bluuebunny/crossref_metadata_2025 huggingface dataset:
Auroral signatures of the plasma injection and dipolarization in the inner magnetosphere
Authors: Sergeev V. A. , Kornilova T. A. , Kornilov I. A. , Angelopoulos V. , Kubyshkina M. V. , Fillingim M. , Nakamura R. , McFadden J. P. , Larson D.
Published: February 2010

Using auroral TV data and particle precipitation data from low‐altitude satellites, we identify the ionospheric signature of magnetotail dipolarizations and substorm injections measured in the near‐Earth near‐equatorial plasma sheet by Time History of Events and Macroscale Interactions during Substorms (THEMIS). Field line mapping exploits a recently developed time‐dependent adaptive model which minimizes the variance to THEMIS in situ magnetotail observations. We present strong evidence that the equatorward edge of the auroral bulge corresponds to the innermost extent of earthward propagating dipolarization fronts in the magnetosphere, whereas individual equatorward moving auroral enhancements correspond to the motion of individual injection fronts reaching at times distances as close to Earth as 5.5 RE. The region of tail dipolarization corresponds to the auroral bulge, a broad spatial region of enhanced but structured auroral emissions, bounded on the poleward side by discrete auroral forms and on the equatorward side by a sharp drop in auroral luminosity and particle precipitation. Particle precipitation within the bulge is enhanced considerably at the energies above 30 keV. Ionospheric protons are isotropic and electrons are anisotropic but with fluctuating fluxes which are below, but on occasion comparable with, trapped levels. The equatorward edge of the bulge, herein termed the “Equatorward edge of Auroral Bulge” propagates during substorm expansion toward lower latitudes, initially fast (corresponding to 100 km/s in space at r ∼ 7 RE) but with decreasing speed after onset. Our adaptive model mapping suggests that equatorial points at near‐geosynchronous altitude can map to ionospheric magnetic latitudes up to 2°–3° off of predictions using standard T96 models. The offsets can be either toward lower latitudes due to field line stretching before auroral breakup or toward higher latitudes after breakup due to the near‐Earth tail dipolarization.
On the origin of high m magnetospheric waves
Authors: Beharrell M. , Kavanagh A. J. , Honary F.
Published: February 2010

A survey of Advanced Rio‐Imaging Experiment in Scandinavia data reveals evidence for a previously overlooked generation mechanism of high azimuthal wave number magnetospheric waves. Here we present observations of pulsating cosmic noise absorption with azimuthal wave numbers as high as 380, suggestive of precipitation modulation by magnetospheric waves. Dispersion relations of the small‐scale precipitation pulsations are indicative of the proposed origin. Previous studies of magnetospheric waves, together with data from the Charge And Mass Magnetospheric Ion Composition Experiment (Magnetospheric Ion Composition Sensor) instrument aboard the Polar spacecraft, provide support for the theory.
Harmonic generation of interfacial waves at a submerged bathymetric ridge
Authors: Hult E. L. , Troy C. D. , Koseff J. R.
Published: February 2010

When two‐layer, periodic, interfacial wave trains pass over a Gaussian ridge, waves of higher harmonic frequency can be excited at the ridge, which then propagate downstream independently of the incident wave. In laboratory experiments, the amount of energy transferred to higher harmonic frequencies increases with the nonlinearity of the main wave over the ridge crest. When the wave nonlinearity is increased to the point where breaking occurs over the ridge, harmonic generation can still occur. The length scale of the obstacle relative to the wavelength can also influence the energy transfer, which is consistent with analogous surface wave studies. The upper limit for which harmonic frequencies can be excited is set by the stratification. This wave‐topography interaction provides a possible mechanism for transferring energy in the internal wavefield to smaller scales.
A novel method for measuring the timing of bed erosion during debris flows and floods
Authors: Berger Catherine , McArdell Brian W. , Fritschi Bruno , Schlunegger Fritz
Published: February 2010

We describe a novel channel bed erosion sensor and the first results of its usage. The sensor is based on a resistance chain built into a column of 5 cm tall cylindrical aluminum elements. The timing and change in resistance as elements are removed from the column are logged outside of the channel. Five sensor columns were placed in the Illgraben torrent bed prior to the start of the 2008 flow season. Before the first debris flow event, 0.1 m of sediment was deposited by small flood events. During the 16 June 2008 debris flow, this layer was eroded, and erosion was therefore first measured 44 min after front arrival and took place progressively over the next 12 min. The results at the erosion sensors are consistent with measurements over the entire reach using traditional surveying methods, and data from the adjacent debris flow monitoring station provide a basis for interpretation. The main limitation is that this sensor records only the rate and timing of the maximum bed erosion and cannot be used to determine deposition and subsequent erosion within a given event.
Affinity maturation of a TNFα‐binding Affibody molecule by Darwinian survival selection
Authors: Löfdahl Per‐Åke , Nygren Per‐Åke
Published: February 2010

