bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytic model of near-field radio-frequency sheaths. I. Tenuous plasma limit
Authors: D’Ippolito D. A. , Myra J. R.
Published: February 2009

An analytic model is derived for electromagnetic radio-frequency (rf) wave propagation in a waveguide filled by a tenuous plasma with a slightly tilted equilibrium magnetic field B, i.e., by=By/B⪡1. The calculation includes the self-consistent coupling between the rf fields and the sheaths at the sheath-plasma interface and can be used to describe antenna sheath formation in the ion cyclotron range of frequencies. The sheaths are treated as thin vacuum regions separating the plasma and metal wall. It is shown that (i) the launched fast wave is coupled parasitically to the slow wave by the magnetic field structure when by≠0 and by the sheath boundary condition, (ii) the sheath voltage Vsh is dependent on the wave parity (the “antenna phasing”), and (iii) integrating the vacuum rf fields, Vvac=−∫dzE∥(vac), gives an overestimate of the sheath voltage. An expression for the self-consistent Vsh including plasma effects and satisfying the Child–Langmuir law is obtained.
Hydrogen storage behavior in C15 Laves phase compound TiCr2 by first principles
Authors: Li Fen , Zhao Jijun , Tian Dongxu , Zhang Hualei , Ke Xuezhi , Johansson Börje
Published: February 2009

Hydrogen storage in TiCr2 alloy of AB2 type with C15 Laves phase structure has been studied using density functional theory and plane-wave pseudopotential technique. The H atom interacts stronger with Cr atoms than with Ti and tends to occupy the g (2A2B) site due to the largest interstitial space. The g sites together with e (1A3B) sites form a three-dimensional clathratelike network, providing a diffusion pathway for H atoms, and the energy barriers for the H diffusion along these paths were computed. Interaction between two interstitial H atoms inside the TiCr2 lattice can be considered as a screened Coulomb repulsion, which seems to control the maximum hydrogen content in the metal hydrides. The absorption energies and electronic structures of metal hydrides TiCr2Hx with x=0.5–12 have been computed, and the theoretical maximum hydrogen storage capacity (between 2.6 and 3.8 wt %) agrees with experiments. The effects of the lattice expansion due to hydrogen absorption of different amounts have also been investigated.
An analytical model of nonproportional scintillator light yield in terms of recombination rates
Authors: Bizarri G. , Moses W. W. , Singh J. , Vasil’ev A. N. , Williams R. T.
Published: February 2009

Analytical expressions for the local light yield as a function of the local deposited energy (−dE/dx) and total scintillation yield integrated over the track of an electron of initial energy E are derived from radiative and/or nonradiative rates of first through third order in density of electronic excitations. The model is formulated in terms of rate constants, some of which can be determined independently from time-resolved spectroscopy and others estimated from measured light yield efficiency as a constraint assumed to apply in each kinetic order. The rates and parameters are used in the theory to calculate scintillation yield versus primary electron energy for comparison to published experimental results on four scintillators. Influence of the track radius on the yield is also discussed. Results are found to be qualitatively consistent with the observed scintillation light yield. The theory can be applied to any scintillator if the rates of the radiative and nonradiative processes are known.
Temperature and excitation power dependence of photoluminescence from high quality GaSb grown on AlSb and GaSb buffer layers
Authors: Park J. H. , Lee T. K. , Noh Y. K. , Kim M. D. , Oh Eunsoon
Published: February 2009

High quality GaSb layers were grown on semi-insulating (001) GaAs substrates by molecular-beam epitaxy, using AlSb and GaSb buffer layers. We observed strong photoluminescence even for temperatures higher than 100 K. The photoluminescence intensity was significantly increased when AlSb/GaSb superlattices were grown on the GaSb layer. With increasing the excitation power, the ratio of the acceptor-bound exciton with respect to the donor-acceptor pair transition is increased due to the saturation of the donor-acceptor pair transitions. We also observed an abnormal increase in the intensity with increasing temperatures up to 100 K. This unusual behavior is attributed to the influence of deep centers.
Composition and strain contrast of Si1−xGex (x=0.20) and Si1−yCy (y≤0.015) epitaxial strained films on (100) Si in annular dark field images
Authors: Wu X. , Baribeau J.-M.
Published: February 2009

The annular dark field (ADF) image contrast of Si1−xGex (x=0.20) and Si1−yCy (y≤0.015) strained epitaxial films on (100) Si is investigated in a 200 kV scanning transmission electron microscope (STEM) with ADF detector inner semiangles ranging from 26 to 92 mrad. For the Si1−xGex/Si system, the contrast increases with increasing ADF detector semiangle and decreases with increasing thickness to remain almost constant after the TEM sample thickness reaches 120 nm. The opposite trend is seen in the Si1−yCy/Si system, where the contrast increases with increasing sample thickness and decreases with increasing ADF detector semiangle, and remains almost constant after the sample thickness exceeds 200 nm. In the dilute Si1−yCy/Si system the lower average atomic number strained Si1−yCy layers are brighter than the higher average atomic number Si for an ADF detector semiangle of up to 92 mrad when the sample thickness is greater than 200 nm. This anomalous contrast dependence is also observed for an ADF detector semiangle of up to 50 mrad in thinner TEM samples. The observed ADF-STEM image contrast is explained in relation to the atomic scattering and multislice simulations. The normalized intensity line scan profiles of ADF-STEM images coincide with the composition profiles determined from analytical TEM techniques: energy dispersive x-ray spectroscopy and electron energy loss spectroscopy, as well as secondary ion mass spectrometry.
Effect of doping with Co and/or Cu on electronic structure and optical properties of ZnO
Authors: Xu M. , Zhao H. , Ostrikov K. , Duan M. Y. , Xu L. X.
Published: February 2009

