bluuebunny/crossref_metadata_2025 huggingface dataset:
Computer‐aided tissue engineering: overview, scope and challenges
Authors: Sun Wei , Darling Andrew , Starly Binil , Nam Jae
Published: December 2008

Advances in computer‐aided technology and its application with biology, engineering and information science to tissue engineering have evolved a new field of computer‐aided tissue engineering (CATE). This emerging field encompasses computer‐aided design (CAD), image processing, manufacturing and solid free‐form fabrication (SFF) for modelling, designing, simulation and manufacturing of biological tissue and organ substitutes. The present Review describes some salient advances in this field, particularly in computer‐aided tissue modeling, computer‐aided tissue informatics and computer‐aided tissue scaffold design and fabrication. Methodologies of development of CATE modelling from high‐resolution non‐invasive imaging and image‐based three‐dimensional reconstruction, and various reconstructive techniques for CAD‐based tissue modelling generation will be described. The latest development in SFF to tissue engineering and a framework of bio‐blueprint modelling for three‐dimensional cell and organ printing will also be introduced.
Expression of GAL genes in a mutant strain of Saccharomyces cerevisiae lacking GAL80: quantitative model and experimental verification
Authors: Verma Malkhey , Bhat Paike Jayadeva , Venkatesh K. V.
Published: December 2008

The regulatory network of GAL genes is a model system for the production of foreign proteins. A mathematical model based on steady state was developed for the expression of GAL (galactosidase) genes in a mutant strain of Saccharomyces cerevisiae lacking GAL80. The transcriptional and translational responses of the GAL switch were predicted at various steady‐state glucose concentrations. The model predicted ultrasensitive transcriptional response with a Hill coefficient (h) of 1.9 and 3.2 for genes with one and two binding sites respectively. Further, a lesser degree of ultrasensitivity was predicted for translational response with an h value of 1.3 for genes with one binding site and 2.1 for genes with two binding sites. The ultrasensitivity was due to dimerization of regulatory protein Gal4p and co‐operative binding of Gal4p to DNA. The steady‐state predictions were experimentally verified through measurements of α‐galactosidase (for one binding site) and β‐galactosidase (for two binding sites). The steady state model was further extended to represent the dynamic expression profile and the same was verified experimentally. The growth phase and the synthesis of foreign protein could be distinctly separated using a mutant strain of Saccharomyces cerevisiae (baker's yeast).
REVIEW: Synergies of microtissue design, viral transduction and adjustable transgene expression for regenerative medicine
Authors: Kelm Jens M. , Kramer Beat P. , Gonzalez‐Nicolini Valeria , Ley Bettina , Fussenegger Martin
Published: December 2008

In the past decade, regenerative medicine has evolved as an interdisciplinary field, integrating expertise from the medical, life‐ and material‐science communities. Recent advances in tissue engineering, gene therapy, gene‐function analysis, animal‐free drug testing, drug discovery, biopharmaceutical manufacturing and cell‐phenotype engineering have capitalized on a core technology portfolio including artificial microtissue design, viral transduction and precise transcription dosing of therapeutic or phenotype‐modulating transgenes. We provide a detailed overview on recent progress in these core technologies and comment on their synergistic impact on current and future human therapies.
René Couteaux (1909–1999) and the morphological identification of synapses
Authors: Tsuji Shigeru
Published: December 2008

During a historical research, we realized that René Couteaux (1909–1999) was the first histologist who stained the postsynaptic structure of the neuromuscular junction. By means of Janus Green B dye, he revealed the membranous ‘subneural apparatus’ related to the ‘synaptic gutter’. Hence, he justified the use of the physiological term ‘synapse’ in histology. A few years later, Couteaux localized acetylcholinesterase activity on this subneural apparatus with a histo‐enzymatic method. The histochemical staining confirmed his histological observations that the subneural apparatus of the muscle cells was distinct from the nerve terminal. Thus Couteaux not only supported Cajal's neuron theory, but also gave decisive morphological basis to the concept of the synapse, thought to be up to that time a physiological entity. These observations were performed several years before the first electron microscopic data obtained in the U.S.A. When the electron microscopy became available in Europe, Couteaux studied the ultrastructural details of the myoneural synapse. He found evidence for the presynaptic ‘active zone’ as a restricted zone of the thickened presynaptic membrane flanked on both sides with synaptic vesicles, some of which were observed to be opening into the synaptic cleft by exocytosis. Furthermore, the synaptic vesicles were shown to be displayed in two rows along the linearly prolonged active zone which is situated just above the ‘trench‐like’ junctional folds of the muscle membrane. The discontinuity of the synaptic structure was confirmed by the three‐dimensional observation of the intraneuronal network of neurofibrils with the first prototype of high‐voltage electron microscope.
Magic angle spinning magnetic resonance: a novel method opening up translational research into NAFLD?
Authors: Boesch Chris
Published: December 2008