The introduction of different methodologies for the construction and screening of complex protein libraries has provided powerful means in protein engineering for the development of molecules with desired traits. A challenge faced in many situations is to adapt a given methodology for efficient and rapid identification of the most interesting variants present in a library. In the present study, the concept of Darwinian selection based on a growth advantage for clones having the desired trait has been investigated. Using a β‐lactamase‐based PCA (protein fragment complementation assay), affinity maturation of a TNFα (tumour necrosis factor α)‐binding Affibody molecule with an initial 2 nM affinity for the target has been performed. Initial characterization of the PCA system, based on the affinity‐driven reconstitution of β‐lactamase activity in the periplasm of cells harbouring a library member showing affinity for a co‐expressed target protein, showed that the system was responsive to promoter induction level, interaction affinity and applied selection pressure. Using combinatorial protein engineering principles, a 107 library of second‐generation Affibody molecules was constructed and subjected to selection of improved variants by library growth in liquid culture. The results show that, after a pre‐selection step on semi‐solid medium to eliminate non‐binding variants, present in the majority, two rounds of selection in liquid culture resulted in an enrichment for binders showing up to 8‐fold higher affinity for the TNFα target than the ancestral variant. Biosensor analyses showed that the major factor for the improved affinity could be attributed to reduced off‐rate constants.
On superconformal characters and partition functions in three dimensions
Authors: Dolan F. A.
Published: February 2010

Possible short and semishort positive energy, unitary representations of the Osp(2N|4) superconformal group in three dimensions are discussed. Corresponding character formulas are obtained, consistent with character formulas for the SO(3,2) conformal group, revealing long multiplet decomposition at unitarity bounds in a simple way. Limits, corresponding to reduction to various Osp(2N|4) subalgebras, are taken in the characters that isolate contributions from fewer states, at a given unitarity threshold, leading to considerably simpler formula. Via these limits, applied to partition functions, closed formula for the generating functions for numbers of BPS operators in the free field limit of superconformal U(n)×U(n) N=6 Chern–Simons theory and its supergravity dual are obtained in the large n limit. Partial counting of semishort operators is performed and consistency between operator counting for the free field and supergravity limits with long multiplet decomposition rules is explicitly demonstrated. Partition functions counting certain protected scalar primary semishort operators, and their superconformal descendants, are proposed and computed for large n. Certain chiral ring partition functions are discussed from a combinatorial perspective.
Ground state entanglement in one-dimensional translationally invariant quantum systems
Authors: Irani Sandy
Published: February 2010

We examine whether it is possible for one-dimensional translationally invariant Hamiltonians to have ground states with a high degree of entanglement. We present a family of translationally invariant Hamiltonians {Hn} for the infinite chain. The spectral gap of Hn is Ω(1/poly(n)). Moreover, for any state in the ground space of Hn and any m, there are regions of size m with entanglement entropy Ω(min{m,n}). A similar construction yields translationally invariant Hamiltonians for finite chains that have unique ground states exhibiting high entanglement. The area law proven by Hastings [“An area law for one dimensional quantum systems,” J. Stat. Mech.: Theory Exp. 2007 (08024)] gives a constant upper bound on the entanglement entropy for one-dimensional ground states that is independent of the size of the region but exponentially dependent on 1/Δ, where Δ is the spectral gap. This paper provides a lower bound, showing a family of Hamiltonians for which the entanglement entropy scales polynomially with 1/Δ. Previously, the best known such bound was logarithmic in 1/Δ.
Symmetric Novikov superalgebras
Authors: Ayadi Imen , Benayadi Saïd
Published: February 2010

We study Novikov superalgebras with nondegenerate associative supersymmetric bilinear forms which are called symmetric Novikov superalgebras. We show that Novikov symmetric superalgebras are associative superalgebras with additional condition. Several examples of symmetric Novikov superalgebras are included, in particular, examples of symmetric Novikov superalgebras which are not 2-nilpotent. Finally, we introduce some notions of double extensions in order to give inductive descriptions of symmetric Novikov superalgebras.
Phase transition solutions in geometrically constrained magnetic domain wall models
Authors: Chen Shouxin , Yang Yisong
Published: February 2010

Recent work on magnetic phase transition in nanoscale systems indicates that new physical phenomena, in particular, the Bloch wall width narrowing, arise as a consequence of geometrical confinement of magnetization and leads to the introduction of geometrically constrained domain wall models. In this paper, we present a systematic mathematical analysis on the existence of the solutions of the basic governing equations in such domain wall models. We show that, when the cross section of the geometric constriction is a simple step function, the solutions may be obtained by minimizing the domain wall energy over the constriction and solving the Bogomol’nyi equation outside the constriction. When the cross section and potential density are both even, we establish the existence of an odd domain wall solution realizing the phase transition process between two adjacent domain phases. When the cross section satisfies a certain integrability condition, we prove that a domain wall solution always exists which links two arbitrarily designated domain phases.
Sorption properties of NO2 gas and its strong influence on hole concentration of H-terminated diamond surfaces
Authors: Kubovic Michal , Kasu Makoto , Kageshima Hiroyuki
Published: February 2010

