissipation parameters and di. It also demonstrates that both open X-point and elongated diffusion regions allow dissipation-independent reconnection and reveals a possibility of strong dependence of the reconnection rates on di.
High performance organic photovoltaic devices using amorphous molecular materials with high charge-carrier drift mobilities
Authors: Kageyama Hiroshi , Ohishi Hitoshi , Tanaka Masatake , Ohmori Yutaka , Shirota Yasuhiko
Published: February 2009

p n -Heterojunction organic photovoltaic devices (OPVs) using amorphous molecular materials with high hole drift mobilities of 10−2 cm2 V−1 s−1, tris[4-(2-thienyl)phenyl]amine and tris[4-(5-phenylthiophen-2-yl)phenyl]amine, as electron donors and fullerene as an electron acceptor were fabricated. In spite of the use of amorphous materials instead of crystalline materials, the devices exhibited high performance with fill factors of 0.62–0.71 and power conversion efficiencies of 1.5%–1.7% under air-mass 1.5 G illumination at an intensity of 100 mW cm−2.
Aluminum gettering of iron in silicon as a problem of the ternary phase diagram
Authors: Abdelbarey D. , Kveder V. , Schröter W. , Seibt M.
Published: February 2009

Deep level transient spectroscopy is used to study the segregation of Fe from crystalline Si to an Al:Si liquid at its surface, which is the basic mechanism of aluminum gettering used in silicon photovoltaics. The measured segregation coefficient is smaller than estimates from the binary Fe:Si and Al:Fe phase diagrams. This apparent discrepancy originates from the ternary character of the system where the solubility of Fe in Si in equilibrium with the Al-doped α-FeSi2 has to be taken as a reference. Our data suggest that this solubility exceeds that in the binary Fe:Si system by two orders of magnitude.
Ordered Au/Pb nanoring arrays on Pb-induced Si(111)-1×1 surface
Authors: Tang Lin , Guan Ze-Lei , Hao Dan , Ma Xu-Cun , Jia Jin-Feng , Xue Qi-Kun
Published: February 2009

Growth and morphology of Au on a homogenous Si(111)-1×1-Pb surface are investigated using scanning tunneling microscopy. The deposited Au atoms grow on the Si(111)-1×1-Pb surface in two-dimensional mode and a long-range ordered 8×8 reconstruction with ringlike structure is observed following room temperature deposition. Upon thermal annealing to 500 K, the 8×8 structure transforms into a hexagonal-ring array with a 4×4 superstructure. The mechanism for the formation of the two self-organized nanostructures is discussed in terms of interface diffusion, alloying, and energy minimization.
Homogeneous deformation of Au-based metallic glass micropillars in compression at elevated temperatures
Authors: Song S. X. , Lai Y. H. , Huang J. C. , Nieh T. G.
Published: February 2009

We performed high-temperature microcompression tests on micron-sized pillar samples fabricated from Au49Ag5.5Pd2.3Cu26.9Si16.3 metallic glass near the glass transition temperature to investigate the homogeneous deformation behavior. Samples were invariably deformed uniformly. The strength was observed to decrease with increasing temperature and decreasing strain rate. Plastic flow behavior can be described by a shear transition zone model. The activation energy and the size of the basic flow unit were both deduced and compared favorably with the theory.
TRPA1 regulates gastrointestinal motility through serotonin release from enterochromaffin cells
Authors: Nozawa Katsura , Kawabata-Shoda Eri , Doihara Hitoshi , Kojima Ryosuke , Okada Hidetsugu , Mochizuki Shinobu , Sano Yorikata , Inamura Kohei , Matsushime Hitoshi , Koizumi Tomonobu , Yokoyama Toshihide , Ito Hiroyuki
Published: February 2009

Serotonin (5-hydroxytryptamine; 5-HT) is abundantly present throughout the gastrointestinal tract and stored mostly in enterochromaffin (EC) cells, which are located on the mucosal surface. 5-HT released from EC cells stimulate both intrinsic and extrinsic nerves, which results in various physiological and pathophysiological responses, such as gastrointestinal contractions. EC cells are believed to have the ability to respond to the chemical composition of the luminal contents of the gut; however, the underlying molecular and cellular mechanisms have not been identified. Here, we demonstrate that the transient receptor potential (TRP) cation channel TRPA1, which is activated by pungent compounds or cold temperature, is highly expressed in EC cells. We also found that TRPA1 agonists, including allyl isothiocyanate and cinnamaldehyde, stimulate EC cell functions, such as increasing intracellular Ca2+levels and 5-HT release, by using highly concentrated EC cell fractions and a model of EC cell function, the RIN14B cell line. Furthermore, we showed that allyl isothiocyanate promotes the contraction of isolated guinea pig ileum via the 5-HT3receptor. Taken together, our results indicate that TRPA1 acts as a sensor molecule for EC cells and may regulate gastrointestinal function.
Synergistic effects of genetic variation in nicotinic and muscarinic receptors on visual attention but not working memory
Authors: Greenwood P. M. , Lin M.-K. , Sundararajan R. , Fryxell K. J. , Parasuraman R.
Published: February 2009