This paper reports on ab initio numerical simulations of the effect of Co and Cu dopings on the electronic structure and optical properties of ZnO, pursued to develop diluted magnetic semiconductors vitally needed for spintronic applications. The simulations are based upon the Perdew-Burke-Enzerh generalized gradient approximation on the density functional theory. It is revealed that the electrons with energies close to the Fermi level effectively transfer only between Cu and Co ions which substitute Zn atoms, and are located in the neighbor sites connected by an O ion. The simulation results are consistent with the experimental observations that addition of Cu helps achieve stable ferromagnetism of Co-doped ZnO. It is shown that simultaneous insertion of Co and Cu atoms leads to smaller energy band gap, redshift of the optical absorption edge, as well as significant changes in the reflectivity, dielectric function, refractive index, and electron energy loss function of ZnO as compared to the doping with either Co or Cu atoms. These highly unusual optical properties are explained in terms of the computed electronic structure and are promising for the development of the next-generation room-temperature ferromagnetic semiconductors for future spintronic devices on the existing semiconductor micromanufacturing platform.
Temperature-dependent polarity reversal in Au/TlGaSe2 Schottky junctions
Authors: Seyidov MirHasan Yu. , Suleymanov Rauf A. , Bakış Yakup
Published: February 2009

Temperature-dependent reversal of the rectifying polarity has been observed in Au/TlGaSe2 Schottky junctions. To explain the experimental findings the important role of the tunneling current was taken into account. Besides, it was found that the temperature range, where the rectifying polarity reversal is observed, coincides with the temperature interval where an electronic phase transition takes place in TlGaSe2 crystals. The interface permittivity is significantly changed as a result of phase transitions, thus changing the Schottky barrier’s width and consequently the contributions of tunneling and usual thermally assisted transitions. Schottky barrier method becomes a powerful tool investigating phase transitions in semiconductors.
Negative permittivity and permeability of gold square nanospirals
Authors: Abdeddaïm R. , Guida G. , Priou A. , Gallas B. , Rivory J.
Published: February 2009

The optical properties of square nanospirals made of gold have been investigated numerically in the hundred terahertz range as a function of the geometrical parameters of the nanospirals. It is shown that the permittivity values of the nanospirals originate from the longitudinal surface plasmon resonances of the arms composing the nanospirals. A magnetic resonance was also observed whose magnitude and position increased with the number of winding. Above three windings the gold nanospirals exhibited negative values of the real part of the permeability above 400 THz.
ErAs epitaxial Ohmic contacts to InGaAs/InP
Authors: Singisetti Uttam , Zimmerman Jeramy D. , Wistey Mark A. , Cagnon Joël , Thibeault Brian J. , Rodwell Mark J. W. , Gossard Arthur C. , Stemmer Susanne , Bank Seth R.
Published: February 2009

We report epitaxial ErAs semimetal Ohmic contacts onto n-type In0.53Ga0.47As grown on InP. The contacts were formed by molecular beam epitaxial growth of ErAs on InAs/InGaAs. Transmission line measurements showed minimum specific contact resistivities of 1.5±0.4 Ω μm2 (horizontal specific contact resistivity ρH, 4.20 Ω μm) for the ErAs/InAs/InGaAs contact. The extracted contact resistance is larger than the true value because of the lateral oxidation of ErAs. The contacts degrade over time and at elevated temperatures because of the oxidation of the ErAs, making it difficult to use as surface contacts, but they are suitable as low-resistance buried contacts.
High resolution pair-distance distribution function P(r) of protein solutions
Authors: Hong Xinguo , Hao Quan
Published: February 2009

A high resolution pair-distance distribution function P(r) of protein molecules has been obtained from the complete solution scattering curve made by combining accurate small-angle and wide-angle x-ray scattering data out to 2.15 Å resolution. Both indirect and direct Fourier transforms exhibit two distinct peaks at 1.4 and 5.1 Å in P(r). X-ray crystallographic data demonstrate that these peaks correspond to two intramolecular distances: the average bond length between C, N, and O atoms and the pitch of an α-helix, respectively. Hence some high resolution aspects of the structure and function of a protein may be investigated in a solution.
Electronic properties of a metallic nanoparticle coupled to a graphene nanoribbon: A single-electron field effect transistor
Authors: Mizuno M. , Kim Eugene H.
Published: February 2009

The electronic properties of a metallic nanoparticle coupled to a graphene nanoribbon are discussed. Results for the nanoribbon’s electronic structure as well as the system’s transport properties are presented. This device is shown to behave as a field effect transistor operating at the single-electron level; its properties could be of utility in a variety of applications such as charge sensing and terahertz photonics.
What is Meant by Impaired Configural Processing in Acquired Prosopagnosia?
Authors: Barton Jason J S
Published: February 2009