The hole concentration of hydrogen-terminated diamond surfaces was studied during exposure to different concentrations of NO2 gas. The hole concentration increased during adsorption of NO2 molecules on the diamond surface, and decreased when the exposure stopped and NO2 molecules desorbed from the surface. The increase in hole concentration can be directly linked to the NO2 concentration. The low NO2 concentration in air (∼20 ppb) is responsible the hole concentration normally measured in air, and with increasing NO2 concentration the maximum hole concentration increases even more. The time evolution of hole concentration was analyzed using the Elovich sorption model. Further analysis based on the Ritchie model indicated that an adsorbed NO2 molecule occupies two different surface sites. Temperature-dependent measurements indicate low activation energy between 0.1 and 0.2 eV.
Evolution of electron states at an n-type InSb surface in a depletion-layer formation process: Effect of nonparabolicity of the conduction-band dispersion
Authors: Takeshita Noboru , Inaoka Takeshi
Published: February 2010

Advancing adsorption on an n-type InSb(110) surface induces gradual formation of a carrier-depletion layer at the surface. Incorporating a highly nonparabolic (NP) dispersion of the conduction band into the local-density-functional formalism in a complete manner, we investigate evolution of electron states at the n-type InSb surface in the depletion-layer formation process. By comparing the calculated results for the NP dispersion with those for the parabolic (P) dispersion corresponding to the band-edge effective mass, we evaluate the effects of the nonparabolicity on surface electron states. The nonparabolicity is found to make significant differences in the effective one-electron potential and the carrier-density distribution at the surface. The band bending occurs in the closer vicinity of the surface and with a smaller bending magnitude in the NP dispersion than in the P dispersion. This can be explained by the fact that carrier electrons operate to screen positive charges of ionized donors in the depletion layer more effectively in the NP dispersion than in the P dispersion. Accurate treatment of the nonparabolicity is indispensable in evaluating the surface electron states at each stage of the formation process.
Dielectrophoretic integration of single- and few-layer graphenes
Authors: Burg Brian R. , Schneider Julian , Maurer Simon , Schirmer Niklas C. , Poulikakos Dimos
Published: February 2010

The dielectrophoretic integration of single- and few-layered graphenes from three distinct graphene suspensions is presented, enabling the parallel assembly of individual two-dimensional nanostructures at predefined locations. The first suspension is an aqueous solution of graphene oxide, the second is ultrasonically exfoliated pristine graphene in N-methyl-pyrrolidone (NMP), and the third is exfoliated graphene in surfactant-stabilized 1 wt % aqueous SDBS solutions. The most crucial aspect for the successful thin flake deposition is the solution quality of the exfoliated graphene. After dielectrophoresis, single-layer graphene oxide is placed between the electrodes, which, while initially insulating, recovers its electrical conductivity following thermal reduction. From the chemically unmodified graphene-NMP solutions, the directed assembly of electrically active few-layer graphene flakes is realized, with flake thicknesses in the range 8–30 nm. Liquid phase exfoliation in water-surfactant solutions yields significantly thicker flake dimensions from 50 to several 100 nm due to the higher enthalpy of mixing in the dispersion. To achieve single-layer pristine graphene dielectrophoretic deposition, higher solution qualities must be available, consisting largely of single-layer graphene sheets. The reported research provides an important framework for parallel fabrication approaches of graphene-based devices.
Origin of platelike granular structure for the ultrananocrystalline diamond films synthesized in H2-containing Ar/CH4 plasma
Authors: Wang Chuan-Sheng , Chen Huang-Chin , Cheng Hsiu-Fung , Lin I-Nan
Published: February 2010

The modification on microstructure of diamond films due to the incorporation of H2 species into the Ar/CH4 plasma was systematically investigated. While the hydrogen-free plasma produced the ultrananocrystalline diamond films with equiaxed grains (about 5 nm in size), the hydrogen-containing plasma resulted in platelike grains (about 100×300 nm2 in size). The size of the platelike grains increased with the H2 content in the plasma. Transmission electron microscopy and optical emission spectroscopy reveal that only 0.1%H2 incorporated in the Ar/CH4 plasma is sufficient for inducing the formation of platelike grains, suggesting that the platelike grains are formed via the competition between the attachment and the etching of hydrocarbons onto the existing diamond surfaces. In Ar plasma, the diamond grains were always passivated with hydrocarbons and the active carbon species in the plasma can only renucleate to form nanocrystalline diamond grains. Incorporation of H2 species in the plasma leads to partial etching of hydrocarbons adhered onto the diamond grains, such that active carbon species in the plasma can attach to diamond surface anisotropically, resulting in diamond flakes and dendrites geometry.
Relativistic quantum Monte Carlo method using zeroth-order regular approximation Hamiltonian
Authors: Nakatsuka Yutaka , Nakajima Takahito , Nakata Maho , Hirao Kimihiko
Published: February 2010

