bluuebunny/crossref_metadata_2025 huggingface dataset:
Anisotropy in structural and physical properties in tetrathiafulvalene derivatives-based zone-cast layers as seen by Raman spectroscopy, UV-visible spectroscopy, and field effect measurements
Authors: Kotarba Sylwia , Jung Jaroslaw , Kowalska Aneta , Marszalek Tomasz , Kozanecki Marcin , Miskiewicz Pawel , Mas-Torrent Marta , Rovira Concepció , Veciana Jaume , Puigmarti-Luis Josep , Ulanski Jacek
Published: July 2010

We have studied anisotropy of thin layers of amphiphilic tetrathiafulvalene derivatives (TTF-4SCn, with n=12, 18, and 22) obtained by zone-casting technique. All the films show optical anisotropy, as seen by polarized optical microscopy and polarized UV-visible spectroscopy. By using polarized Raman spectroscopy an angular dependence of intensity of different vibrational modes in respect to the zone-casting direction was determined. It was found that intensities of the modes related to central and ring C=C vibrations in the TTF core depend very strongly on the angle between the zone-cast direction and polarization plane of incident laser light. Comparison of the deduced orientation of the molecules in one of the films (TTF-4SC18) with its crystal structure shows that the polarized Raman spectroscopy can be useful for controlling orientation of molecules in thin films (e.g., for online monitoring). Organic field effect transistors (OFETs), with channels oriented in parallel and perpendicularly to the zone-casting direction, were built using the oriented TTF-4SCn films. In all cases a strong anisotropy of the charge carrier mobility (μ) was found; the best results were obtained for OFETs with TTF-4SC18, for which μ∥=0.25 cm2/V s, ON/OFF>105, and μ∥/μ⊥≈170.
Simulation of pattern effect induced by millisecond annealing used in advanced metal-oxide-semiconductor technologies
Authors: Cacho F. , Bono H. , Beneyton R. , Dumont B. , Colin A. , Morin P.
Published: July 2010

The submelt millisecond annealing process was introduced in the context of complementary metal-oxide semiconductor technology downscaling to enhance the activation of dopants. However, circuit designs can produce nonuniform local radiative and thermal dispersion properties at the front side of a wafer. Nonuniformities lead to local variations in annealing temperature and, therefore, to variability in device electrical properties and performance. This so-called pattern effect, well known in the context of lamp-based rapid thermal processing systems, is investigated here by simulation of the annealing process on the millisecond time scale. The multiphysics simulation models both optical and thermal properties. Real design inputs were imported from layout files and a finite element method simulation was used to compute transient temperature fields during the process. The absorptivities of a variety of periodic patterned structures were investigated by optical modeling. The radiative and thermal properties of the devices were mapped at the circuit scale. Finally, a three-dimensional thermal simulation was performed to evaluate the intradie thermal dispersions, which were found to be as large as 45°C in the real system.
A variational formulation of the polarizable continuum model
Authors: Lipparini Filippo , Scalmani Giovanni , Mennucci Benedetta , Cancès Eric , Caricato Marco , Frisch Michael J.
Published: July 2010

Continuum solvation models are widely used to accurately estimate solvent effects on energy, structural and spectroscopic properties of complex molecular systems. The polarizable continuum model (PCM) is one of the most versatile among the continuum models because of the variety of properties that can be computed and the diversity of methods that can be used to describe the solute from molecular mechanics (MM) to sophisticated quantum mechanical (QM) post-self-consistent field methods or even hybrid QM/MM methods. In this contribution, we present a new formulation of PCM in terms of a free energy functional whose variational parameters include the continuum polarization (represented by the apparent surface charges), the solute’s atomic coordinates and—possibly—its electronic density. The problem of finding the optimized geometry of the (polarized) solute, with the corresponding self-consistent reaction field, is recast as the minimization of this free energy functional, simultaneously with respect to all its variables. The numerous potential applications of this variational formulation of PCM are discussed, including simultaneous optimization of solute’s geometry and polarization charges and extended Lagrangian dynamics. In particular, we describe in details the simultaneous optimization procedure and we include several numerical examples.
Carrier transport mechanisms of organic bistable devices fabricated utilizing colloidal ZnO quantum dot-polymethylmethacrylate polymer nanocomposites
Authors: Son Dong Ick , You Chan Ho , Jung Jae Hun , Kim Tae Whan
Published: July 2010

Organic bistable devices (OBDs) fabricated utilizing ZnO quantum dots (QDs) embedded in a poly(methyl methacrylate) (PMMA) layer were fabricated by using a spin-coating technique. Transmission electron microscopy images revealed that 5-nm-diameter ZnO QDs were formed inside the PMMA polymer layer. Current-voltage (I-V) measurements on Al/ZnO QDs embedded in PMMA layer/indium-tin-oxide devices at 300 K showed electrical bistability. The maximum ON/OFF ratio of the current bistability for the OBDs was as large as 4×104. Carrier transport mechanisms for the OBDs are described by using several models to fit the experimental I-V data.
Branching ratios and anisotropy parameters in ICl photolysis from 400 to 570 nm using slice imaging
Authors: Samartzis Peter C. , Kitsopoulos Theofanis N.
Published: July 2010

