bluuebunny/crossref_metadata_2025 huggingface dataset:
Subwavelength electromagnetic diode: One-way response of cascading nonlinear meta-atoms
Authors: Fan Yuancheng , Han Jin , Wei Zeyong , Wu Chao , Cao Yang , Yu Xing , Li Hongqiang
Published: April 2011

We propose a scheme for subwavelength electromagnetic diode by employing cascading nonlinear meta-atoms. One-way response is conceptually demonstrated on a microwave transmission line comprising of three metallic ring resonators acting as meta-atoms and a varactor as the nonlinear medium inclusion. Experiments show that our implementation can operate simultaneously as forward diode and backward diode at different frequencies. A transmission contrast of up to 14.7 dB was achieved between forward and backward transmission. Subwavelength size of our diode should be useful for miniaturization of integrated optical nanocircuits.
Ultracompact, broadband slot waveguide polarization splitter
Authors: Lin Shiyun , Hu Juejun , Crozier Kenneth B.
Published: April 2011

In this letter, we demonstrate an ultracompact polarization splitter design leveraging the giant birefringence of silicon-on-insulator slot waveguides. The fabricated splitter device has a coupling length of only 13.6 μm, and shows average polarization extinction ratios of 21 dB and 17 dB for the TE and TM polarizations, respectively, over the entire C-band.
Multilevel programming at a low-voltage step using junction avalanche hot carrier injections
Authors: An Ho-Myoung , Kim Hee-Dong , Kim Tae Geun
Published: April 2011

A highly efficient program method is proposed for multilevel programming with a low-voltage step in a conventional polycrystalline silicon-oxide-nitride-oxide-silicon structure. This method uses junction avalanche hot carriers for charge storage in the nitride layer. A multilevel storage is easily obtained by using a low-voltage step of 0.1 V at each level of the three programmed states along with a fast program time of 1 μs. In addition, a localized charge-injection near the junction edge is clearly observed with an acceptable read margin and threshold voltage difference between the forward and the reverse read at the three programmed states.
Mechanisms of nonlocal effect on the vibration of nanoplates
Authors: Wang C. Y. , Murmu T. , Adhikari S.
Published: April 2011

This letter presents a study of the mechanisms of nonlocal effect on the transverse vibration of two-dimensional (2D) nanoplates, e.g., monolayer layer graphene and boron-nitride sheets. It is found that such a nonlocal effect stems from a distributed transverse force due to (1) the curvature change in the nanoplates and (2) the surface stress due to the nonlocal atom-atom interaction. A single equivalent vibration wavelength is defined to measure the nonlocal effect on the vibration of 2D nanoplates. The critical equivalent wavelength of order 0.55 to 2.23 nm is obtained for significant nonlocal effect on monolayer graphene.
Transport and strain relaxation in wurtzite InAs–GaAs core-shell heterowires
Authors: Kavanagh Karen L. , Salfi Joe , Savelyev Igor , Blumin Marina , Ruda Harry E.
Published: April 2011

Indium-arsenide–gallium-arsenide (InAs–GaAs) core-shell, wurtzite nanowires have been grown on GaAs (001) substrates. The core-shell geometries (core radii 11 to 26 nm, shell thickness >2.5 nm) exceeded equilibrium critical values for strain relaxation via dislocations, apparent from transmission electron microscopy. Partial axial relaxation is detected in all nanowires increasing exponentially with size, while radial strain relaxation is >90%, but undetected in nanowires with both smaller core radii <16 nm and shell thicknesses <5 nm. Electrical measurements on individual core-shell nanowires show that the resulting dislocations are correlated with reduced electron field-effect mobility compared to bare InAs nanowires.
Defect-reduced green GaInN/GaN light-emitting diode on nanopatterned sapphire
Authors: Li Yufeng , You Shi , Zhu Mingwei , Zhao Liang , Hou Wenting , Detchprohm T. , Taniguchi Y. , Tamura N. , Tanaka S. , Wetzel C.
Published: April 2011

Green GaInN/GaN quantum well light-emitting diode (LED) wafers were grown on nanopatterned c-plane sapphire substrate by metal-organic vapor phase epitaxy. Without roughening the chip surface, such LEDs show triple the light output over structures on planar sapphire. By quantitative analysis the enhancement was attributed to both, enhanced generation efficiency and extraction. The spectral interference and emission patterns reveal a 58% enhanced light extraction while photoluminescence reveals a doubling of the internal quantum efficiency. The latter was attributed to a 44% lower threading dislocation density as observed in transmission electron microscopy. The partial light output power measured from the sapphire side of the unencapsulated nanopatterned substrate LED die reaches 5.2 mW at 525 nm at 100 mA compared to 1.8 mW in the reference LED.
Simultaneous measurement of orthogonal components of polarization in a free-space propagating terahertz signal using electro-optic detection
Authors: Byrne M. B. , Shaukat M. U. , Cunningham J. E. , Linfield E. H. , Davies A. G.
Published: April 2011

We report a polarization-sensitive terahertz time-domain spectroscopy system, which allows the simultaneous measurement of orthogonal components of the polarization of a free-space propagating terahertz beam using a dual electro-optic detection scheme. We demonstrate the operation of our system by measuring the birefringence of lithium niobate, simultaneously obtaining terahertz spectra from two orthogonal crystallographic directions.
Roles of nanolayer and particle size on thermophysical characteristics of ethylene glycol-based copper nanofluids
Authors: Lin Yung-Sheng , Hsiao Pai-Yi , Chieng Ching-Chang
Published: April 2011