NAFLD (non-alcoholic fatty liver disease) and NASH (non-alcoholic steatohepatitis) are of increasing importance, both in connection with insulin resistance and with the development of liver cirrhosis. Histological samples are still the ‘gold standard’ for diagnosis; however, because of the risks of a liver biopsy, non-invasive methods are needed. MAS (magic angle spinning) is a special type of NMR which allows characterization of intact excised tissue without need for additional extraction steps. Because clinical MRI (magnetic resonance imaging) and MRS (magnetic resonance spectroscopy) are based on the same physical principle as NMR, translational research is feasible from excised tissue to non-invasive examinations in humans. In the present issue of Clinical Science, Cobbold and co-workers report a study in three animal strains suffering from different degrees of NAFLD showing that MAS results are able to distinguish controls, fatty infiltration and steatohepatitis in cohorts. In vivo MRS methods in humans are not obtainable at the same spectral resolution; however, know-how from MAS studies may help to identify characteristic changes in crowded regions of the magnetic resonance spectrum.
Dorsal Cochlear Nucleus Hyperactivity and Tinnitus: Are They Related?
Authors: Kaltenbach James A. , Godfrey Donald A.
Published: December 2008

Purpose

Eight lines of evidence implicating the dorsal cochlear nucleus (DCN) as a tinnitus contributing site are reviewed. We now expand the presentation of this model, elaborate on its essential details, and provide answers to commonly asked questions regarding its validity.

Conclusions

Over the past decade, numerous studies have converged to support the hypothesis that the DCN may be an important brain center in the generation and modulation of tinnitus. Although other auditory centers have been similarly implicated, the DCN deserves special emphasis because, as a primary acoustic nucleus, it occupies a potentially pivotal position in the hierarchy of functional processes leading to the emergence of tinnitus percepts. Moreover, because a great deal is known about the underlying cellular categories and the details of synaptic circuitry within the DCN, this brain center offers a potentially powerful model for probing mechanisms underlying tinnitus.
Minimal supporting subtrees for the free energy of polymers on disordered trees
Authors: Mörters Peter , Ortgiese Marcel
Published: December 2008

We consider a model of directed polymers on a regular tree with a disorder given by independent, identically distributed weights attached to the vertices. For suitable weight distributions this model undergoes a phase transition with respect to its localization behavior. We show that, for high temperatures, the free energy is supported by a random tree of positive exponential growth rate, which is strictly smaller than that of the full tree. The growth rate of the minimal supporting subtree decreases to zero as the temperature decreases to the critical value. At the critical value and all lower temperatures, a single polymer suffices to support the free energy. Our proofs rely on elegant martingale methods adapted from the theory of branching random walks.
A density matrix-based quasienergy formulation of the Kohn–Sham density functional response theory using perturbation- and time-dependent basis sets
Authors: Thorvaldsen Andreas J. , Ruud Kenneth , Kristensen Kasper , Jørgensen Poul , Coriani Sonia
Published: December 2008

A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn–Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.
Electron acoustic solitary waves in unmagnetized two electron population dense plasmas
Authors: Mahmood S. , Masood W.
Published: December 2008

The electron acoustic solitary waves are studied in unmagnetized two population electron quantum plasmas. The quantum hydrodynamic model is employed with the Sagdeev potential approach to describe the arbitrary amplitude electron acoustic waves in a two electron population dense Fermi plasma. It is found that hot electron density hump structures are formed in the subsonic region in such type of quantum plasmas. The wave amplitude as well as the width of the soliton are increased with the increase of percentage presence of cold (thinly populated) electrons in a multicomponent quantum plasma. It is found that an increase in quantum diffraction parameter broadens the nonlinear structure. Furthermore, the amplitude of the nonlinear electron acoustic wave is found to increase with the decrease in Mach number. The numerical results are also presented to understand the formation of solitons in two electron population Fermi plasmas.
Microstructure of Cs-implanted zirconia: Role of temperature
Authors: Vincent L. , Thomé L. , Garrido F. , Kaitasov O. , Houdelier F.
Published: December 2008

The aim of this study was to identify experimentally the phase which includes cesium in yttria stabilized zirconia (YSZ). The solubility and retention of cesium in YSZ were studied at high temperature (HT). Cesium was ion implanted (at 300 keV) into YSZ at room temperature (RT), 750 °C, or 900 °C at fluences up to 5×1016 cm−2. The temperature dependence of the radiation-induced damage and of the cesium distribution in YSZ single crystals was investigated by Rutherford backscattering spectrometry and ion channeling. Transmission electron microscopy (TEM) studies were performed in order to determine the damage nature and search for a predicted ternary phase of cesium zirconate. Whatever the implantation temperature, the thickness of the damaged layer increases inwards with ion fluence. At RT, amorphization occurs, caused by the high Cs concentration (7at.%). In situ TEM during postannealing shows recrystallization of cubic zirconia after release of cesium. A high implantation temperature has a significant influence on the nature of radiation defects and on the retained Cs concentration. At HT, dislocation loops and voids are formed but no amorphization is observed whereas polygonization occurs at high fluence. The implanted cesium concentration reaches a saturation value of 1.5 at. % above which Cs can no longer be retained in the matrix and is then released at the surface. At that concentration, cesium forms a solid solution in YSZ; no other phase is formed, neither during irradiation nor after thermal annealing.
Influences of light intensity on fluorescence lifetime of nanorods and quantum dots
Authors: Yeh Yi-Cheun , Yuan Chi-Tsu , Kang Chia-Cheng , Chou Pi-Tai , Tang Jau
Published: December 2008