Apperceptive prosopagnosia is supposedly characterised by impaired configural processing, which could refer to either perception of spatial structure or holistic mechanisms. Ten prosopagnosic patients were tested with (i) dot patterns, to determine if manipulations of complexity, size, orientation, or the regularity of global structure generated effects consistent with the holistic hypothesis; and (ii) hierarchical letters, to probe for a global ‘whole-object’ processing deficit. With dot patterns (experiment 1) patients were impaired even for simple two-dot stimuli, but did better with more complex patterns, when size or orientation varied, or with a regular global structure. In experiment 2, they demonstrated normal latency effects of global-level processing. Apperceptive prosopagnosia, including that from lesions encompassing the right fusiform gyrus, is thus associated with a ‘configural deficit’ that impairs perception of spatial structure, not just for faces but also for non-facial patterns. While it cannot be concluded that holistic processing is entirely normal in these subjects, their performance shows significant modulation by whole-object structure, indicating that some whole-object processing is occurring in these patients.
RE-1–silencing transcription factor shows tumor-suppressor functions and negatively regulates the oncogenic
TAC1
in breast cancer cells
Authors: Reddy Bobby Y. , Greco Steven J. , Patel Prem S. , Trzaska Katarzyna A. , Rameshwar Pranela
Published: February 2009

Breast cancer remains the most prevalent cancer among women in the United States. Substance P, a peptide derived from the
TAC1
gene, mediates oncogenic properties in breast and other cancers.
TAC1
expression facilitates the entry of breast cancer cells into bone marrow. The transcriptional repressor element 1–silencing transcription factor (REST) has been implicated in both oncogenic and tumor-suppressor functions. REST binds to the 5′ untranslated region of the
TAC1
promoter and suppresses its expression. This study investigated a role for
REST
in
TAC1
induction in breast cancer. Western blots and real-time PCR indicated that
REST
expression in breast cancer cells was inversely proportional to the cells' aggressiveness, for both cell lines and primary breast cancer cells.
REST
knockdown in low-metastatic T47D cells and nontumorigenic MCF12A cells resulted in increases in
TAC1
induction, proliferation, and migration. These parameters were negatively affected by ectopic expression of
REST
in highly aggressive MDA-MB-231 cells. Together, these findings show a central role for
REST
in the oncogenic function of
TAC1
and suggest a tumor-suppressor role for
REST
in breast cancer.
Peroxisome-associated matrix protein degradation in
Arabidopsis
Authors: Lingard Matthew J. , Monroe-Augustus Melanie , Bartel Bonnie
Published: February 2009

Peroxisomes are ubiquitous eukaryotic organelles housing diverse enzymatic reactions, including several that produce toxic reactive oxygen species. Although understanding of the mechanisms whereby enzymes enter peroxisomes with the help of peroxin (PEX) proteins is increasing, mechanisms by which damaged or obsolete peroxisomal proteins are degraded are not understood. We have exploited unique aspects of plant development to characterize peroxisome-associated protein degradation (PexAD) in
Arabidopsis
. Oilseed seedlings undergo a developmentally regulated remodeling of peroxisomal matrix protein composition in which the glyoxylate cycle enzymes isocitrate lyase (ICL) and malate synthase (MLS) are replaced by photorespiration enzymes. We found that mutations expected to increase or decrease peroxisomal H
2
O
2
levels accelerated or delayed ICL and MLS disappearance, respectively, suggesting that oxidative damage promotes peroxisomal protein degradation. ICL, MLS, and the β-oxidation enzyme thiolase were stabilized in the
pex4–1 pex22–1
double mutant, which is defective in a peroxisome-associated ubiquitin-conjugating enzyme and its membrane tether. Moreover, the stabilized ICL, thiolase, and an ICL-GFP reporter remained peroxisome associated in
pex4–1 pex22–1
. ICL also was stabilized and peroxisome associated in
pex6–1
, a mutant defective in a peroxisome-tethered ATPase. ICL and thiolase were mislocalized to the cytosol but only ICL was stabilized in
pex5–10
, a mutant defective in a matrix protein import receptor, suggesting that peroxisome entry is necessary for degradation of certain matrix proteins. Together, our data reveal new roles for PEX4, PEX5, PEX6, and PEX22 in PexAD of damaged or obsolete matrix proteins in addition to their canonical roles in peroxisome biogenesis.
Multiple gustatory receptors required for the caffeine response in
Drosophila
Authors: Lee Youngseok , Moon Seok Jun , Montell Craig
Published: February 2009

