bluuebunny/crossref_metadata_2025 huggingface dataset:
Core structures of the a-edge dislocation in InN
Authors: Lei H. P. , Ruterana P. , Nouet G. , Jiang X. Y. , Chen J.
Published: March 2007

Stillinger-Weber potential parameters were optimized for InN by fitting to the bulk material properties and point defect energy in order to calculate the core structure of the a-edge dislocation. The initial displacement field is imposed in the perfect crystal according to isotropic linear elasticity theory, and then the system is relaxed to the minimum energy. The different origins of the displacement field generate three cores with four, eight or five/seven atoms. The calculated energies indicate that the four-atom core structure is the most stable for InN.
Current transport characteristics across shallow hybrid-orientation silicon bonded interfaces
Authors: Wagener M. C. , Zhang R. H. , Rozgonyi G. A. , Seacrist M. , Ries M.
Published: March 2007

This letter describes the current transport across the interface of hybrid-orientation direct silicon bonded wafers. It is observed that the position of the bonding interface relative to the wafer surface directly impacts the transport behavior. Varistor behavior occurs in the case of an interface several microns below the surface, while rectifying behavior occurs when the bonding interface is sufficiently close to the surface (200nm) for the interface potential to fully deplete the region above the bonding interface. This phenomenon is expected to be applicable to all near-surface interfaces that have a defect-state density sufficient to pin the Fermi level within the band gap.
Self-focused high frequency ultrasonic transducers based on ZnO piezoelectric films
Authors: Zhou Q. F. , Sharp C. , Cannata J. M. , Shung K. K. , Feng G. H. , Kim E. S.
Published: March 2007

A micromachined self-focusing high frequency ultrasonic transducer was fabricated with a 13μm thick ZnO film deposited on a silicon substrate by sputtering. X-ray diffraction shows that the film has a high (002) orientation. The element aperture size of the transducer was 2.5mm, and the fundamental resonant frequency was designed to be over 200MHz with approximately 28% bandwidth through only one matching layer. Experimental results show that this type of focused high frequency ultrasound device may have potential for cellular microstructure imaging and skin cancer detection.
Study of thermal parameters’ temperature dependence in solids using photothermal radiometry
Authors: Depriester M. , Hus P. , Delenclos S. , Hadj Sahraoui A.
Published: March 2007

A photothermal radiometry configuration that allows the measurement of the temperature dependence of thermal parameters of solid materials is described. Two procedures are proposed. The first one is based on a combination of phase and amplitude signal data collected at a single frequency and the second one makes use of the information contained in the phase signal data, obtained at two different chopping frequencies. The methods are recommended for calorimetric studies requiring temperature scans at a constant chopping frequency.
Enhanced pyroelectric sensitivity using ferroelectric active mode detection
Authors: Mantese Joseph V. , Micheli Adolph L. , Schubring Norman W. , Putty Michael W. , Thompson Margarita P. , Chang Scott , Troxell John R. , Oberdier Larry , Celinska Jolanta , Paz de Araujo Carlos
Published: March 2007

Active pyroelectric detection (APD), using ferroelectrics as the sensing materials, is described and compared to traditional-passive pyroelectric modes of operation. The active approach yields a number of distinct advantages over its passive counterparts, including greater effective pyroelectric coefficient and improved signal to noise ratio. Thin film test structures formed from strontium bismuth tantalate (SrBi2Ta2O9) are used to demonstrate the APD principle.
Tuning InAs quantum dots for high areal density and wideband emission
Authors: Ngo C. Y. , Yoon S. F. , Fan W. J. , Chua S. J.
Published: March 2007

The authors report the effect of growth temperature and monolayer coverage on areal density and photoluminescence spectral width of InAs quantum dot (QD). Areal density and spectral width were found to be strongly dependent on growth temperature and monolayer coverage, respectively. Upon proper tuning, both high areal density and large photoluminescence spectral width were obtained. Areal density of 1.5×1011cm−2 is four times higher than those previously reported, while spectral width of 136nm is the broadest spectral width obtained without any forms of band gap engineering. These results will contribute to an improvement in the performance of QD superluminescent diode.
Quasimonochromatic emission spectra in the near field by polar semiconductor thermal sources
Authors: Sokolov V. N. , Kong B. D. , Kim K. W. , Trew R. J.
Published: March 2007

The near-field spectra of the electromagnetic field emitted from a planar surface are theoretically investigated for a number of polar semiconductor and dielectric materials that support surface phonon polaritons. All of the studied materials, InP, GaAs, GaN, SiC, and α-Al2O3 (sapphire), exhibit quasimonochromatic thermal emission symbolized by strong peaks of evanescent modes at well-defined frequencies in the near field that correspond to the appropriate peaks in the density of states for surface phonon polaritons. It is also found that the materials with lower polariton frequencies (e.g., InP and GaAs) generally demonstrate a higher peak spectral energy density compared to those with higher frequencies (e.g., SiC). This trend is maintained over the entire range of temperature (300–600K) and the distance from the surface (⩽10μm) considered in the calculation. Thus, the results clearly indicate that among the studied materials InP and GaAs are the best candidates to provide the quasicoherent thermal emission for potential use as a nanoscale thermal source. The energy density stored in the evanescent peaks, when close to the surface, is estimated to be many orders of magnitude larger than that in the blackbody radiation.
Evaluation of the thermal stability of Nd60Al20Co20 bulk metallic glass
Authors: Xia L. , Ding D. , Shan S. T. , Dong Y. D.
Published: March 2007