In this letter we investigate light-intensity dependence of the fluorescence lifetime for CdSe nanorods (NRs) and quantum dots (QDs) measured by time-correlated single photon counting techniques. We report extremely narrow lifetime distribution for NRs as the light intensity increases, although the change for QDs is not so pronounced. In addition, the averaged lifetimes for NRs and QDs all become shortened at higher light intensities. Some possible mechanisms for these effects are discussed.
An accurate global potential energy surface, dipole moment surface, and rovibrational frequencies for NH3
Authors: Huang Xinchuan , Schwenke David W. , Lee Timothy J.
Published: December 2008

A global potential energy surface (PES) that includes short and long range terms has been determined for the NH3 molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born–Oppenheimer correction was added. Our best purely ab initio PES, denoted “mixed,” is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10300cm−1 above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J=0–2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J=0–6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J=0–2 is 0.023cm−1 and that for each band is always ⩽0.06cm−1. For J=3–5 the rms error is always ⩽0.15cm−1. This agreement means that transition energies computed with our refined PES should be useful in the assignment of new high-resolution NH3 spectra and in correcting mistakes in previous assignments. Ideas for further improvements to our refined PES and for extension to other isotopolog are discussed.
Electrostatic mode associated with the pinch velocity in reversed field pinch simulations
Authors: Delzanno Gian Luca , Chacón Luis , Finn John M.
Published: December 2008

The existence of a new phenomenon in reversed field pinch (RFP) simulations related to the equilibrium pinch flow is discussed. This behavior is due to the inward equilibrium flow, but is strongly affected by boundary conditions on the perturbed azimuthal flow. It is important to understand and control this mechanism in single helicity simulations of RFPs. This mechanism can be explained in terms of an electrostatic instability related to a mode which can occur in fluid dynamics. In a simple linear model, it is shown that the mode, which is related to the inward advection of angular momentum from the edge, can be stabilized by using homogeneous Dirichlet (no-slip) boundary conditions at the wall. Behavior due to this mode is present in nonlinear simulations with zero-viscous-stress boundary conditions on the tangential velocity at the wall and, even in the presence of the usual magnetohydrodynamic modes, this mode can dominate the nonlinear dynamics of the velocity. In nonlinear simulations with Dirichlet boundary conditions on the tangential velocity, behavior associated with this electrostatic mode is not observed.
Simulations of the emission spectra of fac-tris(2-phenylpyridine) iridium and Duschinsky rotation effects using the Herman–Kluk semiclassical initial value representation method
Authors: Wu Yinghua , Brédas Jean-Luc
Published: December 2008

The phosphorescent emission spectra of fac-tris(2-phenylpyridine) iridium [fac-Ir(ppy)3] due to the lowest triplet T1 and T2 states are simulated using the harmonic oscillator approximation for the S0, T1, and T2 potential energy surfaces (PESs) and taking the Duschinsky rotation into account. The simulations involve the propagation of 177-dimensional wave packets on the coupled PES according to the Herman–Kluk (HK) semiclassical (SC) initial value representation (IVR) method. The HK SC-IVR method is employed because of its accuracy for the PES with mode mixing and its efficiency in dealing with coupled degrees of freedom for large systems. The simulated emission spectrum due to T1 reproduces the structures of the emission spectra observed experimentally, while T2 is found very unlikely to participate in the phosphorescent emission. Although the effect of the Duschinsky mode mixing is small for the T1 state, neglecting it blueshifts the spectrum due to the T2 state by 800 cm−1 and changes the relative intensities, indicating that the importance of the Duschinsky rotation is rather unpredictable and should not be overlooked. The present simulations demonstrate that the simple harmonic oscillator approximation combined with the Duschinsky rotation can adequately describe the photophysics of fac-Ir(ppy)3 and that the HK SC-IVR method is a powerful tool in studies of this kind.
Asymptotic model of the inertial migration of particles in a dilute suspension flow through the entry region of a channel
Authors: Osiptsov Andrei A. , Asmolov Evgeny S.
Published: December 2008