Calculation of thermal conductivity and the characterization of the molecular-level mechanisms of ethylene-glycol-based copper nanofluid are conducted using the molecular dynamics (MD) Simulation when the nanoparticle size ranges from 6 to 14 Å. Layer–Maxwell model is developed for the calculation of effective thermal conductivity of the nanofluid with nanoparticle size up to 2000 Å by the application of distinct thermal conductivity in the nanolayers around nanoparticle obtained from MD simulations. The comparison between computational and experimental results reveals the roles of interfacial layer and nanoparticle size in the thermal conductivity enhancement.
Neodymium zirconate (Nd2Zr2O7) transparent ceramics as a solid state laser material
Authors: Feng Tao , Clarke David R. , Jiang Danyu , Xia Jinfeng , Shi Jianlin
Published: April 2011

Transparent neodymium zirconate (Nd2Zr2O7) ceramics have been fabricated from nanoparticles prepared by combustion synthesis. Emission at 1054.5 nm has been demonstrated using a laser diode pump at 800 nm. A transmittance of 60% at wavelengths longer than ∼900 nm was achieved. A consequence of the very high concentration of Nd ions (1.32×1028 ions/m3) is that the absorption bands are wider than those of Nd doped Y3Al5O12 (Nd:YAG) facilitating pumping over a broader range of wavelengths. The full width at half maximum of the emission peak is also larger than that of Nd:YAG, and the decay time is 460 μs making Nd2Zr2O7 an excellent candidate for efficient high-power microchip lasers emitting at 1054 nm with diode pumping at ∼800 or ∼900 nm.
The stability of a homogeneous suspension of chemotactic bacteria
Authors: Subramanian G. , Koch Donald L. , Fitzgibbon Sean R.
Published: April 2011

The linear stability of a homogeneous dilute suspension of chemotactic bacteria in a constant chemoattractant gradient is analyzed. The bacteria execute a run-and-tumble motion, typified by the species E. coli, wherein periods of smooth swimming (runs) are interrupted by abrupt uncorrelated changes in swimming direction (tumbles). Bacteria tumble less frequently when swimming toward regions of higher chemoattractant concentration, leading to a mean bacterial orientation and velocity in the base state. The stability of an unbounded suspension, both with and without a chemoattractant, is controlled by coupled long wavelength perturbations of the fluid velocity and bacterial orientation fields. In the former case, the most unstable perturbations have their wave vector oriented along the chemoattractant gradient. Chemotaxis reduces the critical bacteria concentration, for the onset of collective swimming, compared with that predicted by Subramanian and Koch [“Critical bacterial concentration for the onset of collective swimming,” J. Fluid Mech. 632, 359 (2009)] in the absence of a chemoattractant. A part of this decrease may be attributed to the increase in the mean tumbling time in the presence of a chemoattractant gradient. A second destabilizing influence comes from the ability of the shearing motion, associated with a velocity perturbation in which the velocity and chemical gradients are aligned, to sweep prealigned bacteria into the local extensional quadrant thereby creating a stronger destabilizing active stress than in an initially isotropic suspension. The chemoattractant gradient also fundamentally alters the unstable spectrum for any finite wavenumber. In suspensions of bacteria that do not tumble, Saintillan and Shelley [“Instabilities and pattern formation in active particle suspensions: Kinetic theory and continuum simulations,” Phys. Rev. Lett. 100, 178103 (2008); “Instabilities, pattern formation and mixing in active suspensions,” Phys. Fluids 20, 123304 (2008)] showed that the growth rate has two real solutions (stationary modes) below a critical wavenumber at which the two solutions merge and then bifurcate to form a pair of complex conjugate solutions (propagating modes) for larger wavenumbers. The discrete spectrum terminates at a second critical wavenumber, and beyond this wavenumber, the only remaining solutions are neutrally stable waves comprising the continuous spectrum. In the presence of a chemoattractant gradient, however, the aforementioned perfect bifurcation is broken and a pair of traveling wave solutions is found for all wavenumbers. Furthermore, instead of terminating at a critical wavenumber, the solutions for the growth rate asymptote to the negative of the tumbling frequency at large wavenumbers.
Note: A portable, light-emitting diode-based ruby fluorescence spectrometer for high-pressure calibration
Authors: Feng Yejun
Published: April 2011

Ruby (Al2O3, with ∼0.5 wt. % Cr doping) is one of the most widely used manometers at the giga-Pascal scale. Traditionally, its fluorescence is excited with intense laser sources. Here, I present a simple, robust, and portable design that employs light-emitting diodes (LEDs) instead. This LED-based system is safer in comparison with laser-based ones.
A New Space for Knowledge and People? Henri Lefebvre, Representations of Space, and the Production of 22@Barcelona
Authors: Charnock Greig , Ribera-Fumaz Ramon
Published: April 2011