It is widely appreciated that neurotransmission systems interact in their effects on human cognition, but those interactions have been little studied. We used genetics to investigate pharmacological evidence of synergisms in nicotinic/muscarinic interactions on cognition. We hypothesized that joint influences of nicotinic and muscarinic systems would be reflected in cognitive effects of normal variation in known SNPs in nicotinic (CHRNA4 rs1044396) and muscarinic (CHRM2 rs8191992) receptor genes. Exp. 1 used a task of cued visual search. The slope of the cue size/reaction time function showed a trend level effect of the muscarinic CHRM2 SNP, no effect of the nicotinic CHRNA4 SNP, but a significant interaction between the 2 SNPs. Slopes were steepest in individuals who were both CHRNA4 C/C and CHRM2 T/T homozygotes. To determine the specificity of this synergism, Exp. 2 assessed working memory for 1–3 locations over 3 s and found no significant effects on either SNP. Interpreting these results in light of Sarter's [Briand LA,et al.(2007) Modulators in concert for cognition: Modulator interactions in the prefrontal cortex.Prog Neurobiol83:69–91] claims of tonic and phasic modes of cholinergic activity, we argue that reorienting attention to the target after invalid cues requires a phasic response, dependent on the nicotinic system, whereas orienting attention to valid cues requires a tonic response, dependent on the muscarinic system. Consistent with that, shifting and scaling after valid cues (tonic) were strongest in CHRNA4 C/C homozygotes who were also CHRM2 T/T homozygotes. This shows synergistic effects within the human cholinergic system.
Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation
Authors: Chang Tsung-Cheng , Zeitels Lauren R. , Hwang Hun-Way , Chivukula Raghu R. , Wentzel Erik A. , Dews Michael , Jung Jason , Gao Ping , Dang Chi V. , Beer Michael A. , Thomas-Tikhonenko Andrei , Mendell Joshua T.
Published: February 2009

Direct control of microRNA (miRNA) expression by oncogenic and tumor suppressor networks results in frequent dysregulation of miRNAs in cancer cells and contributes to tumorigenesis. We previously demonstrated that activation of the c-Myc oncogenic transcription factor (Myc) broadly influences miRNA expression and in particular leads to widespread miRNA down-regulation. miRNA transcripts repressed by Myc include several with potent tumor suppressor activity such as miR-15a/16–1, miR-34a, and let-7 family members. In this study, we have investigated mechanisms downstream of Myc that contribute to miRNA repression. Consistent with transcriptional down-regulation, Myc activity results in the decreased abundance of multiple miRNA primary transcripts. Surprisingly, however, primary transcripts encoding several let-7 miRNAs are not reduced in the high Myc state, suggesting a posttranscriptional mechanism of repression. The Lin-28 and Lin-28B RNA binding proteins were recently demonstrated to negatively regulate let-7 biogenesis. We now show that Myc induces Lin-28B expression in multiple human and mouse tumor models. Chromatin immunoprecipitation and reporter assays reveal direct association of Myc with the Lin-28B promoter resulting in transcriptional transactivation. Moreover, we document that activation of Lin-28B is necessary and sufficient for Myc-mediated let-7 repression. Accordingly, Lin-28B loss-of-function significantly impairs Myc-dependent cellular proliferation. These findings highlight an important role for Lin-28B in Myc-driven cellular phenotypes and uncover an orchestration of transcriptional and posttranscriptional mechanisms in Myc-mediated reprogramming of miRNA expression.
Radially expanding transglial calcium waves in the intact cerebellum
Authors: Hoogland Tycho M. , Kuhn Bernd , Göbel Werner , Huang Wenying , Nakai Junichi , Helmchen Fritjof , Flint Jane , Wang Samuel S.-H.
Published: February 2009

Multicellular glial calcium waves may locally regulate neural activity or brain energetics. Here, we report a diffusion-driven astrocytic signal in the normal, intact brain that spans many astrocytic processes in a confined volume without fully encompassing any one cell. By using 2-photon microscopy in rodent cerebellar cortex labeled with fluorescent indicator dyes or the calcium-sensor protein G-CaMP2, we discovered spontaneous calcium waves that filled approximately ellipsoidal domains of Bergmann glia processes. Waves spread in 3 dimensions at a speed of 4–11 μm/s to a diameter of ≈50 μm, slowed during expansion, and were reversibly blocked by P2 receptor antagonists. Consistent with the hypothesis that ATP acts as a diffusible trigger of calcium release waves, local ejection of ATP triggered P2 receptor-mediated waves that were refractory to repeated activation. Transglial waves represent a means for purinergic signals to act with local specificity to modulate activity or energetics in local neural circuits.
Dodging the crisis of folding proteins with knots
Authors: Sułkowska Joanna I. , Sułkowski Piotr , Onuchic José
Published: February 2009

Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, that involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in ≈1–2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.
Pathogenesis of retinitis pigmentosa associated with apoptosis-inducing mutations in carbonic anhydrase IV
Authors: Datta Rupak , Waheed Abdul , Bonapace Giuseppe , Shah Gul N. , Sly William S.
Published: February 2009

Missense mutations in the carbonic anhydrase IV (CA IV) gene have been identified in patients with an autosomal dominant form of retinitis pigmentosa (RP17). We used two transient expression systems to investigate the molecular mechanism by which the newly identified CA IV mutations, R69H and R219S, contribute to retinal pathogenesis. Although the R219S mutation drastically reduced the activity of the enzyme, the R69H mutation had a minimal effect, suggesting that loss of CA activity is not the molecular basis for their pathogenesis. Defective processing was apparent for both mutant proteins. Cell surface-labeling techniques showed that the R69H and R219S mutations both impaired the trafficking of CA IV to the cell surface, resulting in their abnormal intracellular retention. Expression of both CA IV mutants induced elevated levels of the endoplasmic reticulum (ER) stress markers, BiP and CHOP, and led to cell death by apoptosis. They also had a dominant-negative effect on the secretory function of the ER. These properties are similar to those of R14W CA IV, the signal sequence variant found in the original patients with RP17. These findings suggest that toxic gain of function involving ER stress-induced apoptosis is the common mechanism for pathogenesis of this autosomal-dominant disease. Apoptosis induced by the CA IV mutants could be prevented, at least partially, by treating the cells with dorzolamide, a CA inhibitor. Thus, the use of a CA inhibitor as a chemical chaperone to reduce ER stress may delay or prevent the onset of blindness in RP17.
Comparative genomics allows the discovery ofcis-regulatory elements in mosquitoes
Authors: Sieglaff Douglas H. , Dunn W. Augustine , Xie Xiaohui S. , Megy Karyn , Marinotti Osvaldo , James Anthony A.
Published: February 2009

The discovery and mapping ofcis-regulatory elements is important for understanding regulation of gene transcription in mosquito vectors of human diseases. Genome sequence data are available for 3 species,Aedes aegypti,Anopheles gambiae, andCulex quinquefasciatus(Diptera: Culicidae), representing 2 subfamilies (Culicinae and Anophelinae) that are estimated to have diverged 145 to 200 million years ago. Comparative genomics tools were used to screen genomic DNA fragments located in the 5′-end flanking regions of orthologous genes. These analyses resulted in the identification of 137 sequences, designated “mosquito motifs,” 7 to 9 nucleotides in length, representing 18 families of putativecis-regulatory elements conserved significantly among the 3 species when compared to the fruit fly,Drosophila melanogaster. Forty-one of the motifs were implicated previously in experiments as sites for binding transcription factors or functioning in the regulation of mosquito gene expression. Further analyses revealed associations between specific motifs and expression profiles, particularly in those genes that show increased or decreased mRNA abundance in females following a blood meal, and those accumulating transcription products exclusively or preferentially in the midgut, fat bodies, or ovaries. These results validate the methodology and support a relationship between the discovered motifs and the conservation of hematophagy in mosquitoes.
Extending NGOMSL Model for Human‐Humanoid Robot Interaction in the Soccer Robotics Domain
Authors: Mohan Rajesh Elara , Acosta Calderon Carlos Antonio , Zhou Changjiu , Yue Pik Kong
Published: February 2009

In the field of human‐computer interaction, the Natural Goals, Operators, Methods, and Selection rules Language (NGOMSL) model is one of the most popular methods for modelling knowledge and cognitive processes for rapid usability evaluation. The NGOMSL model is a description of the knowledge that a user must possess to operate the system represented as elementary actions for effective usability evaluations. In the last few years, mobile robots have been exhibiting a stronger presence in commercial markets and very little work has been done with NGOMSL modelling for usability evaluations in the human‐robot interaction discipline. This paper focuses on extending the NGOMSL model for usability evaluation of human‐humanoid robot interaction in the soccer robotics domain. The NGOMSL modelled human‐humanoid interaction design of Robo‐Erectus Junior was evaluated and the results of the experiments showed that the interaction design was able to find faults in an average time of 23.84 s. Also, the interaction design was able to detect the fault within the 60 s in 100% of the cases. The Evaluated Interaction design was adopted by our Robo‐Erectus Junior version of humanoid robots in the RoboCup 2007 humanoid soccer league.
Improving conditional discrimination learning and memory in five-year-old children: Differential outcomes effect using different types of reinforcement
Authors: Martínez Lourdes , Estévez Angeles F. , Fuentes Luis J. , Overmier J. Bruce
Published: February 2009