ICl photolysis in the visible region of the spectrum (400–570 nm) is studied using the slice imaging technique. The Cl(P21/2)/Cl(P23/2) branching ratio between the I(P23/2)+Cl(P23/2) and I(P23/2)+Cl(P21/2) channels is extracted from the iodine photofragment images and it is found to range from 0 to 2.5, rising from 570 to 490 nm and dropping at higher photolysis energies. The I+Cl angular distribution exhibits a similar trend, changing from purely perpendicular at 570 nm to isotropic at 545 nm, fairly parallel at 490 nm and again perpendicular at 440 nm. Following previous work, we discuss these changes in light of avoided curve crossing and determine the crossing probability as a function of wavelength. The angular anisotropy parameter beta of the second channel ranges between 0.6 and 1.4.
Simplified manual fabrication of cubic-zirconia gem anvils for extended energy-range spectroscopic studies to routine high pressures of 100–150 kbar (10–15 GPa)
Authors: Jackson N. R. , Erasmus R. M. , Hearne G. R.
Published: July 2010

Methodology has been developed so as to attain routine extreme conditions as high as 10–15 GPa in a gem anvil optical pressure cell using hand (manual) processed gem anvils. The anvils polished by a simplified hand held tool are inexpensive single crystal cubic zirconia (CZ) gems that have various optical advantages over diamond anvils. Appreciable pressures are attained with culet and corresponding sample cavity dimensions that are relatively convenient to load with sample material. Some technical details are provided as regards the simplified manual fabrication process, thus emphasizing the relative ease and cost effectiveness of the hand polishing technique for fabricating such high pressure anvils. Raman spectroscopy measurements, in triple subtractive mode with a confocal pinhole geometry, are used to exemplify the usefulness of the CZ gem anvil cell methodology in pressure tuning experiments. This is particularly convenient for conventional low wave-number (lattice mode regime) Raman high pressure studies, which have not been reported previously in this context. Various other applications of such anvils are suggested.
Defect structure and materials “hardening” in Fe2O3-doped [Bi0.5Na0.5]TiO3 ferroelectrics
Authors: Aksel Elena , Erdem Emre , Jakes Peter , Jones Jacob L. , Eichel Rüdiger-A.
Published: July 2010

The effect of Fe2O3-doping on the defect structure and piezoelectric properties of [Bi0.5Na0.5]TiO3 ceramics is studied by means of electron paramagnetic resonance spectroscopy. The results show that the Fe3+ functional centers are incorporated at the perovskite B-site, and clearly can be attributed to the formation of (FeTi′–VO••)• defect complexes with charge compensating oxygen vacancies. Correspondingly, they act as acceptors which promotes materials “hardening.”
Electron and hole mobility reduction and Hall factor in phosphorus-compensated p-type silicon
Authors: Rougieux F. E. , Macdonald D. , Cuevas A. , Ruffell S. , Schmidt J. , Lim B. , Knights A. P.
Published: July 2010

The conductivity mobility for majority carrier holes in compensated p-type silicon is determined by combined measurement of the resistivity and the net doping, the latter via electrochemical capacitance-voltage measurements. The minority electron mobility was also measured with a technique based on measurements of surface-limited effective carrier lifetimes. While both minority and majority carrier mobilities are found to be significantly reduced by compensation, the impact is greater on the minority electron mobility. The Hall factor, which relates the Hall mobility to the conductivity mobility, has also been determined using the Hall method combined with the capacitance-voltage measurements. Our results indicate a similar Hall factor in both compensated and noncompensated samples.
Real-time dissociation dynamics of the Ne2Br2 van der Waals complex
Authors: Pio Jordan M. , Taylor Molly A. , van der Veer Wytze E. , Bieler Craig R. , Cabrera Jose A. , Janda Kenneth C.
Published: July 2010

We have characterized the vibrational predissociation (VP) of the Ne2Br2 van der Waals complex using time- and frequency-resolved pump-probe spectroscopy. After exciting Br2 within the complex to a vibrational level 16≤ν′≤23 in the B state, we follow the flow of halogen vibrational energy to the van der Waals modes in real time by recording the time-dependent behavior of Ne2Br2 (ν′), the NeBr2 (ν′−m) intermediates, and the Br2 (ν′−n) products. For Ne2Br2 (ν′=16–18), the only intermediate observed is NeBr2 (ν′−1), and the majority of the final product is Br2 (ν′−2), indicating the dissociation happens via two sequential direct VP steps. We fit the time-dependent behavior of these species to a sequential mechanism and extracted time constants for each step. For higher ν′ levels, the results show that the dissociation occurs via multiple pathways. Product Br2 from levels lower than (ν′−2) becomes much more important, with products as low as (ν′−5) being observed. For ν′=21, we observe both NeBr2 (ν′−1) and (ν′−2) intermediates. The intermediates have significantly different kinetics, with the decay rate of the (ν′−1) transient being nearly twice that of the (ν′−2) transient. Similarly, both Br2 (ν′−2) and (ν′−3) are formed in almost equal amounts, but the (ν′−2) product formation rate is faster than the (ν′−3) rate. The broad vibrational product state distributions and multiple dissociation pathways indicate that intramolecular vibrational energy redistribution becomes increasingly important for ν′>19. We also report vibrational product state distributions for direct excitation to NeBr2 16≤ν′≤23. For NeBr2, the dominant product channel is Br2 (ν′−1) for all initial ν′ studied, consistent with this complex dissociating primarily via direct VP.
Steady-state simulations using weighted ensemble path sampling
Authors: Bhatt Divesh , Zhang Bin W. , Zuckerman Daniel M.
Published: July 2010

