bluuebunny/crossref_metadata_2025 huggingface dataset:
A calibration-independent method for accurate complex permittivity determination of liquid materials
Authors: Hasar U. C.
Published: September 2008

This note presents a calibration-independent method for accurate complex permittivity determination of liquid materials. There are two main advantages of the proposed method over those in the literature, which require measurements of two cells with different lengths loaded by the same liquid material. First, it eliminates any inhomogeneity or impurity present in the second sample and decreases the uncertainty in sample thickness. Second, it removes the undesired impacts of measurement plane deterioration on measurements of liquid materials. For validation of the proposed method, we measure the complex permittivity of distilled water and compare its extracted permittivity with the theoretical datum obtained from the Debye equation.
A gravity-driven low-rate particle feeder
Authors: Chen Wei-Yin , Gowan George , Shi Guang , Wan Shaolong
Published: September 2008

A gravity-driven particle feeder has been designed, fabricated, and tested to feed particles at low rates. A solenoid and a digital timer regulate the feed rate. This design avoids moving parts at the system periphery and thus avoids possible air leakages. It does not use pressurized gas to blow the particles into the desired location and thus pressure disturbance is avoided. The feeder can be operated at either a batch or a near continuous mode. Moreover, feeding a single large particle at a desired time is also feasible in such gaseous environments.
Modulation of single quantum dot energy levels by a surface-acoustic-wave
Authors: Gell J. R. , Ward M. B. , Young R. J. , Stevenson R. M. , Atkinson P. , Anderson D. , Jones G. A. C. , Ritchie D. A. , Shields A. J.
Published: September 2008

This letter presents an experimental investigation into the effect of a surface-acoustic-wave (SAW) on the emission of a single InAs quantum dot. The SAW causes the energy of the transitions within the dot to oscillate at the frequency of the SAW, producing a characteristic broadening of the emission lines in their time-averaged spectra. This periodic tuning of the transition energy is used as a method to regulate the output of a device containing a single quantum dot and we study the system as a high-frequency periodic source of single photons.
Light reflection from a metal surface with subwavelength cavities
Authors: Huang Cheng-ping , Li Jia-qi , Wang Qian-jin , Yin Xiao-gang , Zhu Yong-yuan
Published: September 2008

The interaction of light with the localized/delocalized system, i.e., a metal surface with rectangular cavities of finite depth, has been studied. Reflection spectrum has been measured in the optical frequencies, and resonant minima have been observed. We have developed an analytical model, which agrees well with the experiment. The localized waveguide resonance and delocalized surface resonance have been identified and discussed. The results may be useful for manipulating the coupling between light and matters.
Contact formation at the C60/alkali-metal fluoride/Al interface
Authors: Helander M. G. , Wang Z. B. , Lu Z. H.
Published: September 2008

Efficient contact formation is critical in organic electroluminescence and photovoltaic devices that utilize fullerene (C60). Unlike traditional electron transport molecules, such as tris-(8-hydroxy-quinolinato)aluminum (Alq3), C60 is found to be highly selective of injection layers. Charge injection properties of alkali-metal fluoride injection layers at the C60∕Al cathode interface of organic light emitting diodes were studied. LiF is found to be unique amongst the alkali-metal fluorides in producing an Ohmic contact. The device performance is strongly linked to the size of the vapor phase fluoride molecules. The observed phenomena are explained by an intercalation region at the metal/organic interface.
Tunnel magnetoresistance of 604% at 300K by suppression of Ta diffusion in CoFeB∕MgO∕CoFeB pseudo-spin-valves annealed at high temperature
Authors: Ikeda S. , Hayakawa J. , Ashizawa Y. , Lee Y. M. , Miura K. , Hasegawa H. , Tsunoda M. , Matsukura F. , Ohno H.
Published: September 2008

The authors observed tunnel magnetoresistance (TMR) ratio of 604% at 300K in Ta∕Co20Fe60B20∕MgO∕Co20Fe60B20∕Ta pseudo-spin-valve magnetic tunnel junction annealed at 525°C. To obtain high TMR ratio, it was found critical to anneal the structure at high temperature above 500°C, while suppressing the Ta diffusion into CoFeB electrodes and in particular to the CoFeB∕MgO interface. X-ray diffraction measurement of MgO on SiO2 or Co20Fe60B20 shows that an improvement of MgO barrier quality, in terms of the degree of the (001) orientation and stress relaxation, takes place at annealing temperatures above 450°C. The highest TMR ratio observed at 5K was 1144%.
Fully epitaxial Fe(110)/MgO(111)/Fe(110) magnetic tunnel junctions: Growth, transport, and spin filtering properties
Authors: Hauch J. O. , Fonin M. , Fraune M. , Turban P. , Guerrero R. , Aliev F. G. , Mayer J. , Rüdiger U. , Güntherodt G.
Published: September 2008

Fully epitaxial Fe(110)/MgO(111)/Fe(110) magnetic tunnel junctions (MTJs) have been tested with respect to symmetry-enforced spin filtering. The Fe(110) electrodes exhibit Σ1↑ and Σ1↓ spin states, both crossing the Fermi level, but with a group velocity about 50% smaller for the minority states compared to the majority ones. These epitaxial but symmetry-mismatched MTJs yield tunneling magnetoresistance (TMR) values of 54% at 1.5 K and 28% at room temperature. The TMR value and the estimated tunneling spin polarization are consistent with a partial spin filtering due to the Σ1↑ states partially compensated by the Σ1↓ states.
Nonpolar 4H-AlN grown on 4H-SiC (11¯00) with reduced stacking fault density realized by persistent layer-by-layer growth
Authors: Horita Masahiro , Kimoto Tsunenobu , Suda Jun
Published: September 2008