The ability of insects to detect and avoid ingesting naturally occurring repellents and insecticides is essential for their survival. Nevertheless, the gustatory receptors enabling them to sense toxic botanical compounds are largely unknown. The only insect gustatory receptor shown to be required for avoiding noxious compounds is the
Drosophila
caffeine receptor, Gr66a. However, this receptor is not sufficient for the caffeine response, suggesting that Gr66a may be a subunit of a larger receptor. Here, we report that mutations in the gene encoding the gustatory receptor, Gr93a, result in a phenotype identical to that caused by mutations in
Gr66a
. This includes an inability to avoid caffeine or the related methylxanthine present in tea, theophylline. Caffeine-induced action potentials were also eliminated in
Gr93a
-mutant animals, while the flies displayed normal responses to other aversive compounds or to sugars. The Gr93a protein was coexpressed with Gr66a in avoidance-gustatory receptor neurons (GRNs), and functioned in the same GRNs as Gr66a. However, misexpression of both receptors in GRNs that normally do not express either Gr93a or Gr66a does not confer caffeine sensitivity to these GRNs. Because Gr93a- and Gr66a-mutant animals exhibit the identical phenotypes and function in the same cells, we propose that they may be caffeine coreceptors. In contrast to mammalian and
Drosophila
olfactory receptors and mammalian taste receptors, which are monomeric or dimeric receptors, we propose that
Drosophila
taste receptors that function in avoidance of bitter compounds are more complex and require additional subunits that remain to be identified.
Atomic structure reveals the unique capsid organization of a dsRNA virus
Authors: Pan Junhua , Dong Liping , Lin Li , Ochoa Wendy F. , Sinkovits Robert S. , Havens Wendy M. , Nibert Max L. , Baker Timothy S. , Ghabrial Said A. , Tao Yizhi Jane
Published: February 2009

For most dsRNA viruses, the genome-enclosing capsid comprises 120 copies of a single capsid protein (CP) organized into 60 icosahedrally equivalent dimers, generally identified as 2 nonsymmetricallyinteracting CP molecules with extensive lateral contacts. The crystal structure of a partitivirus,
Penicillium stoloniferum
virus F (PsV-F), reveals a different organization, in which the CP dimer is related by almost-perfect local 2-fold symmetry, forms prominent surface arches, and includes extensive structure swapping between the 2 subunits. An electron cryomicroscopy map of PsV-F shows that the disordered N terminus of each CP molecule interacts with the dsRNA genome and probably participates in its packaging or transcription. Intact PsV-F particles mediate semiconservative transcription, and transcripts are likely to exit through negatively charged channels at the icosahedral 5-fold axes. Other findings suggest that the PsV-F capsid is assembled from dimers of CP dimers, with an arrangement similar to flavivirus E glycoproteins.
Variations in Hd1 proteins,
Hd3a
promoters, and
Ehd1
expression levels contribute to diversity of flowering time in cultivated rice
Authors: Takahashi Yasuyuki , Teshima Kosuke M. , Yokoi Shuji , Innan Hideki , Shimamoto Ko
Published: February 2009

Rice is a facultative short-day plant, and molecular genetic studies have identified the major genes involved in short-day flowering. However, the molecular mechanisms promoting the diversity of flowering time in cultivated rice are not known. We used a core collection of 64 rice cultivars that represent the genetic diversity of 332 accessions from around the world and studied the expression levels and polymorphisms of 6 genes in the short-day flowering pathway. The RNA levels of
Heading date 3a
(
Hd3a
), encoding a floral activator, are highly correlated with flowering time, and there is a high degree of polymorphism in the Heading date 1 (Hd1) protein, which is a major regulator of
Hd3a
expression. Functional and nonfunctional alleles of
Hd1
are associated with early and late flowering, respectively, suggesting that
Hd1
is a major determinant of variation in flowering time of cultivated rice. We also found that the type of
Hd3a
promoter and the level of
Ehd1
expression contribute to the diversity in flowering time and
Hd3a
expression level. We evaluated the contributions of these 3 factors by a statistical analysis using a simple linear model, and the results supported our experimental observations.
Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in
Enterococcus faecalis
Authors: Fox Kristina A. , Ramesh Arati , Stearns Jennifer E. , Bourgogne Agathe , Reyes-Jara Angelica , Winkler Wade C. , Garsin Danielle A.
Published: February 2009

Ethanolamine, a product of the breakdown of phosphatidylethanolamine from cell membranes, is abundant in the human intestinal tract and in processed foods. Effective utilization of ethanolamine as a carbon and nitrogen source may provide a survival advantage to bacteria that inhabit the gastrointestinal tract and may influence the virulence of pathogens. In this work, we describe a unique series of posttranscriptional regulatory strategies that influence expression of ethanolamine utilization genes (
eut
) in
Enterococcus
,
Clostridium
, and
Listeria
species. One of these mechanisms requires an unusual 2-component regulatory system. Regulation involves specific sensing of ethanolamine by a sensor histidine kinase (EutW), resulting in autophosphorylation and subsequent phosphoryl transfer to a response regulator (EutV) containing a RNA-binding domain. Our data suggests that EutV is likely to affect downstream gene expression by interacting with conserved transcription termination signals located within the
eut
locus. Breakdown of ethanolamine requires adenosylcobalamin (AdoCbl) as a cofactor, and, intriguingly, we also identify an intercistronic AdoCbl riboswitch that has a predicted structure different from previously established AdoCbl riboswitches. We demonstrate that association of AdoCbl to this riboswitch prevents formation of an intrinsic transcription terminator element located within the intercistronic region. Together, these results suggest an intricate and carefully coordinated interplay of multiple regulatory strategies for control of ethanolamine utilization genes. Gene expression appears to be directed by overlapping posttranscriptional regulatory mechanisms, each responding to a particular metabolic signal, conceptually akin to regulation by multiple DNA-binding transcription factors.
Ordered water structure at hydrophobic graphite interfaces observed by 4D, ultrafast electron crystallography
Authors: Yang Ding-Shyue , Zewail Ahmed H.
Published: February 2009

