bluuebunny/crossref_metadata_2025 huggingface dataset:
Diurnally variable δ18O signatures of soil CO2 fluxes indicate carbonic anhydrase activity in a forest soil
Authors: Seibt U. , Wingate L. , Lloyd J. , Berry J. A.
Published: November 2006

Oxygen isotopes are valuable tools for studying the gas exchange between terrestrial ecosystems and the atmosphere. We determined the δ18O signatures of soil CO2 fluxes from soil chamber measurements over the diurnal cycle in September 2000, May 2001 and July 2001 in a Sitka spruce plantation in Scotland. Concurrent estimates of the δ18O composition of soil water were obtained from soil samples collected in the vicinity of the chambers. The observed δ18O signatures of net soil CO2 fluxes were diurnally variable and strongly depleted compared to those expected from a simple evasion of respired CO2 at isotopic equilibrium with soil water. We then simulated the δ18O signatures of soil CO2 fluxes using a model of soil gas exchange that includes atmospheric invasion of CO2 with concurrent isotopic equilibration with soil water and evasion of the equilibrated CO2. This brought the modeled δ18O signatures closer to the observations, but complete agreement was only achieved when acceleration of isotopic exchange between CO2 and soil water by carbonic anhydrase activity was included. We hypothesize that carbonic anhydrase is present in the litter or surface soil layers. This introduces a feedback that can result in diurnally variable δ18O signatures of net soil CO2 fluxes. Such effects can only be captured in models that have an explicit description of the canopy air space with a variable δ18O signature of CO2.
Stress evolution in nanocrystalline diamond films produced by chemical vapor deposition
Authors: Li Hao , Sheldon Brian W. , Kothari Abhishek , Ban Zhigang , Walden Barbara L.
Published: November 2006

Nanocrystalline diamond films were grown on silicon substrates by microwave plasma enhanced chemical vapor deposition with 1% methane, 2%–10% hydrogen, and argon. High resolution transmission electron microscope images and selected area electron diffraction patterns confirm that the films consist of 10–20nm sized diamond grains. The residual and intrinsic stresses were investigated using wafer curvature. Intrinsic stresses were always tensile, with higher H2 concentrations generally leading to higher stresses. Annealing the films in a hydrogen plasma significantly increased these stresses. These hydrogen induced changes also appear to alter stress levels and stress gradients during the growth process itself. Raman spectra revealed subtle changes in the chemical bonding that were correlated with some of the stress variations. These results suggest that grain boundary bonding and hydrogen induced reactions at the grain boundaries can influence the intrinsic stresses in nanocrystalline diamond films.
The electronic properties of amorphous and crystallized In2O3 films
Authors: Nakazawa Hiromi , Ito Yuko , Matsumoto Eiji , Adachi Kenji , Aoki Nobuyuki , Ochiai Yuichi
Published: November 2006

Polycrystalline In2O3 films with high crystallinity were prepared by annealing the amorphous In2O3 films deposited at room temperature by using dc/rf sputtering method. General electronic behaviors of both these amorphous and polycrystalline films have been investigated by means of Hall effect and resistivity measurements at temperatures between 4.2 and 300K. For the amorphous films, ionized impurity scattering dominates the electronic transport, and Hall mobility agrees well with the theory of degenerate semiconductors with divalent impurity scattering centers. On the other hand, the conduction mechanism of the polycrystalline films is governed dominantly by phonon scattering, since these films exhibit a clearly positive temperature coefficient of resistivity with the maximum Hall mobility of 150cm2∕Vs at 300K and 230cm2∕Vs at 4.2K, with little change in carrier concentration between these temperatures. Conductivity of both the amorphous and polycrystalline films is found to show a linear relationship in a double-logarithmic plot against carrier concentration between 4×1015 and 5×1020cm−3, a typical behavior of the impurity semiconductors with parabolic conduction band. For each set of films with the same thermal history, Hall mobility is found to vary on a convex upward curve with respect to carrier concentration. This behavior suggests a general and strong correlation of the structural defects introduced upon deposition and localization of conduction electrons with electron mobility, which led to a proposition of three categories for temperature coefficient of resistivity with major transport mechanisms of phonon scattering, divalent impurity scattering, and weak localization, respectively.
Dielectric response of perforated two-dimensional lossy heterostructures: A finite-element approach
Authors: Mejdoubi Abdelilah , Brosseau Christian
Published: November 2006

Finite-element simulations of the effective complex permittivity of perforated two-dimensional (2D) lossy heterostructures are reported. The method is computationally inexpensive and is suited for simulations where the tacit assumptions are the following: (1) the composite behaves like a homogeneous medium with an effective (relative) permittivity ε=ε′−jε″ and (2) the porous medium is characterized by a perforated 2D object having arbitrary shape, e.g., split rings, honeycomb lattice, and Sierpinski carpet. These shape functionals have many applications to the scattering of wave and are also important for describing effective properties of particle dispersions. Our calculations provide insights into a variety of tuning parameters influencing ε including the surface fraction and perimeter of inclusion, the permittivity contrast between the inclusion and the matrix, and the shape of the holes. For a 2D composite structure containing a deterministic fractal inclusion we explicitly demonstrate that the ε′ and ε″ changes with reduced perimeter can be modeled according to the same similarity transformation, at least for the first four iterations of the fractal pattern. We quantify the effect of increasing the internal porosity on ε′ and ε″ for different types of perforated structures and show that composites containing split rings can achieve very small ε′ and ε″ in a large range of porosity. We find also that such geometries are auspicious for local field enhancement. The origin of these enhancements lies in the breakdown of the dipolar approximation which is often used to evaluate the effective permittivity of composite materials. These results can provide the experimenter with a method for assessing permittivity measurements and suggest that the successful integration of voided material in microwave electronic devices depends on the morphology of the embedded porosity.
X-ray diffraction study of crystal plane distortion in silicon carbide substrates
Authors: Mastro M. A. , Fatemi M. , Gaskill D. K. , Lew K.-K. , Van Mil B. L. , Eddy C. R. , Wood C. E. C.
Published: November 2006

