bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of intense femtosecond pumping on ultrafast electronic-vibrational dynamics in molecular systems with relaxation
Authors: Egorova Dassia , Gelin Maxim F. , Thoss Michael , Wang Haobin , Domcke Wolfgang
Published: December 2008

We investigate the influence of strong femtosecond optical pulses on the ultrafast dynamics of molecular systems. The study is based on a series of generic molecular models of increasing complexity, which incorporate multiple and mutually coupled electronic states, electronic-vibrational interaction, and vibrational relaxation. The influence of vibrational relaxation is treated using multilevel Redfield theory. Comparisons to benchmark results of the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method demonstrate the validity of the field-free implementation of Redfield theory employed in this work for weak system-bath interaction. The calculated electronic population and vibrational wave-packet dynamics demonstrate the intricate interplay of strong-field excitation, laser-induced Rabi oscillations, electronic interaction, vibronic coupling, and dissipation. In particular, we show that the interaction with a strong laser pulse may result in pronounced coherent vibrational motion in a dissipative system, even for laser pulses that are longer than the vibrational period. Furthermore, vibrational relaxation in combination with strong laser pulse excitation can lead to revivals of the electronic population after the excitation pulse is over.
Analytic theory of L→H transition, barrier structure, and hysteresis for a simple model of coupled particle and heat fluxes
Authors: Malkov M. A. , Diamond P. H.
Published: December 2008

The two-field (pressure/density) model for the L→H transition is extended and analyzed qualitatively. In its original form the model is ambiguous as to the location of the transition within the range of bistability of particle and thermal fluxes. Here, the model is regularized by including (i) hyperdiffusion, (ii) time dependence, and (iii) curvature of the pressure profile. The regularizations (i)–(ii) agree and indicate that the Maxwell rule for the forward and back transition applies, as opposed to the maximum flux forward and minimum flux backward transition rules (which yields hysteresis) as suggested previously. Regarding (i)–(ii), simple models suggest that for a pressure gradient driven electric field shear bifurcation, the basic scale of the pedestal is inexorably tied to the particle fueling depth, which normally is the neutral penetration depth. There is no hysteresis predicted by the local model of transport suppression. However, the effect of pressure profile curvature (iii) changes these results substantially. When it dominates, the curvature effect reduces the transition threshold to the lower end of the range of heating power, which falls within the phase coexistence region for both forward and back transitions. This softens the transition threshold requirements. In this limit, the model with pressure curvature also predicts transitions which occur in regimes of flat density and driven exclusively by the temperature gradient. This allows the pedestal to extend beyond the fueling depth, and also allows some decoupling of density and pressure profiles. In a parameter range where the pressure curvature is less important the transition occurs somewhere between the above two limits.
Columnar phases of discotic spherocylinders
Authors: Cuetos Alejandro , Martínez-Haya Bruno
Published: December 2008

The liquid crystal phase diagram of the discotic hard spherocylinder fluid is investigated by Monte Carlo simulations. Thickness-to-diameter aspect ratios within L/D=0.2–0.5 are considered. Three distinct columnar phases are found, namely, a hexatic interdigitated phase (Dhi), a hexatic ordered phase (Dho), both with long-range spatial correlations, and a hexatic disordered phase (Dhd), in which the columns become fluidlike. Local domains of stacked particles are also observed in the isotropic phase. The stability of the Dho and Dhd phases is favored with increasing anisotropy of the particle shape. As a consequence, the packing fraction versus the aspect ratio representation of the phase diagram features Dho-Dhd-I and Dhi-Dho-I triple points. The study involved the development of an efficient algorithm to compute the shortest distance between two oblate spherocylinder particles. The study provides a general coarse-grain methodology to explore discotic behavior, with fundamental advantages against alternative molecular models.
Molecular dynamics with time dependent quantum Monte Carlo
Authors: Christov Ivan P.
Published: December 2008

In this paper we propose an ab initio method to solve quantum many-body problems of molecular dynamics where both electronic and nuclear degrees are represented by ensembles of trajectories and guiding waves in physical space. Both electrons and nuclei can be treated quantum mechanically where the guiding waves obey a set of coupled Schrödinger equations (quantum-quantum description) or, alternatively, coupled Schrödinger–Newtonian equations are solved for the quantum-classical approximation. The method takes into account local and nonlocal quantum correlation effects in a self-consistent manner. The general formalism is applied to one- and two-dimensional hydrogen molecules subjected to a strong ultrashort optical pulse. Comparison is made with the results from the “exact” Ehrenfest molecular dynamics for the molecular ionization and for the evolution of the internuclear distance as the molecule dissociates.
Visible luminescence mechanism in nano ZnO under weak confinement regime
Authors: Irimpan Litty , Nampoori V. P. N. , Radhakrishnan P.
Published: December 2008

We describe the structure of luminescence spectrum in the visible region in nano-ZnO in colloidal and thin film forms under weak confinement regime by modeling the transition from excited state energy levels of excitons to their ground state. Measurements on nanocrystallites indicate the presence of luminescence due to excitonic emissions when excited with 255 nm. The relevant energy levels showing the transitions corresponding to the observed peaks in the emission spectrum of ZnO of particle size 18 nm are identified.
Plastic deformation during indentation unloading in multilayered materials
Authors: Tang G. , Shen Y.-L. , Chawla N.
Published: December 2008