Previous studies have demonstrated that discriminative learning is facilitated when a particular outcome is associated with each relation to be learned. When this training procedure is applied (the differential outcomes procedure; DOP), learning is faster and better than when the typical common outcomes procedure or nondifferential outcomes (NDO) is used. Our primary purpose in the two experiments reported here was to assess the potential advantage of DOP in 5-year-old children using three different strategies of reinforcement in which (a) children received a reinforcer following a correct choice (“ + ”), (b) children lost a reinforcer following an incorrect choice (“ − ”), or (c) children received a reinforcer following a correct choice and lost one following an incorrect choice (“ + / − ”). In Experiment 1, we evaluated the effects of the presence of DOP and different types of reinforcement on learning and memory of a symbolic delayed matching-to-sample task using secondary and primary reinforcers. Experiment 2 was similar to the previous one except that only primary reinforcers were used. The results from these experiments indicated that, in general, children learned the task faster and showed higher performance and persistence of learning whenever differential outcomes were arranged independent of whether it was differential gain, loss, or combinations. A novel finding was that they performed the task better when they lost a reinforcer following an incorrect choice (type of training “ − ”) in both experiments. A further novel finding was that the advantage of the DOP over the nondifferential outcomes training increased in a retention test.
Complete Restriction of Fluoroquinolone Use to Control an Outbreak ofClostridium difficileInfection at a Community Hospital
Authors: Kallen Alexander J. , Thompson Angela , Ristaino Polly , Chapman Leigh , Nicholson Ainsley , Sim Bich-Thuy , Lessa Fernanda , Sharapov Umid , Fadden Elaine , Boehler Richard , Gould Carolyn , Limbago Brandi , Blythe David , McDonald L. Clifford
Published: February 2009

Objective.

To review the effect of interventions, including a complete restriction in the use of fluoroquinolones (FQs), used to control an outbreak of hospital-onsetClostridium difficileinfection (HO-CDI) caused primarily by the epidemic North American pulsed-field gel electrophoresis type 1 strain.

Design.

Retrospective cohort and case-control study of all episodes of HO-CDI both before and after 2 interventions.

Setting.

Community hospital; January 1, 2005, through March 31, 2007.

Interventions.

Complete, 5-month, facility-wide restriction of fluoroquinolone use, during which a change in the environmental-services contractor occurred.

Results.

During a 27-month period, 319 episodes of HO-CDI occurred. The hospital-wide mean defined daily doses of antimicrobials decreased 22% after restricting FQ use, primarily because of a 66% decrease in the use of FQs. The interventions were also associated with a significant change in the HO-CDI incidence trends and with an absolute decrease of 22% in HO-CDI cases caused by the epidemic strain (from 66% before the intervention period to 44% during and after the intervention period;P= .02). Univariate analysis revealed that case patients with HO-CDI due to the epidemic strain were more likely than control patients, who did not have diarrhea, to receive a FQ, whereas case patients with HO-CDI due to a nonepidemic strain were not. However, FQ use was not significantly associated with HO-CDI in multivariable analysis.

Conclusions.

An outbreak of epidemic-strain HO-CDI was controlled at a community hospital after an overall decrease in antimicrobial use, primarily because of a restriction of FQ use and a change in environmental-services contractors. The restriction of FQ use may be useful as an adjunct control measure in a healthcare facilities during outbreaks of epidemic-strain HO-CDI.
Dynamics of Telomeres and Promyelocytic Leukemia Nuclear Bodies in a Telomerase-negative Human Cell Line
Authors: Jegou Thibaud , Chung Inn , Heuvelman Gerrit , Wachsmuth Malte , Görisch Sabine M. , Greulich-Bode Karin M. , Boukamp Petra , Lichter Peter , Rippe Karsten
Published: February 2009

Telomerase-negative tumor cells maintain their telomeres via an alternative lengthening of telomeres (ALT) mechanism. This process involves the association of telomeres with promyelocytic leukemia nuclear bodies (PML-NBs). Here, the mobility of both telomeres and PML-NBs as well as their interactions were studied in human U2OS osteosarcoma cells, in which the ALT pathway is active. A U2OS cell line was constructed that had lac operator repeats stably integrated adjacent to the telomeres of chromosomes 6q, 11p, and 12q. By fluorescence microscopy of autofluorescent LacI repressor bound to the lacO arrays the telomere mobility during interphase was traced and correlated with the telomere repeat length. A confined diffusion model was derived that describes telomere dynamics in the nucleus on the time scale from seconds to hours. Two telomere groups were identified that differed with respect to the nuclear space accessible to them. Furthermore, translocations of PML-NBs relative to telomeres and their complexes with telomeres were evaluated. Based on these studies, a model is proposed in which the shortening of telomeres results in an increased mobility that could facilitate the formation of complexes between telomeres and PML-NBs.
Protein Kinase D Controls the Integrity of Golgi Apparatus and the Maintenance of Dendritic Arborization in Hippocampal Neurons
Authors: Czöndör Katalin , Ellwanger Kornelia , Fuchs Yannick F. , Lutz Sylke , Gulyás Márton , Mansuy Isabelle M. , Hausser Angelika , Pfizenmaier Klaus , Schlett Katalin
Published: February 2009