Bulk growth of 4H-SiC is challenging due to the required high growth temperatures and gradients used in sublimation physical vapor transport that are difficult to control, particularly over large diameter boules. We used x-ray diffraction mapping to show concave crystal plane curvature in substrates from five commercial suppliers with two suppliers producing wafers with ⩽2° curvature. The extent of curvature varied little for substrates from any particular supplier. Maps of peak position and full width at half maximum from symmetric and asymmetric reflections were used to identify defective regions in the crystal. Closer examination of the rocking curves in the defective regions found a low density of low angle grain boundaries only in substrates from one supplier.
Optical band gap studies on lithium aluminum silicate glasses doped with Cr3+ ions
Authors: El-Diasty Fouad , Abdel Wahab Fathy A. , Abdel-Baki Manal
Published: November 2006

Lithium aluminum silicate glass system (LAS) implanted with chromium ions is prepared. The reflectance and transmittance measurements are used to determine the dispersion of absorption coefficient. The optical data are explained in terms of the different oxidation states adopted by the chromium ions into the glass network. It is found that the oxidation state of the chromium depends on its concentration. Across a wide spectral range, 0.2–1.6μm, analysis of the fundamental absorption edge provides values for the average energy band gaps for allowed direct and indirect transitions. The optical absorption coefficient just below the absorption edge varies exponentially with photon energy indicating the presence of Urbach’s tail. Such tail is decreased with the increase of the chromium dopant. From the analysis of the optical absorption data, the absorption peak at ground state exciton energy, the absorption at band gap, and the free exciton binding energy are determined. The extinction coefficient data are used to determine the Fermi energy level of the studied glasses. The metallization criterion is obtained and discussed exploring the nature of the glasses. The measured IR spectra of the different glasses are used to throw some light on the optical properties of the present glasses correlating them with their structure and composition.
Injection, trapping, and acceleration of electrons in a three-dimensional nonlinear laser wakefield
Authors: Kalmykov S. Yu. , Gorbunov L. M. , Mora P. , Shvets G.
Published: November 2006

It is demonstrated that the accelerating and focusing phases of the nonlinear three-dimensional axisymmetric laser wake can almost entirely overlap starting from a certain distance behind the laser pulse in homogeneous plasma. Such field structure results from the curvature of phase fronts due to the radially inhomogeneous relativistic shift of plasma frequency. Consequently, the number of trapped low-energy electrons can be much greater than that predicted by the linear wake theory. This effect is favorable for quasimonoenergetic acceleration of a considerable charge (several hundreds of pC) to about 1GeV per electron in the plasma wakefield driven by an ultrashort (∼30fs) weakly focused (r0∼100μm) petawatt laser pulse.
Transport and noise in resonant tunneling diode using self-consistent Green’s function calculation
Authors: Do V. Nam , Dollfus P. , Lien Nguyen V.
Published: November 2006

The fully self-consistent nonequilibrium Green’s function approach to quantum transport is developed to investigate one-dimensional nanoscale devices. Numerical calculations performed for resonant tunneling diodes of different designs and at different temperatures show reasonable results for the potential and electron density profiles, as well as for the transmission coefficient and the current-voltage characteristics. The resonant behavior is discussed in detail with respect to the quantum-well width, the barrier thickness, and the temperature. It is also shown that the current noise spectral density can be straightforwardly calculated for both the coherent and the sequential tunneling models. In qualitative agreement with experiments, the obtained results highlight the role of charge interaction, which causes a fluctuation of the density of states in the well and therefore a noise enhancement in the negative differential conductance region.
Acoustic attenuation measurements in transparent materials in the hypersonic range by picosecond ultrasonics
Authors: Emery P. , Devos A.
Published: November 2006

The authors report on acoustic attenuation measurements in transparent thin films by picosecond ultrasonics. This ultrafast technique has already been proposed for such measurements but usually attenuation is overestimated and a specific sample configuration is needed. Here they present another way of using this technique which overcomes both difficulties. Experimental results obtained for silica show a very good agreement with literature. This validates the protocol which is then applied to various other materials used in microelectronics.
Growth and fabrication of InGaNP-based yellow-red light emitting diodes
Authors: Odnoblyudov V. A. , Tu C. W.
Published: November 2006