Long-term thermal stability of Nd60Al20Co20 bulk metallic glass (BMG) with excellent glass forming ability was investigated by Kissinger and Vogel-Fulcher-Tammann (VFT) analyses, respectively. The heating rate dependence of crystallization temperature of the BMG was found to follow the VFT nonlinear relationship rather than Kissinger’s linear fittings. It is suggested that the continuous heating crystallization diagrams obtained from VFT equation should be more adequate to estimate the long-term thermal stability of Nd60Al20Co20 bulk metallic glass according to the time-temperature-transformation diagram based on isothermal annealing.
Enhanced mass sensitivity of stress-free, silicon nanowire-grown microcantilever sensors
Authors: Lee Dongkyu , Kim Eun-Ha , Yoo Myungsun , Jung Namchul , Lee Kun-Hong , Jeon Sangmin
Published: March 2007

A thin catalytic layer of nickel was evaporated onto one side of silicon microcantilevers and amorphous silicon nanowires were synthesized on the nickel surface. When nanowire-grown cantilevers were exposed to mercaptohexanol vapor, their mass sensitivity was almost two orders of magnitude greater than that of the corresponding plain cantilever due to the increase in surface area afforded by the nanowires, whereas adsorption of mercaptohexanol induced negligible deflection of the nanowire-grown cantilevers. This indicates that the gold-coated nanowire-grown cantilever can be used as a sensitive, stress-free sensor whose spring constant is not affected by the adsorption of alkanethiols.
Ultrafast plasma shutter for shielding high-energy ions from a laser-produced plasma
Authors: Yashiro H. , Tomie T.
Published: March 2007

A laser-produced plasma was employed as an ultrafast shutter for shielding high-energy ions. Fast ions with energy on the order of keV were prevented from reaching the detector by a shutter plasma. The ion signal was suppressed to 1% of the unshielded peak ion signal. Suppression of the ion signal was observed up to 10mm from the target surface of the shutter plasma. The shutter closing time was 40ns at the distance of 2mm. The plasma shutter could operate even at a 100kHz repetition rate. The high-density plasma acts as a shutter by capturing a low-density plasma.
Enhanced photosensitivity in silicate optical fibers by thermal treatment
Authors: Brambilla Gilberto , Pruneri Valerio
Published: March 2007

Enhanced photosensitivity using thermal treatment has been observed on several silicate optical fibers. The effect of the treatment on fibers with different dopants has been tested via Bragg grating inscription. The presence of Ge or Sn atom has been established to be fundamental for the effect to occur. To explain the main features a model involving defect dynamics is proposed.
Picosecond water dynamics adjacent to charged paramagnetic ions measured by magnetic relaxation dispersion
Authors: Lisitza Natasha , Bryant Robert G.
Published: March 2007

Measurements of water-proton spin-lattice relaxation rate constants as a function of magnetic field strength [magnetic relaxation dispersion (MRD)] in aqueous solutions of paramagnetic solutes reveal a peak in the MRD profile. These previously unobserved peaks require that the time correlation functions describing the water-proton-electron dipolar coupling have a periodic contribution. In aqueous solutions of iron(III) ion the peak corresponds to a frequency of 8.7cm−1, which the authors ascribe to the motion of water participating in the second coordination sphere of the triply charged solute ion. Similar peaks of weaker intensity in the same time range are observed for aqueous solutions of chromium(III) chloride as well as for ion pairs formed by ammonium ion with trioxalatochromate(III) ion. The widths of the dispersion peaks are consistent with a lifetime for the periodic motion in the range of 5ps or longer.
What Really Gives a Quantum Computer Its Power?
Authors: Fitzgerald Richard
Published: March 2007

Quantum computers have been predicted to be exponentially faster than their classical counterparts for some computations, such as the factoring of large numbers. (See the article by Charles Bennett in PHYSICS TODAY, October 1995, page 24.) Whereas classical computers perform operations on information stored as classical bits, which can be in one of two discrete states, quantum computers perform operations on quantum bits, or “qubits,” which can be put into any superposition of two quantum states.
Retinal Imaging and Vision at the Frontiers of Adaptive Optics
Authors: Miller Donald T.
Published: March 2007

Vision is a most acute human sense, so it is rather surprising that the very first step in the visual process—the formation of an image on the retina—is often defective. One reason is that the human eye has significant optical defects, aberrations, that distort the passing optical wavefront, blur the retinal image, and degrade our visual experience. Diffraction, which is caused by the finite size of the eye's pupil, is the other reason for blurri-ness. Together, aberrations and diffraction limit not only what the eye sees looking out, but also determine the smallest internal structures that can be observed when looking into the eye with a microscope (see box 1 on page 33). Spectacles and contact lenses can correct the eye's major aberrations, but if all the aberrations could be quantified and corrected while, at the same time, minimizing diffraction, high-resolution retinal microscopy could become routinely feasible—and we might eventually achieve supernormal vision.
Researchers Perform Quite a Magic Trick: Making Nickel-48 Materialize
Authors: Levi Barbara Goss
Published: March 2007