The Barcelona model of urban transformation has for some time now been considered a paradigmatic case of successful regeneration. Urban change is ongoing in the city, albeit in a changed global context in which cities are increasingly being seen as the principal drivers of economic growth and competitiveness in the ‘new’ or ‘knowledge’ economy. The paper draws on the writing of Henri Lefebvre and on his critique of representations of space, in particular, in order to examine the current strategic transformation of the Poblenou district of Barcelona into 22@Barcelona: An innovation district. The paper endorses Lefebvre's work as a point of departure in critically analysing contemporary strategies to engineer urban competitiveness. It argues that the functionalist and reductive representations of 22@Barcelona betray an ideological concern with the globally competitive abstract space, the reduction of differences, and the closing of the circuit of everyday life in Poblenou.
Soil erosion in the Three Gorges Reservoir area
Authors: Xu Xibao , Tan Yan , Yang Guishan , Li Hengpeng , Su Weizhong
Published: April 2011

Spatial and temporal change in soil erosion in the Three Gorges Reservoir area since the water storage of the reservoir began filling to 135 m in 2003 is poorly understood. Using a modified soil erosion model, this study quantifies and analyses change in the extent and intensity of soil erosion in the region from 2000 to 2008. MODIS-NDVI remote sensing data (with 250 m spatial resolution) are used in the modelling and analysis of the study. The total amount, area, and intensity of soil erosion in the reservoir region presented a declining trend from 2000 to 2008. Yet there was an anomaly in the trend, in which extreme soil erosion occurred in 2003 and lasted until 2005. The average volume of soil erosion per year decreased by 4.10 × 106 t and the mean area of land experiencing soil erosion reduced by 1129.6 km2 from the pre-storage period (2000–02) to post-storage period II (2006–08). Land suffering soil erosion at high, very high, and severe levels mainly comprises forest and cropland on slopes with gradients ≥15° and is largely distributed in the eastern and south-western sections of the reservoir area. Land experiencing soil erosion at slight or moderate levels mainly involves cropland and forest on slopes with gradients ≥10° in the central section of the reservoir area. The impact of the Three Gorges Project on soil erosion since 2000 has been mainly mediated through three mechanisms: near-resettlement of rural and urban people; increased frequency and severity of geological hazards induced by rising storage of the reservoir; and implementation of ecological projects in the region. Through the former two mechanisms, soil erosion in the affected communities has been exacerbated, while the ongoing ecological projects appear to offset both the extent and intensity of soil erosion in the reservoir region. Other important factors influencing soil erosion include urban reconstruction and expansion, varying intensity of precipitation, and soil degradation.
Discovery of stream-cling-goby assemblages (Stiphodon species) in the Australian Wet Tropics
Authors: Ebner Brendan C. , Thuesen Paul
Published: April 2011

Amphidromous stream-cling-gobies of the genus Stiphodon comprise an important component of the fish communities in insular streams of tropical Indo-Pacific high islands. We aimed to develop an effective and rapid method of surveying Stiphodon atratus in a continental stream and then apply the method in an untested stream. Triple-pass snorkelling of a single pool revealed the reliability of single-pass estimates of the abundance of S. atratus. Single-pass survey of a reach in each of two streams then confirmed the presence of S. atratus, Stiphodon semoni and Stiphodon rutilaureus, in Australia. However, Stiphodon were in low abundance (S. atratus, Cooper Creek, n = 38, Pauls Pocket Creek, n = 45; S. semoni, Cooper Creek, n = 4, Pauls Pocket Creek, n = 14; S. rutilaureus, Cooper Creek, n = 0, Pauls Pocket Creek, n = 38). Preliminary indications are that particular streams provide critical habitat for newly discovered assemblages of Stiphodon within the Australian Wet Tropics. Small population sizes, coupled with the attractiveness of Stiphodon as aquarium pets, warrants that national protective status is provided to this genus until a comprehensive understanding of species distribution, abundance and population genetic structure is achieved.
Serum factors in older individuals change cellular clock properties
Authors: Pagani Lucia , Schmitt Karen , Meier Fides , Izakovic Jan , Roemer Konstanze , Viola Antoine , Cajochen Christian , Wirz-Justice Anna , Brown Steven A. , Eckert Anne
Published: April 2011

Human aging is accompanied by dramatic changes in daily sleep–wake behavior: Activity shifts to an earlier phase, and the consolidation of sleep and wake is disturbed. Although this daily circadian rhythm is brain-controlled, its mechanism is encoded by cell-autonomous circadian clocks functioning in nearly every cell of the body. In fact, human clock properties measured in peripheral cells such as fibroblasts closely mimic those measured physiologically and behaviorally in the same subjects. To understand better the molecular mechanisms by which human aging affects circadian clocks, we characterized the clock properties of fibroblasts cultivated from dermal biopsies of young and older subjects. Fibroblast period length, amplitude, and phase were identical in the two groups even though behavior was not, thereby suggesting that basic clock properties of peripheral cells do not change during aging. Interestingly, measurement of the same cells in the presence of human serum from older donors shortened period length and advanced the phase of cellular circadian rhythms compared with treatment with serum from young subjects, indicating that a circulating factor might alter human chronotype. Further experiments demonstrated that this effect is caused by a thermolabile factor present in serum of older individuals. Thus, even though the molecular machinery of peripheral circadian clocks does not change with age, some age-related circadian dysfunction observed in vivo might be of hormonal origin and therefore might be pharmacologically remediable.
Cargo binding activates myosin VIIA motor function in cells
Authors: Sakai Tsuyoshi , Umeki Nobuhisa , Ikebe Reiko , Ikebe Mitsuo
Published: April 2011