The authors describe the growth and fabrication of InGaNP quantum well (QW)-based yellow-red light emitting diodes (LEDs) grown directly on transparent GaP (100) wafers. The dependence of InyGa1−yN0.005P0.995∕GaP conduction and valence band offsets on the In composition was calculated, and the dependence of AlxGa1−xP∕GaP band offsets on the Al concentration was also calculated. Using Al0.14Ga0.86P cladding layers increases the light output from a LED chip by 15%. InGaNP∕GaP multiple QW LED structures show an increase of light output and saturation current.
Detection of acoustically induced electromagnetic radiation
Authors: Ikushima Kenji , Watanuki Shunsuke , Komiyama Susumu
Published: November 2006

Electromagnetomechanical response of materials is detected through electromagnetic radiation induced by ultrasound waves. Target specimens are placed in the focusing zone of the ultrasound waves at a distance of ∼60mm from an acoustic generator. The radiation is picked up by a narrow-band loop antenna tuned to the ultrasound frequency. Due to the delay time caused by ultrasound wave propagation in the medium (water), the pulsed electromagnetic radiation from a target is well separated (temporally by ∼40μs) from the apparent signal attributed to the generator, allowing unambiguous and sensitive detection of true signals. Upon stimulation with ultrasounds, emission of electromagnetic radiation is found in bones, woods, plastics, and ferrites as well as a standard piezoelectric material (GaAs).
Nanodroplets deposited in microarrays by femtosecond Ti:sapphire laser-induced forward transfer
Authors: Banks David P. , Grivas Christos , Mills John D. , Eason Robert W. , Zergioti Ioanna
Published: November 2006

The authors present the deposition of nanoscale droplets of Cr using femtosecond Ti:sapphire laser-induced forward transfer. Deposits around 300nm in diameter, significantly smaller than any previously reported, are obtained from a 30nm thick source film. Deposit size, morphology, and adhesion to a receiver substrate as functions of applied laser fluence are investigated. The authors show that deposits can be obtained from previously irradiated areas of the source material film with negligible loss of deposition quality, allowing subspot size period microarrays to be produced without the need to move the source film.
Initial cation stoichiometry and current-voltage behavior in Sc-doped calcium copper titanate
Authors: Chung Sung-Yoon , Lee Sirk-Ihl , Choi Jin-Hoon , Choi Si-Young
Published: November 2006

It is demonstrated that either a strong nonlinear or a nearly Ohmic behavior in current-voltage relationship can be distinctively represented in Sc-doped polycrystalline CaCu3Ti4O12, with variation in the initial composition of samples. Through conductive atomic force microscopy and impedance spectroscopy, such a definitive difference in the electrical property was found to depend on the presence of a large electrostatic barrier at the grain boundaries. The effect of Sc ions on the boundary potential barrier and the conductance of single grains is discussed. Findings suggest a different site selectivity of Sc in the lattice in terms of the initial cation stoichiometry.
The evaluation of the far-field integral in the Green’s function representation for steady Oseen flow
Authors: Fishwick Nina , Chadwick Edmund
Published: November 2006

Consider the Green’s function representation of an exterior problem in steady Oseen flow. The far-field integral in the formulation is shown to be zero.
Identification of the α2-δ-1 subunit of voltage-dependent calcium channels as a molecular target for pain mediating the analgesic actions of pregabalin
Authors: Field Mark J. , Cox Peter J. , Stott Emma , Melrose Heather , Offord James , Su Ti-Zhi , Bramwell Steve , Corradini Laura , England Steven , Winks Joanna , Kinloch Ross A. , Hendrich Jan , Dolphin Annette C. , Webb Tony , Williams Dic
Published: November 2006

Neuropathic pain is a debilitating condition affecting millions of people around the world and is defined as pain that follows a lesion or dysfunction of the nervous system. This type of pain is difficult to treat, but the novel compounds pregabalin (Lyrica) and gabapentin (Neurontin) have proven clinical efficacy. Unlike traditional analgesics such as nonsteroidal antiinflammatory drugs or narcotics, these agents have no frank antiinflammatory actions and no effect on physiological pain. Although extensive preclinical studies have led to a number of suggestions, until recently their mechanism of action has not been clearly defined. Here, we describe studies on the analgesic effects of pregabalin in a mutant mouse containing a single-point mutation within the gene encoding a specific auxiliary subunit protein (α2-δ-1) of voltage-dependent calcium channels. The mice demonstrate normal pain phenotypes and typical responses to other analgesic drugs. We show that the mutation leads to a significant reduction in the binding affinity of pregabalin in the brain and spinal cord and the loss of its analgesic efficacy. These studies show conclusively that the analgesic actions of pregabalin are mediated through the α2-δ-1 subunit of voltage-gated calcium channels and establish this subunit as a therapeutic target for pain control.
Hexim1 sequesters positive transcription elongation factor b from the class II transactivator on MHC class II promoters
Authors: Kohoutek Jiri , Blazek Dalibor , Peterlin B. Matija
Published: November 2006