Nonpolar AlN layers were grown on 4H-SiC (11¯00) substrates by plasma-assisted molecular-beam epitaxy. By using SiC substrates with well-formed step-and-terrace structures, stable layer-by-layer growth of 4H-AlN (11¯00) can be realized. The layer-by-layer growth is confirmed by observations of anisotropic two-dimensional AlN islands on the grown surface as well as persistent reflection high-energy electron diffraction intensity oscillations. Cross-sectional transmission electron microscopy observations reveal that stacking fault generation during growth is suppressed and the stacking fault density is reduced to 1×106 cm−1.
Reversible separation of single-walled carbon nanotubes in bundles
Authors: Sahoo Sangeeta , Maranganti Ravi , Lastella Sarah , Mallick Govind , Karna Shashi , Sharma Pradeep , Ajayan Pulickel M.
Published: September 2008

We show that electrostatic charging of nanotubes and the consequent repulsion can lead to reversible separation of individual single-walled carbon nanotubes in bundles. Low-energy electron beam irradiation leads to this completely reversible phenomenon. A simple semianalytical model is used to explain the observed separation mechanism. The reversibility of the separation process is attributed to discharging and thermal-fluctuation induced motion of the nanotubes in ambient air. Further, the separation impacts the electrical conductance of small nanotube bundled devices.
Energy distribution of interface traps in germanium metal-oxide-semiconductor field effect transistors with HfO2 gate dielectric and its impact on mobility
Authors: Xie Ruilong , Wu Nan , Shen Chen , Zhu Chunxiang
Published: September 2008

The energy distribution of interface trap density (Dit) in HfO2 gated germanium metal-oxide-semiconductor field effect transistors (MOSFETs) is investigated by using charge pumping method with variable rise/fall-time measurement. Our results reveal that a high density of interface traps is present in the upper half of the Ge bandgap. As a result, the inversion-layer electron mobility of Ge n-channel MOSFETs was significantly degraded by the Coulomb scatterings. These results are also consistent with the abnormal capacitance-voltage (C-V) characteristics of Ge MOS capacitors.
The density of states in thin film copper phthalocyanine measured by Kelvin probe force microscopy
Authors: Celebi K. , Jadhav P. J. , Milaninia K. M. , Bora M. , Baldo M. A.
Published: September 2008

The density of states (DOS) is an important factor in understanding charge transport in organic semiconductors. We use Kelvin probe force microscopy to find the DOS in thin films of copper phthalocyanine (CuPC). We find an exponential DOS with a characteristic energy of 0.11 eV over a 0.5 eV range of the highest occupied molecular orbital of CuPC. We also find that the technique is limited by charge trapping and hysteresis at low DOSs, and nonuniform potential profiles within the CuPC film at high DOSs.
High-bias breakdown of Au/1,4-benzenedithiol/Au junctions
Authors: Teramae Yumi , Horiguchi Kazunori , Hashimoto Shuhei , Tsutsui Makusu , Kurokawa Shu , Sakai Akira
Published: September 2008

We have studied the high-bias breakdown of Au/1,4-benzenedithiol (BDT)/Au junctions at room temperature. Exploiting the break junction technique, we held a Au/BDT/Au junction and ruptured it by applying a voltage ramp. The conductance first changes gradually with the bias and then abruptly increases at breakdown. We found that the breakdown voltage shows a broad distribution and takes a maximum at ∼(1.2–1.5)V. The breakdown voltage is unaffected by the ambient atmosphere but tends to slightly decrease with increasing the junction conductance. We consider that the Au electrode becomes unstable at the breakdown voltage and collapses to crush the junction.
Atomic-scale bonding of bulk metallic glass to crystalline aluminum
Authors: Liu K. X. , Liu W. D. , Wang J. T. , Yan H. H. , Li X. J. , Huang Y. J. , Wei X. S. , Shen J.
Published: September 2008

A Ti40Zr25Cu12Ni3Be20 bulk metallic glass (BMG) was welded to a crystalline aluminum by the parallel plate explosive welding method. Experimental evidence and numerical simulation show that atomic-scale bonding between the BMG and the crystalline aluminum can be achieved, and the weldment on the BMG side can retain its amorphous state without any indication of crystallization in the welding process. Nanoindentation tests reveal that the interface of the explosive joints exhibits a significant increase in hardness compared to the matrix on its two sides. The joining of BMG and crystalline materials opens a window to the applications of BMGs in engineering.
Effect of atomic hydrogen on boron-doped germanium: An ab initio study
Authors: Wu R. Q. , Yang M. , Feng Y. P. , Ouyang Y. F.
Published: September 2008

Interaction between interstitial hydrogen (H) and boron (B) in germanium (Ge) is studied by at initio calculations to explore the effect of hydrogen on p-type Ge. The geometry, electronic structure, and frequency of local vibrational mode (LVM) of H in the stable B–H complex are determined. The interstitial hydrogen is found to reside between the B and Ge atoms and deactivate B dopant. The dissociation energy of the defect complex is calculated to be 1.06 eV, higher than that in Si. The frequency of LVM of isolated H at the Ge–Ge bond center and at the most stable bond minimum sites is also given and compared to experimental observations.
Imaging of magnetic colloids under the influence of magnetic field by cryogenic transmission electron microscopy
Authors: Wu Jinsong , Aslam M. , Dravid Vinayak P.
Published: September 2008