Chalk up another one for the shell model…maybe its last one for a while. The model has had a long run in predicting which nuclei would have special stability compared to their neighboring isotopes because they had the right numbers of protons and neutrons—magic numbers—to completely fill the available shells, or energy levels. By now, experimenters have found about ten doubly magic nuclei (in which the numbers of protons and neutrons are both magic) but still sought one elusive holdout: Ni48. A group of researchers working at the Grande Accélérateur National d'Ions Lourds (GANIL) in France has now produced this lightest of nickel's isotopes. (Two other isotopes of nickel are also doubly magic.)
The Road to the Neutrino
Authors: Franklin Allan
Published: March 2007

The usual potted history of the neutrino hypothesis that we find in textbooks goes something like this: Radioactivity—the spontaneous transformation of one element into another—produces α particles, or β particles, or γ rays. Experimental work on the energy of the electrons emitted in β decay began early in the 20th century, and the observations posed a problem: If there were only two bodies (the daughter nucleus and an electron) in the final state of a β decay, the conservation of energy and momentum would require that the spectrum of decay electrons must be monoenergetic. Thus, the observation of a continuous spectrum—electrons emitted with all energies from zero up to a maximum that depended on the radioactive element—cast doubt on both of these conservation laws. Or perhaps the electrons lost varying amounts of energy in escaping the radioactive substance, thus accounting for the continuous energy spectrum. But careful experiments showed that this was not the case. So the problem persisted. In the early 1930s, Wolfgang Pauli suggested that an undetected neutral particle of low mass was also emitted in β decay. Enrico Fermi dubbed this putative particle the “neutrino.” That solved the problem of the continuous spectrum, because, in a three-body decay, the energy of the electron is no longer required to be unique. The energy and momentum conservation laws were saved.
Physicists Triumph at Guess My Number
Authors: Steane Andrew M. , van Dam Wim
Published: March 2007

Let's meet tonight's lucky contestants, ladies and gentlemen, all ready to play Guess My Number, for the grand prize of “ONE MILLION DOLLARS!”
Learning about High-Tc Superconductors from Their Imperfections
Authors: Levi Barbara Goss
Published: March 2007

In the old nursery rhyme, little Jack Horner stuck in his thumb and pulled out a plum. That's more or less what experimenters from the University of California, Berkeley, and the University of Tokyo did recently: They stuck a zinc atom into the copper site of a high-Tc superconductor and extracted a plum of an image using a specially developed scanning tunneling microscope (STM). That image provided dramatic visual confirmation of the d-wave nature of the electron pairing state in such materials (see the cover of this issue).
Nonequilibrium Patterns in Granular Mixing and Segregation
Authors: Shinbrot Troy , Muzzio Fernando J.
Published: March 2007

For over 5000 years, granular mixing has been a topic of acutely practical concern. Paleolithic cave painters mixed their colors from blends of ochre and animal products; ancient Chinese and Egyptians blended inks and cosmetics from pork soot, crushed pearls, and compounds of lead; Aztec priests prepared drugs from concoctions of herbs and roots; and Michelangelo pigmented the Sistine chapel frescoes with blends including chalk, charcoal, and lead.
Liquid Crystals and Carbon Materials
Authors: Hurt Robert H. , Chen Zhong-Ying
Published: March 2007

Carbon atoms can be found in a variety of structures, including the tetrahedra of diamond, the stacked planes of graphite, and the celebrated fullerene spheres and nanotubes. The graphite family alone includes a rich variety of materials, ranging from pencil “lead” to interstellar dust to chimney soot, and from metallurgical coke to activated charcoal for water filtration to lightweight composites for aerospace components—such as the nose cone of the space shuttle, for which carbon composites were chosen because of their high strength at elevated temperatures.
Explorers Focus More Sharply on Their Prey: Weakly Interacting Dark Matter
Authors: Levi Barbara Goss
Published: March 2007

What you see is not what you get when it comes to mass in the universe. We've known for more than 50 years, for example, that spiral galaxies rotate much faster than one would expect based on the mass in their twinkling stars and the intervening gases. Furthermore, large-scale observations of the universe imply that the cosmic mass density is so large that radiant mass accounts for no more than a few percent of the total. So, what is the missing mass?
Ultracold Neutrons are Magnetically Trapped at NIST
Authors: Lubkin Gloria B.
Published: March 2007

Although the neutron was discovered in 1932, its lifetime wasn't measured until 18 years later, when nuclear reactors became available. Obtaining a precise measurement was a tough experimental challenge back then. John Robson was the first to report such a measurement—at the Chalk River reactor in Canada. Fifty years later, improving the precision is still challenging experimenters.
Magnetic Semiconductors Enable Efficient Electrical Spin Injection
Authors: Fitzgerald Richard
Published: March 2007

Dreams of exploiting the spin of the electron in solid-state devices underlie the nascent field of “spintronics.” Aspirations for semiconductors have been spurred by the development, in metals, of giant magneto-resistance devices—as found in the read heads of current high-density computer hard drives—and nonvolatile magnetic memory (see the PHYSICS TODAY special issue on magnetoelectronics, April 1995).
Novel Composite Medium Exhibits Reversed Electromagnetic Properties
Authors: Fitzgerald Richard
Published: March 2007