The class II transactivator (CIITA) is the master integrator of expression of MHC class II genes. It interacts with variety of basal transcription factors to initiate and elongate transcription of these genes. Among others, it recruits positive transcription elongation factor b (P-TEFb) to MHC class II promoters. In cells, P-TEFb is found in small active or large inactive complexes. The large complex is composed of P-TEFb, 7SK small nuclear RNA, and hexamethylene bisacetamide-inducible protein 1 (Hexim1). The present study identifies Hexim1 as a potent inhibitor of CIITA-mediated transcription. Not only the exogenously expressed but also IFN-γ-induced CIITA was inhibited by Hexim1. This inhibition did not result from an association between Hexim1 and CIITA but depended on the intact Cyclin T1-binding domain in Hexim1. Importantly, Hexim1 sequestered P-TEFb from CIITA, as documented by binding competition and ChIP assays. Conversely, the depletion of Hexim1 from cells by siRNA increased CIITA-mediated transcription. Thus, modulating ratios between active and inactive P-TEFb complexes is an additional mechanism of regulating transcriptional activators such as CIITA.
Angiopoietin-like protein 4 converts lipoprotein lipase to inactive monomers and modulates lipase activity in adipose tissue
Authors: Sukonina Valentina , Lookene Aivar , Olivecrona Thomas , Olivecrona Gunilla
Published: November 2006

Lipoprotein lipase (LPL) has a central role in lipoprotein metabolism to maintain normal lipoprotein levels in blood and, through tissue specific regulation of its activity, to determine when and in what tissues triglycerides are unloaded. Recent data indicate that angiopoietin-like protein (Angptl)-4 inhibits LPL and retards lipoprotein catabolism. We demonstrate here that the N-terminal coiled-coil domain of Angptl-4 binds transiently to LPL and that the interaction results in conversion of the enzyme from catalytically active dimers to inactive, but still folded, monomers with decreased affinity for heparin. Inactivation occurred with less than equimolar ratios of Angptl-4 to LPL, was strongly temperature-dependent, and did not consume the Angptl-4. Furthermore, we show that Angptl-4 mRNA in rat adipose tissue turns over rapidly and that changes in the Angptl-4 mRNA abundance are inversely correlated to LPL activity, both during the fed-to-fasted and fasted-to-fed transitions. We conclude that Angptl-4 is a fasting-induced controller of LPL in adipose tissue, acting extracellularly on the native conformation in an unusual fashion, like an unfolding molecular chaperone.
Adaptive wavefront correction in two-photon microscopy using coherence-gated wavefront sensing
Authors: Rueckel Markus , Mack-Bucher Julia A. , Denk Winfried
Published: November 2006

The image quality of a two-photon microscope is often degraded by wavefront aberrations induced by the specimen. We demonstrate here that resolution and signal size in two-photon microcopy can be substantially improved, even in living biological specimens, by adaptive wavefront correction based on sensing the wavefront of coherence-gated backscattered light (coherence-gated wavefront sensing, CGWS) and wavefront control by a deformable mirror. A nearly diffraction-limited focus can be restored even for strong aberrations. CGWS-based wavefront correction should be applicable to samples with a wide range of scattering properties and it should be possible to perform real-time pixel-by-pixel correction even at fast scan speeds.
Kv1.3 channels are a therapeutic target for T cell-mediated autoimmune diseases
Authors: Beeton Christine , Wulff Heike , Standifer Nathan E. , Azam Philippe , Mullen Katherine M. , Pennington Michael W. , Kolski-Andreaco Aaron , Wei Eric , Grino Alexandra , Counts Debra R. , Wang Ping H. , LeeHealey Christine J. , S. Andrews Brian , Sankaranarayanan Ananthakrishnan , Homerick Daniel , Roeck Werner W. , Tehranzadeh Jamshid , Stanhope Kimber L. , Zimin Pavel , Havel Peter J. , Griffey Stephen , Knaus Hans-Guenther , Nepom Gerald T. , Gutman George A. , Calabresi Peter A. , Chandy K. George
Published: November 2006

Autoreactive memory T lymphocytes are implicated in the pathogenesis of autoimmune diseases. Here we demonstrate that disease-associated autoreactive T cells from patients with type-1 diabetes mellitus or rheumatoid arthritis (RA) are mainly CD4+CCR7−CD45RA−effector memory T cells (TEMcells) with elevated Kv1.3 potassium channel expression. In contrast, T cells with other antigen specificities from these patients, or autoreactive T cells from healthy individuals and disease controls, express low levels of Kv1.3 and are predominantly naïve or central-memory (TCM) cells. In TEMcells, Kv1.3 traffics to the immunological synapse during antigen presentation where it colocalizes with Kvβ2, SAP97, ZIP, p56lck, and CD4. Although Kv1.3 inhibitors [ShK(L5)-amide (SL5) and PAP1] do not prevent immunological synapse formation, they suppress Ca2+-signaling, cytokine production, and proliferation of autoantigen-specific TEMcells at pharmacologically relevant concentrations while sparing other classes of T cells. Kv1.3 inhibitors ameliorate pristane-induced arthritis in rats and reduce the incidence of experimental autoimmune diabetes in diabetes-prone (DP-BB/W) rats. Repeated dosing with Kv1.3 inhibitors in rats has not revealed systemic toxicity. Further development of Kv1.3 blockers for autoimmune disease therapy is warranted.
Apoptosis in retinal degeneration involves cross-talk between apoptosis-inducing factor (AIF) and caspase-12 and is blocked by calpain inhibitors
Authors: Sanges Daniela , Comitato Antonella , Tammaro Roberta , Marigo Valeria
Published: November 2006