The application of superparamagnetic nanoparticles for in vivo magnetic resonance imaging (MRI) under external ac magnetic field has attracted considerable research efforts in recent years. However, it is unclear how superparamagnetic nanostructures arrange themselves in fluidic environment under external magnetic field. Here, we report direct visualization of the effect of applied magnetic field to the ferrofluids (about 6 nm superparamagnetic magnetite (Fe3O4) nanoparticle “colloidal” suspension) using the cryogenic transmission electron microscopy (cryo-TEM). While long dipole chains (up to millimeter range) of the magnetite along the magnetic lines are found in samples dried inside the magnetic field, only short dipole chains (within tens of nanometer scale) with random orientations are observed in the wet sample observed by cryo-TEM. In the wet sample, aggregations of medium-length dipole chains (up to hundreds of nanometer) can be observed at the areas where the nanoparticles are “solidified” when phase separation occurs. In situ formation of flux-closure rings is observed at the edge where vitreous ice sublimes due to high-energy electron radiation that leaves magnetite nanoparticles isolated in the vacuum. Such observations may help elucidate the nature of magnetic field-induced assembly in fluidic environment as in the physiological aqueous conditions in MRI and related applications.
High output power GaN-based light-emitting diodes using an electrically reverse-connected p-Schottky diode and p-InGaN–GaN superlattice
Authors: Jang Ja-Soon
Published: September 2008

We demonstrate the high-performance and excellent reliability characteristics of InGaN–GaN light-emitting diodes (LEDs) using an electrically reverse-connected p-Schottky diode and p-InGaN–GaN superlattice (SL). Measurements show that the LED with the Schottky diode and SL yields lower series resistance and higher output power compared to normal LEDs. In addition, the device degradation rate of the proposed LED is 33 times as low as that of the normal LED at high electrical stress of 410 A/cm2, indicating excellent reliability behavior. These results mean that the use of p-Schottky diode and p-SL is very promising for the realization of high-performance GaN-based LEDs.
Room temperature luminescent InGaAs/GaAs core-shell nanowires
Authors: Jabeen F. , Rubini S , Grillo V , Felisari L. , Martelli F.
Published: September 2008

InGaAs/GaAs core-shell nanowires have been grown by molecular beam epitaxy. The core-shell nanowires show room temperature photoluminescence. At low temperatures their luminescence intensity is two to three orders of magnitudes larger than that of parent InGaAs nanowires grown without external GaAs shell. The nanowires have been structurally characterized by scanning electron microscopy and transmission electron microscopy.
Experimental investigations on channel backscattering characteristics of gate-all-around silicon nanowire transistors from top-down approach
Authors: Wang Runsheng , Huang Ru , Zhang Liangliang , Liu Hongwei , Kim Dong-Won , Park Donggun , Wang Yangyuan
Published: September 2008

In this letter, the channel backscattering characteristics and ballistic efficiency of gate-all-around silicon nanowire transistors (SNWTs) are experimentally investigated. A modified experimental extraction methodology for SNWTs is proposed, which takes into account the impact of contact resistance. It was found that without this correction, the characterized results will severely overestimate the channel backscattering in SNWTs due to the temperature sensitivity of the source contact resistance. The highest ballistic efficiency is observed in sub-40-nm SNWTs due to their quasi-one-dimensional properties, demonstrating their potential as an alternative device structure for near-ballistic transport from top-down approach.
A combined experimental and simulation study on thickness dependence of the emission characteristics in multicolor single layer organic light-emitting diodes
Authors: Stathopoulos N. A. , Vasilopoulou M. , Palilis L. C. , Georgiadou D. G. , Argitis P.
Published: September 2008

The impact of the active layer thickness on the emission characteristics of multicolor single layer organic light-emitting diodes based on poly(9-vinylcarbazole) is examined by combining experimental results with model simulations. We compare experimental electroluminescence spectra with simulations using photon-emitting point dipoles and find a very good agreement. We also simulate the location of the recombination zone, considering that the emission probability distribution has a peak located 25 nm from the cathode, which decays exponentially above and below that point. Simulated radiation patterns show that microcavity effects dominate the thickness dependent emitting properties of these devices.
Bandgap bowing in BGaN thin films
Authors: Ougazzaden A. , Gautier S. , Moudakir T. , Djebbour Z. , Lochner Z. , Choi S. , Kim H. J. , Ryou J.-H. , Dupuis R. D. , Sirenko A. A.
Published: September 2008

We report on the bandgap variation in thin films of BxGa1−xN grown on AlN/sapphire substrates using metal-organic vapor phase epitaxy. Optical transmission, photoluminescence, and x-ray diffraction were utilized to characterize the materials’ properties of the BxGa1−xN films. In contrast to the common expectation for the bandgap variation, which is based on the linear interpolation between the corresponding GaN and BN values, a significant bowing (C=9.2±0.5 eV) of the bandgap was observed. A decrease in the optical bandgap by 150 meV with respect to that of GaN was measured for the increase in the boron composition from 0% to 1.8%.
Defect dependent ferromagnetism in MgO doped with Ni and Co
Authors: Narayan J. , Nori Sudhakar , Pandya D. K. , Avasthi D. K. , Smirnov A. I.
Published: September 2008

We have investigated magnetic properties of MgO single crystals doped with Ni and Co impurities, and studied changes in magnetic properties after heavy ion irradiation. These results are compared with doped single-crystal thin films that contain a higher concentration of trapped defects. The as-grown bulk single crystals, which contain a small equilibrium concentration of vacancies, exhibit a perfect paramagnetic behavior throughout the temperature range and magnetic field. By introducing defects either by ion irradiation or by thin film deposition, which have trapped defects, we are able to achieve defect-mediated ferromagnetic ordering.
To Abalone Unbound
Authors: Glashow Sheldon L.
Published: September 2008

