bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of Bacteroidetes in high‐altitude saline evaporitic basins in northern Chile
Authors: Dorador Cristina , Meneses Daniela , Urtuvia Viviana , Demergasso Cecilia , Vila Irma , Witzel Karl‐Paul , Imhoff Johannes F.
Published: August 2009

The phylum Bacteroidetes represents one of the most abundant bacterial groups of marine and freshwater bacterioplankton. We investigated the diversity of Bacteroidetes in water and sediment samples from three evaporitic basins located in the highlands of northern Chile. We used both 16S rRNA gene clone libraries created with targeted Bacteroidetes‐specific primers and separation of specifically amplified gene fragments by denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed a reduced richness of these organisms in samples from Salar de Huasco (two to four DGGE bands) increasing in Salar de Ascotán (two to seven DGGE bands) and Laguna Tebenquiche at Salar de Atacama (four to eight DGGE bands). Cluster analysis (WPGMA) of DGGE bands showed that bands from Salar de Huasco and Salar de Ascotán grouped together and samples from Salar de Atacama formed separate clusters in water and sediment samples, reflecting different Bacteroidetes communities between sites. Most of the sequences analyzed belonged to the family Flavobacteriaceae and clustered with the genera Psychroflexus, Gillisia, Maribacter, Muricauda, Flavobacterium, and Salegentibacter. The most abundant phylotype was highly related to Psychroflexus spp. and was recovered from all three study sites. The similarity of the analyzed sequences with their closest relatives in GenBank was typically <97% and notably lower when compared with type strains, demonstrating the unique character of these sequences. Culture efforts will be necessary to get a better description of the diversity of this group in saline evaporitic basins of northern Chile.
Translation and dispersion of sediment pulses in flume experiments simulating gravel augmentation below dams
Authors: Sklar Leonard S. , Fadde Jessica , Venditti Jeremy G. , Nelson Peter , Wydzga M. Aleksandra , Cui Yantao , Dietrich William E.
Published: August 2009

The effectiveness of gravel augmentation as a river restoration strategy depends on the extent and duration of the topographic and bed texture changes created by the pulse of added sediment. Previous work has emphasized the strong tendency for natural sediment waves to propagate primarily by dispersion; however, pulse translation may occur for gravel additions to armored channels downstream of dams where added sediments are finer than the preexisting bed material. Here we report results of a laboratory investigation in which we created an immobile, armored bed and documented the spatial and temporal evolution of the bed topography and bed texture in response to gravel pulses of various volumes and grain sizes. The introduced sediment waves evolved by a combination of translation and dispersion, with a significant translational component. Pulse translation and dispersion can be readily discerned on a graph of the time evolution of the downstream cumulative distribution of elevation differences from the preexisting bed topography. Translation was most evident for smaller volumes of added sediment. Pulses of finer‐grained gravel moved through the flume more rapidly, resulting in a larger magnitude but shorter duration of bed fining. More work is needed to understand the influence of bar‐pool topography and flow magnitude and duration before the grain size and volume of gravel additions can be selected to achieve optimal patterns of pulse propagation.
Hydrologic modeling to screen potential environmental management methods for malaria vector control in Niger
Authors: Gianotti Rebecca L. , Bomblies Arne , Eltahir Elfatih A. B.
Published: August 2009

This paper describes the first use of Hydrology‐Entomology and Malaria Transmission Simulator (HYDREMATS), a physically based distributed hydrology model, to investigate environmental management methods for malaria vector control in the Sahelian village of Banizoumbou, Niger. The investigation showed that leveling of topographic depressions where temporary breeding habitats form during the rainy season, by altering pool basin microtopography, could reduce the pool persistence time to less than the time needed for establishment of mosquito breeding, approximately 7 days. Undertaking soil surface plowing can also reduce pool persistence time by increasing the infiltration rate through an existing pool basin. Reduction of the pool persistence time to less than the rainfall interstorm period increases the frequency of pool drying events, removing habitat for subadult mosquitoes. Both management approaches could potentially be considered within a given context. This investigation demonstrates that management methods that modify the hydrologic environment have significant potential to contribute to malaria vector control in water‐limited, Sahelian Africa.
Dissection of a composite volcanic earthquake at Santiaguito, Guatemala
Authors: Johnson J. B. , Sanderson R. , Lyons J. , Escobar‐Wolf R. , Waite G. , Lees J. M.
Published: August 2009