Interfacial water has unique properties in various functions. Here, using 4-dimensional (4D), ultrafast electron crystallography with atomic-scale spatial and temporal resolution, we report study of structure and dynamics of interfacial water assembly on a hydrophobic surface. Structurally, vertically stacked bilayers on highly oriented pyrolytic graphite surface were determined to be ordered, contrary to the expectation that the strong hydrogen bonding of water on hydrophobic surfaces would dominate with suppressed interfacial order. Because of its terrace morphology, graphite plays the role of a template. The dynamics is also surprising. After the excitation of graphite by an ultrafast infrared pulse, the interfacial ice structure undergoes nonequilibrium “phase transformation” identified in the hydrogen-bond network through the observation of structural isosbestic point. We provide the time scales involved, the nature of ice-graphite structural dynamics, and relevance to properties related to confined water.
RETRACTED: GCK is essential to systemic inflammation and pattern recognition receptor signaling to JNK and p38
Authors: Zhong Jian , Gavrilescu L. Cristina , Molnár Árpád , Murray Lauren , Garafalo Stephen , Kehrl John H. , Simon Amy R. , Van Etten Richard A. , Kyriakis John M.
Published: February 2009

Systemic inflammation arising from the organismal distribution of pathogen-associated molecular patterns is a major cause of clinical morbidity and mortality. Herein we report a critical and previously unrecognized in vivo role for germinal center kinase (GCK, genome nomenclature:
map4k2
), a mammalian
Sterile 20
(
STE20
) orthologue, in PAMP signaling, and systemic inflammation. We find that disruption of
gck
in mice strongly impairs PAMP-stimulated macrophage cytokine and chemokine release and renders mice resistant to endotoxin-mediated lethality. Bone marrow transplantation studies show that hematopoietic cell GCK signaling is essential to systemic inflammation. Disruption of
gck
substantially reduces PAMP activation of macrophage Jun-N-terminal kinase (JNK) and p38 mitogen-activated protein kinases (MAPKs) via reduced activation of the MAPK-kinase-kinases (MAP3Ks) mixed lineage kinases (MLKs)-2 and -3. Extracellular signal-regulated kinase (ERK) and nuclear factor-κB (NF-κB) activation are largely unaffected. Thus, GCK is an essential PAMP effector coupling JNK and p38, but not ERK or NF-κB to systemic inflammation.
A role for LYNX2 in anxiety-related behavior
Authors: Tekinay Ayse B. , Nong Yi , Miwa Julie M. , Lieberam Ivo , Ibanez-Tallon Ines , Greengard Paul , Heintz Nathaniel
Published: February 2009

Anxiety disorders are the most prevalent mental disorders in developed societies. Although roles for the prefrontal cortex, amygdala, hippocampus and mediodorsal thalamus in anxiety disorders are well documented, molecular mechanisms contributing to the functions of these structures are poorly understood. Here we report that deletion of
Lynx2
, a mammalian prototoxin gene that is expressed at high levels in anxiety associated brain areas, results in elevated anxiety-like behaviors. We show that LYNX2 can bind to and modulate neuronal nicotinic receptors, and that loss of
Lynx2
alters the actions of nicotine on glutamatergic signaling in the prefrontal cortex. Our data identify
Lynx2
as an important component of the molecular mechanisms that control anxiety, and suggest that altered glutamatergic signaling in the prefrontal cortex of
Lynx2
mutant mice contributes to increased anxiety-related behaviors.
Mechanisms contributing to synaptic Ca
2+
signals and their heterogeneity in hair cells
Authors: Frank Thomas , Khimich Darina , Neef Andreas , Moser Tobias
Published: February 2009

Sound coding at hair cell ribbon synapses is tightly regulated by Ca
2+
. Here, we used patch-clamp, fast confocal Ca
2+
imaging and modeling to characterize synaptic Ca
2+
signaling in cochlear inner hair cells (IHCs) of hearing mice. Submicrometer fluorescence hotspots built up and collapsed at the base of IHCs within a few milliseconds of stimulus onset and cessation. They most likely represented Ca
2+
microdomains arising from synaptic Ca
2+
influx through Ca
V
1.3 channels. Synaptic Ca
2+
microdomains varied substantially in amplitude and voltage dependence even within single IHCs. Testing putative mechanisms for the heterogeneity of Ca
2+
signaling, we found the amplitude variability unchanged when blocking mitochondrial Ca
2+
uptake or Ca
2+
-induced Ca
2+
release, buffering cytosolic Ca
2+
by millimolar concentrations of EGTA, or elevating the Ca
2+
channel open probability by the dihydropyridine agonist BayK8644. However, we observed substantial variability also for the fluorescence of immunolabeled Ca
V
1.3 Ca
2+
channel clusters. Moreover, the Ca
2+
microdomain amplitude correlated positively with the size of the corresponding synaptic ribbon. Ribbon size, previously suggested to scale with the number of synaptic Ca
2+
channels, was approximated by using fluorescent peptide labeling. We propose that IHCs adjust the number and the gating of Ca
V
1.3 channels at their active zones to diversify their transmitter release rates.
Circulating microRNAs, potential biomarkers for drug-induced liver injury
Authors: Wang Kai , Zhang Shile , Marzolf Bruz , Troisch Pamela , Brightman Amy , Hu Zhiyuan , Hood Leroy E. , Galas David J.
Published: February 2009