We propose a new relativistic treatment in the quantum Monte Carlo (QMC) technique using the zeroth-order regular approximation (ZORA) Hamiltonian. The novel ZORA local energy is derived, and its availability is examined with some variational Monte Carlo calculations. We optimize the wave functions variationally and evaluate the relativistic and correlation effects simultaneously. It is shown that our ZORA-QMC method with Jastrow–Slater wave functions can recover not only relativistic effects but also almost the same amount of electron correlations as the nonrelativistic QMC method can by evaluating the ionization potentials of the first row atoms, Li–Ne.
Enormously high-peak-power optical pulse generation from a single-transverse-mode GaInN blue-violet laser diode
Authors: Kuramoto Masaru , Oki Tomoyuki , Sugahara Tomoya , Kono Shunsuke , Ikeda Masao , Yokoyama Hiroyuki
Published: February 2010

We have demonstrated extraordinary optical pulse generation with a peak-power of 55 W and pulse duration of 15 ps by intense electrical pulse excitation of a 401 nm GaInN laser diode (LD). Electrical pulse excitation of a GaInN LD which contained a thicker electron blocking layer gave rise to abnormal behavior with a several nanosecond-long delay and apparent Q-switching under intense excitation. Operation of this LD under such excitation was found to produce highly intense optical pulses even in semiconductor lasers with a single-transverse-mode.
Binary liquid crystal alignments based on photoalignment in azo dye-doped liquid crystals and their application
Authors: Fuh Andy Ying-Guey , Chen Ju-Chin , Huang San-Yi , Cheng Ko-Ting
Published: February 2010

This work demonstrates the feasibility of binary liquid crystal (LC) alignments, in which two forms of LC alignment are in a single pixel or a specific area using a surface-treated alignment layer and a photoalignment film of the adsorption of azo dyes onto the polymer surface in azo dye-doped liquid crystals. Binary LC alignments that involve two of common LC alignments, which are homogeneous, homeotropic, hybrid, and twisted nematic alignments, are initially demonstrated. Then, a binary LC alignment that comprises hybrid and homeotropic alignments is adopted to fabricate a viewing-angle-dependent liquid crystal display, which displays two images by changing viewing angles.
Spin filter effect of manganese phthalocyanine contacted with single-walled carbon nanotube electrodes
Authors: Shen Xin , Sun Lili , Benassi Enrico , Shen Ziyong , Zhao Xingyu , Sanvito Stefano , Hou Shimin
Published: February 2010

We present a theoretical study of the spin transport through a manganese phthalocyanine (MnPc) molecule sandwiched between two semi-infinite armchair single-walled carbon nanotube (SWCNT) electrodes. Ab initio modeling is performed by combing the nonequilibrium Green’s function formalism with spin density functional theory. Our calculations show that MnPc not only can act as a nearly perfect spin filter, but also has a large transmission around the Fermi level, which is dominated by the highest occupied molecule orbital (HOMO). The HOMO of MnPc is found to be a singly filled doubly degenerate molecular orbital, where the electrodes’ Fermi level can easily pin. The spin filter effect of MnPc is very robust regardless of whether the open ends of the SWCNT electrodes are terminated by hydrogen, fluorine, or carbon dimers, demonstrating its promising applications in future molecular spintronics.
Multimode resonances in metallically confined square-resonator microlasers
Authors: Che Kai-Jun , Yang Yue-De , Huang Yong-Zhen
Published: February 2010

Directional emission InP/AlGaInAs square-resonator microlasers with a side length of 20 μm are fabricated by standard photolithography and inductively coupled-plasma etching technique. Multimode resonances with about seven distinct mode peaks in a free-spectral range are observed from 1460 to 1560 nm with the free-spectral range of 12.1 nm near the wavelength of 1510 nm, and the mode refractive index versus the photon energy E (eV) as 3.07152+0.18304E are obtained by fitting the laser spectra with an analytical mode wavelength formula derived by light ray method. In addition, mode field pattern is simulated for cold cavity by two dimensional finite-difference time-domain technique.
Obama, detroit push the limits of electric vehicle batteries
Authors: Kramer David
Published: February 2010

The first plug-in hybrid and all-electric cars are just around the corner, but their batteries still need work.
Accelerator school travels university circuit
Authors: Feder Toni
Published: February 2010

With the use of accelerators on the rise, a mobile school aims to fill in where universities fall short.
Molecular defects of the glycine 41 variants of alanine glyoxylate aminotransferase associated with primary hyperoxaluria type I
Authors: Cellini Barbara , Montioli Riccardo , Paiardini Alessandro , Lorenzetto Antonio , Maset Fabio , Bellini Tiziana , Oppici Elisa , Voltattorni Carla Borri
Published: February 2010