The following piece of doggerel was delivered in an after-dinner talk by Harvard particle theorist Sheldon L. Glashow, once a California physicist himself. He spoke at the APS New England Sectional Meeting on 12 October at Northeastern University.
Calving icebergs may cause glacial earthquakes in Greenland
Authors: Wilson Mark
Published: September 2008

Recent local measurements and numerical simulations constrain the possible mechanisms for glacial dynamics that occur on the time scale of minutes.
Shaped light waves can pass through opaque material
Authors: Miller Johanna
Published: September 2008

A decades-old theoretical prediction about random scattering has just received its first experimental confirmation.
Physics flourishes in Hong Kong
Authors: Day Charles
Published: September 2008

In just two decades, scientific research in Hong Kong has been transformed from an underfunded pastime into a world-class enterprise.
G8 nations commit to building a score of CO2 sequestration demonstration projects
Authors: Kramer David
Published: September 2008

But Congress could block the Bush administration’s plan to finance 10 commercial-scale CO2 capture and storage projects at coal-fired power plants.
Giant telescope teams seek funding
Authors: Feder Toni
Published: September 2008

Neither of the huge telescopes spearheaded in the US is a sure bet, but project members say that for the country to remain internationally competitive in optical astronomy, both need to get built.
Modeling the physics of storm surges
Authors: Resio Donald T. , Westerink Joannes J.
Published: September 2008

Despite the potentially catastrophic consequences of storm surges, the physics of surge generation and propagation has historically been poorly understood, and many misconceptions about surges still exist.
The Chinese nuclear tests, 1964–1996
Authors: Reed Thomas C.
Published: September 2008

A combination of intellectual rigor, technical sophistication, hard work, and intelligence gathering brought China into the world’s nuclear club in record-shattering time.
Tennis physics, anyone?
Authors: Cross Rodney
Published: September 2008

After a tennis ball lands on the court, it slows down, spins up, and squashes. Friction on the ball can even reverse direction, pushing it forward.
Debate on a comprehensive nuclear weapons test ban: Con
Authors: Barker Robert B.
Published: September 2008

We are seeing today an unprecedented public interest in the control of nuclear arms. The resulting plethora of books and articles on all aspects of nuclear weapons and nuclear-weapon strategies is providing the basis for a new, informed discussion of arms-control objectives and priorities. While there may be a general desire for the elimination of all nuclear weapons, there is also an appreciation that nuclear weapons will be with us for the foreseeable future, and that we will achieve bilateral and verifiable reductions only over time. The public understands that even as we work for reductions in nuclear arms, those nuclear weapons that do exist should continue to preserve deterrence and stability between the two nuclear-weapons superpowers, the Soviet Union and the United States. Hence we should measure all proposals for arms control or arms reductions against their ability to reduce the numbers of nuclear weapons while preserving deterrence and stability.
Chemical dynamics of vibrationally excited molecules: Controlling reactions in gases and on surfaces
Authors: Crim F. Fleming
Published: September 2008

Experimental studies of the chemical reaction dynamics of vibrationally excited molecules reveal the ability of different vibrations to control the course of a reaction. This Perspective describes those studies for the prototypical reaction of vibrationally excited methane and its isotopologues in gases and on surfaces and looks to the prospects of similar studies in liquids. The influences of vibrational excitation on the CH bond cleavage in a single collision reaction with Cl and in dissociative adsorption on a Ni surface bear some striking similarities. Both reactions are bond-selective processes in which the initial preparation of a molecular eigenstate containing a large component of CH stretching results in preferential cleavage of that bond. It is possible to cleave either the CH bond or CD bond in the reaction of Cl with CH3D, CH2D2, or CHD3and, similarly, to use initial excitation of the CH stretch to promote dissociation of CHD3to CD3and H on a Ni surface. Different vibrational modes, such as the symmetric and antisymmetric stretches in CH3D or CH4, lead to very different reactivities, and molecules with the symmetric stretching vibration excited can be as much as 10 times more reactive than ones with the antisymmetric stretch excited. The origin of this behavior lies in the change in the vibrational motion induced by the interaction with the atomic reaction partner or the surface.
Magnetic resonance imaging of primary cerebral gliosarcoma: a report of 15 cases
Authors: Han L. , Zhang X. , Qiu S. , Li X. , Xiong W. , Zhang Y. , Qu H. , Chang R. , Chen B. , Wang W. , Li S.
Published: September 2008

Background: Gliosarcomas are rare tumors with mixed glial and mesenchymal components. Many of their radiologic features resemble those of other primary brain malignancies.

Purpose: To investigate the magnetic resonance (MR) imaging features of gliosarcomas.

Material and Methods: We retrospectively reviewed the MR images, pathology reports, and clinical information of 11 male and four female patients aged 15–71 years to evaluate the location, morphology, enhancement, and other features of their pathologically confirmed gliosarcomas.

Results: Apart from one tumor in the right cerebellar hemisphere, all were supratentorial. Two tumors were intraventricular, and four involved the corpus callosum. The tumors were well demarcated, with an inhomogeneous or cystic appearance and moderate-to-extensive surrounding edema. Thick walls with strong rim and ring-like enhancement were observed in 13 (87%). Seven (47%) showed intratumoral paliform enhancement.