The indentation behavior of a heterogeneous material with constituents having distinctly different mechanical properties was studied numerically. The microstructural heterogeneity was represented by an elastic-plastic finite element model featuring explicit metal/ceramic nanolayers. Internal deformation fields as well as stress and strain histories at selected points in the material were analyzed during the loading and unloading history. We show that the metallic layers experience plastic deformation even during the unloading part of indentation, while indentation contact is present. Thus, the unloading response in these heterogeneous materials is much more complex than the conventional purely elastic recovery process observed in single-phase metals.
Optimizing the geometry of an in vitro tunneling magnetoresistance biosensor using an immobilized ferrimagnetic nanoparticle agent
Authors: Kim Sunwook , Bae Seongtae
Published: December 2008

Spatial interactions of the magnetic field produced by an immobilized ferrimagnetic nanoparticle agent on the sensing layer have been numerically calculated considering the longitudinal and transverse components of the magnetic field. Based on the calculations, the sensor geometry to obtain the maximum sensing performance of an in vitro exchange biased tunneling magnetoresistance (TMR) based biosensor can be determined prior to fabrication. Numerical analysis considering the one-dimensional (longitudinal) component of the magnetic field along the magnetization of the ferrimagnetic nanoparticle agent found that the geometrical parameters of the biosensor can be determined by simply considering the effective distance (δ). The effective distance (δ) is determined by the remnant magnetization and radius of the ferrimagnetic nanoparticle agent and the detectable field limit (BDL) relevant to the exchange bias field of the TMR sensor. The optimized sensor geometry in terms of the critical length (lc) and width (wc) is approximated as wc/lc≈3.14. For a more accurate optimization of the sensor geometry, the two-dimensional magnetic field distributions on the sensing surface are numerically analyzed by employing the astroid curve model (or Stoner–Wohlfarth model). According to the numerical results using this model, the effective sensing area is found to have been extended due to the transverse component of the magnetic field. The extended effective sensing area in the optimized sensor geometry resulting from the spatial field interaction caused by the two-dimensional magnetic field is expected to enhance the output signal of the in vitro TMR based biosensor. However, in considering the two-dimensional magnetic field distribution, the undetectable area formed in the vicinity of the center of the optimized sensing area due to the spatial field interaction is a problem in designing a more accurate sensor geometry. Making a TMR sensor with a larger exchange bias field and introducing an especially designed sensor structure with a magnetic shield with a high permeability are suggested as solutions to this technical problem.
Strain promoted conductivity of doped carbon nanotubes
Authors: Kuo Hsin-Fu , Hsu Ching-Tung , Lien Der-Hsien , Syue Sen-Hong , Kao Yin-Shen , Li Ching-Chen , Li Yi-Fan , Chin Wei , Chang Shih-Chin , Wei Bee-Yu , Hsu Wen-Kuang
Published: December 2008

Strain promoted conductivity is detected in boron-doped carbon nanotubes and conductance biased at 3.5, 3.8, −4.6, −5.7, and −6.4 V exceeds 0.5G0. Deflection induced degeneracy of BC3-π bands accounts for conductance increment.
Temperature-dependent photoluminescence and photoluminescence excitation of aluminum monodoped and aluminum-indium dual-doped ZnO nanorods
Authors: Lin Shisheng , He Haiping , Ye Zhizhen , Zhao Binghui , Huang Jingyun
Published: December 2008

The authors report fabrication of aluminum monodoped ZnO (AlZnO) and aluminum-indium dual-doped ZnO (AlInZnO) nanorods arrays. Optical properties of AlZnO and AlInZnO nanorods are studied through temperature-dependent photoluminescence (PL) and PL excitation (PLE). Compared to AlInZnO nanorods, AlZnO nanorods possess better PL properties, as evidenced by a higher ratio of intensity of band-edge emission to green emission at 10 K and a higher PL intensity at room temperature. As supported by x-ray diffraction patterns, AlZnO nanorods also have higher crystallinity than AlInZnO nanorods. Indium doping induces a pronounced donor-acceptor pair transition of ∼3.22 eV at 10 K, the mechanism of which is discussed. Temperature-dependent energies of the A free exciton (FXA) and neutral donor bound exciton (D0X) are analyzed and the Einstein temperature is deduced to be ∼310 K. An activation energy of ∼8 meV is determined from the quenching of D0X as a function of temperature in AlInZnO nanorods. It is interpreted that nonradiative centers caused by indium segregation result in the small activation energy. Moreover, temperature-dependent PLE of AlZnO and AlInZnO nanorods reveals that the donor levels of aluminum and indium are 75 and 102 meV, respectively. Considering that the donor level of Al is shallower than that of In and that the optical and crystal properties of AlZnO nanorods are better than those of AlInZnO nanorods, aluminum is a better n-type dopant than indium for ZnO nanorods.
Ab initio description and visualization of charge transport in durene crystals
Authors: Ortmann Frank , Hannewald Karsten , Bechstedt Friedhelm
Published: December 2008

We study the charge transport through crystalline durene which exhibits large hole mobilities. By means of ab initio calculations, we determine the temperature-dependent polaron bandwidth and the mobility tensor of the charge carriers. The origin of the bandlike mobility curves is discussed, and the strong anisotropy of the mobility is analyzed in detail. We put a special focus on the relationship between crystal packing geometry, molecular wave function overlap, and charge transport properties. The results include a visualization of the transport channels in durene which can be regarded as a prototypical herringbone-stacked crystal.
Evolution of an electron energy distribution function in a weak dc magnetic field in solenoidal inductive plasma
Authors: Lee Min-Hyong , Choi Seong Wook
Published: December 2008