According to Maxwell's equations, lossless propagation of electromagnetic waves requires the index of refraction n, given by (εμ)1/2, to be real, where ε is the electrical permittivity or dielectric constant and μ is the magnetic permeability. All familiar materials have a positive μ and, for the most part, positive ε. But at the March Meeting of the American Physical Society, held in Minneapolis, a group of researchers from the University of California, San Diego, led by David Smith and Sheldon Schultz, reported having built a composite medium with an effective μ that is negative. By combining that medium with one that has a negative ε, they have created a composite material that allows transmission of microwaves that would be blocked by either medium alone. But the propagation inside the composite is predicted to have unusual properties, such as a negative index of refraction.
Have Heavy Ion Collisions at CERN Reached the Quark–Gluon Plasma?
Authors: Schwarzschild Bertram
Published: March 2007

With Brookhaven's Relativistic Heavy Ion Collider (RHIC) about to begin its experimental program and CERN's heavy-ion program winding down at the venerable Super Proton Synchrotron (SPS), a celebratory day of talks at CERN was convoked in February to summarize six years of investigating nuclear matter in extremis at the SPS with a relativistic beam of lead ions. Much of the discussion that day revolved around the question of whether or not the CERN experiments had achieved fleeting visits to the quark–gluon plasma—the promised land envisioned by quantum chromodynamics. QCD is the standard field theory of nuclear matter in terms of its quark constituents and the gluons that bind them.
Modern Classical Physics Through the Work of G. I. Taylor
Authors: Brenner Michael P. , Stone Howard A.
Published: March 2007

During the spring of 1998 we co-taught a graduate course on modern classical physics that aimed to cover the fundamentals while also conveying the directions and sense of current research. As we talked about the subject, we realized that many of the important discoveries underlying a wide range of topics of current interest in physics and engineering were made by a single individual, the British scientist Geoffrey Ingram (G. I.) Taylor (1886–1975). Although many researchers are familiar with one or another of Taylor's contributions, few seem to be aware of the incredible breadth of his scientific publications and their relevance to important research questions today. The same person who is commonly remembered as the namesake for several basic fluid flow instabilities (Taylor–Couette, Rayleigh–Taylor, and Saffman–Taylor) also was the first to show experimentally that a diffraction pattern produced by shining light on a needle does not change when the intensity of light is decreased. And these topics are only the beginning. Taylor made fundamental contributions to turbulence, championing the need for developing a statistical theory, and performing the first measurements of the effective diffusivity and viscosity of the atmosphere. He wrote one of the first scientific papers using random walks; gave the first consistent theory of the structure of shocks in gases; and explained the importance of dislocations for determining the strength of solids. He also described the counterintuitive physics of fluid motion in a rotating environment, providing the basic principles for important aspects of atmospheric and oceanic dynamics.
Pattern regulation in the stripe of zebrafish suggests an underlying dynamic and autonomous mechanism
Authors: Yamaguchi Motoomi , Yoshimoto Eiichi , Kondo Shigeru
Published: March 2007

The mechanism by which animal markings are formed is an intriguing problem that has remained unsolved for a long time. One of the most important questions is whether the positional information for the pattern formation is derived from a covert prepattern or an autonomous mechanism. In this study, using the zebrafish as the model system, we attempted to answer this classic question. We ablated the pigment cells in limited areas of zebrafish skin by using laser irradiation, and we observed the regeneration of the pigmentation pattern. Depending on the area ablated, different patterns regenerated in a specific time course. The regenerated patterns and the transition of the stripes during the regeneration process suggest that pattern formation is independent of the prepattern; furthermore, pattern formation occurs by an autonomous mechanism that satisfies the condition of “local self-enhancement and long-range inhibition.” Because the zebrafish is the only striped animal for which detailed molecular genetic studies have been conducted, our finding will facilitate the identification of the molecular and cellular mechanisms that underlie skin pattern formation.
Innateness and culture in the evolution of language
Authors: Kirby Simon , Dowman Mike , Griffiths Thomas L.
Published: March 2007

Human language arises from biological evolution, individual learning, and cultural transmission, but the interaction of these three processes has not been widely studied. We set out a formal framework for analyzing cultural transmission, which allows us to investigate how innate learning biases are related to universal properties of language. We show that cultural transmission can magnify weak biases into strong linguistic universals, undermining one of the arguments for strong innate constraints on language learning. As a consequence, the strength of innate biases can be shielded from natural selection, allowing these genes to drift. Furthermore, even when there is no natural selection, cultural transmission can produce apparent adaptations. Cultural transmission thus provides an alternative to traditional nativist and adaptationist explanations for the properties of human languages.
Deletion of
kasB
in
Mycobacterium tuberculosis
causes loss of acid-fastness and subclinical latent tuberculosis in immunocompetent mice
Authors: Bhatt Apoorva , Fujiwara Nagatoshi , Bhatt Kiranmai , Gurcha Sudagar S. , Kremer Laurent , Chen Bing , Chan John , Porcelli Steven A. , Kobayashi Kazuo , Besra Gurdyal S. , Jacobs William R.
Published: March 2007