G41 is an interfacial residue located within the α-helix 34–42 of alanine:glyoxylate aminotransferase (AGT). Its mutations on the major (AGT-Ma) or the minor (AGT-Mi) allele give rise to the variants G41R-Ma, G41R-Mi, and G41V-Ma causing hyperoxaluria type 1. Impairment of dimerization in these variants has been suggested to be responsible for immunoreactivity deficiency, intraperoxisomal aggregation, and sensitivity to proteasomal degradation. However, no experimental evidence supports this view. Here we report that G41 mutations, besides increasing the dimer-monomer equilibrium dissociation constant, affect the protein conformation and stability, and perturb its active site. As compared to AGT-Ma or AGT-Mi, G41 variants display different near-UV CD and intrinsic emission fluorescence spectra, larger exposure of hydrophobic surfaces, sensitivity to Met53-Tyr54 peptide bond cleavage by proteinase
K
, decreased thermostability, reduced coenzyme binding affinity, and catalytic efficiency. Additionally, unlike AGT-Ma and AGT-Mi, G41 variants under physiological conditions form insoluble inactive high-order aggregates (∼5,000 nm) through intermolecular electrostatic interactions. A comparative molecular dynamics study of the putative structures of AGT-Mi and G41R-Mi predicts that G41 → R mutation causes a partial unwinding of the 34–42 α-helix and a displacement of the first 44 N-terminal residues including the active site loop 24–32. These simulations help us to envisage the possible structural basis of AGT dysfunction associated with G41 mutations. The detailed insight into how G41 mutations act on the structure-function of AGT may contribute to achieve the ultimate goal of correcting the effects of these mutations.
Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication
Authors: Speller Camilla F. , Kemp Brian M. , Wyatt Scott D. , Monroe Cara , Lipe William D. , Arndt Ursula M. , Yang Dongya Y.
Published: February 2010

Although the cultural and nutritive importance of the turkey (
Meleagris gallopavo
) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC–AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (
Meleagris gallopavo gallopavo
) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices.
Plasmonic nanorod absorbers as orientation sensors
Authors: Chang Wei-Shun , Ha Ji Won , Slaughter Liane S. , Link Stephan
Published: February 2010

Nanoparticles are actively exploited as biological imaging probes. Of particular interest are gold nanoparticles because of their nonblinking and nonbleaching absorption and scattering properties that arise from the excitation of surface plasmons. Nanoparticles with anisotropic shapes furthermore provide information about the probe orientation and its environment. Here we show how the orientation of single gold nanorods (25 × 73 nm) can be determined from both the transverse and longitudinal surface plasmon resonance by using polarization-sensitive photothermal imaging. By measuring the orientation of the same nanorods separately using scanning electron microscopy, we verified the high accuracy of this plasmon-absorption-based technique. However, care had to be taken when exciting the transverse plasmon absorption using a large numerical aperture objective as out-of-plane plasmon oscillations were also excited then. For the size regime studied here, being able to establish the nanorod orientation from the transverse mode is unique to photothermal imaging and almost impossible with conventional dark-field scattering spectroscopy. This is important because the transverse surface plasmon resonance is mostly insensitive to the medium refractive index and nanorod aspect ratio allowing nanorods of any length to be used as orientation sensors without changing the laser frequency.
Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon
Ignicoccus hospitalis
Authors: Küper Ulf , Meyer Carolin , Müller Volker , Rachel Reinhard , Huber Harald
Published: February 2010

ATP synthase catalyzes ATP synthesis at the expense of an electrochemical ion gradient across a membrane that can be generated by different exergonic reactions. Sulfur reduction is the main energy-yielding reaction in the hyperthermophilic strictly anaerobic Crenarchaeon
Ignicoccus hospitalis.
This organism is unusual in having an inner and an outer membrane that are separated by a huge intermembrane compartment. Here we show, on the basis of immuno-EM analyses of ultrathin sections and immunofluorescence experiments with whole
I. hospitalis
cells, that the ATP synthase and H
2
:sulfur oxidoreductase complexes of this organism are located in the outer membrane. These two enzyme complexes are mandatory for the generation of an electrochemical gradient and for ATP synthesis. Thus, among all prokaryotes possessing two membranes in their cell envelope (including Planctomycetes, Gram-negative bacteria),
I. hospitalis
is a unique organism, with an energized outer membrane and ATP synthesis within the periplasmic space. In addition, DAPI staining and EM analyses showed that DNA and ribosomes are localized in the cytoplasm, leading to the conclusion that in
I. hospitalis
energy conservation is separated from information processing and protein biosynthesis. This raises questions regarding the function of the two membranes, the interaction between these compartments, and the general definition of a cytoplasmic membrane.
No difference in kinetics of tau or histone phosphorylation by CDK5/p25 versus CDK5/p35 in vitro
Authors: Peterson Dylan W. , Ando D. Michael , Taketa Daryl A. , Zhou Hongjun , Dahlquist Fredrick W. , Lew John
Published: February 2010

CDK5/p35 is a cyclin-dependent kinase essential for normal neuron function. Proteolysis of the p35 subunit in vivo results in CDK5/p25 that causes neurotoxicity associated with a number of neurodegenerative diseases. Whereas the mechanism by which conversion of p35 to p25 leads to toxicity is unknown, there is common belief that CDK5/p25 is catalytically hyperactive compared to CDK5/p35. Here, we have compared the steady-state kinetic parameters of CDK5/p35 and CDK5/p25 towards both histone H1, the best known substrate for both enzymes, and the microtubule-associated protein, tau, a physiological substrate whose in vivo phosphorylation is relevant to Alzheimer’s disease. We show that the kinetics of both enzymes are the same towards either substrate in vitro. Furthermore, both enzymes display virtually identical kinetics towards individual phosphorylation sites in tau monitored by NMR. We conclude that conversion of p35 to p25 does not alter the catalytic efficiency of the CDK5 catalytic subunit by using histone H1 or tau as substrates, and that neurotoxicity associated with CDK5/p25 is unlikely attributable to CDK5 hyperactivation, as measured in vitro.
Analysis of a gain-of-function FGFR2 Crouzon mutation provides evidence of loss of function activity in the etiology of cleft palate
Authors: Snyder-Warwick Alison K. , Perlyn Chad A. , Pan Jing , Yu Kai , Zhang Lijuan , Ornitz David M.
Published: February 2010