We investigated the evolution of the electron energy distribution function (EEDF) in a solenoidal inductively coupled plasma surrounded by an axial dc magnetic field. The increase in the dc magnetic field caused the EEDF to evolve from a bi-Maxwellian to a Maxwellian distribution. At the discharge center, the number of low energy electrons was significantly reduced while the high energy electron population showed little change when a weak dc magnetic field was present. However, at the discharge radial boundary, the high energy electron population decreased significantly with the magnetic field while the change in low energy population was not prominent compared to the discharge boundary. These changes in EEDFs at the boundary and center of the discharge are due to the radial confinement and the restriction of radial transport of electrons by dc magnetic field.
Efficient energy transfer for Ce to Nd in Nd∕Ce codoped yttrium aluminum garnet
Authors: Meng Jian Xin , Li Jin Qing , Shi Zhao Pu , Cheah Kok Wai
Published: December 2008

A two order of enhancement in near-infrared emission from Nd3+ in Ce3+∕Nd3+ codoped yttrium aluminum garnet (YAG) matrix is obtained. This is due to efficient absorption by the allowed 4f-5d transition of Ce3+ ions then transfer to Nd3+ ions via a well matched energy level. This is among the most efficient near-infrared emission from Nd3+ ions strongly sensitized by exciting with an allowed transition in an inorganic matrix. This means that a new class of material, YAG:Ce,Nd, was produced and it potentially can be an efficient near-infrared phosphor that could be easily excited by a GaN light emitting diode, producing a new type of near-infrared emitter.
Action-angle variables for the continuous spectrum of ideal magnetohydrodynamics
Authors: Hirota M. , Fukumoto Y.
Published: December 2008

Action-angle variables corresponding to singular (or improper) eigenmodes are rigorously formulated for the Alfvén and slow (or cusp) continuous spectra of ideal magnetohydrodynamics. The perturbation energy is then transformed into the normal form, namely, the eigenfrequency multiplied by the action variable. It is shown that the Laplace transform approach expedites this action-angle formulation more efficiently than the existing ones devoted to other kinds of continuous spectra. The presence of flow that is either nonparallel to the magnetic field or supersonic at some places brings about singular eigenmodes with negative energy. The Alfvén and slow singular eigenmodes are neutrally stable even in the presence of any external potential fields, but may cause instability when coupled with another singular or nonsingular eigenmode with the opposite sign of energy.
A taxonomic revision of Hemigenia section Malleantha sect. nov. (Lamiaceae: Westringieae)
Authors: Guerin G. R.
Published: December 2008

A new section of Hemigenia, Hemigenia sect. Malleantha G.R.Guerin sect. nov., is split from the typical section of Hemigenia, as its members do not belong with the type species of the genus (and therefore of the typical section), H. purpurea R.Br. A taxonomic revision of Hemigenia sect. Malleantha is presented which recognises 27 species, including the following 13 new species: H. appressa G.R.Guerin, H. benthamii G.R.Guerin, H. botryphylla G.R.Guerin, H. bracteosa G.R.Guerin, H. buccinata G.R.Guerin, H. ciliata G.R.Guerin, H. dulca G.R.Guerin, H. pachyphylla G.R.Guerin, H. royceana G.R.Guerin, H. tenelliflora G.R.Guerin, H. tomentosa G.R.Guerin, H. virescens G.R.Guerin and H. wandooana G.R.Guerin. Hemigenia parviflora Bartl. is reinstated from synonymy under H. sericea var. parviflora (Bartl.) Benth. Hemigenia eutaxioides C.R.P.Andrews is synonymised with H. teretiuscula F.Muell. and H. sericea var. lanosa F.Muell. ex Benth. is synonymised with H. argentea Bartl.
Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation
Authors: Ding Feng , Dokholyan Nikolay V.
Published: December 2008

Misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1) is implicated in neuronal death in amyotrophic lateral sclerosis. Each SOD1 monomer binds to 1 copper and 1 zinc ion and maintains its disulfide bond (Cys-57–Cys-146) in the reducing cytoplasm of cell. Mounting experimental evidence suggests that metal loss and/or disulfide reduction are important for initiating misfolding and aggregation of SOD1. To uncover the role of metals and the disulfide bond in the SOD1 folding, we systemically study the folding thermodynamics and structural dynamics of SOD1 monomer and dimer with and without metal binding and under disulfide-intact or disulfide-reduced environments in computational simulations. We use all-atom discrete molecular dynamics for sampling. Our simulation results provide dynamical evidence to the stabilizing role of metal ions in both dimer and monomer SOD1. The disulfide bond anchors a loop (Glu-49 to Asn-53) that contributes to the dimer interface. The reduction of the disulfide bond in SOD1 with metal ions depleted results in a flexible Glu-49–Asn-53 loop, which, in turn, disrupts dimer formation. Interestingly, the disulfide bond reduction does not affect the thermostability of monomer SOD1 as significantly as the metal ions do. We further study the structural dynamics of metal-free SOD1 monomers, the precursor for aggregation, in simulations and find inhomogeneous local unfolding of β-strands. The strands protected by the metal-binding and electrostatic loops are found to unfold first after metal loss, leading to a partially unfolded β-sheet prone to aggregation. Our simulation study sheds light on the critical role of metals and disulfide bond in SOD1 folding and aggregation.
Carbonic anhydrase II-positive pancreatic cells are progenitors for both endocrine and exocrine pancreas after birth
Authors: Inada Akari , Nienaber Cameron , Katsuta Hitoshi , Fujitani Yoshio , Levine Jared , Morita Rina , Sharma Arun , Bonner-Weir Susan
Published: December 2008