Mycobacterium tuberculosis
, the causative agent of tuberculosis, has two distinguishing characteristics: its ability to stain acid-fast and its ability to cause long-term latent infections in humans. Although this distinctive staining characteristic has often been attributed to its lipid-rich cell wall, the specific dye-retaining components were not known. Here we report that targeted deletion of
kasB
, one of two
M. tuberculosis
genes encoding distinct β-ketoacyl- acyl carrier protein synthases involved in mycolic acid synthesis, results in loss of acid-fast staining. Biochemical and structural analyses revealed that the Δ
kasB
mutant strain synthesized mycolates with shorter chain lengths. An additional and unexpected outcome of
kasB
deletion was the loss of ketomycolic acid
trans
-cyclopropanation and a drastic reduction in methoxymycolic acid
trans
-cyclopropanation, activities usually associated with the
trans
-cyclopropane synthase CmaA2. Although deletion of
kasB
also markedly altered the colony morphology and abolished classic serpentine growth (cording), the most profound effect of
kasB
deletion was the ability of the mutant strain to persist in infected immunocompetent mice for up to 600 days without causing disease or mortality. This long-term persistence of Δ
kasB
represents a model for studying latent
M. tuberculosis
infections and suggests that this attenuated strain may represent a valuable vaccine candidate against tuberculosis.
Hypoxia-inducible factor 1α stabilization by carbon monoxide results in cytoprotective preconditioning
Authors: Chin Beek Y. , Jiang Ge , Wegiel Barbara , Wang Hong J. , MacDonald Theresa , Zhang Xu Chen , Gallo David , Cszimadia Eva , Bach Fritz H. , Lee Patty J. , Otterbein Leo E.
Published: March 2007

The most salient feature of carbon monoxide (CO)-mediated cytoprotection is the suppression of inflammation and cell death. One of the important cellular targets of CO is the macrophage (mφ). Many studies have shown that exposure of mφ to CO results in the generation of an antiinflammatory phenotype; however, these reports have ignored the effect of CO alone on the cell before stimulation. Most investigations have focused on the actions of CO in modulating the response to noxious stimuli. We demonstrate here that exposure of mφ to CO results in a significant and transient burst of reactive oxygen species (ROS) arising from the mitochondria (mitochondria-deficient mφ do not respond to CO to produce ROS). The ROS promote rapid activation and stabilization of the transcription factor hypoxia-inducible factor 1α (HIF-1α), which regulates expression of genes involved in inflammation, metabolism, and cell survival. The increase in HIF-1α expression induced by CO results in regulated expression of TGF-β, a potent antiinflammatory cytokine. CO-induced HIF-1α and TGF-β expression are necessary to prevent anoxia/reoxygenation-induced apoptosis in mφ. Furthermore, blockade of HIF-1α using RNA interference and HIF-1α-cre-lox mφ resulted in a loss of TGF-β expression and CO-induced protection. A similar mechanism of CO-induced protection was operationalin vivoto protect against lung ischemia-reperfusion injury. Taken together, we conclude that CO conditions the mφ via a HIF-1α and TGF-β-dependent mechanism and we elucidate the earliest events in mφ signaling that lead to and preserve cellular homeostasis at the site of injury.
Bound anionic states of adenine
Authors: Harańczyk Maciej , Gutowski Maciej , Li Xiang , Bowen Kit H.
Published: March 2007

Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the newfound anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike the dipole-bound state, could exist in condensed phases and might be relevant to radiobiological damage. The discovery of these valence anionic states of adenine was facilitated by the development of (
i
) an experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (
ii
) a combinatorial/quantum chemical approach for identification of the most stable tautomers of organic molecules.
Model-based assessment of the role of human-induced climate change in the 2005 Caribbean coral bleaching event
Authors: Donner Simon D. , Knutson Thomas R. , Oppenheimer Michael
Published: March 2007

Episodes of mass coral bleaching around the world in recent decades have been attributed to periods of anomalously warm ocean temperatures. In 2005, the sea surface temperature (SST) anomaly in the tropical North Atlantic that may have contributed to the strong hurricane season caused widespread coral bleaching in the Eastern Caribbean. Here, we use two global climate models to evaluate the contribution of natural climate variability and anthropogenic forcing to the thermal stress that caused the 2005 coral bleaching event. Historical temperature data and simulations for the 1870–2000 period show that the observed warming in the region is unlikely to be due to unforced climate variability alone. Simulation of background climate variability suggests that anthropogenic warming may have increased the probability of occurrence of significant thermal stress events for corals in this region by an order of magnitude. Under scenarios of future greenhouse gas emissions, mass coral bleaching in the Eastern Caribbean may become a biannual event in 20–30 years. However, if corals and their symbionts can adapt by 1–1.5°C, such mass bleaching events may not begin to recur at potentially harmful intervals until the latter half of the century. The delay could enable more time to alter the path of greenhouse gas emissions, although long-term “committed warming” even after stabilization of atmospheric CO2levels may still represent an additional long-term threat to corals.
Loss of androgen receptor binding to selective androgen response elements causes a reproductive phenotype in a knockin mouse model
Authors: Schauwaers Kris , De Gendt Karel , Saunders Philippa T. K. , Atanassova Nina , Haelens Annemie , Callewaert Leen , Moehren Udo , Swinnen Johannes V. , Verhoeven Guido , Verrijdt Guy , Claessens Frank
Published: March 2007