Molecular mechanisms underlying apoptosis in retinitis pigmentosa, as in other neurodegenerative diseases, are still elusive, and this fact hampers the development of a cure for this blinding disease. We show that two apoptotic pathways, one from the mitochondrion and one from the endoplasmic reticulum, are coactivated during the degenerative process in an animal model of retinitis pigmentosa, the
rd1
mouse. We found that both AIF and caspase-12 translocate to the nucleus of dying photoreceptors
in vivo
and in an
in vitro
cellular model. Translocation of both apoptotic factors depends on changes in intracellular calcium homeostasis and on calpain activity. Knockdown experiments defined that AIF plays the major role in this apoptotic event, whereas caspase-12 has a reinforcing effect. This study provides a link between two executor caspase-independent apoptotic pathways involving mitochondrion and endoplasmic reticulum in a degenerating neuron.
Quinone sensing by the circadian input kinase of the cyanobacterial circadian clock
Authors: Ivleva Natalia B. , Gao Tiyu , LiWang Andy C. , Golden Susan S.
Published: November 2006

Circadian rhythms are endogenous cellular programs that time metabolic and behavioral events to occur at optimal times in the daily cycle. Light and dark cycles synchronize the endogenous clock with the external environment through a process called entrainment. Previously, we identified the bacteriophytochrome-like circadian input kinase CikA as a key factor for entraining the clock in the cyanobacterium
Synechococcus elongatus
PCC 7942. Here, we present evidence that CikA senses not light but rather the redox state of the plastoquinone pool, which, in photosynthetic organisms, varies as a function of the light environment. Furthermore, CikA associates with the Kai proteins of the circadian oscillator, and it influences the phosphorylation state of KaiC during resetting of circadian phase by a dark pulse. The abundance of CikA varies inversely with light intensity, and its stability decreases in the presence of the quinone analog 2,5-dibromo-3-methyl-6-isopropyl-
p
-benzoquinone (DBMIB). The pseudo-receiver domain of CikA is crucial for sensitivity to DBMIB, and it binds the quinone directly, a demonstration of a previously unrecognized ligand-binding role for the receiver fold. Our results suggest that resetting the clock in
S. elongatus
is metabolism-dependent and that it is accomplished through the interaction of the circadian oscillator with CikA.
An essential role of NF-κB in the “tumor-like” phenotype of arthritic synoviocytes
Authors: Li Xiangli , Makarov Sergei S.
Published: November 2006

A hallmark of rheumatoid arthritis is the formation of an aggressive, tumor-like structure called pannus that erodes the joint. A major cellular component of the pannus is the fibroblast-like synoviocyte (FLS), whose morphology strikingly resembles that of a transformed cell, but underlying mechanisms of this “transformation” are not known. Here, using animal models of rheumatoid arthritis, we show that arthritic FLS contain a substantial (>30%) fraction of bone marrow-derived precursors that can differentiatein vitrointo various mesenchymal cell types, but inflammation prevents the multilineage differentiation. We show that the transcription factor NF-κB plays the key role in the repression of osteogenic and adipogenic differentiation of arthritic FLS. Furthermore, we show that specific activation of NF-κB profoundly enhances proliferation, motility, and matrix-degrading activity of FLS. We thus propose that arthritic FLS are mesenchymal stem cells whose differentiation is arrested at early stages of differentiation by activation of NF-κB.
Self-renewal of embryonic stem cells by a small molecule
Authors: Chen Shuibing , Do Jeong Tae , Zhang Qisheng , Yao Shuyuan , Yan Feng , Peters Eric C. , Schöler Hans R. , Schultz Peter G. , Ding Sheng
Published: November 2006

A cell-based screen of chemical libraries was carried out to identify small molecules that control the self-renewal of ES cells. A previously uncharacterized heterocycle, SC1, was discovered that allows one to propagate murine ES cells in an undifferentiated, pluripotent state under chemically defined conditions in the absence of feeder cells, serum, and leukemia inhibitory factor. Long-term SC1-expanded murine ES cells can be differentiated into cells of the three primary germ layers
in vitro
and also can generate chimeric mice and contribute to the germ line
in vivo
. Biochemical and cellular experiments suggest that SC1 works through dual inhibition of RasGAP and ERK1. Molecules of this kind may not only facilitate practical applications of stem cells in research and therapy, but also provide previously undescribed insights into the complex biology of stem cells.
Recent Southeast Asian domestication and Lapita dispersal of sacred male pseudohermaphroditic “tuskers” and hairless pigs of Vanuatu
Authors: Lum J. Koji , McIntyre James K. , Greger Douglas L. , Huffman Kirk W. , Vilar Miguel G.
Published: November 2006