Myosin VIIA, thought to be involved in human auditory function, is a gene responsible for human Usher syndrome type 1B, which causes hearing and visual loss. Recent studies have suggested that it can move processively if it forms a dimer. Nevertheless, it exists as a monomer in vitro, unlike the well-known two-headed processive myosin Va. Here we studied the molecular mechanism, which is currently unknown, of activating myosin VIIA as a cargo-transporting motor. Human myosin VIIA was present throughout cytosol, but it moved to the tip of filopodia upon the formation of dimer induced by dimer-inducing reagent. The forced dimer of myosin VIIA translocated its cargo molecule, MyRip, to the tip of filopodia, whereas myosin VIIA without the forced dimer-forming module does not translocate to the filopodial tips. These results suggest that dimer formation of myosin VIIA is important for its cargo-transporting activity. On the other hand, myosin VIIA without the forced dimerization module became translocated to the filopodial tips in the presence of cargo complex, i.e., MyRip/Rab27a, and transported its cargo complex to the tip. Coexpression of MyRip promoted the association of myosin VIIA to vesicles and the dimer formation. These results suggest that association of myosin VIIA monomers with membrane via the MyRip/Rab27a complex facilitates the cargo-transporting activity of myosin VIIA, which is achieved by cluster formation on the membrane, where it possibly forms a dimer. Present findings support that MyRip, a cargo molecule, functions as an activator of myosin VIIA transporter function.
Using the base-of-the-pyramid perspective to catalyze interdependence-based collaborations
Authors: London Ted , Anupindi Ravi
Published: April 2011

Improving food security and nutrition in the developing world remains among society's most intractable challenges and continues despite a wide variety of investments. Both donor- and enterprise-led initiatives, for example, have explored including smallholder farmers in their value chains. However, these efforts have had only modest success, partly because the private and development sectors prefer to maintain their independence. Research from the base-of-the-pyramid domain offers new insights into how collaborative interdependence between sectors can enhance the connection between profits and the alleviation of poverty. In this article, we identify the strengths and weaknesses of donor-led and enterprise-led value chain initiatives. We then explore how insights from the base-of-the-pyramid domain yield a set of interdependence-based collaboration strategies that can achieve more sustainable and scalable outcomes.
l
-Fucose utilization provides
Campylobacter jejuni
with a competitive advantage
Authors: Stahl Martin , Friis Lorna M. , Nothaft Harald , Liu Xin , Li Jianjun , Szymanski Christine M. , Stintzi Alain
Published: April 2011

Campylobacter jejuni
is a prevalent gastrointestinal pathogen in humans and a common commensal of poultry. When colonizing its hosts,
C. jejuni
comes into contact with intestinal carbohydrates, including
l
-fucose, released from mucin glycoproteins. Several strains of
C. jejuni
possess a genomic island (
cj0480c–cj0490
) that is up-regulated in the presence of both
l
-fucose and mucin and allows for the utilization of
l
-fucose as a substrate for growth. Strains possessing this genomic island show increased growth in the presence of
l
-fucose and mutation of
cj0481
,
cj0486
,
and cj0487
results in the loss of the ability to grow on this substrate. Furthermore, mutants in the putative fucose permease (
cj0486
) are deficient in fucose uptake and demonstrate a competitive disadvantage when colonizing the piglet model of human disease, which is not paralleled in the colonization of poultry. This identifies a previously unrecorded metabolic pathway in select strains of
C. jejuni
associated with a virulent lifestyle.
Route to three-dimensional fragments using diversity-oriented synthesis
Authors: Hung Alvin W. , Ramek Alex , Wang Yikai , Kaya Taner , Wilson J. Anthony , Clemons Paul A. , Young Damian W.
Published: April 2011

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of
sp
2
-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various “difficult” targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly
sp
3
-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules.
Deficit in switching between functional brain networks underlies the impact of multitasking on working memory in older adults
Authors: Clapp Wesley C. , Rubens Michael T. , Sabharwal Jasdeep , Gazzaley Adam
Published: April 2011

Multitasking negatively influences the retention of information over brief periods of time. This impact of interference on working memory is exacerbated with normal aging. We used functional MRI to investigate the neural basis by which an interruption is more disruptive to working memory performance in older individuals. Younger and older adults engaged in delayed recognition tasks both with and without interruption by a secondary task. Behavioral analysis revealed that working memory performance was more impaired by interruptions in older compared with younger adults. Functional connectivity analyses showed that when interrupted, older adults disengaged from a memory maintenance network and reallocated attentional resources toward the interrupting stimulus in a manner consistent with younger adults. However, unlike younger individuals, older adults failed to both disengage from the interruption and reestablish functional connections associated with the disrupted memory network. These results suggest that multitasking leads to more significant working memory disruption in older adults because of an interruption recovery failure, manifest as a deficient ability to dynamically switch between functional brain networks.
HDL promotes rapid atherosclerosis regression in mice and alters inflammatory properties of plaque monocyte-derived cells
Authors: Feig Jonathan E. , Rong James X. , Shamir Raanan , Sanson Marie , Vengrenyuk Yuliya , Liu Jianhua , Rayner Katey , Moore Kathryn , Garabedian Michael , Fisher Edward A.
Published: April 2011