Conclusion: Gliosarcoma demonstrates certain characteristic MR features, such as supratentorial and peripheral location, well-demarcated, abutting a dural surface, uneven and thick-walled rim-like or ring enhancement, as well as intratumoral strip enhancement. These findings, combined with patient age, can aid the differential diagnosis of gliosarcomas from more common primary brain tumors.
Book Review
Authors: Bogren H.
Published: September 2008

The Chest X-Ray: A Survival Guide. 3rd edition. By G. de Lacey, S. Morley, & L. Berman. Amsterdam: Saunders, Elsevier, 2008. ISBN: 978-0-7020-3046-8. 352 pages. Price (paperback): USD 75.00.
RanBPM regulates cell shape, arrangement, and capacity of the female germline stem cell niche in Drosophila melanogaster
Authors: Dansereau David A. , Lasko Paul
Published: September 2008

Experiments in cultured cells with Ran-binding protein M (RanBPM) suggest that it links cell surface receptors and cell adhesion proteins. In this study, we undertake a genetic study of RanBPM function in the germline stem cell (GSC) niche of Drosophila melanogaster ovaries. We find that two RanBPM isoforms are produced from alternatively spliced transcripts, the longer of which is specifically enriched in the GSC niche, a cluster of somatic cells that physically anchors GSCs and expresses signals that maintain GSC fate. Loss of the long isoform from the niche causes defects in niche organization and cell size and increases the number of GSCs attached to the niche. In genetic mosaics for a null RanBPM allele, we find a strong bias for GSC attachment to mutant cap cells and observe abnormal accumulation of the adherens junction component Armadillo (β-catenin) and the membrane skeletal protein Hu-li tai shao in mutant terminal filament cells. These results implicate RanBPM in the regulation of niche capacity and adhesion.
IGFBP-5 regulates muscle cell differentiation by binding to IGF-II and switching on the IGF-II auto-regulation loop
Authors: Ren Hongxia , Yin Ping , Duan Cunming
Published: September 2008

IGF-II stimulates both mitogenesis and myogenesis through its binding and activation of the IGF-I receptor (IGF-IR). How this growth factor pathway promotes these two opposite cellular responses is not well understood. We investigate whether local IGF binding protein-5 (IGFBP-5) promotes the myogenic action of IGF-II. IGFBP-5 is induced before the elevation of IGF-II expression during myogenesis. Knockdown of IGFBP-5 impairs myogenesis and suppresses IGF-II gene expression. IGF-II up-regulates its own gene expression via the PI3K-Akt signaling pathway. Adding IGF-II or constitutively activating Akt rescues the IGFBP-5 knockdown-caused defects. However, an IGF analogue that binds to the IGF-IR but not IGFBP has only a limited effect. When added with low concentrations of IGF-II, IGFBP-5 restores IGF-II expression and myogenic differentiation, whereas an IGF binding–deficient IGFBP-5 mutant has no effect. These findings suggest that IGFBP-5 promotes muscle cell differentiation by binding to and switching on the IGF-II auto-regulation loop.
TLR ligand–induced podosome disassembly in dendritic cells is ADAM17 dependent
Authors: West Michele A. , Prescott Alan R. , Chan Kui Ming , Zhou Zhongjun , Rose-John Stefan , Scheller Jürgen , Watts Colin
Published: September 2008

Toll-like receptor (TLR) signaling induces a rapid reorganization of the actin cytoskeleton in cultured mouse dendritic cells (DC), leading to enhanced antigen endocytosis and a concomitant loss of filamentous actin–rich podosomes. We show that as podosomes are lost, TLR signaling induces prominent focal contacts and a transient reduction in DC migratory capacity in vitro. We further show that podosomes in mouse DC are foci of pronounced gelatinase activity, dependent on the enzyme membrane type I matrix metalloprotease (MT1-MMP), and that DC transiently lose the ability to degrade the extracellular matrix after TLR signaling. Surprisingly, MMP inhibitors block TLR signaling–induced podosome disassembly, although stimulated endocytosis is unaffected, which demonstrates that the two phenomena are not obligatorily coupled. Podosome disassembly caused by TLR signaling occurs normally in DC lacking MT1-MMP, and instead requires the tumor necrosis factor α–converting enzyme ADAM17 (a disintegrin and metalloprotease 17), which demonstrates a novel role for this “sheddase” in regulating an actin-based structure.
Separase cooperates with Zds1 and Zds2 to activate Cdc14 phosphatase in early anaphase
Authors: Queralt Ethel , Uhlmann Frank
Published: September 2008

Completion of mitotic exit and cytokinesis requires the inactivation of mitotic cyclin-dependent kinase (Cdk) activity. A key enzyme that counteracts Cdk during budding yeast mitotic exit is the Cdc14 phosphatase. Cdc14 is inactive for much of the cell cycle, sequestered by its inhibitor Net1 in the nucleolus. At anaphase onset, separase-dependent down-regulation of PP2ACdc55 allows phosphorylation of Net1 and consequent Cdc14 release. How separase causes PP2ACdc55 down-regulation is not known. Here, we show that two Cdc55-interacting proteins, Zds1 and Zds2, contribute to timely Cdc14 activation during mitotic exit. Zds1 and Zds2 are required downstream of separase to facilitate nucleolar Cdc14 release. Ectopic Zds1 expression in turn is sufficient to down-regulate PP2ACdc55 and promote Net1 phosphorylation. These findings identify Zds1 and Zds2 as new components of the mitotic exit machinery, involved in activation of the Cdc14 phosphatase at anaphase onset. Our results suggest that these proteins may act as separase-regulated PP2ACdc55 inhibitors.
The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression
Authors: Grund Stefanie E. , Fischer Tamás , Cabal Ghislain G. , Antúnez Oreto , Pérez-Ortín José E. , Hurt Ed
Published: September 2008