The inertial migration of particles in a dilute suspension flow through the entry region of a plane channel (or a circular pipe) is considered. Within the two-fluid approach, an asymptotic one-way coupling model of the dilute suspension flow in the entry region of a channel is constructed. The carrier phase is a viscous incompressible Newtonian fluid, and the dispersed phase consists of identical noncolloidal rigid spheres. In the interphase momentum exchange, we take into account the drag force, the virtual mass force, the Archimedes force, and the inertial lift force with a correction factor due to the wall effect and an arbitrary particle slip velocity. The channel Reynolds number is high and the particle-to-fluid density ratio is of order unity or significantly larger unity. The solution is constructed using the matched asymptotic expansion method. The problem of finding the far-downstream cross-channel profile of particle number concentration is reduced to solving the equations of the two-phase boundary layer developing on the channel walls. The full Lagrangian approach is used to study the evolution of the cross-flow particle concentration profile. The inertial migration results in particle accumulation on two symmetric planes (an annulus) distanced from the walls, with a nonuniform concentration profile between the planes (inside the annulus) and particle-free layers near the walls. When the particle-to-fluid density ratio is of order unity, an additional local maximum of the particle concentration on inner planes (an inner annulus) is revealed. The inclusion of the corrected lift force makes it possible to resolve the nonintegrable singularity in the concentration profile on the wall, which persisted in all previously published solutions for the dilute suspension flow in a boundary layer. The numerical results are compared to the tubular pinch effect observed in experiments, and a qualitative analogy is found.
Low-temperature characterization and micropatterning of coevaporated Bi2Te3 and Sb2Te3 films
Authors: Huang Baoling , Lawrence Chris , Gross Andrew , Hwang Gi-Suk , Ghafouri Niloufar , Lee Sang-Woo , Kim Hanseup , Li Chang-Peng , Uher Ctirad , Najafi Khalil , Kaviany Massoud
Published: December 2008

Thermoelectric (TE) properties of the coevaporated Bi2Te3 and Sb2Te3 films are measured from 100 to 300 K for Seebeck coefficient αS and from 5 to 300 K for electrical resistivity ρe, mobility μe, and Hall coefficient RH. For the low-temperature characterization of TE films, the conditions for coevaporation deposition of Bi, Te, and Sb to form Bi2Te3 and Sb2Te3 films are also investigated, including substrate material, substrate temperature Tsub, and elemental flux ratio (FR). The resublimation of Te occurring above 473 K significantly affects the film composition and quality. Our optimal deposition conditions for Bi2Te3 films are Tsub=533 K and FR=2.4, and those for Sb2Te3 films are Tsub=503 K and FR=3.0. The TE properties of both films are strongly temperature dependent, while Bi2Te3 films show a stronger temperature dependence than Sb2Te3 films due to different major scattering mechanisms. αS of both the coevaporated films are close to or higher than those of bulk materials, but ρe is much higher (due to lower carrier concentrations for Sb2Te3 films and lower μe for Bi2Te3 films). Also, no freeze-out regime is found for both Bi2Te3 and Sb2Te3 films at low temperatures. The room-temperature power factors of αS2/ρe for Bi2Te3 and Sb2Te3 films are 2.3 and 2.0 mW/K2 m, and the maxima are 2.7 mW/K2 m for Bi2Te3 at T=220 K and 2.1 mW/K2 m for Sb2Te3 at T=280 K. Shadow mask technique is successfully used for the micropatterning (20 μm) of TE films with no significant change in properties.
A robust floating nanoammeter
Authors: Sauer B. E. , Kara D. M. , Hudson J. J. , Tarbutt M. R. , Hinds E. A.
Published: December 2008

A circuit capable of measuring nanoampere currents while floating at voltages up to at least 25kV is described. The circuit relays its output to ground potential via an optical fiber. We particularly emphasize the design and construction techniques, which allow robust operation in the presence of high voltage spikes and discharges.
Photonic band gaps of polygonal and circular dielectric rods in square lattices
Authors: Chang K. P. , Yang S. L. , Shen L. F. , Yang T. J.
Published: December 2008

The plane-wave method is employed to determine the band structures and the field patterns of the photonic crystals with polygonal and circular rods in square lattices. Isotropic and anisotropic N-fold polygonal rods are used to assess the effects of the shapes and symmetries of polygonal rods on E- and H-polarization modes. The photonic band structures of the polygonal rods approach those of the circular rods as N increases above a value that is determined by the optical properties of the photonic crystal. Moreover, for comparable geometric structures, anisotropic polygonal-rod photonic crystals can provide larger absolute photonic band gaps than isotropic photonic crystals.
The acoustic response from individual attached and unattached rigid shelled microbubbles
Authors: Butler Mairead B. , Thomas David H. , Pye Stephen D. , Moran Carmel M. , McDicken W. Norman , Sboros Vassilis
Published: December 2008

A comparison of the acoustic response of attached and unattached individual microbubbles is presented. biSphere™ was insonated by 1.6 MHz ultrasound, peak negative acoustic pressures of 550 and 800 kPa, and the unprocessed radio frequency echo data collected. Comparison of the mean backscatter pressure from unattached and attached biSphere™ at these pressures showed no significant difference. No backscatter was detected for attached microbubbles insonated at 300 kPa. We surmised that at 550 and 800 kPa the rigid-shelled microbubble cracked on insonation, resulting in backscatter from an air microbubble in both cases. The dissolution rate of the gas was slower for attached biSphere™.
Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks
Authors: Ollinger S. V. , Richardson A. D. , Martin M. E. , Hollinger D. Y. , Frolking S. E. , Reich P. B. , Plourde L. C. , Katul G. G. , Munger J. W. , Oren R. , Smith M.-L. , Paw U K. T. , Bolstad P. V. , Cook B. D. , Day M. C. , Martin T. A. , Monson R. K. , Schmid H. P.
Published: December 2008