HDL cholesterol (HDL-C) plasma levels are inversely related to cardiovascular disease risk. Previous studies have shown in animals and humans that HDL promotes regression of atherosclerosis. We hypothesized that this was related to an ability to promote the loss of monocyte-derived cells (CD68+, primarily macrophages and macrophage foam cells) from plaques. To test this hypothesis, we used an established model of atherosclerosis regression in which plaque-bearing aortic arches from apolipoprotein E-deficient (apoE−/−) mice (low HDL-C, high non–HDL-C) were transplanted into recipient mice with differing levels of HDL-C and non–HDL-C: C57BL6 mice (normal HDL-C, low non–HDL-C), apoAI−/−mice (low HDL-C, low non–HDL-C), or apoE−/−mice transgenic for human apoAI (hAI/apoE−/−; normal HDL-C, high non–HDL-C). Remarkably, despite persistent elevated non–HDL-C in hAI/apoE−/−recipients, plaque CD68+cell content decreased by >50% by 1 wk after transplantation, whereas there was little change in apoAI−/−recipient mice despite hypolipidemia. The decreased content of plaque CD68+cells after HDL-C normalization was associated with their emigration and induction of their chemokine receptor CCR7. Furthermore, in CD68+cells laser-captured from the plaques, normalization of HDL-C led to decreased expression of inflammatory factors and enrichment of markers of the M2 (tissue repair) macrophage state. Again, none of these beneficial changes were observed in the apoAI−/−recipients, suggesting a major requirement for reverse cholesterol transport for the beneficial effects of HDL. Overall, these results establish HDL as a regulator in vivo of the migratory and inflammatory properties of monocyte-derived cells in mouse atherosclerotic plaques, and highlight the phenotypic plasticity of these cells.
Variability in krill biomass links harvesting and climate warming to penguin population changes in Antarctica
Authors: Trivelpiece Wayne Z. , Hinke Jefferson T. , Miller Aileen K. , Reiss Christian S. , Trivelpiece Susan G. , Watters George M.
Published: April 2011

The West Antarctic Peninsula (WAP) and adjacent Scotia Sea support abundant wildlife populations, many of which were nearly extirpated by humans. This region is also among the fastest-warming areas on the planet, with 5–6 °C increases in mean winter air temperatures and associated decreases in winter sea-ice cover. These biological and physical perturbations have affected the ecosystem profoundly. One hypothesis guiding ecological interpretations of changes in top predator populations in this region, the “sea-ice hypothesis,” proposes that reductions in winter sea ice have led directly to declines in “ice-loving” species by decreasing their winter habitat, while populations of “ice-avoiding” species have increased. However, 30 y of field studies and recent surveys of penguins throughout the WAP and Scotia Sea demonstrate this mechanism is not controlling penguin populations; populations of both ice-loving Adélie and ice-avoiding chinstrap penguins have declined significantly. We argue in favor of an alternative, more robust hypothesis that attributes both increases and decreases in penguin populations to changes in the abundance of their main prey, Antarctic krill. Unlike many other predators in this region, Adélie and chinstrap penguins were never directly harvested by man; thus, their population trajectories track the impacts of biological and environmental changes in this ecosystem. Linking trends in penguin abundance with trends in krill biomass explains why populations of Adélie and chinstrap penguins increased after competitors (fur seals, baleen whales, and some fishes) were nearly extirpated in the 19th to mid-20th centuries and currently are decreasing in response to climate change.
Essential role for Abi1 in embryonic survival and WAVE2 complex integrity
Authors: Dubielecka Patrycja M. , Ladwein Kathrin I. , Xiong Xiaoling , Migeotte Isabelle , Chorzalska Anna , Anderson Kathryn V. , Sawicki Janet A. , Rottner Klemens , Stradal Theresia E. , Kotula Leszek
Published: April 2011

Abl interactor 1 (Abi1) plays a critical function in actin cytoskeleton dynamics through participation in the WAVE2 complex. To gain a better understanding of the specific role of Abi1, we generated a conditional Abi1-KO mouse model and MEFs lacking Abi1 expression. Abi1-KO cells displayed defective regulation of the actin cytoskeleton, and this dysregulation was ascribed to altered activity of the WAVE2 complex. Changes in motility of Abi1-KO cells were manifested by a decreased migration rate and distance but increased directional persistence. Although these phenotypes did not correlate with peripheral ruffling, which was unaffected, Abi1-KO cells exhibited decreased dorsal ruffling. Western blotting analysis of Abi1-KO cell lysates indicated reduced levels of the WAVE complex components WAVE1 and WAVE2, Nap1, and Sra-1/PIR121. Although relative Abi2 levels were more than doubled in Abi1-KO cells, the absolute Abi2 expression in these cells amounted only to a fifth of Abi1 levels in the control cell line. This finding suggests that the presence of Abi1 is critical for the integrity and stability of WAVE complex and that Abi2 levels are not sufficiently increased to compensate fully for the loss of Abi1 in KO cells and to restore the integrity and function of the WAVE complex. The essential function of Abi1 in WAVE complexes and their regulation might explain the observed embryonic lethality of Abi1-deficient embryos, which survived until approximately embryonic day 11.5 and displayed malformations in the developing heart and brain. Cells lacking Abi1 and the conditional Abi1-KO mouse will serve as critical models for defining Abi1 function.
Atomistic simulation of ion solvation in water explains surface preference of halides
Authors: Caleman Carl , Hub Jochen S. , van Maaren Paul J. , van der Spoel David
Published: April 2011