Volcano earthquake sources associated with eruptions at Santiaguito volcano in Guatemala are complex. Rock fracture, fluid flow, and gas expansion occur at variable time scales and induce superposed ground motions, including both static and dynamic deformation, and atmospheric pressure disturbances. Dissection of this composite event is facilitated through extra‐seismic observations, such as infrasound, geodetic, and visual monitoring. Multi‐parametric investigation of an eruptive event on Jan. 4th 2009 reveals increased degassing, apparent as both geodetic tilt and harmonic seismo‐infrasonic tremor, preceding an explosive event. The explosive event itself entails surface dome uplift, multiple eruptive pulses, and subsequent re‐equilibration of the volcanic edifice manifested in derived tilt. We report here on an integrated approach to discerning the physical processes at the actively effusing and exploding Santiaguito volcano and describe the composite earthquake that occurs here.
Phase variation has a role in Burkholderia ambifaria niche adaptation
Authors: Vial Ludovic , Groleau Marie-Christine , Lamarche Martin G , Filion Geneviève , Castonguay-Vanier Josée , Dekimpe Valérie , Daigle France , Charette Steve J , Déziel Eric
Published: August 2009

Members of the Burkholderia cepacia complex (Bcc), such as B. ambifaria, are effective biocontrol strains, for instance, as plant growth-promoting bacteria; however, Bcc isolates can also cause severe respiratory infections in people suffering from cystic fibrosis (CF). No distinction is known between isolates from environmental and human origins, suggesting that the natural environment is a potential source of infectious Bcc species. While investigating the presence and role of phase variation in B. ambifaria HSJ1, an isolate recovered from a CF patient, we identified stable variants that arose spontaneously irrespective of the culture conditions. Phenotypic and proteomic approaches revealed that the transition from wild-type to variant types affects the expression of several putative virulence factors. By using four different infection models (Drosophila melanogaster, Galleria mellonella, macrophages and Dictyostelium discoideum), we showed that the wild-type was more virulent than the variant. It may be noted that the variant showed reduced replication in a human monocyte cell line when compared with the wild-type. On the other hand, the variant of isolate HSJ1 was more competitive in colonizing plant roots than the wild-type. Furthermore, we observed that only clinical B. ambifaria isolates generated phase variants, and that these variants showed the same phenotypes as observed with the HSJ1 variant. Finally, we determined that environmental B. ambifaria isolates showed traits that were characteristic of variants derived from clinical isolates. Our study therefore suggest that B. ambifaria uses phase variation to adapt to drastically different environments: the lung of patients with CF or the rhizosphere.
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
Authors: Hamady Micah , Lozupone Catherine , Knight Rob
Published: August 2009

Next-generation sequencing techniques, and PhyloChip, have made simultaneous phylogenetic analyses of hundreds of microbial communities possible. Insight into community structure has been limited by the inability to integrate and visualize such vast datasets. Fast UniFrac overcomes these issues, allowing integration of larger numbers of sequences and samples into a single analysis. Its new array-based implementation offers orders of magnitude improvements over the original version. New 3D visualization of principal coordinates analysis results, with the option to view multiple coordinate axes simultaneously, provides a powerful way to quickly identify patterns that relate vast numbers of microbial communities. We show the potential of Fast UniFrac using examples from three data types: Sanger-sequencing studies of diverse free-living and animal-associated bacterial assemblages and from the gut of obese humans as they diet, pyrosequencing data integrated from studies of the human hand and gut, and PhyloChip data from a study of citrus pathogens. We show that a Fast UniFrac analysis using a reference tree recaptures patterns that could not be detected without considering phylogenetic relationships and that Fast UniFrac, coupled with BLAST-based sequence assignment, can be used to quickly analyze pyrosequencing runs containing hundreds of thousands of sequences, showing patterns relating human and gut samples. Finally, we show that the application of Fast UniFrac to PhyloChip data could identify well-defined subcategories associated with infection. Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac.
Immigrational Background Affects the Effectiveness of a School‐based Overweight Prevention Program Promoting Water Consumption
Authors: Muckelbauer Rebecca , Libuda Lars , Clausen Kerstin , Toschke André M. , Reinehr Thomas , Kersting Mathilde
Published: August 2009