Cleft palate is a common birth defect in humans and is a common phenotype associated with syndromic mutations in
fibroblast growth factor receptor 2
(
Fgfr2
). Cleft palate occurred in nearly all mice homozygous for the Crouzon syndrome mutation C342Y in the mesenchymal splice form of
Fgfr2
. Mutant embryos showed delayed palate elevation, stage-specific biphasic changes in palate mesenchymal proliferation, and reduced levels of mesenchymal glycosaminoglycans (GAGs). Reduced levels of feedback regulators of FGF signaling suggest that this gain-of-function mutation in FGFR2 ultimately resembles loss of FGF function in palate mesenchyme. Knowledge of how mesenchymal FGF signaling regulates palatal shelf development may ultimately lead to pharmacological approaches to reduce cleft palate incidence in genetically predisposed humans.
Identification of an unconventional E3 binding surface on the UbcH5 ∼ Ub conjugate recognized by a pathogenic bacterial E3 ligase.
Authors: Levin Itay , Eakin Catherine , Blanc Marie-Pierre , Klevit Rachel E. , Miller Samuel I. , Brzovic Peter S.
Published: February 2010

Gram-negative bacteria deliver a cadre of virulence factors directly into the cytoplasm of eukaryotic host cells to promote pathogenesis and/or commensalism. Recently, families of virulence proteins have been recognized that function as E3 Ubiquitin-ligases. How these bacterial ligases integrate into the ubiquitin (Ub) signaling pathways of the host and how they differ functionally from endogenous eukaryotic E3s is not known. Here we show that the bacterial E3 SspH2 from
S. typhimurium
selectively binds the human UbcH5 ∼ Ub conjugate recognizing regions of both UbcH5 and Ub subunits. The surface of the E2 UbcH5 involved in this interaction differs substantially from that defined for other E2/E3 complexes involving eukaryotic E3-ligases. In vitro, SspH2 directs the synthesis of K48-linked poly-Ub chains, suggesting that cellular protein targets of SspH2-catalyzed Ub transfer are destined for proteasomal destruction. Unexpectedly, we found that intermediates in SspH2-directed reactions are activated poly-Ub chains directly tethered to the UbcH5 active site (UbcH5 ∼ Ub

n

). Rapid generation of UbcH5 ∼ Ub

n

may allow for bacterially directed modification of eukaryotic target proteins with a completed poly-Ub chain, efficiently tagging host targets for destruction.
Downstream class switching leads to IgE antibody production by B lymphocytes lacking IgM switch regions
Authors: Zhang Tingting , Franklin Andrew , Boboila Cristian , McQuay Amy , Gallagher Michael P. , Manis John P. , Khamlichi Ahmed Amine , Alt Frederick W.
Published: February 2010

Ig heavy chain (IgH) class-switch recombination (CSR) replaces the IgH Cμ constant region exons with one of several sets of downstream IgH constant region exons (e.g., Cγ, Cε, or Cα), which affects switching from IgM to another IgH class (e.g., IgG, IgE, or IgA). Activation-induced cytidine deaminase (AID) initiates CSR by promoting DNA double-strand breaks (DSBs) within switch (S) regions flanking the donor Cμ (Sμ) and a downstream acceptor CH(e.g., Sγ, Sε, Sα) that are then joined to complete CSR. DSBs generated in Sμ frequently are joined within Sμ to form internal switch region deletions (ISD). AID-induced ISD and mutations have been considered rare in downstream S regions, suggesting that AID targeting to these S regions requires its prior recruitment to Sμ. We have now assayed for CSR and ISD in B cells lacking Sμ (Sμ−/−B cells). In Sμ−/−B cells activated for CSR to IgG1 and IgE, CSR to IgG1 was greatly reduced; but, surprisingly, CSR to IgE occurred at nearly normal levels. Moreover, normal B cells had substantial Sγ1 ISD and increased mutations in and near Sγ1, and levels of both were greatly increased in Sμ−/−B cells. Finally, Sμ−/−B cells underwent downstream CSR between Sγ1 and Sε on alleles that lacked Sμ CSR to these sequences. Our findings show that AID targets downstream S regions independently of CSR with Sμ and implicate an alternative pathway for IgE class switching that involves generation and joining of DSBs within two different downstream S regions before Sμ joining.
Persistent hepatitis C virus infection in microscale primary human hepatocyte cultures
Authors: Ploss Alexander , Khetani Salman R. , Jones Christopher T. , Syder Andrew J. , Trehan Kartik , Gaysinskaya Valeriya A. , Mu Kathy , Ritola Kimberly , Rice Charles M. , Bhatia Sangeeta N.
Published: February 2010