We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. A straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when significant metastable intermediates states are present. We therefore develop an enhanced WE scheme, building on existing ideas, which accelerates attainment of steady state in complex systems. We apply both WE approaches to several model systems, confirming their correctness and efficiency by comparison with brute-force results. The enhanced version is significantly faster than the brute force and straightforward WE for systems with WE bins that accurately reflect the reaction coordinate(s). The new WE methods can also be applied to equilibrium sampling, since equilibrium is a steady state.
Fragile-to-strong transition in metallic glass-forming liquids
Authors: Zhang Chunzhi , Hu Lina , Yue Yuanzheng , Mauro John C.
Published: July 2010

Two of the Earth’s most abundant substances, water and silica, exhibit some of the most unusual properties in nature. Among these is an anomalous scaling of liquid dynamics, which appear non-Arrhenius (or “fragile”) at high temperatures yet Arrhenius (or “strong”) at low temperatures. Here we show that this fragile-to-strong (F-S) transition is not limited to a few liquids such as water and silica, but is possibly a general behavior of metallic glass-forming liquids. We also propose a general model for the viscosity of F-S liquids that captures the scaling of dynamics across both the fragile and strong regimes.
Large critical magnetic field and tunneling anomaly behavior of superconducting carbon-coated Sn nanorods and nanoparticles
Authors: Wang Z. H. , Geng D. Y. , Han Z. , Zhang Z. D.
Published: July 2010

The arc-discharge process is usually used to synthesize some kinds of metal nanocrystals or nanoparticles all with high melting temperature. Here, the carbon-coated Sn (with a low melting temperature) nanostructured materials with different shapes, such as carbon-coated Sn nanorods with diameter of about 100 and 50 nm and, correspondingly, the length of 500 and 200 nm, and the carbon-coated Sn nanoparticles, are prepared by a modified arc-discharge process. The carbon shells are found to surround these Sn nanostructures. The carbon shell becomes thick with decreasing the size of the Sn nanostructures. The magnetic and electrical transports are affected by the shape of nanocrystals. The critical magnetic field of the carbon-coated Sn nanorods with diameter of 50 nm and length of 200 nm is almost 25 times higher than that of bulk Sn. The superconductivity of the carbon-coated Sn nanoparticles with particle size of 40 nm is destroyed. The zero bias tunneling anomalies was observed in the carbon-coated Sn nanoparticles.
Shape profile of acoustic radiation-induced static displacement pulses in solids
Authors: Cantrell John H. , Yost William T.
Published: July 2010

In a recent article Narasimha et al. [J. Appl. Phys. 105, 073506 (2009)] claim to show that the shape of static displacement pulses generated by ultrasonic tone-bursts in nondispersive solids is that of a growing trapezoid in the spatial domain that leads to a flat-topped pulse shape in the time domain for a fixed spatial position. Flaws in their theoretical arguments are corrected to show that their model actually predicts a right-triangular pulse shape for nondispersive monocrystals in both the spatial and time domains as originally reported by Yost and Cantrell [Phys. Rev. B 30, 3221 (1984)] and Cantrell et al. [Phys. Rev. B 35, 9780 (1987)].
Nanoscale rectification at the LaAlO3/SrTiO3 interface
Authors: Bogorin Daniela F. , Bark Chung Wung , Jang Ho Won , Cen Cheng , Folkman Chad M. , Eom Chang-Beom , Levy Jeremy
Published: July 2010

Control over electron transport at scales that are comparable to the Fermi wavelength or mean-free path can lead to a variety of electronic devices. Here we report electrical rectification in nanowires formed by nanoscale control of the metal-insulator transition at the interface between LaAlO3 and SrTiO3. Controlled in-plane asymmetry in the confinement potential produces electrical rectification in the nanowire, analogous to what occurs naturally for Schottky diodes or by design in structures with engineered structural inversion asymmetry. Nanostructures produced in this manner may be useful in developing a variety of nanoelectronic, electro-optic, and spintronic devices.
Conductance asymmetry in point-contacts on epitaxial thin films of Ba(Fe0.92Co0.08)2As2
Authors: Mehta Manan , Sheet Goutam , Dikin D. A. , Lee S. , Bark C. W. , Jiang J. , Weiss J. D. , Hellstrom E. E. , Rzchowski M. S. , Eom C. B. , Chandrasekhar V.
Published: July 2010

One of the most common observations in point-contact spectra on the recently discovered ferropnictide superconductors is a large conductance asymmetry with respect to voltage across the point-contact. In this paper, we show that the antisymmetric part of the point-contact spectrum between a silver tip and an epitaxial thin film of Ba(Fe0.92Co0.08)2As2 shows certain unique features that have an interesting evolution with increasing temperature up to a temperature far above the critical temperature Tc. We associate this observation with the existence of a gap above Tc that might originate from strong fluctuations of the phase of the superconducting order parameter.
Single carrier devices with electrical doped layers for the characterization of charge-carrier transport in organic thin-films
Authors: Schober Matthias , Olthof Selina , Furno Mauro , Lüssem Björn , Leo Karl
Published: July 2010

We introduce single-carrier devices with electrical doped layers as a concept for the characterization of charge-carrier transport in organic semiconductors. In this approach, individual organic layers from a multilayer device are investigated in single-carrier test devices, where they are enclosed by symmetrically arranged electrical doped layers of equal thickness and composition. Single carrier devices without electrical doped layers are usually difficult to interpret due to an uncertainty about interface dipole effects between the metal contacts and pristine organic layers. In comparison, our devices show Ohmic contacts at the electrodes as well as zero built-in voltage and thus allow a more direct insight into charge-carrier transport. State-of-the-art simulation models are applied to analyze current-voltage characteristics and evaluate crucial parameters such as energy barriers between adjacent organic layers and mobilities.
Band-gap narrowing of TiO2 doped with Ce probed with x-ray absorption spectroscopy
Authors: Chen S. W. , Lee J. M. , Lu K. T. , Pao C. W. , Lee J. F. , Chan T. S. , Chen J. M.
Published: July 2010