Protein kinase D (PKD) is known to participate in various cellular functions, including secretory vesicle fission from the Golgi and plasma membrane-directed transport. Here, we report on expression and function of PKD in hippocampal neurons. Expression of an enhanced green fluorescent protein (EGFP)-tagged PKD activity reporter in mouse embryonal hippocampal neurons revealed high endogenous PKD activity at the Golgi complex and in the dendrites, whereas PKD activity was excluded from the axon in parallel with axonal maturation. Expression of fluorescently tagged wild-type PKD1 and constitutively active PKD1S738/742E (caPKD1) in neurons revealed that both proteins were slightly enriched at the trans-Golgi network (TGN) and did not interfere with its thread-like morphology. By contrast, expression of dominant-negative kinase inactive PKD1K612W (kdPKD1) led to the disruption of the neuronal Golgi complex, with kdPKD1 strongly localized to the TGN fragments. Similar findings were obtained from transgenic mice with inducible, neuron-specific expression of kdPKD1-EGFP. As a prominent consequence of kdPKD1 expression, the dendritic tree of transfected neurons was reduced, whereas caPKD1 increased dendritic arborization. Our results thus provide direct evidence that PKD activity is selectively involved in the maintenance of dendritic arborization and Golgi structure of hippocampal neurons.
Nutrient-dependent mTORC1 Association with the ULK1–Atg13–FIP200 Complex Required for Autophagy
Authors: Hosokawa Nao , Hara Taichi , Kaizuka Takeshi , Kishi Chieko , Takamura Akito , Miura Yutaka , Iemura Shun-ichiro , Natsume Tohru , Takehana Kenji , Yamada Naoyuki , Guan Jun-Lin , Oshiro Noriko , Mizushima Noboru
Published: February 2009

Autophagy is an intracellular degradation system, by which cytoplasmic contents are degraded in lysosomes. Autophagy is dynamically induced by nutrient depletion to provide necessary amino acids within cells, thus helping them adapt to starvation. Although it has been suggested that mTOR is a major negative regulator of autophagy, how it controls autophagy has not yet been determined. Here, we report a novel mammalian autophagy factor, Atg13, which forms a stable ∼3-MDa protein complex with ULK1 and FIP200. Atg13 localizes on the autophagic isolation membrane and is essential for autophagosome formation. In contrast to yeast counterparts, formation of the ULK1–Atg13–FIP200 complex is not altered by nutrient conditions. Importantly, mTORC1 is incorporated into the ULK1–Atg13–FIP200 complex through ULK1 in a nutrient-dependent manner and mTOR phosphorylates ULK1 and Atg13. ULK1 is dephosphorylated by rapamycin treatment or starvation. These data suggest that mTORC1 suppresses autophagy through direct regulation of the ∼3-MDa ULK1–Atg13–FIP200 complex.
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
Authors: Kubatko Laura S. , Carstens Bryan C. , Knowles L. Lacey
Published: February 2009

Summary: STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree.

Availability: The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/.

Contact:  lkubatko@stat.osu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Water Relations of Chusquea ramosissima and Merostachys claussenii in Iguazu National Park, Argentina
Authors: Saha Sonali , Holbrook Noel M. , Montti Lía , Goldstein Guillermo , Cardinot Gina Knust
Published: February 2009

Bamboos are prominent components of many tropical ecosystems, yet little is known about the physiological mechanisms utilized by these gigantic forest grasses. Here, we present data on the water transport properties of Chusquea ramosissima and Merostachys claussenii, monocarpic bamboo grasses native to the subtropical Atlantic forests of Argentina. C. ramosissima and M. claussenii differed in their growth form and exhibited contrasting strategies of water transport. Maximum xylem hydraulic conductivity of C. ramosissima culms was 2-fold higher than that of M. claussenii. C. ramosissima cavitated at relatively high water potentials (50% loss of conductivity at ≥1 MPa), whereas M. claussenii was more drought tolerant (50% loss at ≤3 MPa). Both species exhibited significant loss of hydraulic conductivity during the day, which was reversed overnight due to the generation of root pressure. The photosynthetic capacities of both bamboo species, estimated based on electron transport rates, were moderate, reflecting both the large amount of leaf area supported by culms and diurnal loss of hydraulic conductivity due to cavitation. Leaf hydraulic conductance was also relatively low for both species, congruent with their modest photosynthetic capacities. Within its native range, C. ramosissima is highly invasive due to its ability to colonize and persist in both forest gaps and land cleared for agriculture. We propose that a highly vulnerable vasculature, coupled with diurnal root pressure and an allometry that allows substantial leaf area to be supported on relatively slender culms, are key traits contributing to the ecological success of C. ramosissima.
Drought and Abscisic Acid Effects on Aquaporin Content Translate into Changes in Hydraulic Conductivity and Leaf Growth Rate: A Trans-Scale Approach
Authors: Parent Boris , Hachez Charles , Redondo Elise , Simonneau Thierry , Chaumont François , Tardieu François
Published: February 2009