Inner nuclear membrane proteins containing a LEM (LAP2, emerin, and MAN1) domain participate in different processes, including chromatin organization, gene expression, and nuclear envelope biogenesis. In this study, we identify a robust genetic interaction between transcription export (TREX) factors and yeast Src1, an integral inner nuclear membrane protein that is homologous to vertebrate LEM2. DNA macroarray analysis revealed that the expression of the phosphate-regulated genes PHO11, PHO12, and PHO84 is up-regulated in src1Δ cells. Notably, these PHO genes are located in subtelomeric regions of chromatin and exhibit a perinuclear location in vivo. Src1 spans the nuclear membrane twice and exposes its N and C domains with putative DNA-binding motifs to the nucleoplasm. Genome-wide chromatin immunoprecipitation–on-chip analyses indicated that Src1 is highly enriched at telomeres and subtelomeric regions of the yeast chromosomes. Our data show that the inner nuclear membrane protein Src1 functions at the interface between subtelomeric gene expression and TREX-dependent messenger RNA export through the nuclear pore complexes.
Caprin-2 enhances canonical Wnt signaling through regulating LRP5/6 phosphorylation
Authors: Ding Yu , Xi Ying , Chen Ting , Wang Ji-yong , Tao Dong-lei , Wu Zhi-Li , Li Yi-ping , Li Chen , Zeng Rong , Li Lin
Published: September 2008

The low-density lipoprotein receptor–related proteins 5 and 6 (LRP5/6) are coreceptors for Frizzled and transmit signals from the plasma membrane to the cytosol. However, the mechanism for LRP5/6 signal transmission remains undefined. Here, we identify cytoplasmic activation/proliferation-associated protein 2 (Caprin-2) as a LRP5/6-binding protein. Our data show that Caprin-2 stabilizes cytosolic β-catenin and enhances lymphoid enhancer-binding factor 1/T cell factor–dependent reporter gene activity as well as the expression of Wnt target genes in mammalian cells. Morpholino-mediated knockdown of Caprin-2 in zebrafish embryos inhibits Wnt/β-catenin signaling and results in a dorsalized phenotype. Moreover, Caprin-2 facilitates LRP5/6 phosphorylation by glycogen synthase kinase 3, and thus enhances the interaction between Axin and LRP5/6. Therefore, Caprin-2 promotes activation of the canonical Wnt signaling pathway by regulating LRP5/6 phosphorylation.
Inactivation of clathrin heavy chain inhibits synaptic recycling but allows bulk membrane uptake
Authors: Kasprowicz Jaroslaw , Kuenen Sabine , Miskiewicz Katarzyna , Habets Ron L.P. , Smitz Liesbet , Verstreken Patrik
Published: September 2008

Synaptic vesicle reformation depends on clathrin, an abundant protein that polymerizes around newly forming vesicles. However, how clathrin is involved in synaptic recycling in vivo remains unresolved. We test clathrin function during synaptic endocytosis using clathrin heavy chain (chc) mutants combined with chc photoinactivation to circumvent early embryonic lethality associated with chc mutations in multicellular organisms. Acute inactivation of chc at stimulated synapses leads to substantial membrane internalization visualized by live dye uptake and electron microscopy. However, chc-inactivated membrane cannot recycle and participate in vesicle release, resulting in a dramatic defect in neurotransmission maintenance during intense synaptic activity. Furthermore, inactivation of chc in the context of other endocytic mutations results in membrane uptake. Our data not only indicate that chc is critical for synaptic vesicle recycling but they also show that in the absence of the protein, bulk retrieval mediates massive synaptic membrane internalization.
ERK regulates Golgi and centrosome orientation towards the leading edge through GRASP65
Authors: Bisel Blaine , Wang Yanzhuang , Wei Jen-Hsuan , Xiang Yi , Tang Danming , Miron-Mendoza Miguel , Yoshimura Shin-ichiro , Nakamura Nobuhiro , Seemann Joachim
Published: September 2008

Directed cell migration requires the orientation of the Golgi and centrosome toward the leading edge. We show that stimulation of interphase cells with the mitogens epidermal growth factor or lysophosphatidic acid activates the extracellular signal–regulated kinase (ERK), which phosphorylates the Golgi structural protein GRASP65 at serine 277. Expression of a GRASP65 Ser277 to alanine mutant or a GRASP65 1–201 truncation mutant, neither of which can be phosphorylated by ERK, prevents Golgi orientation to the leading edge in a wound assay. We show that phosphorylation of GRASP65 with recombinant ERK leads to the loss of GRASP65 oligomerization and causes Golgi cisternal unstacking. Furthermore, preventing Golgi polarization by expressing mutated GRASP65 inhibits centrosome orientation, which is rescued upon disassembly of the Golgi structure by brefeldin A. We conclude that Golgi remodeling, mediated by phosphorylation of GRASP65 by ERK, is critical for the establishment of cell polarity in migrating cells.
Comments on ‘On correcting the overestimation of the permutation-based false discovery rate estimator’
Authors: Xie Yang
Published: September 2008

Contact: Yang.xie@utsouthwestern.edu
Bosque: integrated phylogenetic analysis software
Authors: Ramírez-Flandes Salvador , Ulloa Osvaldo
Published: September 2008

Summary: Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (users have sometimes to leave their programs, on their desktop computers, running for extended periods of time). To address these problems we have developed ‘Bosque’, a multi-platform client–server software that performs standard phylogenetic tasks either locally or remotely on servers, and integrates the results on a local relational database. Bosque performs sequence alignments and graphical visualization and editing of trees, thus providing a powerful environment that integrates all the steps of phylogenetic analyses.