The regenerative process in the pancreas is of particular interest because diabetes results from an inadequate number of insulin-producing beta cells and pancreatic cancer may arise from the uncontrolled growth of progenitor/stem cells. Continued and substantial growth of islet tissue occurs after birth in rodents and humans, with additional compensatory growth in response to increased demand. In rodents there is clear evidence of pancreatic regeneration after some types of injury, with proliferation of preexisting differentiated cell types accounting for some replacement. Additionally, neogenesis or the budding of new islet cells from pancreatic ducts has been reported, but the existence and identity of a progenitor cell have been debated. We hypothesized that the progenitor cells are duct epithelial cells that after replication undergo a regression to a less differentiated state and then can form new endocrine and exocrine pancreas. To directly test whether ductal cells serve as pancreatic progenitors after birth and give rise to new islets, we generated transgenic mice expressing human carbonic anhydrase II (CAII) promoter: Cre recombinase (Cre) or inducible CreER
TM
to cross with ROSA26 loxP-Stop-loxP LacZ reporter mice. We show that CAII-expressing cells within the pancreas act as progenitors that give rise to both new islets and acini normally after birth and after injury (ductal ligation). This identification of a differentiated pancreatic cell type as an in vivo progenitor of all differentiated pancreatic cell types has implications for a potential expandable source for new islets for replenishment therapy for diabetes.
Depolarization-activated gating pore current conducted by mutant sodium channels in potassium-sensitive normokalemic periodic paralysis
Authors: Sokolov Stanislav , Scheuer Todd , Catterall William A.
Published: December 2008

Some inherited periodic paralyses are caused by mutations in skeletal muscle Na
V
1.4 sodium channels that alter channel gating and impair action potential generation. In the case of hypokalemic periodic paralysis, mutations of one of the outermost two gating charges in the S4 voltage sensor in domain II of the Na
V
1.4 α subunit induce gating pore current, resulting in a leak of sodium or protons through the voltage sensor that causes depolarization, sodium overload, and contractile failure correlated with low serum potassium. Potassium-sensitive normokalemic periodic paralysis (NormoPP) is caused by mutations in the third gating charge in domain II of the Na
V
1.4 channel. Here, we report that these mutations in rat Na
V
1.4 (R669Q/G/W) cause gating pore current that is activated by depolarization and therefore is conducted in the activated state of the voltage sensor. In addition, we find that this gating pore current is retained in the slow-inactivated state and is deactivated only at hyperpolarized membrane potentials. Gating pore current through the mutant voltage sensor of slow-inactivated NormoPP channels would cause increased sodium influx at the resting membrane potential and during trains of action potentials, depolarize muscle fibers, and lead to contractile failure and cellular pathology in NormoPP.
Contrast agent-enhanced computed tomography of articular cartilage: Association with tissue composition and properties
Authors: Silvast T. S. , Jurvelin J. S. , Aula A. S. , Lammi M. J. , Töyräs J.
Published: December 2008

Background: Contrast agent-enhanced computed tomography may enable the noninvasive quantification of glycosaminoglycan (GAG) content of articular cartilage. It has been reported that penetration of the negatively charged contrast agent ioxaglate (Hexabrix) increases significantly after enzymatic degradation of GAGs. However, it is not known whether spontaneous degradation of articular cartilage can be quantitatively detected with this technique.

Purpose: To investigate the diagnostic potential of contrast agent-enhanced cartilage tomography (CECT) in quantification of GAG concentration in normal and spontaneously degenerated articular cartilage by means of clinical peripheral quantitative computed tomography (pQCT).

Material and Methods: In this in vitro study, normal and spontaneously degenerated adult bovine cartilage ( n=32) was used. Bovine patellar cartilage samples were immersed in 21 mM contrast agent (Hexabrix) solution for 24 hours at room temperature. After immersion, the samples were scanned with a clinical pQCT instrument. From pQCT images, the contrast agent concentration in superficial as well as in full-thickness cartilage was calculated. Histological and functional integrity of the samples was quantified with histochemical and mechanical reference measurements extracted from our earlier study.

Results: Full diffusion of contrast agent into the deep cartilage was found to take over 8 hours. As compared to normal cartilage, a significant increase (11%, P<0.05) in contrast agent concentration was seen in the superficial layer of spontaneously degenerated samples. Significant negative correlations were revealed between the contrast agent concentration and the superficial or full-thickness GAG content of tissue (| R| > 0.5, P<0.01). Further, pQCT could be used to measure the thickness of patellar cartilage.

Conclusion: The present results suggest that CECT can be used to diagnose proteoglycan depletion in spontaneously degenerated articular cartilage with a clinical pQCT scanner. Possibly, the in vivo use of clinical pQCT for CECT arthrography of human joints is feasible.
Effects of methylprednisolone on bone mineral density and microarchitecture of trabecular bones in rats with administration time and assessed by micro-computed tomography
Authors: Liu S. P. , Liao E. Y. , Chen J. , Yang S. M. , Li J. W. , Sheng Z. F. , Mo H. , Wu X. P. , Yao L. , Dai R. C.
Published: December 2008

Background: Little research exists on the dynamic effects of glucocorticoids on bone mineral density (BMD) and microarchitecture of trabecular bones of rats assessed by micro-computed tomography (micro-CT).