The availability of nitrogen represents a key constraint on carbon cycling in terrestrial ecosystems, and it is largely in this capacity that the role of N in the Earth's climate system has been considered. Despite this, few studies have included continuous variation in plant N status as a driver of broad-scale carbon cycle analyses. This is partly because of uncertainties in how leaf-level physiological relationships scale to whole ecosystems and because methods for regional to continental detection of plant N concentrations have yet to be developed. Here, we show that ecosystem CO
2
uptake capacity in temperate and boreal forests scales directly with whole-canopy N concentrations, mirroring a leaf-level trend that has been observed for woody plants worldwide. We further show that both CO
2
uptake capacity and canopy N concentration are strongly and positively correlated with shortwave surface albedo. These results suggest that N plays an additional, and overlooked, role in the climate system via its influence on vegetation reflectivity and shortwave surface energy exchange. We also demonstrate that much of the spatial variation in canopy N can be detected by using broad-band satellite sensors, offering a means through which these findings can be applied toward improved application of coupled carbon cycle–climate models.
Basal Body Components Exhibit Differential Protein Dynamics during Nascent Basal Body Assembly
Authors: Pearson Chad G. , Giddings Thomas H. , Winey Mark
Published: December 2008

Basal bodies organize cilia that are responsible for both mechanical beating and sensation. Nascent basal body assembly follows a series of well characterized morphological events; however, the proteins and their assembly dynamics for new basal body formation and function are not well understood. High-resolution light and electron microscopy studies were performed in Tetrahymena thermophila to determine how proteins assemble into the structure. We identify unique dynamics at basal bodies for each of the four proteins analyzed (α-tubulin, Spag6, centrin, and Sas6a). α-Tubulin incorporates only during new basal body assembly, Spag6 continuously exchanges at basal bodies, and centrin and Sas6a exhibit both of these patterns. Centrin loads and exchanges at the basal body distal end and stably incorporates during new basal body assembly at the nascent site of assembly and the microtubule cylinder. Conversely, both dynamic and stable populations of Sas6a are found only at a single site, the cartwheel. The bimodal dynamics found for centrin and Sas6a reveal unique protein assembly mechanisms at basal bodies that may reflect novel functions for these important basal body and centriolar proteins.
Infective Potential of Sporangia and Zoospores of Phytophthora ramorum
Authors: Widmer T. L.
Published: December 2008

Phytophthora species produce sporangia that either germinate directly or release zoospores, depending upon environmental conditions. Previous Phytophthora spp. inoculation trials have used both sporangia and zoospores as the inoculum type. However, it is unknown what impact propagule type has on disease. Rhododendron leaf disks were inoculated with P. ramorum zoospores (75, 500, or 2,400 per disk), sporangia (75 per disk), or sporangia plus trifluoperazine hydrochloride (TFP) (75 per disk), a chemical that inhibits zoospore formation. Combining results from two different isolates, the highest concentration of zoospores (2,400 per disk) induced a significantly higher percentage of necrotic leaf disk area (96.6%) than sporangia (87.6%) and 500 zoospores per disk (88.7%). The sporangia plus TFP treatment had the lowest necrosis at 47.5%. Rooted rhododendron cuttings had a higher percentage of necrotic leaves per plant when inoculated with zoospores (3,000 or 50,000 per ml) or cysts (50,000 per ml) than with sporangia (3,000 per ml) with or without TFP. The percentage of necrotic leaf area was significantly higher when cysts or zoospores were inoculated at 50,000 per ml than sporangia without TFP and zoospores at 3,000 per ml. All treatments were significantly higher in the percentage of necrotic leaf area than the leaves treated with sporangia plus TFP. This demonstrates that the full inoculum potential may not be achieved when sporangia are used as the inoculum propagule.
Occurrence and Characterization of Dimethachlon Insensitivity in Sclerotinia sclerotiorum in Jiangsu Province of China
Authors: Ma Hui-Xia , Feng Xi-Jie , Chen Yu , Chen Chang-Jun , Zhou Ming-Guo
Published: December 2008

Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, is the main fungal disease of oilseed rape (Brassica napus) in China. Numerous fungicide applications are required for control. Dimethachlon, one of the dicarboximide fungicides, has been the major fungicide for disease control after benzimidazole resistance became widespread. Fungal populations were collected throughout Jiangsu Province between 2006 and 2007 in order to determine their sensitivity to dimethachlon. A total of 1,066 single-sclerotium isolates of S. sclerotiorum were collected, and most of the isolates were considered sensitive to dimethachlon. Five isolates collected in Yancheng and Changzhou showed normal growth at 5 μg/ml dimethachlon with the resistance factor ≈10 (resistance factor was estimated as ratios between the EC50 values of resistant isolates and the average EC50 values of sensitive ones) compared to the sensitive isolates (EC50 is the concentration of fungicide causing 50% reduction in growth). Through in vitro selection for resistance to the fungicide, 25 dimethachlon-resistant mutants were derived from 10 wild-type isolates of S. sclerotiorum. The resistance factors for the isolates ranged from 198 to 484, and the isolates were considered highly resistant to dimethachlon. Therefore, at least two different mechanisms of resistance seem to be involved: one that may provide a moderate resistance (insensitivity) and a second that may give a high resistance level under laboratory conditions. There was positive cross-resistance between dimethachlon and other dicarboximide fungicides, such as iprodione and procymidone, in these S. sclerotiorum isolates. The field dimethachlon-insensitive and the laboratory-induced dimethachlon-resistant isolates appeared to have mycelial growth, sclerotial production, and pathogenicity comparable to their wild-type parental isolates. Also, results of osmotic tests showed that there were no significant difference in mycelial radial growth between the field dimethachlon-sensitive and field dimethachlon-insensitive isolates on potato dextrose agar plates amended with 2, 4, 6, or 8% (wt/vol) NaCl, but the laboratory-induced dimethachlon-resistant isolates grew significantly more slowly than their wild-type sensitive parents under all concentrations of NaCl. Because these studies yielded a high frequency of laboratory resistance in S. sclerotiorum, together with the occurrence of field insensitivity, appropriate precautions against resistance development in natural populations should be taken.
First Report of Garlic common latent virus in Garlic from India
Authors: Majumder S. , Baranwal V. K.
Published: December 2008

Garlic (Allium sativum L.) is one of the most important culinary herbs in the Indian subcontinent. Several viruses belonging to genera Potyvirus, Carlavirus, and Allexivirus are known to infect garlic (2,3). Garlic accessions grown on the research farm of the Indian Agricultural Research Institute, New Delhi, were tested for the presence of Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV). Leaves showing mild to severe mosaic symptoms were collected in January of 2008 from five accessions of garlic (Pusa Selection-34, G-1, Selection-17, G-282, and PGS-14) from the experimental plots. Direct antigen coated (DAC)-ELISA was performed with antisera to OYDV, GarCLV (Bioreba, Reinach, Switzerland), and Garlic latent virus (GarLV) (synonym for SLV) obtained from D. E. Lesemann, (Braunschweig, Germany). Total RNA was extracted from 100 mg of leaves with the RNeasy Plant Mini kit (Qiagen, Maryland) according to the manufacturer's protocol. Reverse transcription (RT)-PCR and DAC-ELISA confirmed the presence of OYDV and SLV in all selection lines, both of which were reported previously from garlic in India (1). The occurrence of GarCLV was confirmed by DAC-ELISA and RT- PCR using a primer pair 5′-AAATGTTAATCGCTAAACGACC-3′ and 5′-CTTTGTGGATTTTCGGTAAG-3′ designed from the conserved region of open reading frame (ORF) 5 (coat protein) and ORF 6 (nucleic acid binding protein) of GarCLV (GenBank Accession Nos. AB004566, X81138, and X81139). Expected amplicons of ∼500 bp for GarCLV were obtained from all garlic lines tested, confirming that all five garlic lines had mixed infections of OYDV, SLV, and GarCLV. The amplicons obtained from Pusa Selection-34 were directly sequenced and the 536-bp nucleotide sequence (GenBank Accession No. FJ154841) showed a sequence identity of 87% compared with GarCLV (GenBank Accession No. AB004566). To our knowledge, this is the first report of GarCLV in garlic cultivars in India. Our study demonstrates that GarCLV occurs frequently in mixed infections with OYDV and SLV and the potential impact of these mixed infections on garlic production needs to be evaluated.

References: (1) S. Majumder et al. J. Plant Pathol. 90:369, 2008. (2) P. Van Dijk. Acta Hortic. 358:299, 1994. (3) D. G. A. Walkey and D. N. Antill. J. Hortic. Sci, 64:53, 1989.
An Outbreak of Head Rot of Cabbage Caused by Rhizoctonia solani AG2-1 in Central China
Authors: Zhang L. , Zheng L. , Hsiang T. , Lv R. , Huang J.
Published: December 2008

In July of 2007, an outbreak of head rot of cabbage (Brassica oleracea) occurred on more than 2,500 ha in Changyang County, Hubei Province, China. On average, yields were reduced by approximately 50%. Affected plants were first observed in 2006, and symptoms were considered physiological or nutritional disorders by growers. In 2007, the more extensive summer rains favored an increase in disease severity. Initial symptoms consisted of irregular, brown-to-black lesions on leaves and sometimes a wet decay of the base of outer leaves. Lesions expanded until entire heads were rotted. Rhizoctonia solani was recovered consistently from symptomatic plant tissues. Five isolates were used to evaluate cultural and morphological characteristics of the pathogen. On potato dextrose agar (PDA), all isolates yielded colonies that became brown after 5 days of incubation. The hyphae, 4.9 to 8.0 μm in diameter, branched at right or acute angles near the septa and each cell usually had six to eight nuclei. Dark brown sclerotia, 0.5 to 5 mm in diameter, appeared after 10 days of incubation. Genomic DNA of a representative isolate, CY-1, was extracted, and the rDNA-internal transcribed spacer sequence showed 99.5% identity to R. solani AG2-1 (Accession No. EU513147) in GenBank. Pathogenicity tests were completed in the laboratory by placing 6-mm-diameter mycelial plugs from 3-day-old PDA cultures of the five isolates onto 30 cabbage leaves detached from 5-week-old cabbage plants. The inoculated leaves were incubated at 28°C with 95% relative humidity in a controlled environment chamber. Two days after inoculation, black, wet lesions were observed on all inoculated leaves, while no symptoms were apparent on leaves inoculated with noncolonized PDA plugs. Koch's postulates were fulfilled by reisolating R. solani from diseased leaves. R. solani AG1 (1), AG2-1 (2), and AG4 (4) have been reported as causal agents of diseases of cabbage and related plants, and AG2-1 has been previously isolated from cabbage grown in southwest China (3), but to our knowledge, this is the most severe outbreak reported from China.