Availability:  http://bosque.udec.cl

Contact:  sram@profc.udec.cl
Diseases of the European edible crab (Cancer pagurus): a review
Authors: Stentiford Grant D.
Published: September 2008

Stentiford, G. D. 2008. Diseases of the European edible crab (Cancer pagurus): a review. – ICES Journal of Marine Science, 65: 1578–1592. The edible crab (Cancer pagurus) supports an important fishery in European waters. The fishery is increasing in size and in relative importance as stocks of marine finfish decline. Despite its importance, though, studies on the pathogens and parasites of this crab species are relatively lacking compared with studies of commercially exploited finfish and molluscan hosts. Recent basic surveys of C. pagurus stocks from the English Channel carried out by the Cefas laboratory at Weymouth have identified a new viral infection (C. pagurus bacilliform virus, CpBV) in juvenile crabs, and several new species of protistan parasite (Hematodinium sp., Paramarteilia canceri, and Enterospora canceri) in the adult population. The histopathology and prevalence of each of these pathogens suggests that each can induce host mortality and, further, that specific pathogens are differentially prevalent in juvenile and adult cohorts from similar geographic locations and at different times of the year. In this review, these newly discovered pathogens are placed in context with previously described bacterial, fungal, protistan, and metazoan pathogens of C. pagurus, and the potential for these pathogens to impact on the health of individuals and populations within the English Channel fishery is discussed.
Facialmetric similarities mediate mate choice: sexual imprinting on opposite-sex parents
Authors: Bereczkei Tamas , Hegedus Gabor , Hajnal Gabor
Published: September 2008

Former studies have suggested that imprinting-like processes influence the shaping of human mate preferences. In this study, we provide more direct evidence for assessing facial resemblance between subjects' partner and subjects' parents. Fourteen facial proportions were measured on 312 adults belonging to 52 families, and the correlations between family members were compared with those of pairs randomly selected from the population. Spouses proved to be assortatively mated in the majority of measured facial proportions. Significant correlations have been found between the young men and their partner's father (but not his mother), especially on facial proportions belonging to the central area of the face. Women also showed resemblance to their partner's mother (but not to their father) in the facial characteristics of their lower face. Replicating our previous studies, facial photographs of participants were also matched by independent judges who ascribed higher resemblance between partners, and subjects and their partners' opposite-sex parents, compared with controls. Our results support the sexual imprinting hypothesis which states that children shape a mental template of their opposite-sex parents and search for a partner who resembles that perceptual schema. The fact that only the facial metrics of opposite-sex parents showed resemblance to the partner's face tends to rule out the role of familiarity in shaping mating preferences. Our findings also reject several other rival hypotheses. The adaptive value of imprinting-related human mating is discussed, and a hypothesis is made of why different facial areas are involved in males' and females' search for resemblance.
Deciphering the function of canonical Wnt signals in development and disease: conditional loss- and gain-of-function mutations of β-catenin in mice
Authors: Grigoryan Tamara , Wend Peter , Klaus Alexandra , Birchmeier Walter
Published: September 2008

Wnt signaling is one of a handful of powerful signaling pathways that play crucial roles in the animal life by controlling the genetic programs of embryonic development and adult homeostasis. When disrupted, these signaling pathways cause developmental defects, or diseases, among them cancer. The gateway of the canonical Wnt pathway, which contains >100 genes, is an essential molecule called β-catenin (Armadillo in Drosophila). Conditional loss- and gain-of-function mutations of β-catenin in mice provided powerful tools for the functional analysis of canonical Wnt signaling in many tissues and organs. Such studies revealed roles of Wnt signaling that were previously not accessible to genetic analysis due to the early embryonic lethality of conventional β-catenin knockout mice, as well as the redundancy of Wnt ligands, receptors, and transcription factors. Analysis of conditional β-catenin loss- and gain-of-function mutant mice demonstrated that canonical Wnt signals control progenitor cell expansion and lineage decisions both in the early embryo and in many organs. Canonical Wnt signaling also plays important roles in the maintenance of various embryonic or adult stem cells, and as recent findings demonstrated, in cancer stem cell types. This has opened new opportunities to model numerous human diseases, which have been associated with deregulated Wnt signaling. Our review summarizes what has been learned from genetic studies of the Wnt pathway by the analysis of conditional β-catenin loss- and gain-of-function mice.
A new mechanism controlling kinetochore–microtubule interactions revealed by comparison of two dynein-targeting components: SPDL-1 and the Rod/Zwilch/Zw10 complex
Authors: Gassmann Reto , Essex Anthony , Hu Jia-Sheng , Maddox Paul S. , Motegi Fumio , Sugimoto Asako , O’Rourke Sean M. , Bowerman Bruce , McLeod Ian , Yates John R. , Oegema Karen , Cheeseman Iain M. , Desai Arshad
Published: September 2008