Androgens influence transcription of their target genes through the activation of the androgen receptor (AR) that subsequently interacts with specific DNA motifs in these genes. These DNA motifs, called androgen response elements (AREs), can be classified in two classes: the classical AREs, which are also recognized by the other steroid hormone receptors; and the AR-selective AREs, which display selectivity for the AR. Forin vitrointeraction with the selective AREs, the androgen receptor DNA-binding domain is dependent on specific residues in its second zinc-finger. To evaluate the physiological relevance of these selective elements, we generated a germ-line knockin mouse model, termed SPARKI (SPecificity-affecting AR KnockIn), in which the second zinc-finger of the AR was replaced with that of the glucocorticoid receptor, resulting in a chimeric protein that retains its ability to bind classical AREs but is unable to bind selective AREs. The reproductive organs of SPARKI males are smaller compared with wild-type animals, and they are also subfertile. Intriguingly, however, they do not display any anabolic phenotype. The expression of two testis-specific, androgen-responsive genes is differentially affected by the SPARKI mutation, which is correlated with the involvement of different types of response elements in their androgen responsiveness. In this report, we present the firstin vivoevidence of the existence of two functionally different types of AREs and demonstrate that AR-regulated gene expression can be targeted based on this distinction.
Evidence of spatially bound gene regulation in
Mus musculus
: Decreased gene expression proximal to microRNA genomic location
Authors: Inaoka Hidenori , Fukuoka Yutaka , Kohane Isaac S.
Published: March 2007

The extent, spatially and in time, of the phenomenon of localized decreased expression in the chromosomal vicinity of microRNA (miRNA) previously described in
Caenorhabditis elegans
is reproduced in
Mus musculus
across a wide range of tissues in several independent experiments. Computationally predicted miRNA targets are enriched in the vicinity of miRNAs, and transcription factors are identified as the class of genes that systematically exhibit this localized decrease. Also, those mRNA with AT-rich UTRs, particularly those that are not in the vicinity of CpG islands, most often exhibit this localized decrease. This localization broadens with the shift from developing to mature/differentiated tissues and suggests a developmentally controlled and spatially bound regulation.
PGC-1β controls mitochondrial metabolism to modulate circadian activity, adaptive thermogenesis, and hepatic steatosis
Authors: Sonoda Junichiro , Mehl Isaac R. , Chong Ling-Wa , Nofsinger Russell R. , Evans Ronald M.
Published: March 2007

The transcriptional coactivator peroxisome proliferator-activated receptor-γ coactivator 1β (PGC-1β) is believed to control mitochondrial oxidative energy metabolism by activating specific target transcription factors including estrogen-related receptors and nuclear respiratory factor 1, yet its physiological role is not yet clearly understood. To define its function
in vivo
, we generated and characterized mice lacking the functional PGC-1β protein [PGC-1β knockout (KO) mice]. PGC-1β KO mice are viable and fertile and show no overt phenotype under normal laboratory conditions. However, the KO mice displayed an altered expression in a large number of nuclear-encoded genes governing mitochondrial and metabolic functions in multiple tissues including heart, skeletal muscle, brain, brown adipose tissue, and liver. In contrast to PGC-1α KO mice that are reportedly hyperactive, PGC-1β KO mice show greatly decreased activity during the dark cycle. When acutely exposed to cold, the KO mice developed abnormal hypothermia and morbidity. Furthermore, high-fat feeding induced hepatic steatosis and increased serum triglyceride and cholesterol levels in the KO mice. These results suggest that PGC-1β in mouse plays a nonredundant role in controlling mitochondrial oxidative energy metabolism.
Cytoskeletal dynamics of human erythrocyte
Authors: Li Ju , Lykotrafitis George , Dao Ming , Suresh Subra
Published: March 2007

The human erythrocyte (red blood cell, RBC) demonstrates extraordinary ability to undergo reversible large deformation and fluidity. Such mechanical response cannot be consistently rationalized on the basis of fixed connectivity of the cell cytoskeleton that comprises the spectrin molecular network tethered to phospholipid membrane. Active topological remodeling of spectrin network has been postulated, although detailed models of such dynamic reorganization are presently unavailable. Here we present a coarse-grained cytoskeletal dynamics simulation with breakable protein associations to elucidate the roles of shear stress, specific chemical agents, and thermal fluctuations in cytoskeleton remodeling. We demonstrate a clear solid-to-fluid transition depending on the metabolic energy influx. The solid network's plastic deformation also manifests creep and yield regimes depending on the strain rate. This cytoskeletal dynamics model offers a means to resolve long-standing questions regarding the reference state used in RBC elasticity theory for determining the equilibrium shape and deformation response. In addition, the simulations offer mechanistic insights into the onset of plasticity and void percolation in cytoskeleton. These phenomena may have implication for RBC membrane loss and shape change in the context of hereditary hemolytic disorders such as spherocytosis and elliptocytosis.
Genomic analysis of the Mozambique strain of
Vibrio cholerae
O1 reveals the origin of El Tor strains carrying classical CTX prophage
Authors: Faruque Shah M. , Tam Vincent C. , Chowdhury Nityananda , Diraphat Pornphan , Dziejman Michelle , Heidelberg John F. , Clemens John D. , Mekalanos John J. , Nair G. Balakrish
Published: March 2007