The effects of abscisic acid (ABA) on aquaporin content, root hydraulic conductivity (Lpr), whole plant hydraulic conductance, and leaf growth are controversial. We addressed these effects via a combination of experiments at different scales of plant organization and tested their consistency via a model. We analyzed under moderate water deficit a series of transformed maize (Zea mays) lines, one sense and three antisense, affected in NCED (for 9-cis-epoxycarotenoid dioxygenase) gene expression and that differed in the concentration of ABA in the xylem sap. In roots, the mRNA expression of most aquaporin PIP (for plasma membrane intrinsic protein) genes was increased in sense plants and decreased in antisense plants. The same pattern was observed for the protein contents of four PIPs. This resulted in more than 6-fold differences between lines in Lpr under both hydrostatic and osmotic gradients of water potential. This effect was probably due to differences in aquaporin activity, because it was nearly abolished by a hydrogen peroxide treatment, which blocks the water channel activity of aquaporins. The hydraulic conductance of intact whole plants was affected in the same way when measured either in steady-state conditions or via the rate of recovery of leaf water potential after rewatering. The recoveries of leaf water potential and elongation upon rehydration differed between lines and were accounted for by the experimentally measured Lpr in a model of water transfer. Overall, these results suggest that ABA has long-lasting effects on plant hydraulic properties via aquaporin activity, which contributes to the maintenance of a favorable plant water status.
Exploring the Mechanism of Physcomitrella patens Desiccation Tolerance through a Proteomic Strategy
Authors: Wang Xiao Qin , Yang Ping Fang , Liu Zheng , Liu Wei Zhong , Hu Yong , Chen Hui , Kuang Ting Yun , Pei Zhen Ming , Shen Shi Hua , He Yi Kun
Published: February 2009

The moss Physcomitrella patens has been shown to tolerate abiotic stresses, including salinity, cold, and desiccation. To better understand this plant's mechanism of desiccation tolerance, we have applied cellular and proteomic analyses. Gametophores were desiccated over 1 month to 10% of their original fresh weight. We report that during the course of dehydration, several related processes are set in motion: plasmolysis, chloroplast remodeling, and microtubule depolymerization. Despite the severe desiccation, the membrane system maintains integrity. Through two-dimensional gel electrophoresis and image analysis, we identified 71 proteins as desiccation responsive. Following identification and functional categorization, we found that a majority of the desiccation-responsive proteins were involved in metabolism, cytoskeleton, defense, and signaling. Degradation of cytoskeletal proteins might result in cytoskeletal disassembly and consequent changes in the cell structure. Late embryogenesis abundant proteins and reactive oxygen species-scavenging enzymes are both prominently induced, and they might help to diminish the damage brought by desiccation.
Silencing the Hydroxyproline-Rich Glycopeptide Systemin Precursor in Two Accessions of Nicotiana attenuata Alters Flower Morphology and Rates of Self-Pollination
Authors: Berger Beatrice , Baldwin Ian T.
Published: February 2009

Systemins and their hydroxyproline-rich glycopeptide systemin (ppHS) subfamily members are known to mediate antiherbivore defenses in some solanaceous taxa but not others; functions other than in defense remain largely unexplored. Nicotiana attenuata's ppHS is known not to function in herbivore defense. NappHS transcripts are abundant in flowers, particularly in pistils, and when two N. attenuata accessions from Utah and Arizona were transformed to silence NappHS by RNAi (IRsys), seed capsule production and seed number per capsule were reduced in both accessions. These reductions in reproductive performance could not be attributed to impaired pollen or ovule viability; hand-pollination of all IRsys lines of both accessions restored seed production per capsule to levels found in wild-type plants. Rather, changes in flower morphology that decreased the efficiency of self-pollination are likely responsible: IRsys plants of both accessions have flowers with pistils that protrude beyond their anthers. Because these changes in flower morphology are reminiscent of CORONATINE-INSENSITIVE1-silenced N. attenuata plants, we measured jasmonates (JAs) and their biosynthetic transcripts in different floral developmental stages, and found levels of JA-isoleucine (Ile)/leucine and threonine deaminase transcripts, which are abundant in wild-type pistils, to be significantly reduced in IRsys buds and flowers. Threonine deaminase supplies Ile for JA-Ile biosynthesis, and we propose that ppHS mediates JA signaling during flower development and thereby changes flower morphology. These results suggest that the function of ppHS family members in N. attenuata may have diversified to modulate flower morphology and thereby outcrossing rates in response to biotic or abiotic stresses.
Methyl Jasmonate Reduces Grain Yield by Mediating Stress Signals to Alter Spikelet Development in Rice
Authors: Kim Eun Hye , Kim Youn Shic , Park Su-Hyun , Koo Yeon Jong , Choi Yang Do , Chung Yong-Yoon , Lee In-Jung , Kim Ju-Kon
Published: February 2009