Hepatitis C virus (HCV) remains a major public health problem, affecting approximately 130 million people worldwide. HCV infection can lead to cirrhosis, hepatocellular carcinoma, and end-stage liver disease, as well as extrahepatic complications such as cryoglobulinemia and lymphoma. Preventative and therapeutic options are severely limited; there is no HCV vaccine available, and nonspecific, IFN-based treatments are frequently ineffective. Development of targeted antivirals has been hampered by the lack of robust HCV cell culture systems that reliably predict human responses. Here, we show the entire HCV life cycle recapitulated in micropatterned cocultures (MPCCs) of primary human hepatocytes and supportive stroma in a multiwell format. MPCCs form polarized cell layers expressing all known HCV entry factors and sustain viral replication for several weeks. When coupled with highly sensitive fluorescence- and luminescence-based reporter systems, MPCCs have potential as a high-throughput platform for simultaneous assessment of in vitro efficacy and toxicity profiles of anti-HCV therapeutics.
p53 hides a multitude of CIN
Authors: Short Ben
Published: February 2010

Tumor suppressor stops cells from gaining or losing chromosomes.
Fate-determining mechanisms in epithelial–myofibroblast transition: major inhibitory role for Smad3
Authors: Masszi András , Speight Pam , Charbonney Emmanuel , Lodyga Monika , Nakano Hiroyasu , Szászi Katalin , Kapus András
Published: February 2010

Epithelial–myofibroblast (MF) transition (EMyT) is a critical process in organ fibrosis, leading to α–smooth muscle actin (SMA) expression in the epithelium. The mechanism underlying the activation of this myogenic program is unknown. We have shown previously that both injury to intercellular contacts and transforming growth factor β (TGF-β) are indispensable for SMA expression (two-hit model) and that contact disruption induces nuclear translocation of myocardin-related transcription factor (MRTF). Because the SMA promoter harbors both MRTF-responsive CC(A/T)-rich GG element (CArG) boxes and TGF-β–responsive Smad-binding elements, we hypothesized that the myogenic program is mobilized by a synergy between MRTF and Smad3. In this study, we show that the synergy between injury and TGF-β exclusively requires CArG elements. Surprisingly, Smad3 inhibits MRTF-driven activation of the SMA promoter, and Smad3 silencing renders injury sufficient to induce SMA expression. Furthermore, Smad3 is degraded under two-hit conditions, thereby liberating the myogenic program. Thus, Smad3 is a critical timer/delayer of MF commitment in the epithelium, and EMyT can be dissected into Smad3-promoted (mesenchymal) and Smad3-inhibited (myogenic) phases.
Drosophila Ana2 is a conserved centriole duplication factor
Authors: Stevens Naomi R. , Dobbelaere Jeroen , Brunk Kathrin , Franz Anna , Raff Jordan W.
Published: February 2010

In Caenorhabditis elegans, five proteins are required for centriole duplication: SPD-2, ZYG-1, SAS-5, SAS-6, and SAS-4. Functional orthologues of all but SAS-5 have been found in other species. In Drosophila melanogaster and humans, Sak/Plk4, DSas-6/hSas-6, and DSas-4/CPAP—orthologues of ZYG-1, SAS-6, and SAS-4, respectively—are required for centriole duplication. Strikingly, all three fly proteins can induce the de novo formation of centriole-like structures when overexpressed in unfertilized eggs. Here, we find that of eight candidate duplication factors identified in cultured fly cells, only two, Ana2 and Asterless (Asl), share this ability. Asl is now known to be essential for centriole duplication in flies, but no equivalent protein has been found in worms. We show that Ana2 is the likely functional orthologue of SAS-5 and that it is also related to the vertebrate STIL/SIL protein family that has been linked to microcephaly in humans. We propose that members of the SAS-5/Ana2/STIL family of proteins are key conserved components of the centriole duplication machinery.
Effects of Forward Sales on Spot Markets: Pre‐commitment Sales and Prices for Fresh Strawberries
Authors: Mohapatra Sandeep , Goodhue Rachael E. , Carter Colin A. , Chalfant James A.
Published: February 2010

Increasingly, agricultural markets are vertically coordinated. Often a thinning spot market coexists with coordinated transactions, raising the question of how private coordination affects the market as a whole. One of the greatest challenges when analyzing such market‐level effects is obtaining information on private transactions. We utilize publicly available data to evaluate how informal contracts in the fresh strawberry market affect spot market prices using a generalized autoregressive conditional heteroskedastic in mean (GARCH‐M) model. We find that these informal contracts increased spot prices, as argued by some industry members, while the effect on spot price volatility varied by production region.
Silent ships sometimes do encounter more fish. 1. Vessel comparisons during winter pollock surveys
Authors: De Robertis Alex , Wilson Christopher D. , Williamson Neal J. , Guttormsen Michael A. , Stienessen Sarah
Published: February 2010