The electronic structure of TiO2 doped with Ce was investigated with x-ray absorption and photoluminescence (PL) spectra. Ce doping narrows the band gap of TiO2, as evidenced by a redshift in the absorption edge in the O K-edge spectrum and PL. Narrowing is ascribed to the formation of an impurity band, composed of Ce 4f (Ce3+/Ce4+) and oxygen defect states, that induces tailing of the conduction band. Band gap narrowing extends the photoactivity of TiO2 to visible light. The impurity band located below the minimum of the conduction band traps excited electrons and suppresses recombination, enhancing the photocatalytic activity.
InGaN/GaN self-organized quantum dot green light emitting diodes with reduced efficiency droop
Authors: Zhang Meng , Bhattacharya Pallab , Guo Wei
Published: July 2010

High density (2–5×1010 cm−2) self-organized InGaN/GaN quantum dots were grown by plasma-assisted molecular beam epitaxy. Room temperature photoluminescence shows that the quantum dots have strong emission ranging from 430 to 524 nm. The internal quantum efficiency of dots emitting at 500 nm was determined to be 32% by temperature dependent photoluminescence measurements. A recombination lifetime of 0.57 ns is derived from time resolved photoluminescence measurements. These superior optical properties are attributed to a small piezoelectric field in the quantum dots. Light emitting diodes fabricated with the InGaN/GaN quantum dots and emitting at λ=524 nm demonstrate a small blueshift with current injection and reduced efficiency droop.
Memristive behaviors of LiNbO3 ferroelectric diodes
Authors: Li Haitao , Xia Yidong , Xu Bo , Guo Hongxuan , Yin Jiang , Liu Zhiguo
Published: July 2010

Memristive systems are expected to lead to analog computers that process information the way the human brain does. In this work, memristive behaviors have been revealed in ferroelectric diodes employing LiNbO3. The conduction states in such diodes can be continually modulated by the successive voltage sweeps, which is essentially based on electron tunneling through a thin residual barrier. The role of oxygen vacancies in such memristive behaviors is also discussed.
Cutoff radius effect of the isotropic periodic sum method in homogeneous system. II. Water
Authors: Takahashi Kazuaki , Narumi Tetsu , Yasuoka Kenji
Published: July 2010

Molecular dynamics simulation has been applied for water to compare the isotropic periodic sum (IPS) method [X. Wu and B. R. Brooks, J. Chem. Phys. 122, 044107 (2005)] with the Ewald sum based on the diffusion coefficient and liquid structure. The IPS method gives a good estimation for the self-diffusion coefficient at a cutoff radius, rc, greater than 2.2 nm; however, the radial distribution function g(r) has a notable deviation. The peak of this deviation appears at specific intermolecular distances which are near each cutoff radius and decrease in proportion to the inverse of the cube of rc. Thus the deviation becomes insignificant (less than 1%) at rc greater than 2.2 nm. The distance dependent Kirkwood factor Gk(r) was also calculated, and since the truncation of a long-range interaction of the cutofflike method (such as cutoff with or without the switch function and the reaction field) shows serious shortcomings for dipole-dipole correlations in bulk water systems, this was observed by comparing the shape to that of the Ewald sum [Y. Yonetani, J. Chem. Phys. 124, 204501 (2006); D. van der Spoel and P. J. van Maaren, J. Chem. Theory Comput. 2, 1 (2006)]. The Gk(r) of cutofflike method greatly deviate from that of the Ewald sum. However, the discrepancy of Gk(r) for the IPS method was found to be much less than that of other typical cutofflike methods. In conclusion, the IPS method is an adequately accurate technique for estimating transport coefficients and the liquid structure of water in a homogeneous system at long cutoff distances.
Differential control of TAp73 and ΔNp73 protein stability by the ring finger ubiquitin ligase PIR2
Authors: Sayan Berna S. , Yang Ai Li , Conforti Franco , Tucci Paola , Piro Maria Cristina , Browne Gareth J. , Agostini Massimiliano , Bernardini Sergio , Knight Richard A. , Mak Tak W. , Melino Gerry
Published: July 2010

p73 is a p53-related transcription factor with fundamental roles in development and tumor suppression. Transcription from two different promoters on the p73 gene results in generation of transcriptionally active TAp73 isoforms and dominant negative ΔNp73 isoforms with opposing pro- and anti-apoptotic functions. Therefore, the relative ratio of each isoform is an important determinant of the cell fate. Proteasomal degradation of p73 is mediated by polyubiquitination-dependent and -independent processes both of which appear, thus far, to lack selectivity for the TAp73 and ΔNp73 isoforms. Here, we describe the characterization of another transcriptional target of TAp73; a ring finger domain ubiquitin ligase p73 Induced RING 2 protein (PIR2). Although PIR2 was initially identified a p53-induced gene (p53RFP), low abundance of PIR2 transcript in mouse embryonic fibroblasts of TAp73 KO mice compared with WT mice and comparison of PIR2 mRNA and protein levels following TAp73 or p53 overexpression substantiate TAp73 isoforms as strong inducers of PIR2. Although PIR2 expression was induced by DNA damage, its expression did not alter apoptotic response or cell cycle profile per se. However, coexpression of PIR2 with TAp73 or ΔNp73 resulted in an increase of the TA/ΔNp73 ratio, due to preferential degradation of ΔNp73. Finally, PIR2 was able to relieve the inhibitory effect of ΔNp73 on TAp73 induced apoptosis following DNA damage. These results suggest that PIR2, by being induced by TAp73 and degrading ΔNp73, differentially regulates TAp73/ΔNp73 stability, and, hence, it may offer a therapeutic approach to enhance the chemosensitivity of tumor cells.
Multiple functions of Osterix are required for bone growth and homeostasis in postnatal mice
Authors: Zhou Xin , Zhang Zhaoping , Feng Jian Q. , Dusevich Vladmir M. , Sinha Krishna , Zhang Hua , Darnay Bryant G. , de Crombrugghe Benoit
Published: July 2010