References: (1) G. S. Abawi and S. B. Martin. Plant Dis. 69:158, 1985. (2) L. Corazza et al. Eur. J. Plant Pathol. 101:341, 1995. (3) H. R. Li and H. H. Zhu. J. Yunnan Agric. Univ. 3:247, 1993. (4) G. H. Yang et al. Plant Pathol. 56:351, 2007.
Puccinia jaceae var. solstitialis Teliospore Priming on Yellow Starthistle
Authors: Fisher A. J. , Aegerter B. J. , Gordon T. R. , Smith L. , Woods D. M.
Published: December 2008

Following the introduction of Puccinia jaceae var. solstitialis to California for biological control of yellow starthistle (Centaurea solstitialis, Asteraceae), teliospores, pycnia, and multiple urediniospore generations have been observed in the field. Because urediniospores have a relatively short life span in the field, functioning teliospores are expected to be necessary for the permanent establishment of P. jaceae var. solstitialis in California. To determine if conditions in California were conducive to this, teliospore emergence and priming were evaluated in the field. A factorial experiment in the laboratory with five incubation times and three incubation temperatures was used to determine teliospore priming requirements. Teliospore production coincided with plant senescence in August and September at two sites in 2 years; fewer teliospores were produced in 2006, suggesting inconsistent teliospore production may limit population growth and contribute to local extinctions in some areas. When teliospores were primed in the field, germination was low through the fall and abruptly peaked in January during both years. In the laboratory, teliospore germination increased as incubation time increased from 2 to 6 weeks and temperatures decreased from 12 to 4°C. A degree-hour model derived from laboratory data accurately predicts when teliospores are primed for germination in the field. Based on the results obtained in this study, it is apparent that teliospore germination can occur over a range of priming conditions. However, lower temperatures and longer incubation periods are superior in breaking teliospore dormancy.
Defective Active Silicon Uptake Affects Some Components of Rice Resistance to Brown Spot
Authors: Dallagnol Leandro J. , Rodrigues Fabrício Á. , Mielli Mateus V. B. , Ma Jian F. , Datnoff Lawrence E.
Published: December 2008

Rice is known to accumulate high amounts of silicon (Si) in plant tissue, which helps to decrease the intensity of many economically important rice diseases. Among these diseases, brown spot, caused by the fungus Bipolaris oryzae, is one of the most devastating because it negatively affects yield and grain quality. This study aimed to evaluate the importance of active root Si uptake in rice for controlling brown spot development. Some components of host resistance were evaluated in a rice mutant, low silicon 1 (lsi1), defective in active Si uptake, and its wild-type counterpart (cv. Oochikara). Plants were inoculated with B. oryzae after growing for 35 days in a hydroponic culture amended with 0 or 2 mMol Si. The components of host resistance evaluated were incubation period (IP), relative infection efficiency (RIE), area under brown spot progress curve (AUBSPC), final lesion size (FLS), rate of lesion expansion (r), and area under lesion expansion progress curve (AULEPC). Si content from both Oochikara and lsi1 in the +Si treatment increased in leaf tissue by 219 and 178%, respectively, over the nonamended controls. Plants from Oochikara had 112% more Si in leaf tissue than plants from lsi1. The IP of brown spot from Oochikara increased ≈6 h in the presence of Si and the RIE, AUBSPC, FLS, r, and AULEPC were significantly reduced by 65, 75, 33, 36, and 35%, respectively. In the presence of Si, the IP increased 3 h for lsi1 but the RIE, AUBSPC, FLS, r, and AULEPC were reduced by only 40, 50, 12, 21, and 12%, respectively. The correlation between Si leaf content and IP was significantly positive but Si content was negatively correlated with RIE, AUBSPC, FLS, r, and AULEPC. Single degree-of-freedom contrasts showed that Oochikara and lsi1 supplied with Si were significantly different from those not supplied with Si for all components of resistance evaluated. This result showed that a reduced Si content in tissues of plants from lsi1 dramatically affected its basal level of resistance to brown spot, suggesting that a minimum Si concentration is needed. Consequently, the results of this study emphasized the importance of an active root Si uptake system for an increase in rice resistance to brown spot.
Wnt-induced proteolytic targeting: Figure 1.
Authors: Jones Katherine A. , Kemp Caroline R.
Published: December 2008