Water is a demanding partner. It strongly attracts ions, yet some halide anions—chloride, bromide, and iodide—are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl
-
, Br
-
, and I
-
have shallow minima near the surface. We demonstrate that these minima derive from more favorable water–water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion–water energy, whereas F
-
is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.
Extraneous factors in judicial decisions
Authors: Danziger Shai , Levav Jonathan , Avnaim-Pesso Liora
Published: April 2011

Are judicial rulings based solely on laws and facts? Legal formalism holds that judges apply legal reasons to the facts of a case in a rational, mechanical, and deliberative manner. In contrast, legal realists argue that the rational application of legal reasons does not sufficiently explain the decisions of judges and that psychological, political, and social factors influence judicial rulings. We test the common caricature of realism that justice is “what the judge ate for breakfast” in sequential parole decisions made by experienced judges. We record the judges’ two daily food breaks, which result in segmenting the deliberations of the day into three distinct “decision sessions.” We find that the percentage of favorable rulings drops gradually from ≈65% to nearly zero within each decision session and returns abruptly to ≈65% after a break. Our findings suggest that judicial rulings can be swayed by extraneous variables that should have no bearing on legal decisions.
Analytical results on Casimir forces for conductors with edges and tips
Authors: Maghrebi Mohammad F. , Rahi Sahand Jamal , Emig Thorsten , Graham Noah , Jaffe Robert L. , Kardar Mehran
Published: April 2011

Casimir forces between conductors at the submicron scale are paramount to the design and operation of microelectromechanical devices. However, these forces depend nontrivially on geometry, and existing analytical formulae and approximations cannot deal with realistic micromachinery components with sharp edges and tips. Here, we employ a novel approach to electromagnetic scattering, appropriate to perfect conductors with sharp edges and tips, specifically wedges and cones. The Casimir interaction of these objects with a metal plate (and among themselves) is then computed systematically by a multiple-scattering series. For the wedge, we obtain analytical expressions for the interaction with a plate, as functions of opening angle and tilt, which should provide a particularly useful tool for the design of microelectromechanical devices. Our result for the Casimir interactions between conducting cones and plates applies directly to the force on the tip of a scanning tunneling probe. We find an unexpectedly large temperature dependence of the force in the cone tip which is of immediate relevance to experiments.
Orthograde dihydropyridine receptor signal regulates ryanodine receptor passive leak
Authors: Eltit José Miguel , Li Hongli , Ward Christopher W. , Molinski Tadeusz , Pessah Isaac N. , Allen Paul D. , Lopez José R.
Published: April 2011

The skeletal muscle dihydropyridine receptor (DHPR) and ryanodine receptor (RyR1) are known to engage a form of conformation coupling essential for muscle contraction in response to depolarization, referred to as excitation–contraction coupling. Here we use WT and Ca
V
1.1 null (dysgenic) myotubes to provide evidence for an unexplored RyR1–DHPR interaction that regulates the transition of the RyR1 between gating and leak states. Using double-barreled Ca
2+
-selective microelectrodes, we demonstrate that the lack of Ca
V
1.1 expression was associated with an increased myoplasmic resting [Ca
2+
] ([Ca
2+
]
rest
), increased resting sarcolemmal Ca
2+
entry, and decreased sarcoplasmic reticulum (SR) Ca
2+
loading. Pharmacological control of the RyR1 leak state, using bastadin 5, reverted the three parameters to WT levels. The fact that Ca
2+
sparks are not more frequent in dysgenic than in WT myotubes adds support to the hypothesis that the leak state is a conformation distinct from gating RyR1s. We conclude from these data that this orthograde DHPR-to-RyR1 signal inhibits the transition of gated RyR1s into the leak state. Further, it suggests that the DHPR-uncoupled RyR1 population in WT muscle has a higher propensity to be in the leak conformation. RyR1 leak functions are to keep [Ca
2+
]
rest
and the SR Ca
2+
content in the physiological range and thus maintain normal intracellular Ca
2+
homeostasis.
Mice lacking phosphatase PP2A subunit PR61/B’δ (
Ppp2r5d
) develop spatially restricted tauopathy by deregulation of CDK5 and GSK3β
Authors: Louis Justin V. , Martens Ellen , Borghgraef Peter , Lambrecht Caroline , Sents Ward , Longin Sari , Zwaenepoel Karen , Pijnenborg Robert , Landrieu Isabelle , Lippens Guy , Ledermann Birgit , Götz Jürgen , Van Leuven Fred , Goris Jozef , Janssens Veerle
Published: April 2011

Functional diversity of protein phosphatase 2A (PP2A) enzymes mainly results from their association with distinct regulatory subunits. To analyze the functions of one such holoenzyme in vivo, we generated mice lacking PR61/B’δ (B56δ), a subunit highly expressed in neural tissues. In PR61/B’δ-null mice the microtubule-associated protein tau becomes progressively phosphorylated at pathological epitopes in restricted brain areas, with marked immunoreactivity for the misfolded MC1-conformation but without neurofibrillary tangle formation. Behavioral tests indicated impaired sensorimotor but normal cognitive functions. These phenotypical characteristics were further underscored in PR61/B’δ-null mice mildly overexpressing human tau. PR61/B’δ-containing PP2A (PP2A