Chromosome segregation requires stable bipolar attachments of spindle microtubules to kinetochores. The dynein/dynactin motor complex localizes transiently to kinetochores and is implicated in chromosome segregation, but its role remains poorly understood. Here, we use the Caenorhabditis elegans embryo to investigate the function of kinetochore dynein by analyzing the Rod/Zwilch/Zw10 (RZZ) complex and the associated coiled-coil protein SPDL-1. Both components are essential for Mad2 targeting to kinetochores and spindle checkpoint activation. RZZ complex inhibition, which abolishes both SPDL-1 and dynein/dynactin targeting to kinetochores, slows but does not prevent the formation of load-bearing kinetochore–microtubule attachments and reduces the fidelity of chromosome segregation. Surprisingly, inhibition of SPDL-1, which abolishes dynein/dynactin targeting to kinetochores without perturbing RZZ complex localization, prevents the formation of load-bearing attachments during most of prometaphase and results in extensive chromosome missegregation. Coinhibition of SPDL-1 along with the RZZ complex reduces the phenotypic severity to that observed following RZZ complex inhibition alone. We propose that the RZZ complex can inhibit the formation of load-bearing attachments and that this activity of the RZZ complex is normally controlled by dynein/dynactin localized via SPDL-1. This mechanism could coordinate the hand-off from initial weak dynein-mediated lateral attachments, which help orient kinetochores and enhance their ability to capture microtubules, to strong end-coupled attachments that drive chromosome segregation.
Multiple centrosomes: together they stand, divided they fall
Authors: Gergely Fanni , Basto Renata
Published: September 2008

Cells with extra centrosomes rely entirely on centrosome clustering mechanisms to assemble a bipolar spindle and to divide in a bipolar fashion. To identify the pathways involved in suppression of multipolarity, Kwon, Godinho, and colleagues (pp. 2189–2203) have set up a genome-wide screen in Drosophila S2 cells. Surprisingly, they found that efficient clustering requires a large number of proteins associated with a variety of cellular functions.
Cohesion by topology: sister chromatids interlocked by DNA: Figure 1.
Authors: Bermejo Rodrigo , Branzei Dana , Foiani Marco
Published: September 2008

Sister chromatid cohesion is coupled with chromosome replication and influences chromosome segregation and intra-S repair. Specialized proteins, the cohesins, together with other pathways contribute to tether sister chromatids. In this issue of Genes & Development, Wang and colleagues (pp. 2426–2433 demonstrate that TopoIV, a type II DNA topoisomerase, modulates cohesion in Escherichia coli, by removing interlocked DNA junctions between sister chromatids. They propose that DNA precatenanes, arising during replication fork progression, hold sister chromatids together.
Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli
Authors: Pesavento Christina , Becker Gisela , Sommerfeldt Nicole , Possling Alexandra , Tschowri Natalia , Mehlis Anika , Hengge Regine
Published: September 2008

During the transition from post-exponential to stationary phase, Escherichia coli changes from the motile-planktonic to the adhesive-sedentary “lifestyle.” We demonstrate this transition to be controlled by mutual inhibition of the FlhDC/motility and σS/adhesion control cascades at two distinct hierarchical levels. At the top level, motility gene expression and the general stress response are inversely coordinated by σ70/σFliA/σS competition for core RNA polymerase and the FlhDC-controlled FliZ protein acting as a σS inhibitor. At a lower level, the signaling molecule bis-(3′–5′)-cyclic-diguanosine monophosphate (c-di-GMP) reduces flagellar activity and stimulates transcription of csgD, which encodes an essential activator of adhesive curli fimbriae expression. This c-di-GMP is antagonistically controlled by σS-regulated GGDEF proteins (mainly YegE) and YhjH, an EAL protein and c-di-GMP phosphodiesterase under FlhDC/FliA control. The switch from motility-based foraging to the general stress response and curli expression requires σS-modulated down-regulation of expression of the flagellar regulatory cascade as well as proteolysis of the flagellar master regulator FlhDC. Control of YhjH by FlhDC and of YegE by σS produces a fine-tuned checkpoint system that “unlocks” curli expression only after down-regulation of flagellar gene expression. In summary, these data reveal the logic and sequence of molecular events underlying the motile-to-adhesive “lifestyle” switch in E. coli.
Modulation of Escherichia coli sister chromosome cohesion by topoisomerase IV
Authors: Wang Xindan , Reyes-Lamothe Rodrigo , Sherratt David J.
Published: September 2008

A body of evidence supports the idea that newly replicated Escherichia coli chromosomes segregate progressively as replication progresses, with spatial separation of sister genetic loci occurring ∼15 min after their replication. We show that the time of this cohesion can be modulated by topoisomerase IV (TopoIV) activity. Impairment of TopoIV prevents segregation of newly replicated sister loci and bulk chromosome segregation, whereas modest increases in TopoIV decrease the cohesion time substantially. Therefore, we propose that precatenanes, which form as replication progresses by interwinding of newly replicated sister chromosomes, are responsible for E. coli sister chromosome cohesion.
Antibody Staining of Drosophila Tissues--Helpful Hints
Authors: Rebay Ilaria , Fehon Richard G.
Published: September 2008

INTRODUCTION

The most common reason for generating antibodies against a particular protein in Drosophila is to examine its pattern of endogenous expression during development. Thus, once an antiserum is shown to stain transfected cells, the next step is to try the antiserum on Drosophila tissues, usually embryos, imaginal discs, or ovaries. This article provides suggestions for optimization of antibody staining in Drosophila tissues.
Estimation of Free Thiols and Disulfide Bonds Using Ellman’s Reagent
Authors: Simpson Richard J.
Published: September 2008

INTRODUCTION

This protocol describes a method for quantitating the amount of free thiols and disulfide bond linkages in proteins. It uses the sulfhydryl reagent 5,5′-dithiobis (2-nitrobenzoic acid), or DTNB, which is also referred to as Ellman’s reagent.
Clearing Plant Tissue for Observation of Vascular Strands
Authors: Christensen Sioux
Published: September 2008

INTRODUCTION

Vascular strands constitute an internal tissue that is important for plant growth. The strands are easily imaged by whole-mount analysis after fixation and tissue clearing, as described in this article.