Misregulation of the Wnt pathway is a common route to cancer, including primary breast cancers. In this issue of Genes & Development, Miranda-Carboni and colleagues (3121–3134) demonstrate that the cyclin-dependent kinase inhibitor p27Kip1 is ubiquitylated for proteasomal degradation in Wnt10b-induced mammary tumors exclusively by the Cul4A E3 ligase, which is strongly induced by Wnt signaling. The discovery of a new Wnt-induced proteolytic targeting system has important implications for the mechanism of Wnt-initiated tumorigenesis.
Master and commander: continued expression of Prox1 prevents the dedifferentiation of lymphatic endothelial cells
Authors: Bixel M. Gabriele , Adams Ralf H.
Published: December 2008

Cell differentiation occurs mostly during a specific developmental time window and is irreversible. The homeobox-containing transcription factor Prox1 is a master regulator of lymphatic endothelial cell differentiation in the embryo. A study by Johnson et al. (3282–3291) published in this issue of Genes & Development now shows that continued expression of Prox1 is required to maintain lymphatic endothelial cell identity even in adult mice. These findings indicate that Prox1 is essential for the differentiation and function of the lymphatic vasculature throughout life.
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
Authors: Cuddapah Suresh , Jothi Raja , Schones Dustin E. , Roh Tae-Young , Cui Kairong , Zhao Keji
Published: December 2008

Insulators are DNA elements that prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC-binding factor) is the only known major insulator-binding protein in the vertebrates and has been shown to bind many enhancer-blocking elements. However, it is not clear whether it plays a role in chromatin domain barriers between active and repressive domains. Here, we used ChIP-seq to map the genome-wide binding sites of CTCF in three cell types and identified significant binding of CTCF to the boundaries of repressive chromatin domains marked by H3K27me3. Although we find an extensive overlapping of CTCF-binding sites across the three cell types, its association with the domain boundaries is cell-type-specific. We further show that the nucleosomes flanking CTCF-binding sites are well positioned. Interestingly, we found a complementary pattern between the repressive H3K27me3 and the active H2AK5ac regions, which are separated by CTCF. Our data indicate that CTCF may play important roles in the barrier activity of insulators, and this study provides a resource for further investigation of the CTCF function in organizing chromatin in the human genome.
Soil CO2 efflux in contrasting boreal deciduous and coniferous stands and its contribution to the ecosystem carbon balance
Authors: GAUMONT‐GUAY DAVID , BLACK T. ANDREW , MCCAUGHEY HARRY , BARR ALAN G. , KRISHNAN PRAVEENA , JASSAL RACHHPAL S. , NESIC ZORAN
Published: December 2008

Similar nonsteady‐state automated chamber systems were used to measure and partition soil CO2 efflux in contrasting deciduous (trembling aspen) and coniferous (black spruce and jack pine) stands located within 100 km of each other near the southern edge of the Boreal forest in Canada. The stands were exposed to similar climate forcing in 2003, including marked seasonal variations in soil water availability, which provided a unique opportunity to investigate the influence of climate and stand characteristics on soil CO2 efflux and to quantify its contribution to the net ecosystem CO2 exchange (NEE) as measured with the eddy‐covariance technique. Partitioning of soil CO2 efflux between soil respiration (including forest‐floor vegetation) and forest‐floor photosynthesis showed that short‐ and long‐term temporal variations of soil CO2 efflux were related to the influence of (1) soil temperature and water content on soil respiration and (2) below‐canopy light availability, plant water status and forest‐floor plant species composition on forest‐floor photosynthesis. Overall, the three stands were weak to moderate sinks for CO2 in 2003 (NEE of −103, −80 and −28 g C m−2 yr−1 for aspen, black spruce and jack pine, respectively). Forest‐floor respiration accounted for 86%, 73% and 75% of annual ecosystem respiration, in the three respective stands, while forest‐floor photosynthesis contributed to 11% and 14% of annual gross ecosystem photosynthesis in the black spruce and jack pine stands, respectively. The results emphasize the need to perform concomitant measurements of NEE and soil CO2 efflux at longer time scales in different ecosystems in order to better understand the impacts of future interannual climate variability and vegetation dynamics associated with climate change on each component of the carbon balance.
Flowering range changes across an elevation gradient in response to warming summer temperatures
Authors: CRIMMINS THERESA M. , CRIMMINS MICHAEL A. , DAVID BERTELSEN C.
Published: December 2008

Many studies have demonstrated plant response to warming temperatures, both as advancement in the timing of phenological events and in range shifts. Mountain gradients are ideal laboratories for studying species range changes. In this study of 363 plant species in bloom collected in five segments across a 1200 m (4158 ft) elevation gradient, we look for changes in species flowering ranges over a 20‐year period. Ninety‐three species (25.6%) exhibited a significant change in the elevation at which they flowered from the first half to the second half of the record, with many of these changes occurring at higher elevations. Most of the species exhibiting the changes were perennial plants. Interestingly, though many changes in flowering range were specific to higher elevations, range changes occurred all across the gradient. The changes reported in this study are concurrent with significant increases in summer temperatures across the region and are consistent with observed changes around the globe.