Drug-induced liver injury is a frequent side effect of many drugs, constitutes a significant threat to patient health and has an enormous economic impact on health care expenditures. Numerous efforts have been made to identify reliable and predictive markers to detect the early signs of drug-induced injury to the liver, one of the most vulnerable organs in the body. These studies have, however, not delivered any more informative candidates than the serum aminotransferase markers that have been available for ≈30 years. Using acetaminophen overdose-induced liver injury in the mouse as a model system, we have observed highly significant differences in the spectrum and levels of microRNAs in both liver tissues and in plasma between control and overdosed animals. Based on our survey of microRNA expression among normal tissues, some of the microRNAs, like messenger RNAs, display restricted tissue distributions. A number of elevated circulating microRNAs in plasma collected from acetaminophen-overdosed animals are highly expressed in the liver. We have demonstrated that specific microRNA species, such as mir-122 and mir-192, both are enriched in the liver tissue and exhibit dose- and exposure duration-dependent changes in the plasma that parallel serum aminotransferase levels and the histopathology of liver degeneration, but their changes can be detected significantly earlier. These findings suggest the potential of using specific circulating microRNAs as sensitive and informative biomarkers for drug-induced liver injury.
Combining affinity purification by ADP-ribose-binding
macro
domains with mass spectrometry to define the mammalian ADP-ribosyl proteome
Authors: Dani Nadia , Stilla Annalisa , Marchegiani Adriano , Tamburro Antonio , Till Susanne , Ladurner Andreas G. , Corda Daniela , Di Girolamo Maria
Published: February 2009

Mono-ADP-ribosylation is a reversible posttranslational modification that modulates the function of target proteins. The enzymes that catalyze this reaction in mammalian cells are either bacterial pathogenic toxins or endogenous cellular ADP-ribosyltransferases. For the latter, both the enzymes and their targets have largely remained elusive, mainly due to the lack of specific techniques to study this reaction. The recent discovery of the
macro
domain, a protein module that interacts selectively with ADP-ribose, prompted us to investigate whether this interaction can be extended to the identification of ADP-ribosylated proteins. Here, we report that
macro
domains can indeed be used as selective baits for high-affinity purification of mono-ADP-ribosylated proteins, which can then be identified by mass spectrometry. Using this approach, we have identified a series of cellular targets of ADP-ribosylation reactions catalyzed by cellular ADP-ribosyltransferases and toxins. These proteins include most of the known targets of ADP-ribosylation, indicating the validity of this method, and a large number of other proteins, which now need to be individually validated. This represents an important step toward the discovery of new ADP-ribosyltransferase targets and an understanding of the physiological role and the pharmacological potential of this protein modification.
Biofuel economics from a US perspective: past and future.
Authors: Zhang Z. B. , Wetzstein M.
Published: February 2009

With the vast number of government programmes around the world supporting virtually every phase of biofuels, there is a strong commitment towards the development of these fuels. However, our current knowledge base of biofuel production, marketing and environmental impact is filled with uncertainty. To shed light on the uncertainty, especially from a US perspective, this review of the biofuel economic literature attempts to determine the most fruitful areas of economic research. As a foundation, it is currently accepted that the US maize-based ethanol industry is sustainable with present government incentives and regulations, while cellulosic-based ethanol is not. Thus, without major new government incentives it is unlikely the USA will achieve goals set by various energy policy acts. The literature indicates a governmental system approach is required which advances biofuels to markets. Such an approach integrates research, regulatory initiatives and education. In terms of the food versus fuel issue, markets are very responsive to price shocks which will mitigate food inflation. However, market gyrations will occur, which will negatively impact the world's poor. With government incentives and regulations, the short-run future of biofuels is bright, while in the long run, biofuels will contribute to, but are unlikely to dominate, our future fuel supply.
Viruses transmitted through the food chain: a review of the latest developments.
Authors: Verhoef L. , Boxman I. L. , Koopmans M.
Published: February 2009

The emergence of severe acute respiratory syndrome (SARS), Nipah virus and H5N1 has sparked fears of food-borne dissemination of viruses, resulting in an increased focus on microbiological food safety. Norovirus (NoV) and hepatitis A virus (HAV) have been recognized as priorities based on their illness burden, and as models for prevention studies. In addition, hepatitis E virus is considered an emerging food-borne pathogen. Systematic surveillance for food-borne viral diseases, where present, has to deal with underreporting, with available data biased towards developed countries, making true estimates of the burden of illness challenging. Nevertheless, food-borne viral outbreaks are often reported, whereas current measures undertaken by food safety management organizations are focused primarily on bacterial contamination and are insufficient for viruses in food. There has been a shift towards molecular techniques for the diagnosis and detection of viruses in food, but a definite link to food is still hard to establish owing to the low levels of viruses in foods. Moreover, multiple strains may be involved in sewage-contaminated foods, with the risk of recombination and development of novel strains after ingestion. To enable monitoring of food and food safety, sensitive routine methods are needed, and methods for detection of NoV and HAV in risk foods (shellfish, soft fruit and leafy greens) are currently validated. Norovirus cannot be cultured, but the murine NoV may be a surrogate for studying NoV survival. In all, significant progress has been made in understanding food-borne viral infections, but clear data gaps still exist and should be the focus of future research.
Control of cell growth by brassinosteroids.
Authors: Pereira-Netto A. B.
Published: February 2009