Purpose: To investigate time-related changes in the BMD and microarchitecture of trabeculae in rats exposed to glucocorticoid.

Material and Methods: Female Sprague-Dawley rats were recruited into a baseline group, glucocorticoid-treated groups, or control groups. Glucocorticoid-treated rats were given daily subcutaneous injections of methylprednisolone at a dosage of 3.5 mg/kg for 1 or 9 weeks. A high-resolution micro-CT was used to identify the densitometric and microarchitectural properties of trabeculae in both the proximal metaphysis of tibiae and the sixth lumbar vertebrae (L6).

Results: Compared with baseline rats, volumetric BMD, tissue BMD, bone volume fraction, trabecular number, and degree of anisotropy of trabeculae from tibiae or L6 increased in control rats and glucocorticoid-treated rats with time; however, changes in the latter group were smaller. Compared with control rats at each time point, a decrease occurred in volumetric BMD, tissue BMD, bone volume fraction, trabecular number, degree of anisotropy, and trabecular connectivity density in trabecular bones from tibiae or L6 in glucocorticoid-treated rats. The decrease was greater in week 9 compared to week 1. Contrarily, an increase was noted in trabecular thickness, trabecular separation, and structure model index in glucocorticoid-treated rats. A time-related analysis within glucocorticoid-treated groups in both skeletal regions showed a decline in bone volume fraction, trabecular connectivity density, trabecular number, and degree of anisotropy with time, but trabecular thickness and trabecular separation were elevated.

Conclusion: Methylprednisolone can inhibit bone mineralization and bone mass gain with growth in rats. It can also deteriorate microarchitecture of trabeculae in a time-dependent or an accumulative dose-dependent manner. Further, the remaining trabeculae appear to thicken in order to adapt to altered stress.
Announcing the JCB DataViewer, a browser-based application for viewing original image files
Authors: Hill Emma
Published: December 2008

Over the lifetime of the JCB, the technology available to cell biologists has advanced immensely, producing more complex data with higher information content. Despite the advent of the Internet, the presentation of data in publications has not kept pace. Authors still present single, static, “representative” images and compressed movie files. I am therefore excited and proud to announce the launch of the JCB DataViewer.
Partial Sequence and Survey Analysis Identify a Multipartite, Negative-Sense RNA Virus Associated with Fig Mosaic
Authors: Walia Jeewan Jyot , Salem Nida M. , Falk Bryce W.
Published: December 2008

RNA and nucleotide sequence-based analyses were used to identify viruses in fig mosaic (FM)-affected fig (Ficus carica) trees. Nucleotide sequence analyses of 267 cloned cDNAs identified sequences corresponding to four viruses representing four distinct taxa from fig trees in California. Virus sequences corresponding to members of the family Closteroviridae were most common (55 sequences). We also found two sequences for an Umbravirus, one sequence corresponding to a Luteovirus-associated RNA, and two sequences that showed homology to European mountain ash ringspot-associated virus (EMARAV). Reverse transcription–polymerase chain reaction (RT-PCR) and northern hybridization analyses were used to confirm the presence of specific virus RNAs in fig trees. A survey of 184 fig trees from a germplasm collection, a commercial orchard, backyards, and feral fig trees showed that one virus was most common (detected in 96% of tested samples), while none of the other virus sequences were detected in more than 36% of the fig trees. Based on its association with FM-affected trees, nucleotide sequence-based phylogenetic association, and previous reported properties, we suggest the name of this virus as Fig mosaic-associated virus (FMaV).
Identification of the Wheat Curl Mite as the Vector of Triticum mosaic virus
Authors: Seifers Dallas L. , Martin T. J. , Harvey Tom L. , Fellers John P. , Michaud J. P.
Published: December 2008

Triticum mosaic virus (TriMV) is a newly discovered virus found infecting wheat (Triticum aestivum) in Kansas. This study was conducted to determine if the wheat curl mite (WCM, Aceria tosichella) and the bird cherry oat aphid (Rhopalosiphum padi) could transmit TriMV. Using different sources of WCM and two different isolates of TriMV, we were able to show the WCM is the vector of TriMV. Field analysis by enzyme-linked immunosorbent assay (ELISA) demonstrated natural infection patterns of wheat infected with TriMV, Wheat streak mosaic virus (WSMV), or both TriMV and WSMV, putatively infected by viruliferous WCM from a volunteer source growing adjacent to the wheat. Moreover, by single WCM transfers using WCM obtained from different wheat plants naturally infected with TriMV and WSMV and naturally infested with WCM, we showed that these WCM also transmitted TriMV only to wheat or transmitted both TriMV and WSMV to wheat. The infection rates of wheat with TriMV only using WCM transmission was low in both laboratory and field analyses. However, field analyses by ELISA showed that levels of infection of wheat by both TriMV and WSMV were high. No transmission of TriMV to wheat by R. padi occurred in our studies.
Impact of Different Preplant Cultural Treatments on Survival of Phytophthora nicotianae in Soil
Authors: Matheron M. E. , Porchas M.
Published: December 2008