The transcription factor Osterix (Osx) is required for osteoblast differentiation and bone formation during embryonic development, but it is not known whether Osx has an essential function in postnatal bone growth and in bone homeostasis. Conditional deletion of
Osx
at several time points postnatally revealed that Osx was essential for osteoblast differentiation and new bone formation in growing and adult bones. Additionally, inactivation of
Osx
in bones severely disrupted the maturation, morphology, and function of osteocytes. These findings identify Osx as having an essential role in the cell-specific genetic program of osteocytes. Interestingly,
Osx
inactivation also led to the massive accumulation of unresorbed calcified cartilage in a large area below the growth plate of endochondral bones. This specific area was also marked by an unanticipated almost complete lack of bone marrow cells and a marked decrease in the density and size of osteoclasts. This diminished density of osteoclasts could contribute to the lack of resorption of mineralized cartilage. In addition, we speculate that the abnormally accumulated, mainly naked cartilage represents an unfavorable substrate for osteoclasts. Our study identifies Osx as an essential multifunctional player in postnatal bone growth and homeostasis.
Prion protein interaction with stress-inducible protein 1 enhances neuronal protein synthesis via mTOR
Authors: Roffé Martín , Beraldo Flávio Henrique , Bester Romina , Nunziante Max , Bach Christian , Mancini Gabriel , Gilch Sabine , Vorberg Ina , Castilho Beatriz A. , Martins Vilma Regina , Hajj Glaucia Noeli Maroso
Published: July 2010

Transmissible spongiform encephalopathies are fatal neurodegenerative diseases caused by the conversion of prion protein (PrP
C
) into an infectious isoform (PrP
Sc
). How this event leads to pathology is not fully understood. Here we demonstrate that protein synthesis in neurons is enhanced via PrP
C
interaction with stress-inducible protein 1 (STI1). We also show that neuroprotection and neuritogenesis mediated by PrP
C
–STI1 engagement are dependent upon the increased protein synthesis mediated by PI3K-mTOR signaling. Strikingly, the translational stimulation mediated by PrP
C
–STI1 binding is corrupted in neuronal cell lines persistently infected with PrP
Sc
, as well as in primary cultured hippocampal neurons acutely exposed to PrP
Sc
. Consistent with this, high levels of eukaryotic translation initiation factor 2α (eIF2α) phosphorylation were found in PrP
Sc
-infected cells and in neurons acutely exposed to PrP
Sc
. These data indicate that modulation of protein synthesis is critical for PrP
C
–STI1 neurotrophic functions, and point to the impairment of this process during PrP
Sc
infection as a possible contributor to neurodegeneration.
Repression of tyrosine hydroxylase is responsible for the sex-linked chocolate mutation of the silkworm,
Bombyx mori
Authors: Liu Chun , Yamamoto Kimiko , Cheng Ting-Cai , Kadono-Okuda Keiko , Narukawa Junko , Liu Shi-Ping , Han Yu , Futahashi Ryo , Kidokoro Kurako , Noda Hiroaki , Kobayashi Isao , Tamura Toshiki , Ohnuma Akio , Banno Yutaka , Dai Fang-Ying , Xiang Zhong-Huai , Goldsmith Marian R. , Mita Kazuei , Xia Qing-You
Published: July 2010

Pigmentation patterning has long interested biologists, integrating topics in ecology, development, genetics, and physiology. Wild-type neonatal larvae of the silkworm,
Bombyx mori
, are completely black. By contrast, the epidermis and head of larvae of the homozygous recessive sex-linked chocolate (
sch
) mutant are reddish brown. When incubated at 30 °C, mutants with the
sch
allele fail to hatch; moreover, homozygous mutants carrying the allele
sch lethal
(

sch
l

) do not hatch even at room temperature (25 °C). By positional cloning, we narrowed a region containing
sch
to 239,622 bp on chromosome 1 using 4,501 backcross (BC1) individuals. Based on expression analyses, the best
sch
candidate gene was shown to be tyrosine hydroxylase (
BmTh
).
BmTh
coding sequences were identical among
sch
,

sch
l

, and wild-type. However, in
sch
the ∼70-kb sequence was replaced with ∼4.6 kb of a Tc1-mariner type transposon located ∼6 kb upstream of
BmTh
, and in

sch
l

, a large fragment of an L1Bm retrotransposon was inserted just in front of the transcription start site of
BmTh
. In both cases, we observed a drastic reduction of
BmTh
expression. Use of RNAi with
BmTh
prevented pigmentation and hatching, and feeding of a tyrosine hydroxylase inhibitor also suppressed larval pigmentation in the wild-type strain,

pnd
+

and in a
pS
(black-striped) heterozygote. Feeding L-dopa to
sch
neonate larvae rescued the mutant phenotype from chocolate to black. Our results indicate the
BmTh
gene is responsible for the
sch
mutation, which plays an important role in melanin synthesis producing neonatal larval color.
Cytochrome
c
polymerization by successive domain swapping at the C-terminal helix
Authors: Hirota Shun , Hattori Yoko , Nagao Satoshi , Taketa Midori , Komori Hirofumi , Kamikubo Hironari , Wang Zhonghua , Takahashi Isao , Negi Shigeru , Sugiura Yukio , Kataoka Mikio , Higuchi Yoshiki
Published: July 2010