Brassinosteroids (BRs) comprise a specific class of low-abundance plant steroids of ubiquitous occurrence in plants. Molecular genetic analysis of mutants defective in BR biosynthesis or response has demonstrated that the ability to synthesize, perceive and respond to BRs is critical for normal plant growth. In the last 10 years, more than a dozen reviews have summarized the impressive progress in our understanding of the BRs metabolism, including its regulation, and also in the identification of the various components of their signal transduction pathway. In this review, an insight into the BR-induced changes in biochemical and molecular mechanisms important to control cell growth is provided. Data presented in this review also demonstrate that BR control of cell growth rely on a broad variety of mechanisms.
Proposed strategies for mitigating the impact of high food prices on nutrition and health in Latin America and the Caribbean.
Authors: Valpiani N. , Thorne-Lyman A. L. , Pee S. de , Godfrey S. , Gentilini U. , Bloem M. W.
Published: February 2009

High food prices are expected to have detrimental impacts on the dietary intake of vulnerable populations around the world, exacerbating malnutrition and poor health. Prior to the onset of the price rises, 53 million individuals in Latin America already lacked sufficient daily energy intake, and the rates of anaemia and high child stunting suggest widespread vitamin and mineral deficiencies. Where households cope with high prices by eliminating more expensive, nutrient-dense foods from their diets, the prevalence of micronutrient deficiencies will increase, especially among those with the highest nutrient needs: pregnant and lactating women, young children and the chronically ill. Unaddressed, food price increases will stunt the growth and development of a generation. This paper reviews market-based and non-market-based options for augmenting the emergency nutrition safety net in Latin American and Caribbean nations. Because the region has the unique advantage of numerous established conditional cash transfer programmes enabled by political stability and well-functioning market economies, much focus is given to their strengths, weaknesses and potential to mitigate the effects of high food prices. Yet, as these programmes sometimes fail to target the urban poor or reach marginalized rural communities that lack access to infrastructure and markets, food-based interventions remain indispensable for restoring micronutrient and health status across the region. Contextual factors, including the specific nutrient deficiencies of concern and the condition of and access to infrastructure and markets, should inform the combination of interventions selected.
Advances in sea cucumber aquaculture and prospects for commercial culture of
Holothuria scabra
.
Authors: Raison C. M.
Published: February 2009

Sea cucumbers have been consumed for centuries in Asia as traditional medicinal and prestige foods, said to aid wound healing, joint pain, intestinal problems and as a general health tonic. Increasing prosperity in China over the past 30 years has fuelled growing demand for high-value seafood products in the region which has placed severe pressure on traditional sea cucumber fisheries. Despite the emergence of new fishery locations and increasing international trade, supply has been failing to meet demand, resulting in an increasing price trend. There is evidence that wild-sea cucumber populations are under severe pressure with concerns that depleted stocks may take decades to recover with no clear indication that fisheries management is improving. Growing interest in stock restoration as a fisheries management tool has led to significant advances in culture techniques for the more valuable species of sea cucumber, and this in turn has raised the possibility of culturing the most promising species commercially. This review provides an overview of sea cucumber ecology and biology, international trade, fisheries management issues and advances in culture techniques, and then focuses on prospects for commercial culture of
Holothuria scabra
, the most valuable tropical species.
Practicalities of estimating carbon sequestration - boreal coniferous forests.
Authors: Berg B. , McClaugherty C. , Santo A. V. de
Published: February 2009

We have reviewed literature on the topic 'carbon sequestration in forest soils'. We review a theory/model for the sequestration process based on pine (
Pinus
) needle litter that is transformed into stable matter during decomposition. The decomposition process is divided into two phases with lignified tissue in the latter developing a recalcitrance with a calculable limit value for decomposition. This is just one of several possible models, this one developed for boreal forests. It appears likely that part of the stabilization process is related to oxygen limitation for micro-organisms, high concentrations of heavy metals developed during decomposition and/or allelopathic effects that suppress the decomposition process and allow an accumulation of organic matter. We divide the concept into
primary sequestration
and
secondary sequestration
. Primary sequestration occurs in an organic layer, e.g. a humus layer, and is a process that encompasses the stabilization of decomposing plant litter remains and their accumulation. This layer is vulnerable to e.g. fire and other disturbances. Secondary sequestration occurs in the mineral soil, where the buildup of sequestered carbon is a slower process. This carbon material was leached from the organic layers and has become adsorbed to mineral particles and thus stabilized. We may consider the concept stability as a very relative one. Stability appears to be related to a set of conditions on e.g. environment and micro-organisms. It may also be related to nutrients in the litter and/or environment. The review is based on available data and has its focus on coniferous boreal and northern temperate forests.
The role of vitamin E in the diet.
Authors: Shrapnel B. S.
Published: February 2009