Jasmonic acid (JA) is involved in plant development and the defense response. Transgenic overexpression of the Arabidopsis (Arabidopsis thaliana) jasmonic acid carboxyl methyltransferase gene (AtJMT) linked to the Ubi1 promoter increased levels of methyl jasmonate (MeJA) by 6-fold in young panicles. Grain yield was greatly reduced in Ubi1:AtJMT plants due to a lower numbers of spikelets and lower filling rates than were observed for nontransgenic (NT) controls. Ubi1:AtJMT plants had altered numbers of spikelet organs, including the lemma/palea, lodicule, anther, and pistil. The loss of grain yield and alteration in spikelet organ numbers were reproduced by treating NT plants with exogenous MeJA, indicating that increased levels of MeJA in Ubi1:AtJMT panicles inhibited spikelet development. Interestingly, MeJA levels were increased by 19-fold in young NT panicles upon exposure to drought conditions, resulting in a loss of grain yield that was similar to that observed in Ubi1:AtJMT plants. Levels of abscisic acid (ABA) were increased by 1.9- and 1.4-fold in Ubi1:AtJMT and drought-treated NT panicles, respectively. The ABA increase in Ubi1:AtJMT panicles grown in nondrought conditions suggests that MeJA, rather than drought stress, induces ABA biosynthesis under drought conditions. Using microarray and quantitative polymerase chain reaction analyses, we identified seven genes that were regulated in both Ubi1:AtJMT and drought-treated NT panicles. Two genes, OsJMT1 and OsSDR (for short-chain alcohol dehydrogenase), are involved in MeJA and ABA biosynthesis, respectively, in rice (Oryza sativa). Overall, our results suggest that plants produce MeJA during drought stress, which in turn stimulates the production of ABA, together leading to a loss of grain yield.
AtMyb41 Regulates Transcriptional and Metabolic Responses to Osmotic Stress in Arabidopsis
Authors: Lippold Felix , Sanchez Diego H. , Musialak Magdalena , Schlereth Armin , Scheible Wolf-Ruediger , Hincha Dirk K. , Udvardi Michael K.
Published: February 2009

Myb transcription factors have been implicated in a wide variety of plant-specific processes, including secondary metabolism, cell shape determination, cell differentiation, and stress responses. Very recently, AtMyb41 from Arabidopsis (Arabidopsis thaliana) was described as a gene transcriptionally regulated in response to salinity, desiccation, cold, and abscisic acid. The corresponding transcription factor was suggested to control stress responses linked to cell wall modifications. In this work, we have characterized AtMyb41 further by subjecting independent AtMyb41-overexpressing lines to detailed transcriptome and metabolome analysis. Our molecular data indicate that AtMyb41 is involved in distinct cellular processes, including control of primary metabolism and negative regulation of short-term transcriptional responses to osmotic stress.
A Role for the TOC Complex in Arabidopsis Root Gravitropism
Authors: Stanga John P. , Boonsirichai Kanokporn , Sedbrook John C. , Otegui Marisa S. , Masson Patrick H.
Published: February 2009

Arabidopsis (Arabidopsis thaliana) roots perceive gravity and reorient their growth accordingly. Starch-dense amyloplasts within the columella cells of the root cap are important for gravitropism, and starchless mutants such as pgm1 display an attenuated response to gravistimulation. The altered response to gravity1 (arg1) mutant is known to be involved with the early phases of gravity signal transduction. arg1 responds slowly to gravistimulation and is in a genetically distinct pathway from pgm1, as pgm1 mutants enhance the gravitropic defect of arg1. arg1 seeds were mutagenized with ethylmethane sulfonate to identify new mutants that enhance the gravitropic defect of arg1. Two modifier of arg1 mutants (mar1 and mar2) grow in random directions only when arg1 is present, do not affect phototropism, and respond like the wild type to application of phytohormones. Both have mutations affecting different components of the Translocon of Outer Membrane of Chloroplasts (TOC) complex. mar1 possesses a mutation in the TOC75-III gene; mar2 possesses a mutation in the TOC132 gene. Overexpression of TOC132 rescues the random growth phenotype of mar2 arg1 roots. Root cap amyloplasts in mar2 arg1 appear ultrastructurally normal. They saltate like the wild type and sediment at wild-type rates upon gravistimulation. These data point to a role for the plastidic TOC complex in gravity signal transduction within the statocytes.
MIKC* MADS Domain Heterodimers Are Required for Pollen Maturation and Tube Growth in Arabidopsis
Authors: Adamczyk Benjamin J. , Fernandez Donna E.
Published: February 2009