Cytochrome
c
(cyt
c
) is a stable protein that functions in a monomeric state as an electron donor for cytochrome
c
oxidase. It is also released to the cytosol when permeabilization of the mitochondrial outer membrane occurs at the early stage of apoptosis. For nearly half a century, it has been known that cyt
c
forms polymers, but the polymerization mechanism remains unknown. We found that cyt
c
forms polymers by successive domain swapping, where the C-terminal helix is displaced from its original position in the monomer and Met-heme coordination is perturbed significantly. In the crystal structures of dimeric and trimeric cyt
c
, the C-terminal helices are replaced by the corresponding domain of other cyt
c
molecules and Met80 is dissociated from the heme. The solution structures of dimeric, trimeric, and tetrameric cyt
c
were linear based on small-angle X-ray scattering measurements, where the trimeric linear structure shifted toward the cyclic structure by addition of PEG and (NH
4
)
2
HPO
4
. The absorption and CD spectra of high-order oligomers (∼40 mer) were similar to those of dimeric and trimeric cyt
c
but different from those of monomeric cyt
c
. For dimeric, trimeric, and tetrameric cyt
c
, the Δ
H
of the oligomer dissociation to monomers was estimated to be about -20 kcal/mol per protomer unit, where Met-heme coordination appears to contribute largely to Δ
H
. The present results suggest that cyt
c
polymerization occurs by successive domain swapping, which may be a common mechanism of protein polymerization.
Interneurons of the cerebellar cortex toggle Purkinje cells between up and down states
Authors: Oldfield Claire S. , Marty Alain , Stell Brandon M.
Published: July 2010

We demonstrate that single interneurons can toggle the output neurons of the cerebellar cortex (the Purkinje cells) between their two states. The firing of Purkinje cells has previously been shown to alternate between an “up” state in which the cell fires spontaneous action potentials and a silent “down” state. We show here that small hyperpolarizing currents in Purkinje cells can bidirectionally toggle Purkinje cells between down and up states and that blockade of the hyperpolarization-activated cation channels (H channels) with the specific antagonist ZD7288 (10 μM) blocks the transitions from down to up states. Likewise, hyperpolarizing inhibitory postsnyaptic potentials (IPSPs) produced by small bursts of action potentials (10 action potentials at 50 Hz) in molecular-layer interneurons induce these bidirectional transitions in Purkinje cells. Furthermore, single interneurons in paired interneuron → Purkinje cell recordings, produce bidirectional switches between the two states of Purkinje cells. The ability of molecular-layer interneurons to toggle Purkinje cells occurs when Purkinje cells are recorded under whole-cell patch-clamp conditions as well as when action potentials are recorded in an extracellular loose cell-attached configuration. The mode switch demonstrated here indicates that a single presynaptic interneuron can have opposite effects on the output of a given Purkinje cell, which introduces a unique type of synaptic interaction that may play an important role in cerebellar signaling.
Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex
Authors: Bedogni Francesco , Hodge Rebecca D. , Elsen Gina E. , Nelson Branden R. , Daza Ray A. M. , Beyer Richard P. , Bammler Theo K. , Rubenstein John L. R. , Hevner Robert F.
Published: July 2010

Areas and layers of the cerebral cortex are specified by genetic programs that are initiated in progenitor cells and then, implemented in postmitotic neurons. Here, we report that Tbr1, a transcription factor expressed in postmitotic projection neurons, exerts positive and negative control over both regional (areal) and laminar identity.
Tbr1
null mice exhibited profound defects of frontal cortex and layer 6 differentiation, as indicated by down-regulation of gene-expression markers such as
Bcl6
and
Cdh9
. Conversely, genes that implement caudal cortex and layer 5 identity, such as
Bhlhb5
and
Fezf2
, were up-regulated in
Tbr1
mutants. Tbr1 implements frontal identity in part by direct promoter binding and activation of
Auts2
, a frontal cortex gene implicated in autism. Tbr1 regulates laminar identity in part by downstream activation or maintenance of
Sox5
, an important transcription factor controlling neuronal migration and corticofugal axon projections. Similar to
Sox5
mutants,
Tbr1
mutants exhibit ectopic axon projections to the hypothalamus and cerebral peduncle. Together, our findings show that Tbr1 coordinately regulates regional and laminar identity of postmitotic cortical neurons.
Essential roles for
imuA
′- and
imuB
-encoded accessory factors in DnaE2-dependent mutagenesis in
Mycobacterium tuberculosis
Authors: Warner Digby F. , Ndwandwe Duduzile E. , Abrahams Garth L. , Kana Bavesh D. , Machowski Edith E. , Venclovas Česlovas , Mizrahi Valerie
Published: July 2010