During the life of a citrus planting, the population of Phytophthora pathogens can build to significant levels in orchard soil. A study was initiated to examine the impact of some nonchemical cultural practices on survival of P. nicotianae, the most prevalent Phytophthora sp. in Arizona citrus groves, in soil formerly planted to citrus. In three trials over a 3-year period, P. nicotianae could not be detected at a depth of 10 cm after soil naturally infested with the pathogen was subjected to a dry summer fallow period of at least 31 days in the desert southwest region of Arizona. The mean temperature of soil at this depth during these trials ranged from 37 to 39°C. Furthermore, in two of these trials, after summer dry fallow periods of 38 and 45 days, the pathogen could not be detected at a depth of 15 to 20 cm and was detected in only one of 19 soil samples at a depth of 25 to 30 cm. In comparison, the pathogen was recovered from a high proportion of soil samples subjected to a dry winter fallow period or maintained in the greenhouse and planted with a seedling of citrus, alfalfa, or irrigated without the presence of any plant, where mean temperature of soil ranged from 15 to 30°C. In regions with a hot and dry summer climate, a dry summer fallow treatment of soil after removal of an existing citrus planting and before establishment of a new grove could provide a rapid and relatively inexpensive means of lowering the population of P. nicotianae to virtually nondetectable levels to at least a depth of 30 cm.
Water and Temperature Parameters Associated with Winter Wheat Diseases Caused by Soilborne Pathogens
Authors: Smiley Richard W.
Published: December 2008

Wheat in eastern Oregon is produced mostly as a 2-year rotation of winter wheat and summer fallow. Maximum agronomic yield potential is expected with early September planting dates but actual yields are generally highest for plantings made in mid-October. Field experiments with sequential planting dates from early September to December were performed over 4 years. Associations among yield, disease incidence, and 19 moisture and temperature parameters were evaluated. Incidence of Cephalosporium stripe, crown rot, eyespot, and take-all decreased as planting was delayed. Crown rot and eyespot were negatively correlated more significantly and more frequently with temperature than moisture parameters, and take-all was more associated with moisture than temperature. Rhizoctonia root rot was unrelated to planting date and climatic parameters. Crown rot was identified most frequently (4 of 5 tests) as an important contributor to yield suppression but yield was most closely associated (R2 > 0.96) with effects from a single disease in only two of five location–year tests. Yield was most related to combinations of diseases in three of five tests, complicating development of disease modules for wheat growth-simulation models.
Quantification of Conidia of Diplodia spp. Extracted from Red and Jack Pine Cones
Authors: Munck Isabel A. , Stanosz Glen R.
Published: December 2008

Frequency of detection and inoculum production by the conifer shoot blight and canker pathogens Diplodia pinea and D. scrobiculata on cones of red pine (Pinus resinosa) and jack pine (P. banksiana) were studied. Cones were collected from the ground and from canopies of red and jack pine trees in mixed stands at three sites in each of two different locations during two consecutive summers in Wisconsin. Conidia were extracted in water, quantified, germination tested, and the Diplodia species present was determined using molecular methods. At least one pathogen was detected from each tree at each site in both years. Overall, more conidia were extracted from cones from canopies than cones from the ground and from red pine cones than jack pine cones. Both total numbers of conidia extracted and proportions of cones yielding D. pinea or D. scrobiculata varied by location and pine species. Cones from either the ground or canopies can be used for surveys to detect Diplodia spp. at a given site but cones from canopies may be more useful to determine the relative abundance of potentially available inoculum of these pathogens.
Characterization of Phytophthora infestans Populations in Colombia: First Report of the A2 Mating Type
Authors: Vargas Angela M. , Ocampo Lina M. Quesada , Céspedes Maria Catalina , Carreño Natalia , González Adriana , Rojas Alejandro , Zuluaga A. Paola , Myers Kevin , Fry William E. , Jiménez Pedro , Bernal Adriana J. , Restrepo Silvia
Published: December 2008

Phytophthora infestans, the causal agent of late blight in crops of the Solanaceae family, is one of the most important plant pathogens in Colombia. Not only are Solanum lycopersicum, and S. tuberosum at risk, but also several other solanaceous hosts (Physalis peruviana, S. betaceum, S. phureja, and S. quitoense) that have recently gained importance as new crops in Colombia may be at risk. Because little is known about the population structure of Phytophthora infestans in Colombia, we report here the phenotypic and molecular characterization of 97 isolates collected from these six different solanaceous plants in Colombia. All the isolates were analyzed for mating type, mitochondrial haplotypes, genotype for several microsatellites, and sequence of the internal transcribed spacer (ITS) region. This characterization identified a single individual of A2 mating type (from Physalis peruviana) for the first time in Colombia. All isolates had an ITS sequence that was at least 97% identical to the consensus sequence. Of the 97 isolates, 96 were mitochondrial haplotype IIa, with the single A2 isolate being Ia. All isolates were invariant for the microsatellites. Additionally, isolates collected from S. tuberosum and P. peruviana (64 isolates) were tested for: aggressiveness on both hosts, genotype for the isozymes (glucose-6-phosphate isomerase and peptidase), and restriction fragment length polymorphism fingerprint pattern as detected by RG57. Isolates from S. tuberosum were preferentially pathogenic on S. tuberosum, and isolates from P. peruviana were preferentially pathogenic on P. peruviana. The population from these two hosts was dominated by a single clonal lineage (59 of 64 individuals assayed), previously identified from Ecuador and Peru as EC-1. This lineage was mating type A1, IIa for mitochondrial DNA, invariant for two microsatellites, and invariant for both isozymes. The remaining four A1 isolates were in lineages very closely related to EC-1 (named EC-1.1, CO-1, and CO-2). The remaining lineage (the A2 mating type) had characteristics of the US-8 lineage (previously identified in Mexico, the United States, and Canada). These results have important epidemiological implications for the production of these two crops in Colombia.
Curtovirus–Cucurbit Interaction: Acquisition Host Plays a Role in Leafhopper Transmission in a Host-Dependent Manner
Authors: Chen Li-Fang , Gilbertson Robert L.
Published: December 2008