Recent analyses of global pig populations revealed strict correlations between mtDNA phylogenies and geographic locations. An exception was the monophyletic “Pacific clade” (PC) of pigs not previously linked to any specific location. We examined mtDNA sequences of two varieties of Vanuatu sacred pigs, the male pseudohermaphroditic
Narave
from the island of Malo (
n
= 9) and the hairless
Kapia
from the island of Tanna (
n
= 9), as well as control pigs (
n
= 21) from the islands of Malo, Tanna, and Epi and compared them with GenBank sequences to determine (
i
) the distribution of PC and introduced domestic lineages within Vanuatu, (
ii
) relationship between the
Narave
and
Kapia
, and (
iii
) origin of the PC. All of the
Narave
share two PC mtDNA sequences, one of which matches the sequence of a
Narave
collected in 1927, consistent with an unbroken maternal descent of these intersex pigs from the original pigs brought to Vanuatu 3,200 years ago. One-third of the
Kapia
share a single PC lineage also found in the
Narave
. The remaining
Kapia
lineages are associated with recently introduced, globally distributed domestic breeds. The predominant
Narave
lineage is also shared with two wild boars from Vietnam. These data suggest that PC pigs were recently domesticated within Southeast Asia and dispersed during the human colonization of Remote Oceania associated with the Lapita cultural complex. More extensive sampling of Southeast Asian wild boar diversity may refine the location of Pacific pig domestication and potentially the proximate homeland of the Lapita cultural complex.
Astrocyte elevated gene-1 (
AEG-1
) is a target gene of oncogenic Ha-ras requiring phosphatidylinositol 3-kinase and c-Myc
Authors: Lee Seok-Geun , Su Zao-Zhong , Emdad Luni , Sarkar Devanand , Fisher Paul B.
Published: November 2006

It is well established that Ha-
ras
and c-
myc
genes collaborate in promoting transformation, tumor progression, and metastasis. However, the precise mechanism underlying this cooperation remains unclear. In the present study, we document that astrocyte elevated gene-1 (
AEG-1
) is a downstream target molecule of Ha-
ras
and c-
myc
, mediating their tumor-promoting effects. AEG-1 expression is elevated in diverse neoplastic states, it cooperates with Ha-ras to promote transformation, and its overexpression augments invasion of transformed cells, demonstrating its functional involvement in Ha-ras-mediated tumorigenesis. We now document that AEG-1 expression is markedly induced by oncogenic Ha-ras, activating the phosphatidylinositol 3-kinase signaling pathway that augments binding of c-Myc to key E-box elements in the
AEG-1
promoter, thereby regulating
AEG-1
transcription. In addition, Ha-ras-mediated colony formation is inhibited by
AEG-1
siRNA. This is a demonstration that Ha-ras activation of a tumor-promoting gene is regulated directly by c-Myc DNA binding via phosphatidylinositol 3-kinase signaling, thus revealing a previously uncharacterized mechanism of Ha-ras-mediated oncogenesis through AEG-1.
AMP-activated protein kinase regulates the assembly of epithelial tight junctions
Authors: Zhang Li , Li Ji , Young Lawrence H. , Caplan Michael J.
Published: November 2006

AMP activated protein kinase (AMPK), a sensor of cellular energy status in all eukaryotic cells, is activated by LKB1-dependent phosphorylation. Recent studies indicate that activated LKB1 induces polarity in epithelial cells and that this polarization is accompanied by the formation of tight junction structures. We wished to determine whether AMPK also contributes to the assembly of tight junctions in the epithelial cell polarization process. We found that AMPK is activated during calcium-induced tight junction assembly. Activation of AMPK by 5-aminoimidazole-4-carboxamide ribonucleoside facilitates tight junction assembly under conditions of normal extracellular Ca
2+
concentrations and initiates tight junction assembly in the absence of Ca
2+
as revealed by the relocation of
zonula occludens
1, the establishment of transepithelial electrical resistance, and the paracellular flux assay. Expression of a dominant negative AMPK construct inhibits tight junction assembly in MDCK cells, and this defect in tight junction assembly can be partially ameliorated by rapamycin. These results suggest that AMPK plays a role in the regulation of tight junction assembly.
Adenosine A2A receptor activation reduces hepatic ischemia reperfusion injury by inhibiting CD1d-dependent NKT cell activation
Authors: Lappas Courtney M. , Day Yuan-Ji , Marshall Melissa A. , Engelhard Victor H. , Linden Joel
Published: November 2006

Ischemia reperfusion injury results from tissue damage during ischemia and ongoing inflammation and injury during reperfusion. Liver reperfusion injury is reduced by lymphocyte depletion or activation of adenosine A2A receptors (A2ARs) with the selective agonist 4- {3-[6-amino-9-(5-ethylcarbamoyl-3,4-dihydroxy-tetrahydro-furan-2-yl)-9H-purin-2-yl]- prop-2-ynyl}-cyclohexanecarboxylic acid methyl ester (ATL146e). We show that NKT cells are stimulated to produce interferon (IFN)-γ by 2 h after the initiation of reperfusion, and the use of antibodies to deplete NK1.1-positive cells (NK and NKT) or to block CD1d-mediated glycolipid presentation to NKT cells replicates, but is not additive to, the protection afforded by ATL146e, as assessed by serum alanine aminotransferase elevation, histological necrosis, neutrophil accumulation, and serum IFN-γ elevation. Reduced reperfusion injury observed in RAG-1 knockout (KO) mice is restored to the wild-type (WT) level by adoptive transfer of NKT cells purified from WT or A2AR KO mice but not IFN-γ KO mice. Additionally, animals with transferred A2AR−/− NKT cells are not protected from hepatic reperfusion injury by ATL146e. In vitro, ATL146e potently inhibits both anti-CD3 and α-galactosylceramide–triggered production of IFN-γ by NKT cells. These findings suggest that hepatic reperfusion injury is initiated by the CD1d-dependent activation of NKT cells, and the activation of these cells is inhibited by A2AR activation.
On the origin of biochemistry at an alkaline hydrothermal vent
Authors: Martin William , Russell Michael J
Published: November 2006