Cholera outbreaks in subSaharan African countries are caused by strains of the El Tor biotype of toxigenic
Vibrio cholerae
O1. The El Tor biotype is the causative agent of the current seventh cholera pandemic, whereas the classical biotype, which was associated with the sixth pandemic, is now extinct. Besides other genetic differences the CTX prophages encoding cholera toxin in the two biotypes of
V. cholerae
O1 have distinct repressor (
rstR
) genes. However, recent incidences of cholera in Mozambique were caused by an El Tor biotype
V. cholerae
O1 strain that, unusually, carries a classical type (CTX
class
) prophage. We conducted genomic analysis of the Mozambique strain and its CTX prophage together with chromosomal phage integration sites to understand the origin of this atypical strain and its evolutionary relationship with the true seventh pandemic strain. These analyses showed that the Mozambique strain carries two copies of CTX
class
prophage located on the small chromosome in a tandem array that allows excision of the prophage, but the excised phage genome was deficient in replication and did not produce CTX
class
virion. Comparative genomic microarray analysis revealed that the strain shares most of its genes with the typical El Tor strain N16961 but did not carry the TLC gene cluster, and RS1 sequence, adjacent to the CTX prophage. Our data are consistent with the Mozambique strain's having evolved from a progenitor similar to the seventh pandemic strain, involving multiple recombination events and suggest a model for origination of El Tor strains carrying the classical CTX prophage.
Structure of the N-terminal domain of a type B1 G protein-coupled receptor in complex with a peptide ligand
Authors: Grace Christy Rani R. , Perrin Marilyn H. , Gulyas Jozsef , DiGruccio Michael R. , Cantle Jeffrey P. , Rivier Jean E. , Vale Wylie W. , Riek Roland
Published: March 2007

The corticotropin releasing factor (CRF) family of ligands and their receptors coordinate endocrine, behavioral, autonomic, and metabolic responses to stress and play additional roles within the cardiovascular, gastrointestinal, and other systems. The actions of CRF and the related urocortins are mediated by activation of two receptors, CRF-R1 and CRF-R2, belonging to the B1 family of G protein-coupled receptors. The short-consensus-repeat fold (SCR) within the first extracellular domain (ECD1) of the CRF receptor(s) comprises the major ligand binding site and serves to dock a peptide ligand via its C-terminal segment, thus positioning the N-terminal segment to interact with the receptor's juxtamembrane domains to activate the receptor. Here we present the 3D NMR structure of ECD1 of CRF-R2β in complex with astressin, a peptide antagonist. In the structure of the complex the C-terminal segment of astressin forms an amphipathic helix, whose entire hydrophobic face interacts with the short-consensus-repeat motif, covering a large intermolecular interface. In addition, the complex is characterized by intermolecular hydrogen bonds and a salt bridge. These interactions are quantitatively weighted by an analysis of the effects on the full-length receptor affinities using an Ala scan of CRF. These structural studies identify the major determinants for CRF ligand specificity and selectivity and support a two-step model for receptor activation. Furthermore, because of a proposed conservation of the fold for both the ECD1s and ligands, this structure can serve as a model for ligand recognition for the entire B1 receptor family.
A Drosophila melanogaster model of spinal muscular atrophy reveals a function for SMN in striated muscle
Authors: Rajendra T.K. , Gonsalvez Graydon B. , Walker Michael P. , Shpargel Karl B. , Salz Helen K. , Matera A. Gregory
Published: March 2007

Mutations in human survival motor neurons 1 (SMN1) cause spinal muscular atrophy (SMA) and are associated with defects in assembly of small nuclear ribonucleoproteins (snRNPs) in vitro. However, the etiological link between snRNPs and SMA is unclear. We have developed a Drosophila melanogaster system to model SMA in vivo. Larval-lethal Smn-null mutations show no detectable snRNP reduction, making it unlikely that these animals die from global snRNP deprivation. Hypomorphic mutations in Smn reduce dSMN protein levels in the adult thorax, causing flightlessness and acute muscular atrophy. Mutant flight muscle motoneurons display pronounced axon routing and arborization defects. Moreover, Smn mutant myofibers fail to form thin filaments and phenocopy null mutations in Act88F, which is the flight muscle–specific actin isoform. In wild-type muscles, dSMN colocalizes with sarcomeric actin and forms a complex with α-actinin, the thin filament crosslinker. The sarcomeric localization of Smn is conserved in mouse myofibrils. These observations suggest a muscle-specific function for SMN and underline the importance of this tissue in modulating SMA severity.
Absence of integrin-mediated TGFβ1 activation in vivo recapitulates the phenotype of TGFβ1-null mice
Authors: Yang Zhiwei , Mu Zhenyu , Dabovic Branka , Jurukovski Vladimir , Yu Dawen , Sung Joanne , Xiong Xiaozhong , Munger John S.
Published: March 2007