The last decade has seen many developments in our understanding of vitamin E, its transport and metabolism, and its potential role in the prevention of chronic disease. Of the eight fat-soluble substances comprising vitamin E, α-tocopherol has emerged as central to vitamin E activity in the body, its concentration in the plasma being governed by α-tocopherol transfer protein and maintained in a narrow range. Although new insights into the role of habitual fat intake in determining human requirements for vitamin E have been gained, uncertainties remain and estimates of requirements differ considerably between authorities. Investigation of the potential of this potent chain-breaking antioxidant to prevent or delay conditions thought to be associated with oxidative stress, including cardiovascular disease, cancer, Alzheimer's disease and Parkinson's disease, has challenged nutritionists to reconsider optimal intakes of vitamin E. High-dose supplementation has proved ineffective in reducing risk and may even be associated with increased risk; yet, new evidence suggests that a lifetime diet rich in α-tocopherol may provide protection against heart disease and cancer. Intakes of α-tocopherol are low in some western populations, which may in part be the result of advice to consume low-fat diets, intended to help address rising rates of obesity. An increased focus on fat quality, consistent with advice stemming from the cardiovascular literature, will help ensure adequate intakes of vitamin E in the context of diets moderate in total fat.
Geminivirus resistance breeding in common bean.
Authors: Blair M. W. , Morales F. J.
Published: February 2009

Common bean (
Phaseolus vulgaris
L.) is among the most important food staples worldwide, mainly because of its relatively high protein content and other valuable nutritional qualities. Unfortunately, common beans are highly susceptible to plant viruses in general, including one of the largest families of plant viruses known as the
Geminiviridae
. These viruses, unlike most RNA plant viruses, possess a DNA genome that allows these pathogens to replicate in the nucleus of their plant host cells, thus, causing major damage to susceptible legume crops. Although some geminiviruses, belonging to two (
Mastrevirus
and
Curtovirus
) of the four genera that compose the
Geminiviridae
, can be transmitted by leafhoppers (Cicadellidae) to common bean, most geminiviruses that attack legumes belong to the genus
Begomovirus
, and are transmitted by the whitefly
Bemisia tabaci
(Genn.). In fact, the type species of this genus is bean golden yellow mosaic virus (BGYMV), which attacks over a million hectares of common bean grown in the lowlands and mid-altitude valleys of Central America, southern Mexico, the Caribbean region and northern South America. Another begomovirus, bean golden mosaic virus (BGMV), affects over two million hectares of common bean in Brazil, northern Argentina and the lowlands of Bolivia, in South America. In this region, bean dwarf mosaic virus (BDMV) has also caused the loss of thousands of hectares of highly valuable common bean genotypes in northwestern Argentina. In northwestern Mexico, thousands of hectares of common bean have been under the constant attack of a begomovirus related to a virus originally described in cucurbits, squash leaf curl virus (SLCV), in southwestern USA, currently known in Mexico as bean calico mosaic virus (BCaMV). Fortunately, none of these viruses is present in Eastern Africa, where the common bean is also a major food staple. Another Old World begomovirus reported to attack common bean both in the Old and New World, is tomato yellow leaf curl virus (TYLCV). This review describes the different breeding approaches followed since the 1970s to introduce resistance to begomoviruses infecting important legume crops, particularly common bean. This has been a challenging process, considering that no immune genotypes have been identified in more than 30000 common bean genotypes exposed to begomoviruses, such as BGMV or BGYMV.
How have opinions about GMOs changed over time? The situation in the European Union and the USA.
Authors: Bonny S.
Published: February 2009

This text examines changes in opinions on genetically modified organisms (GMOs) over the past ten years in the EU and the USA. Divergence in opinion on this topic makes it difficult to define common policies and has led to conflicts. The results of diverse surveys and polls taken repeatedly over several years, for example the Eurobarometer polls in the EU, have been used to carry out a meta-analysis of opinions on GMOs. First of all, the data used as well as questions of method and the numerous difficulties arising from such an approach are presented. In the second part, the points of view in the USA and the EU are compared for those years when identical questions were asked on both sides of the Atlantic, demonstrating the differences associated with location. Then, changes in opinions on GMOs over time are analysed, focusing in turn on the USA and then the EU countries. To conclude, we examine whether there is a certain convergence or a widening gap over time between views in the USA and the EU. As regards biotechnology, there is a slight convergence of views over the last few years, Americans having become a little less optimistic and Europeans relatively more optimistic. However, in Europe, the level of opposition to GMOs remains very high and is even growing in some countries.
Food-drug interaction: the case of grapefruit juice.
Authors: Uesawa Y.
Published: February 2009

Here, we present an overview of two decades of work on the interactions between grapefruit juice (GFJ) and drugs, particularly on the mechanisms of these interactions and the interacting components in GFJ. We describe classical examples where GFJ enhances intestinal absorption of drugs, as well as newly discovered interactions with the inhibition of intestinal absorption. Work aimed at understanding the causal compounds in GFJ highlights the relationship between human physiology and food and is clinically important. Further understanding of this interaction may allow patients and their doctors to stop worrying about drug interactions with GFJ.