T
61
δ

) poorly dephosphorylates tau in vitro, arguing against a direct dephosphorylation defect. Rather, the activity of glycogen synthase kinase-3β, a major tau kinase, was found increased, with decreased phosphorylation of Ser-9, a putative cyclin-dependent kinase 5 (CDK5) target. Accordingly, CDK5 activity is decreased, and its cellular activator p35, strikingly absent in the affected brain areas. As opposed to tau, p35 is an excellent PP2A

T
61
δ

substrate. Our data imply a nonredundant function for PR61/B’δ in phospho-tau homeostasis via an unexpected spatially restricted mechanism preventing p35 hyperphosphorylation and its subsequent degradation.
A sequential mechanism for clathrin cage disassembly by 70-kDa heat-shock cognate protein (Hsc70) and auxilin
Authors: Rothnie Alice , Clarke Anthony R. , Kuzmic Petr , Cameron Angus , Smith Corinne J.
Published: April 2011

An essential stage in endocytic coated vesicle recycling is the dissociation of clathrin from the vesicle coat by the molecular chaperone, 70-kDa heat-shock cognate protein (Hsc70), and the J-domain-containing protein, auxilin, in an ATP-dependent process. We present a detailed mechanistic analysis of clathrin disassembly catalyzed by Hsc70 and auxilin, using loss of perpendicular light scattering to monitor the process. We report that a single auxilin per clathrin triskelion is required for maximal rate of disassembly, that ATP is hydrolyzed at the same rate that disassembly occurs, and that three ATP molecules are hydrolyzed per clathrin triskelion released. Stopped-flow measurements revealed a lag phase in which the scattering intensity increased owing to association of Hsc70 with clathrin cages followed by serial rounds of ATP hydrolysis prior to triskelion removal. Global fit of stopped-flow data to several physically plausible mechanisms showed the best fit to a model in which sequential hydrolysis of three separate ATP molecules is required for the eventual release of a triskelion from the clathrin–auxilin cage.
Crystal structure of a covalent intermediate in DNA cleavage and rejoining by
Escherichia coli
DNA topoisomerase I
Authors: Zhang Zhongtao , Cheng Bokun , Tse-Dinh Yuk-Ching
Published: April 2011

DNA topoisomerases control DNA topology by breaking and rejoining DNA strands via covalent complexes with cleaved DNA substrate as catalytic intermediates. Here we report the structure of
Escherichia coli
topoisomerase I catalytic domain (residues 2–695) in covalent complex with a cleaved single-stranded oligonucleotide substrate, refined to 2.3-Å resolution. The enzyme-substrate intermediate formed after strand cleavage was captured due to the presence of the D111N mutation. This structure of the covalent topoisomerase-DNA intermediate, previously elusive for type IA topoisomerases, shows distinct conformational changes from the structure of the enzyme without bound DNA and provides detailed understanding of the covalent catalysis required for strand cleavage to take place. The portion of cleaved DNA 5′ to the site of cleavage is anchored tightly with extensive noncovalent protein–DNA interactions as predicted by the “enzyme-bridged” model. Distortion of the scissile strand at the -4 position 5′ to the cleavage site allows specific selectivity of a cytosine base in the binding pocket. Many antibacterial and anticancer drugs initiate cell killing by trapping the covalent complexes formed by topoisomerases. We have demonstrated in previous mutagenesis studies that accumulation of the covalent complex of bacterial topoisomerase I is bactericidal. This structure of the covalent intermediate provides the basis for the design of novel antibiotics that can trap the enzyme after formation of the covalent complex.
Anchored clathrate waters bind antifreeze proteins to ice
Authors: Garnham Christopher P. , Campbell Robert L. , Davies Peter L.
Published: April 2011

The mechanism by which antifreeze proteins (AFPs) irreversibly bind to ice has not yet been resolved. The ice-binding site of an AFP is relatively hydrophobic, but also contains many potential hydrogen bond donors/acceptors. The extent to which hydrogen bonding and the hydrophobic effect contribute to ice binding has been debated for over 30 years. Here we have elucidated the ice-binding mechanism through solving the first crystal structure of an Antarctic bacterial AFP. This 34-kDa domain, the largest AFP structure determined to date, folds as a Ca
2+
-bound parallel beta-helix with an extensive array of ice-like surface waters that are anchored via hydrogen bonds directly to the polypeptide backbone and adjacent side chains. These bound waters make an excellent three-dimensional match to both the primary prism and basal planes of ice and in effect provide an extensive X-ray crystallographic picture of the AFP∶ice interaction. This unobstructed view, free from crystal-packing artefacts, shows the contributions of both the hydrophobic effect and hydrogen bonding during AFP adsorption to ice. We term this mode of binding the “anchored clathrate” mechanism of AFP action.
Motor-driven intracellular transport powers bacterial gliding motility
Authors: Sun Mingzhai , Wartel Morgane , Cascales Eric , Shaevitz Joshua W. , Mignot Tâm
Published: April 2011