Curly top disease (CTD) of vegetable crops is caused by viruses in the genus Curtovirus (family Geminiviridae). Cucurbits are reported to be susceptible to CTD; however, the disease is rare in California despite annual outbreaks in other hosts (e.g., common bean, pepper, sugar beet, and tomato). Consistent with these observations, no obvious curly top symptoms were observed in melon fields surveyed for CTD in Central California in 2004 and 2005, whereas the disease was readily observed in tomato plants in nearby fields. However, samples of cucurbits from Idaho with curly top-like symptoms, collected in 2005 and 2007, were confirmed to have the disease. The susceptibility of cucurbits (cantaloupe, honeydew melon, pumpkin, and watermelon) to the three curtoviruses known to occur in California (Beet curly top virus, BCTV; Beet severe curly top virus, BSCTV; and Beet mild curly top virus, BMCTV) was evaluated by agroinoculation or leafhopper transmission. Irrespective of the curtovirus species and inoculation method, low rates of infection and mild or symptomless disease phenotypes were observed in cucurbits. In contrast, all inoculated tomato, Nicotiana benthamiana, or shepherd's purse plants were infected and developed severe symptoms. In leafhopper transmission experiments, BMCTV infected cucurbits when leafhoppers acquired the virus from a symptomatic host with a high viral titer (shepherd's purse), whereas no infection occurred when the acquisition host had mild symptoms and a low viral titer (sugar beet); in contrast, the acquisition host did not influence transmission of BMCTV to tomato or shepherd's purse (all plants were infected). This revealed an influence of the acquisition host on leafhopper transmission in a host-specific manner. Our results also indicate that, although cucurbits can develop CTD, they are relatively poor hosts for these curtoviruses.
Lymphatic endothelial cell identity is reversible and its maintenance requires Prox1 activity
Authors: Johnson Nicole C. , Dillard Miriam E. , Baluk Peter , McDonald Donald M. , Harvey Natasha L. , Frase Sharon L. , Oliver Guillermo
Published: December 2008

The activity of the homeobox gene Prox1 is necessary and sufficient for venous blood endothelial cells (BECs) to acquire a lymphatic endothelial cell (LEC) fate. We determined that the differentiated LEC phenotype is a plastic, reprogrammable condition that depends on constant Prox1 activity for its maintenance. We show that conditional down-regulation of Prox1 during embryonic, postnatal, or adult stages is sufficient to reprogram LECs into BECs. Consequently, the identity of the mutant lymphatic vessels is also partially reprogrammed as they acquire some features typical of the blood vasculature. siRNA-mediated down-regulation of Prox1 in LECs in culture demonstrates that reprogramming of LECs into BECs is a Prox1-dependent, cell-autonomous process. We propose that Prox1 acts as a binary switch that suppresses BEC identity and promotes and maintains LEC identity; switching off Prox1 activity is sufficient to initiate a reprogramming cascade leading to the dedifferentiation of LECs into BECs. Therefore, LECs are one of the few differentiated cell types that require constant expression of a certain gene to maintain their phenotypic identity.
UNC-51/ATG1 kinase regulates axonal transport by mediating motor–cargo assembly
Authors: Toda Hirofumi , Mochizuki Hiroaki , Flores Rafael , Josowitz Rebecca , Krasieva Tatiana B. , LaMorte Vickie J. , Suzuki Emiko , Gindhart Joseph G. , Furukubo-Tokunaga Katsuo , Tomoda Toshifumi
Published: December 2008

Axonal transport mediated by microtubule-dependent motors is vital for neuronal function and viability. Selective sets of cargoes, including macromolecules and organelles, are transported long range along axons to specific destinations. Despite intensive studies focusing on the motor machinery, the regulatory mechanisms that control motor–cargo assembly are not well understood. Here we show that UNC-51/ATG1 kinase regulates the interaction between synaptic vesicles and motor complexes during transport in Drosophila. UNC-51 binds UNC-76, a kinesin heavy chain (KHC) adaptor protein. Loss of unc-51 or unc-76 leads to severe axonal transport defects in which synaptic vesicles are segregated from the motor complexes and accumulate along axons. Genetic studies show that unc-51 and unc-76 functionally interact in vivo to regulate axonal transport. UNC-51 phosphorylates UNC-76 on Ser143, and the phosphorylated UNC-76 binds Synaptotagmin-1, a synaptic vesicle protein, suggesting that motor−cargo interactions are regulated in a phosphorylation-dependent manner. In addition, defective axonal transport in unc-76 mutants is rescued by a phospho-mimetic UNC-76, but not a phospho-defective UNC-76, demonstrating the essential role of UNC-76 Ser143 phosphorylation in axonal transport. Thus, our data provide insight into axonal transport regulation that depends on the phosphorylation of adaptor proteins.
Stepping into the ring: the SIN takes on contractile ring assembly: Figure 1.
Authors: Roberts-Galbraith Rachel H. , Gould Kathleen L.
Published: December 2008