A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood–Ljungdahl) pathway of CO2fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood–Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO2reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as probable candidates for central involvement in prebiotic chemistry: metal sulphides, formate, carbon monoxide, methyl sulphide, acetate, formyl phosphate, carboxy phosphate, carbamate, carbamoyl phosphate, acetyl thioesters, acetyl phosphate, possibly carbonyl sulphide and eventually pterins. Carbon might have entered early metabolism via reactions hardly different from those in the modern Wood–Ljungdahl pathway, the pyruvate synthase reaction and the incomplete reverse citric acid cycle. The key energy-rich intermediates were perhaps acetyl thioesters, with acetyl phosphate possibly serving as the universal metabolic energy currency prior to the origin of genes. Nitrogen might have entered metabolism as geochemical NH3via two routes: the synthesis of carbamoyl phosphate and reductive transaminations of α-keto acids. Together with intermediates of methyl synthesis, these two routes of nitrogen assimilation would directly supply all intermediates of modern purine and pyrimidine biosynthesis. Thermodynamic considerations related to formyl pterin synthesis suggest that the ability to harness a naturally pre-existing proton gradient at the vent–ocean interface via an ATPase is older than the ability to generate a proton gradient with chemistry that is specified by genes.
Genetic influences on the neural basis of social cognition
Authors: Skuse David
Published: November 2006

The neural basis of social cognition has been the subject of intensive research in both human and non-human primates. Exciting, provocative and yet consistent findings are emerging. A major focus of interest is the role of efferent and afferent connectivity between the amygdala and the neocortical brain regions, now believed to be critical for the processing of social and emotional perceptions. One possible component is a subcortical neural pathway, which permits rapid and preconscious processing of potentially threatening stimuli, and it leads from the retina to the superior colliculus, to the pulvinar nucleus of the thalamus and then to the amygdala. This pathway is activated by direct eye contact, one of many classes of potential threat, and may be particularly responsive to the ‘whites of the eyes’. In humans, autonomic arousal evoked by this stimulus is associated with the activity in specific cortical regions concerned with processing visual information from faces. The integrated functioning of these pathways is modulated by one or more X-linked genes, yet to be identified. The emotional responsiveness of the amygdala, and its associated circuits, to social threat is also influenced by functional polymorphisms in the promoter of the serotonin transporter gene. We still do not have a clear account of how specific allelic variation, in candidate genes, increases susceptibility to developmental disorders, such as autism, or psychiatric conditions, such as anxiety or depressive illness. However, the regulation of emotional responsiveness to social cues lies at the heart of the problem, and recent research indicates that we may be nearing a deeper and more comprehensive understanding.
Reproductive strategy, sexual development and attraction to facial characteristics
Authors: Cornwell R. Elisabeth , Law Smith Miriam J , Boothroyd Lynda G , Moore Fhionna R , Davis Hasker P , Stirrat Michael , Tiddeman Bernard , Perrett David I
Published: November 2006

Sexual reproduction strategies vary both between and within species in the level of investment in offspring. Life-history theories suggest that the rate of sexual maturation is critically linked to reproductive strategy, with high investment being associated with few offspring and delayed maturation. For humans, age of puberty and age of first sex are two developmental milestones that have been associated with reproductive strategies. Stress during early development can retard or accelerate sexual maturation and reproduction. Early age of menarche is associated with absence of younger siblings, absence of a father figure during early life and increased weight. Father absence during early life is also associated with early marriage, pregnancy and divorce.

Choice of partner characteristics is critical to successful implementation of sexual strategies. It has been suggested that sexually dimorphic traits (including those evident in the face) signal high-quality immune function and reproductive status. Masculinity in males has also been associated with low investment in mate and offspring. Thus, women's reproductive strategy should be matched to the probability of male investment, hence to male masculinity.

Our review leads us to predict associations between the rate of sexual maturation and adult preferences for facial characteristics (enhanced sexual dimorphism and attractiveness). We find for men, engaging in sex at an early age is related to an increased preference for feminized female faces. Similarly, for women, the earlier the age of first sex the greater the preference for masculinity in opposite-sex faces. When we controlled sexual dimorphism in male faces, the speed of sexual development in women was not associated with differences in preference for male facial attractiveness.