De Robertis, A., Wilson, C. D., Williamson, N. J., Guttormsen, M. A., and Stienessen, S. 2010. Silent ships sometimes do encounter more fish. 1. Vessel comparisons during winter pollock surveys. – ICES Journal of Marine Science, 67: 985–995. Avoidance of approaching vessels by fish is a major source of uncertainty in surveys of fish stocks. In an effort to minimize vessel avoidance, international standards for underwater-noise emission by research vessels have been established. Despite widespread investment in noise-reduced vessels, the effectiveness of noise reduction on vessel avoidance remains poorly understood. Here, we report on vessel comparisons of pollock abundance recorded by the NOAA ships “Oscar Dyson” (OD), a noise-reduced vessel, and “Miller Freeman” (MF), a conventionally designed vessel. The comparisons were made during three acoustic surveys of prespawning aggregations of walleye pollock (Theragra chalcogramma) in Alaska. The experiments demonstrate that a noise-reduced vessel will detect significantly more fish backscatter than a conventional vessel in some situations. OD detected 31% more pollock backscatter than MF in the Shumagin Islands, where pollock were distributed between 100 and 200 m deep, and 13% more pollock backscatter in Shelikof Strait, where pollock were primarily distributed 200–300 m deep. However, there was no difference in the Bogoslof Island area where pollock were found at 400–700 m. In the Shumagin and Shelikof areas, the discrepancy between vessels tended to decrease with fish depth, consistent with a decreasing response to a stimulus propagating from the surface. Analysis of the depth distributions of pollock supports the conclusion that the discrepancies in backscatter stem from differential behavioural responses to the two vessels.
The endosymbiotic origin, diversification and fate of plastids
Authors: Keeling Patrick J.
Published: February 2010

Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes andPaulinella(which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.
Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes
Authors: Lithgow Trevor , Schneider André
Published: February 2010

All eukaryotes require mitochondria for survival and growth. The origin of mitochondria can be traced down to a single endosymbiotic event between two probably prokaryotic organisms. Subsequent evolution has left mitochondria a collection of heterogeneous organelle variants. Most of these variants have retained their own genome and translation system. In hydrogenosomes and mitosomes, however, the entire genome was lost. All types of mitochondria import most of their proteome from the cytosol, irrespective of whether they have a genome or not. Moreover, in most eukaryotes, a variable number of tRNAs that are required for mitochondrial translation are also imported. Thus, import of macromolecules, both proteins and tRNA, is essential for mitochondrial biogenesis. Here, we review what is known about the evolutionary history of the two processes using a recently revised eukaryotic phylogeny as a framework. We discuss how the processes of protein import and tRNA import relate to each other in an evolutionary context.
Endosymbiotic associations within protists
Authors: Nowack Eva C. M. , Melkonian Michael
Published: February 2010

The establishment of an endosymbiotic relationship typically seems to be driven through complementation of the host's limited metabolic capabilities by the biochemical versatility of the endosymbiont. The most significant examples of endosymbiosis are represented by the endosymbiotic acquisition of plastids and mitochondria, introducing photosynthesis and respiration to eukaryotes. However, there are numerous other endosymbioses that evolved more recently and repeatedly across the tree of life. Recent advances in genome sequencing technology have led to a better understanding of the physiological basis of many endosymbiotic associations. This review focuses on endosymbionts in protists (unicellular eukaryotes). Selected examples illustrate the incorporation of various new biochemical functions, such as photosynthesis, nitrogen fixation and recycling, and methanogenesis, into protist hosts by prokaryotic endosymbionts. Furthermore, photosynthetic eukaryotic endosymbionts display a great diversity of modes of integration into different protist hosts.

In conclusion, endosymbiosis seems to represent a general evolutionary strategy of protists to acquire novel biochemical functions and is thus an important source of genetic innovation.
Organization and expression of organellar genomes
Authors: Barbrook Adrian C. , Howe Christopher J. , Kurniawan Davy P. , Tarr Sarah J.
Published: February 2010

Protist mitochondrial genomes show a very wide range of gene content, ranging from three genes for respiratory chain components in Apicomplexa and dinoflagellates to nearly 100 genes in
Reclinomonas americana
. In many organisms the rRNA genes are fragmented, although still functional. Some protist mitochondria encode a full set of tRNAs, while others rely on imported molecules. There is similarly a wide variation in mitochondrial genome organization, even among closely related groups. Mitochondrial gene expression and control are generally poorly characterized. Transcription probably relies on a ‘viral-type’ RNA polymerase, although a ‘bacterial-type’ enzyme may be involved in some cases. Transcripts are heavily edited in many lineages. The chloroplast genome generally shows less variation in gene content and organization, although greatly reduced genomes are found in dinoflagellate algae and non-photosynthetic organisms. Genes in the former are located on small plasmids in contrast to the larger molecules found elsewhere. Control of gene expression in chloroplasts involves transcriptional and post-transcriptional regulation. Redox poise and the ATP/ADP ratio are likely to be important determinants. Some protists have an additional extranuclear genome, the nucleomorph, which is a remnant nucleus. Nucleomorphs of two separate lineages have a number of features in common.