In
Mycobacterium tuberculosis
(Mtb), damage-induced mutagenesis is dependent on the C-family DNA polymerase, DnaE2. Included with
dnaE2
in the Mtb SOS regulon is a putative operon comprising
Rv3395c
, which encodes a protein of unknown function restricted primarily to actinomycetes, and
Rv3394c
, which is predicted to encode a Y-family DNA polymerase. These genes were previously identified as components of an
imuA
-
imuB
-
dnaE2
–type mutagenic cassette widespread among bacterial genomes. Here, we confirm that
Rv3395c
(designated
imuA
′) and
Rv3394c
(
imuB
) are individually essential for induced mutagenesis and damage tolerance. Yeast two-hybrid analyses indicate that ImuB interacts with both ImuA′ and DnaE2, as well as with the β-clamp. Moreover, disruption of the ImuB-β clamp interaction significantly reduces induced mutagenesis and damage tolerance, phenocopying
imuA
′,
imuB
, and
dnaE2
gene deletion mutants. Despite retaining structural features characteristic of Y-family members, ImuB homologs lack conserved active-site amino acids required for polymerase activity. In contrast, replacement of DnaE2 catalytic residues reproduces the
dnaE2
gene deletion phenotype, strongly implying a direct role for the α-subunit in mutagenic lesion bypass. These data implicate differential protein interactions in specialist polymerase function and identify the split
imuA
′-
imuB
/
dnaE2
cassette as a compelling target for compounds designed to limit mutagenesis in a pathogen increasingly associated with drug resistance.
Structural basis for the wobbler mouse neurodegenerative disorder caused by mutation in the Vps54 subunit of the GARP complex
Authors: Pérez-Victoria F. Javier , Abascal-Palacios Guillermo , Tascón Igor , Kajava Andrey , Magadán Javier G. , Pioro Erik P. , Bonifacino Juan S. , Hierro Aitor
Published: July 2010

The multisubunit Golgi-associated retrograde protein (GARP) complex is required for tethering and fusion of endosome-derived transport vesicles to the
trans
-Golgi network. Mutation of leucine-967 to glutamine in the Vps54 subunit of GARP is responsible for spinal muscular atrophy in the wobbler mouse, an animal model of amyotrophic lateral sclerosis. The crystal structure at 1.7 Å resolution of the mouse Vps54 C-terminal fragment harboring leucine-967, in conjunction with comparative sequence analysis, reveals that Vps54 has a continuous α-helical bundle organization similar to that of other multisubunit tethering complexes. The structure shows that leucine-967 is buried within the α-helical bundle through predominantly hydrophobic interactions that are critical for domain stability and folding in vitro. Mutation of this residue to glutamine does not prevent integration of Vps54 into the GARP complex but greatly reduces the half-life and levels of the protein in vivo. Severely reduced levels of mutant Vps54 and, consequently, of the whole GARP complex underlie the phenotype of the wobbler mouse.
Long-lived quantum coherence in photosynthetic complexes at physiological temperature
Authors: Panitchayangkoon Gitt , Hayes Dugan , Fransted Kelly A. , Caram Justin R. , Harel Elad , Wen Jianzhong , Blankenship Robert E. , Engel Gregory S.
Published: July 2010

Photosynthetic antenna complexes capture and concentrate solar radiation by transferring the excitation to the reaction center that stores energy from the photon in chemical bonds. This process occurs with near-perfect quantum efficiency. Recent experiments at cryogenic temperatures have revealed that coherent energy transfer—a wave-like transfer mechanism—occurs in many photosynthetic pigment-protein complexes. Using the Fenna–Matthews–Olson antenna complex (FMO) as a model system, theoretical studies incorporating both incoherent and coherent transfer as well as thermal dephasing predict that environmentally assisted quantum transfer efficiency peaks near physiological temperature; these studies also show that this mechanism simultaneously improves the robustness of the energy transfer process. This theory requires long-lived quantum coherence at room temperature, which never has been observed in FMO. Here we present evidence that quantum coherence survives in FMO at physiological temperature for at least 300 fs, long enough to impact biological energy transport. These data prove that the wave-like energy transfer process discovered at 77 K is directly relevant to biological function. Microscopically, we attribute this long coherence lifetime to correlated motions within the protein matrix encapsulating the chromophores, and we find that the degree of protection afforded by the protein appears constant between 77 K and 277 K. The protein shapes the energy landscape and mediates an efficient energy transfer despite thermal fluctuations.
Fas-associated death domain (FADD) is a negative regulator of T-cell receptor–mediated necroptosis
Authors: Osborn Stephanie L. , Diehl Gretchen , Han Seong-Ji , Xue Ling , Kurd Nadia , Hsieh Kristina , Cado Dragana , Robey Ellen A. , Winoto Astar
Published: July 2010

Cell death is an important mechanism to limit uncontrolled T-cell expansion during immune responses. Given the role of death-receptor adapter protein Fas-associated death domain (FADD) in apoptosis, it is intriguing that T-cell receptor (TCR)–induced proliferation is blocked in FADD-defective T cells. Necroptosis is an alternate form of death that can be induced by death receptors and is linked to autophagy. It requires the death domain-containing kinase RIP1 and, in certain instances, RIP3. FADD and its apoptotic partner, Caspase-8, have also been implicated in necroptosis. To accurately assess the role of FADD in mature T-cell proliferation and death, we generated a conditional T-cell–specific FADD knockout mouse strain. The T cells of these mice develop normally, but lack FADD at the mature stage. FADD-deficient T cells respond poorly to TCR triggering, exhibit slow cell cycle entry, and fail to expand over time. We find that programmed necrosis occurs during the late stage of normal T-cell proliferation and that this process is greatly amplified in FADD-deficient T cells. Inhibition of necroptosis using an inhibitor of RIP1 kinase activity rescues the FADD knockout proliferative defect. However, TCR-induced necroptosis did not appear to require autophagy or involve RIP3. Consistent with their defective CD8 T-cell response, these mice succumb to
Toxoplasma gondii
infection more readily than wild-type mice. We conclude that FADD constitutes a mechanism to keep TCR-induced programmed necrotic signaling in check during early phases of T-cell clonal expansion.
Design of an HA2-based
Escherichia coli
expressed influenza immunogen that protects mice from pathogenic challenge
Authors: Bommakanti Gayathri , Citron Michael P. , Hepler Robert W. , Callahan Cheryl , Heidecker Gwendolyn J. , Najar Tariq Ahmad , Lu Xianghan , Joyce Joseph G. , Shiver John W. , Casimiro Danilo R. , ter Meulen Jan , Liang Xiaoping , Varadarajan Raghavan
Published: July 2010