The multifunctional cytokine transforming growth factor (TGF) β1 is secreted in a latent complex with its processed propeptide (latency-associated peptide [LAP]). TGFβ1 must be functionally released from this complex before it can engage TGFβ receptors. One mechanism of latent TGFβ1 activation involves interaction of the integrins αvβ6 and αvβ8 with an RGD sequence in LAP; other putative latent TGFβ1 activators include thrombospondin-1, oxidants, and various proteases. To assess the contribution of RGD-binding integrins to TGFβ1 activation in vivo, we created a mutation in Tgfb1 encoding a nonfunctional variant of the RGD sequence (RGE). Mice with this mutation (Tgfb1RGE/RGE) display the major features of Tgfb1−/− mice (vasculogenesis defects, multiorgan inflammation, and lack of Langerhans cells) despite production of normal levels of latent TGFβ1. These findings indicate that RGD-binding integrins are requisite latent TGFβ1 activators during development and in the immune system.
Chromosome breakage after G2 checkpoint release
Authors: Deckbar Dorothee , Birraux Julie , Krempler Andrea , Tchouandong Leopoldine , Beucher Andrea , Walker Sarah , Stiff Tom , Jeggo Penny , Löbrich Markus
Published: March 2007

DNA double-strand break (DSB) repair and checkpoint control represent distinct mechanisms to reduce chromosomal instability. Ataxia telangiectasia (A-T) cells have checkpoint arrest and DSB repair defects. We examine the efficiency and interplay of ATM's G2 checkpoint and repair functions. Artemis cells manifest a repair defect identical and epistatic to A-T but show proficient checkpoint responses. Only a few G2 cells enter mitosis within 4 h after irradiation with 1 Gy but manifest multiple chromosome breaks. Most checkpoint-proficient cells arrest at the G2/M checkpoint, with the length of arrest being dependent on the repair capacity. Strikingly, cells released from checkpoint arrest display one to two chromosome breaks. This represents a major contribution to chromosome breakage. The presence of chromosome breaks in cells released from checkpoint arrest suggests that release occurs before the completion of DSB repair. Strikingly, we show that checkpoint release occurs at a point when approximately three to four premature chromosome condensation breaks and ∼20 γH2AX foci remain.
Requirement of ZO-1 for the formation of belt-like adherens junctions during epithelial cell polarization
Authors: Ikenouchi Junichi , Umeda Kazuaki , Tsukita Sachiko , Furuse Mikio , Tsukita Shoichiro
Published: March 2007

The molecular mechanisms of how primordial adherens junctions (AJs) evolve into spatially separated belt-like AJs and tight junctions (TJs) during epithelial polarization are not well understood. Previously, we reported the establishment of ZO-1/ZO-2–deficient cultured epithelial cells (1[ko]/2[kd] cells), which lacked TJs completely. In the present study, we found that the formation of belt-like AJs was significantly delayed in 1(ko)/2(kd) cells during epithelial polarization. The activation of Rac1 upon primordial AJ formation is severely impaired in 1(ko)/2(kd) cells. Our data indicate that ZO-1 plays crucial roles not only in TJ formation, but also in the conversion from “fibroblastic” AJs to belt-like “polarized epithelial” AJs through Rac1 activation. Furthermore, to examine whether ZO-1 itself mediate belt-like AJ and TJ formation, respectively, we performed a mutational analysis of ZO-1. The requirement for ZO-1 differs between belt-like AJ and TJ formation. We propose that ZO-1 is directly involved in the establishment of two distinct junctional domains, belt-like AJs and TJs, during epithelial polarization.
Cytokines induced during chronic hepatitis B virus infection promote a pathway for NK cell–mediated liver damage
Authors: Dunn Claire , Brunetto Maurizia , Reynolds Gary , Christophides Theodoros , Kennedy Patrick T. , Lampertico Pietro , Das Abhishek , Lopes A. Ross , Borrow Persephone , Williams Kevin , Humphreys Elizabeth , Afford Simon , Adams David H. , Bertoletti Antonio , Maini Mala K.
Published: March 2007

Hepatitis B virus (HBV) causes chronic infection in more than 350 million people worldwide. It replicates in hepatocytes but is non-cytopathic; liver damage is thought to be immune mediated. Here, we investigated the role of innate immune responses in mediating liver damage in patients with chronic HBV infection. Longitudinal analysis revealed a temporal correlation between flares of liver inflammation and fluctuations in interleukin (IL)-8, interferon (IFN)-α, and natural killer (NK) cell expression of tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) directly ex vivo. A cross-sectional study confirmed these findings in patients with HBV-related liver inflammation compared with healthy carriers. Activated, TRAIL-expressing NK cells were further enriched in the liver of patients with chronic HBV infection, while their hepatocytes expressed increased levels of a TRAIL death–inducing receptor. IFN-α concentrations found in patients were capable of activating NK cells to induce TRAIL-mediated hepatocyte apoptosis in vitro. The pathogenic potential of this pathway could be further enhanced by the ability of the IFN-α/IL-8 combination to dysregulate the balance of death-inducing and regulatory TRAIL receptors expressed on hepatocytes. We conclude that NK cells may contribute to liver inflammation by TRAIL-mediated death of hepatocytes and demonstrate that this non-antigen–specific mechanism can be switched on by cytokines produced during active HBV infection.