Protein-directed intracellular transport has not been observed in bacteria despite the existence of dynamic protein localization and a complex cytoskeleton. However, protein trafficking has clear potential uses for important cellular processes such as growth, development, chromosome segregation, and motility. Conflicting models have been proposed to explain
Myxococcus xanthus
motility on solid surfaces, some favoring secretion engines at the rear of cells and others evoking an unknown class of molecular motors distributed along the cell body. Through a combination of fluorescence imaging, force microscopy, and genetic manipulation, we show that membrane-bound cytoplasmic complexes consisting of motor and regulatory proteins are directionally transported down the axis of a cell at constant velocity. This intracellular motion is transmitted to the exterior of the cell and converted to traction forces on the substrate. Thus, this study demonstrates the existence of a conserved class of processive intracellular motors in bacteria and shows how these motors have been adapted to produce cell motility.
Generation of targeted
Chlamydia trachomatis
null mutants
Authors: Kari Laszlo , Goheen Morgan M. , Randall Linnell B. , Taylor Lacey D. , Carlson John H. , Whitmire William M. , Virok Dezso , Rajaram Krithika , Endresz Valeria , McClarty Grant , Nelson David E. , Caldwell Harlan D.
Published: April 2011

Chlamydia trachomatis
is an obligate intracellular bacterial pathogen that infects hundreds of millions of individuals globally, causing blinding trachoma and sexually transmitted disease. More effective chlamydial control measures are needed, but progress toward this end has been severely hampered by the lack of a tenable chlamydial genetic system. Here, we describe a reverse-genetic approach to create isogenic
C. trachomatis
mutants.
C. trachomatis
was subjected to low-level ethyl methanesulfonate mutagenesis to generate chlamydiae that contained less then one mutation per genome. Mutagenized organisms were expanded in small subpopulations that were screened for mutations by digesting denatured and reannealed PCR amplicons of the target gene with the mismatch specific endonuclease CEL I. Subpopulations with mutations were then sequenced for the target region and plaque-cloned if the desired mutation was detected. We demonstrate the utility of this approach by isolating a tryptophan synthase gene (
trpB
) null mutant that was otherwise isogenic to its parental clone as shown by de novo genome sequencing. The mutant was incapable of avoiding the anti-microbial effect of IFN-γ–induced tryptophan starvation. The ability to genetically manipulate chlamydiae is a major advancement that will enhance our understanding of chlamydial pathogenesis and accelerate the development of new anti-chlamydial therapeutic control measures. Additionally, this strategy could be applied to other medically important bacterial pathogens with no or difficult genetic systems.
Attracting the attention of a fly
Authors: Sareen Preeti , Wolf Reinhard , Heisenberg Martin
Published: April 2011

Organisms with complex visual systems rarely respond to just the sum of all visual stimuli impinging on their eyes. Often, they restrict their responses to stimuli in a temporarily selected region of the visual field (selective visual attention). Here, we investigate visual attention in the fly
Drosophila
during tethered flight at a torque meter. Flies can actively shift their attention; however, their attention can be guided to a certain location by external cues. Using visual cues, we can direct the attention of the fly to one or the other of the two visual half-fields. The cue can precede the test stimulus by several seconds and may also be spatially separated from the test by at least 20° and yet attract attention. This kind of external guidance of attention is found only in the lower visual field.
CO
2
-limitation-inducible Green Recovery of fatty acids from cyanobacterial biomass
Authors: Liu Xinyao , Fallon Sarah , Sheng Jie , Curtiss Roy
Published: April 2011

Using genetically modified cyanobacterial strains, we engineered a Green Recovery strategy to convert membrane lipids into fatty acids for economical and environmentally sustainable biofuel production. The Green Recovery strategy utilizes lipolytic enzymes under the control of promoters induced by CO
2
limitation. Data indicate that strains of the cyanobacterium
Synechocystis
sp. PCC6803 engineered for Green Recovery underwent degradation of membrane diacylglycerols upon CO
2
limitation, leading to release of fatty acids into the culture medium. Recovered fatty acid yields of 36.1 × 10
-12
 mg/cell were measured in one of the engineered strains (SD239). Green Recovery can be incorporated into previously constructed fatty-acid-secretion strains, enabling fatty acid recovery from the remaining cyanobacterial biomass that will be generated during fatty acid biofuel production in photobioreactors.
The association of classroom interactions, year group and social class
Authors: Harris Diane , Williams Julian
Published: April 2011

We investigate differences in the teacher‐learner interactions in Reception, Year 2 and Year 4 science and literacy classrooms through three measures: (i) the proportion of open questions asked by the teacher, (ii) the rate of successful responses, and (iii) wait‐times. A regression analysis of data from 20 schools and 102 lessons suggests that classrooms in socio‐economically disadvantaged areas offer distinctive patterns of interaction, i.e., typically associated with those approximately two years younger in the more affluent school districts. We then closely examine the quality of two contrasting dialogues from reception science classes of schools in poor and affluent areas. We see how teachers’ questions can work or fail to work to achieve the expected quality in scientific dialogue, and thus how effective use of open questioning might be indicative of quality. In conclusion, we discuss quality of talk as an explanation of class differences in learning outcomes of schooling.
Repair defects put stem cells in a fix
Authors: Short Ben
Published: April 2011

Study reveals that mutations in DNA-dependent protein kinase block multiple DNA repair pathways.