MADS box genes encode transcription factors that play important regulatory roles at various stages in plant development. Transcripts encoding the MIKC*-type (for MADS DNA-binding domain, Intervening domain, Keratin-like domain, and C-terminal domain) factors, a divergent clade, are enriched in mature pollen. Previous studies have shown that these proteins bind DNA as heterodimers, which form between S- and P-class MIKC* proteins. In this study, Arabidopsis (Arabidopsis thaliana) pollen with little or no MIKC* activity was produced by combining strong loss-of-function alleles of the S-class proteins AGAMOUS-LIKE66 (AGL66) and AGL104. Double mutant plants produce pollen but have severely reduced fertility due to reduced pollen viability, delayed germination, and aberrant pollen tube growth. Microarray analysis of the mutant pollen revealed that the loss of MIKC* regulation has a major impact on pollen gene expression. Pollen competition assays involving various combinations of AGL65, AGL66, AGL104, and AGL94 mutant alleles provided genetic evidence that at least three heterodimers (AGL30-AGL104, AGL65-AGL104, and AGL30-AGL66) form and function in at least a partially redundant fashion in pollen. Analyses of transcript abundance in wild-type and mutant pollen indicated that AGL65-containing complexes are likely to be more abundant than the others and that accumulation of AGL30 and AGL94 transcripts increases in response to reductions in MIKC* activity. These results were combined to create a model to describe MIKC* heterodimer contributions in pollen.
In vivo comparison of the relative systemic bioavailability of fluticasone propionate from three anti‐static spacers and a metered dose inhaler
Authors: Nair Arun , Menzies Daniel , Hopkinson Pippa , McFarlane Lesley , Lipworth Brian J.
Published: February 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Conventional spacers help overcome problems with co‐ordination and may improve lung deposition and decrease oropharyngeal impaction.

• Antistatic spacers eliminate electrostatic charge and may hence improve respirable dose delivery.

• The systemic bioavailability of inhaled fluticasone propionate is primarily dependent on delivery by the pulmonary route and hence the performance of antistatic spacers can be evaluated using adrenal suppression as a sensitive surrogate for relative bioavailability to the lung after an inhalation.

WHAT THIS STUDY ADDS

• This study compares the relative bioavailability to the lung of inhaled fluticasone delivered via conventional pressurized metered dose inhalers (pMDI) and three antistatic spacers (plastic Zerostat‐V, plastic Aerochamber Max, and metal Nebuchamber) in patients with asthma.

• All three antistatic spacers when compared with pMDI significantly increased the relative bioavailability to the lungs of inhaled fluticasone in terms of relative adrenal suppression, and there were no significant differences between the plastic and metal antistatic spacers.

AIMS

The systemic bioavailability of inhaled fluticasone propionate (FP) depends primarily on lung absorption and can be quantified by measuring suppression of overnight and early morning urinary cortisol/creatinine (OUCC and EMUCC, respectively). The aim of the study was to determine the relative bioavailability of hydrofluoroalkane (HFA) FP to the lungs via anti‐static plastic (Zerostat‐V and Aerochamber Max), metal (Nebuchamber) anti‐static spacers and metered dose inhaler [Flixotide Evohaler (EH) (pMDI)].

METHODS

A randomized, double‐blind, double‐dummy, four‐way crossover design was used. Eighteen mild to moderate asthmatics received single doses of placebo/HFA‐FP 2 mg via the 280‐ml Zerostat‐V (ZS); 250‐ml Nebuchamber (NC); 197‐ml Aerochamber Max (AC); and pMDI (EH). Measurements of OUCC and EMUCC were made at baseline and 10 h after each dose.

RESULTS

Significant suppression of OUCC and EMUCC occurred from baseline with all three spacers, but not Evohaler (geometric mean fold suppression, 95% confidence interval): ZS, 2.74 (1.75, 4.30), P < 0.001; NC, 3.31 (1.81, 6.06), P < 0.001; AC, 4.98 (3.39, 7.31), P < 0.001; and for EH this was 1.42 (0.92, 2.21), P= 0.169 (equating to a 64, 70, 80 and 30% fall in OUCC via the ZS, NC, AC and EH devices, respectively). There were significant differences between all three spacers vs. EH. When compared with the Evohaler, the Zerostat V resulted in 48% greater suppression (P= 0.009); the Nebuchamber 57% greater suppression (P= 0.001); and the Aerochamber Max 71% greater suppression of OUCC (P < 0.001).

CONCLUSION

All three antistatic spacers significantly increased the relative systemic bioavailability of HFA‐FP compared with the standard pMDI.