Influenza HA is the primary target of neutralizing antibodies during infection, and its sequence undergoes genetic drift and shift in response to immune pressure. The receptor binding HA1 subunit of HA shows much higher sequence variability relative to the metastable, fusion-active HA2 subunit, presumably because neutralizing antibodies are primarily targeted against the former in natural infection. We have designed an HA2-based immunogen using a protein minimization approach that incorporates designed mutations to destabilize the low pH conformation of HA2. The resulting construct (HA6) was expressed in
Escherichia coli
and refolded from inclusion bodies. Biophysical studies and mutational analysis of the protein indicate that it is folded into the desired neutral pH conformation competent to bind the broadly neutralizing HA2 directed monoclonal 12D1, not the low pH conformation observed in previous studies. HA6 was highly immunogenic in mice and the mice were protected against lethal challenge by the homologous A/HK/68 mouse-adapted virus. An HA6-like construct from another H3 strain (A/Phil/2/82) also protected mice against A/HK/68 challenge. Regions included in HA6 are highly conserved within a subtype and are fairly well conserved within a clade. Targeting the highly conserved HA2 subunit with a bacterially produced immunogen is a vaccine strategy that may aid in pandemic preparedness.
Adverse interactions between micro-RNAs and target genes from different species
Authors: Tang Tian , Kumar Supriya , Shen Yang , Lu Jian , Wu Mao-Lien , Shi Suhua , Li Wen-Hsiung , Wu Chung-I
Published: July 2010

It is commonly assumed but not proven that microRNAs (miRNAs) and their targets coevolve. Under this assumption, miRNAs and targets from different species may interact adversely, resulting in reduced fitness. However, the strength of the adverse interactions may not be detectable because even outright deletions of miRNAs often manifest only subtle fitness effects. We tested and measured the strength of heterospecific interactions by carrying out transgenic experiments across
Drosophila
species by overexpressing the
miR310s
cluster of
Drosophila melanogaster
(
Dm310s
) and
Drosophila pseudoobscura
(
Dp310s
) in
D. melanogaster
. Flies overexpressing the heterospecific
Dp310s
are only one-third as viable as those overexpressing the conspecific
Dm310s
. The viability effect is easily detectable in comparison to the effect of the deletion of
miR310s
. The number of genes significantly misexpressed under the influence of
Dp310s
is 3–10 times greater than under
Dm310s
. Importantly, the numbers of predicted targets are similar between them. Expression analysis of the predicted target genes suggests that miRNAs may sometimes function to buffer fluctuations in the transcriptome output. After the buffering function has evolved, heterospecific combinations may cause adverse effects.
Microtubule-assisted mechanism for functional metabolic macromolecular complex formation
Authors: An Songon , Deng Yijun , Tomsho John W. , Kyoung Minjoung , Benkovic Stephen J.
Published: July 2010

Evidence has been presented for a metabolic multienzyme complex, the purinosome, that participates in de novo purine biosynthesis to form clusters in the cytoplasm of living cells under purine-depleted conditions. Here we identified, using fluorescent live cell imaging, that a microtubule network appears to physically control the spatial distribution of purinosomes in the cytoplasm. Application of a cell-based assay measuring the rate of de novo purine biosynthesis confirmed that the metabolic activity of purinosomes was significantly suppressed in the absence of microtubules. Collectively, we propose a microtubule-assisted mechanism for functional purinosome formation in HeLa cells.
Viruses and Schizophrenia
Authors: O'Reilly Richard L.
Published: July 2010

A viral hypothesis for the pathogenesis of schizophrenia has been under serious consideration for more than 70 years. To date, attempts have failed to identify a specific virus which contributes to the aetiology of the disorder. There has, however, been a recent resurgence of interest in a possible relationship between viral illness and schizophrenia. This renewed attention is the result of epidemiological evidence suggesting an excess of winter births in patients with schizophrenia, indications of foetal insults in persons who develop schizophrenia and an association between foetal exposure to the influenza virus and the subsequent development of schizophrenia. Advances in our understanding of the pathophysiology of viral diseases and the development of sophisticated techniques to study them have resulted in more complex viral hypotheses of schizophrenic aetiology, such as viral disruption of normal neurodevelopment, viral induced autoimmunity and retroviral integration. These hypotheses are now beginning to be tested experimentally.
Mental Health Law: An Idea whose Time has Passed
Authors: Rosenman Stephen
Published: July 2010

In this paper I argue that specific mental health law should not exist and should be replaced by modern guardianship law which is non-discriminatory and which intervenes according to need rather than diagnostic classification. Substituted consent provided by a guardian protects the patient and the treatment provider. Custody to prevent danger to others should remain with courts rather than informal proceedings where individual rights to freedom are less carefully protected.

Special mental health law stigmatises people with mental illness and degrades their treatment. It also diminishes the standing of the psychiatric profession which advocates the continuation of such laws.