The septation initiation network (SIN) regulates the timing of septum formation in Schizosaccharomyces pombe. However, whether and how the SIN functions in contractile ring formation has remained unclear. In this issue of Genes & Development, Hachet and Simanis (3205–3216) demonstrate that the SIN acts downstream from the Plo1 kinase to control a final step in contractile ring assembly. Furthermore, their careful analysis of contractile ring formation may help bridge two existing models of cytokinetic ring formation.
pVHL is a regulator of glucose metabolism and insulin secretion in pancreatic β cells
Authors: Zehetner Jens , Danzer Carsten , Collins Stephan , Eckhardt Katrin , Gerber Philipp A. , Ballschmieter Pia , Galvanovskis Juris , Shimomura Kenju , Ashcroft Frances M. , Thorens Bernard , Rorsman Patrik , Krek Wilhelm
Published: December 2008

Insulin secretion from pancreatic β cells is stimulated by glucose metabolism. However, the relative importance of metabolizing glucose via mitochondrial oxidative phosphorylation versus glycolysis for insulin secretion remains unclear. von Hippel-Lindau (VHL) tumor suppressor protein, pVHL, negatively regulates hypoxia-inducible factor HIF1α, a transcription factor implicated in promoting a glycolytic form of metabolism. Here we report a central role for the pVHL–HIF1α pathway in the control of β-cell glucose utilization, insulin secretion, and glucose homeostasis. Conditional inactivation of Vhlh in β cells promoted a diversion of glucose away from mitochondria into lactate production, causing cells to produce high levels of glycolytically derived ATP and to secrete elevated levels of insulin at low glucose concentrations. Vhlh-deficient mice exhibited diminished glucose-stimulated changes in cytoplasmic Ca2+ concentration, electrical activity, and insulin secretion, which culminate in impaired systemic glucose tolerance. Importantly, combined deletion of Vhlh and Hif1α rescued these phenotypes, implying that they are the result of HIF1α activation. Together, these results identify pVHL and HIF1α as key regulators of insulin secretion from pancreatic β cells. They further suggest that changes in the metabolic strategy of glucose metabolism in β cells have profound effects on whole-body glucose homeostasis.
Against the oxidative damage theory of aging: superoxide dismutases protect against oxidative stress but have little or no effect on life span in Caenorhabditis elegans
Authors: Doonan Ryan , McElwee Joshua J. , Matthijssens Filip , Walker Glenda A. , Houthoofd Koen , Back Patricia , Matscheski Andrea , Vanfleteren Jacques R. , Gems David
Published: December 2008

The superoxide radical (O2−) has long been considered a major cause of aging. O2− in cytosolic, extracellular, and mitochondrial pools is detoxified by dedicated superoxide dismutase (SOD) isoforms. We tested the impact of each SOD isoform in Caenorhabditis elegans by manipulating its five sod genes and saw no major effects on life span. sod genes are not required for daf-2 insulin/IGF-1 receptor mutant longevity. However, loss of the extracellular Cu/ZnSOD sod-4 enhances daf-2 longevity and constitutive diapause, suggesting a signaling role for sod-4. Overall, these findings imply that O2− is not a major determinant of aging in C. elegans.
A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
Authors: Hampton Oliver A. , Den Hollander Petra , Miller Christopher A. , Delgado David A. , Li Jian , Coarfa Cristian , Harris Ronald A. , Richards Stephen , Scherer Steven E. , Muzny Donna M. , Gibbs Richard A. , Lee Adrian V. , Milosavljevic Aleksandar
Published: December 2008

By applying a method that combines end-sequence profiling and massively parallel sequencing, we obtained a sequence-level map of chromosomal aberrations in the genome of the MCF-7 breast cancer cell line. A total of 157 distinct somatic breakpoints of two distinct types, dispersed and clustered, were identified. A total of 89 breakpoints are evenly dispersed across the genome. A majority of dispersed breakpoints are in regions of low copy repeats (LCRs), indicating a possible role for LCRs in chromosome breakage. The remaining 68 breakpoints form four distinct clusters of closely spaced breakpoints that coincide with the four highly amplified regions in MCF-7 detected by array CGH located in the 1p13.1-p21.1, 3p14.1-p14.2, 17q22-q24.3, and 20q12-q13.33 chromosomal cytobands. The clustered breakpoints are not significantly associated with LCRs. Sequences flanking most (95%) breakpoint junctions are consistent with double-stranded DNA break repair by nonhomologous end-joining or template switching. A total of 79 known or predicted genes are involved in rearrangement events, including 10 fusions of coding exons from different genes and 77 other rearrangements. Four fusions result in novel expressed chimeric mRNA transcripts. One of the four expressed fusion products (RAD51C-ATXN7) and one gene truncation (BRIP1 or BACH1) involve genes coding for members of protein complexes responsible for homology-driven repair of double-stranded DNA breaks. Another one of the four expressed fusion products (ARFGEF2-SULF2) involves SULF2, a regulator of cell growth and angiogenesis. We show that knock-down of SULF2 in cell lines causes tumorigenic phenotypes, including increased proliferation, enhanced survival, and increased anchorage-independent growth.