These developmental influences on partner choice were not mediated by self-rated attractiveness or parental relationships. We conclude that individuals assort in preferences based on the rapidity of their sexual development. Fast developing individuals prefer opposite-sex partners with an increased level of sexually dimorphic facial characteristics.
Behavioural and neurophysiological evidence for face identity and face emotion processing in animals
Authors: Tate Andrew J , Fischer Hanno , Leigh Andrea E , Kendrick Keith M
Published: November 2006

Visual cues from faces provide important social information relating to individual identity, sexual attraction and emotional state. Behavioural and neurophysiological studies on both monkeys and sheep have shown that specialized skills and neural systems for processing these complex cues to guide behaviour have evolved in a number of mammals and are not present exclusively in humans. Indeed, there are remarkable similarities in the ways that faces are processed by the brain in humans and other mammalian species. While human studies with brain imaging and gross neurophysiological recording approaches have revealed global aspects of the face-processing network, they cannot investigate how information is encoded by specific neural networks. Single neuron electrophysiological recording approaches in both monkeys and sheep have, however, provided some insights into the neural encoding principles involved and, particularly, the presence of a remarkable degree of high-level encoding even at the level of a specific face. Recent developments that allow simultaneous recordings to be made from many hundreds of individual neurons are also beginning to reveal evidence for global aspects of a population-based code. This review will summarize what we have learned so far from these animal-based studies about the way the mammalian brain processes the faces and the emotions they can communicate, as well as associated capacities such as how identity and emotion cues are dissociated and how face imagery might be generated. It will also try to highlight what questions and advances in knowledge still challenge us in order to provide a complete understanding of just how brain networks perform this complex and important social recognition task.
Crystal structures of human α‐defensins HNP4, HD5, and HD6
Authors: Szyk Agnieszka , Wu Zhibin , Tucker Kenneth , Yang De , Lu Wuyuan , Lubkowski Jacek
Published: November 2006

Six α‐defensins have been found in humans. These small arginine‐rich peptides play important roles in various processes related to host defense, being the effectors and regulators of innate immunity as well as enhancers of adoptive immune responses. Four defensins, called neutrophil peptides 1 through 4, are stored primarily in polymorphonuclear leukocytes. Major sites of expression of defensins 5 and 6 are Paneth cells of human small intestine. So far, only one structure of human α‐defensin (HNP3) has been reported, and the properties of the intestine defensins 5 and 6 are particularly poorly understood. In this report, we present the high‐resolution X‐ray structures of three human defensins, 4 through 6, supplemented with studies of their antimicrobial and chemotactic properties. Despite only modest amino acid sequence identity, all three defensins share their tertiary structures with other known α‐ and β‐defensins. Like HNP3 but in contrast to murine or rabbit α‐defensins, human defensins 4–6 form characteristic dimers. Whereas antimicrobial and chemotactic activity of HNP4 is somewhat comparable to that of other human neutrophil defensins, neither of the intestinal defensins appears to be chemotactic, and for HD6 also an antimicrobial activity has yet to be observed. The unusual biological inactivity of HD6 may be associated with its structural properties, somewhat standing out when compared with other human α‐defensins. The strongest cationic properties and unique distribution of charged residues on the molecular surface of HD5 may be associated with its highest bactericidal activity among human α‐defensins.
Solution structure of a single‐domain thiosulfate sulfurtransferase from Arabidopsis thaliana
Authors: Cornilescu Gabriel , Vinarov Dmitriy A. , Tyler Ejan M. , Markley John L. , Cornilescu Claudia C.
Published: November 2006

We describe the three‐dimensional structure of the product of Arabidopsis thaliana gene At5g66040.1 as determined by NMR spectroscopy. This protein is categorized as single‐domain sulfurtransferase and is annotated as a senescence‐associated protein (sen1‐like protein) and ketoconazole resistance protein (http://arabidopsis.org/info/genefamily/STR_genefamily.html). The sequence of At5g66040.1 is virtually identical to that of a protein from Arabidopsis found by others to confer ketoconazole resistance in yeast. Comparison of the three‐dimensional structure with those in the Protein Data Bank revealed that At5g66040.1 contains an additional mobile β‐hairpin not found in other rhodaneses that may function in binding specific substrates. This represents the first structure of a single‐domain plant sulfurtransferase. The enzymatically active cysteine‐containing domain belongs to the CDC25 class of phosphatases, sulfide dehydrogenases, and stress proteins such as senescence specific protein 1 in plants, PspE and GlpE in bacteria, and cyanide and arsenate resistance proteins. Versions of this domain that lack the active site cysteine are found in other proteins, such as phosphatases, ubiquitin hydrolases, and sulfuryltransferases.
An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H
Authors: Butterwick Joel A. , Palmer Arthur G.
Published: November 2006

Dynamic processes are inherent properties of proteins and are crucial for a wide range of biological functions. To address how changes in protein sequence and structure affect dynamic processes, a quantitative comparison of microsecond‐to‐microsecond time scale conformational changes, measured by solution NMR spectroscopy, within homologous mesophilic and thermophilic ribonuclease H (RNase H) enzymes is presented. Kinetic transitions between the observed major state (high population) and alternate (low population) conformational state(s) of the substrate‐binding handle region in RNase H from the mesophile Escherichia coli (ecRNH) and thermophile Thermus thermophilus (ttRNH) occur with similar kinetic exchange rate constants, but the difference in stability between exchanging conformers is smaller in ttRNH compared to ecRNH. The altered thermodynamic equilibrium between kinetically exchanging conformers in the thermophile is recapitulated in ecRNH by the insertion of a Gly residue within a putative hinge between α‐helices B and C. This Gly insertion is conserved among thermophilic RNases H, and allows the formation of additional intrahelical hydrogen bonds. A Gly residue inserted between α‐helices B and C appears to relieve unfavorable interactions in the transition state and alternate conformer(s) and represents an important adaptation to adjust conformational changes within RNase H for activity at high temperatures.