We tested whether a simple overweight prevention program promoting water consumption in elementary schools is equally effective in children with an immigrational background (MIG) and in those without (non‐MIG). Thus, a secondary analysis of a controlled cluster trial, lasting one school year, was conducted. Thirty‐two elementary schools located in low socioeconomic districts in two German cities were included. Of the 2,950 school children analyzed, 1,306 were MIG children. Water fountains were installed in the schools of the intervention group (IG) and teachers held lessons to promote water consumption. Control schools (control group (CG)) did not receive any intervention. Before and after intervention, body weight and height was measured. Overweight was defined by age‐ and sex‐specific BMI cutoffs that are linked to an adult BMI of 25 kg/m2. Beverage consumption was assessed in questionnaires. Modification of intervention effects by immigrational background was tested by interaction terms. The immigrational background modified the intervention effect on prevalence and remission of overweight (interaction term: P = 0.03 and P = 0.02), but not on the incidence of overweight (P = 0.06). After intervention, the risk of being overweight was reduced in the IG compared to the CG among non‐MIG (odds ratio = 0.51, 95% confidence interval (CI): 0.31–0.83), but not among MIG children (odds ratio = 1.02, 95% CI: 0.63–1.65). After intervention, water consumption significantly increased in the IG equally among both, non‐MIG and MIG, by ∼1 glass/day. A simple school‐based intervention promoting water consumption prevented overweight in non‐MIG children, but failed in MIG children. Different beverage consumption, among other lifestyle factors, may account for this effect but scientific discussion remains open.
High‐fat Diet Followed by Fasting Disrupts Circadian Expression of Adiponectin Signaling Pathway in Muscle and Adipose Tissue
Authors: Barnea Maayan , Madar Zecharia , Froy Oren
Published: August 2009

The circadian clock controls energy homeostasis by regulating circadian expression of proteins involved in metabolism. Disruption of circadian rhythms leads to obesity and metabolic disorders. Little is known regarding the control of the biological clock over adiponectin signaling pathway in adipose tissue, the adiponectin producer, and muscle, an adiponectin target tissue under fasting, low‐fat (LF), or high‐fat (HF) diet. Mice were fed LF or HF diet for 7 weeks and fasted on the last day. The circadian mRNA expression of clock genes and components of adiponectin metabolic pathway (mAdipoR1, mAdipoR2, mPparα, mPparγ, mAmpk, and mAcc) in the muscle and adipose tissue were tested. Using average daily levels of multiple time points around the circadian cycle, we assessed mRNA levels of the different adiponectin signaling components. In addition, serum glucose, adiponectin, and insulin were measured. Under LF diet, adiponectin signaling pathway components exhibited circadian rhythmicity at the mRNA levels. Fasting and HF diet followed by fasting disrupted this circadian expression causing a phase advance or delay, respectively. Changes were also found in the expression levels of adiponectin receptor, mAmpk, mAcc, mPparα, and mPparγ reflecting a defect in adiponectin signaling. As both peroxisome proliferator‐activated receptor α (PPARα) and mAMPK are linked to the core clock mechanism, they could mediate the disruptions seen in clock gene expression under HF diet. In turn, the circadian clock affects the daily rhythm of these adiponectin signaling components.
Significance of Overvaluation of Shape/Weight in Binge‐eating Disorder: Comparative Study With Overweight and Bulimia Nervosa
Authors: Grilo Carlos M. , Masheb Robin M. , White Marney A.
Published: August 2009

Increasing empirical evidence supports the validity of binge‐eating disorder (BED) and its inclusion as a formal diagnosis in the Diagnostic and Statistical Manual of Mental Disorders (DSM‐V). Contention exists regarding the criteria for BED, including whether, like bulimia nervosa (BN), it should be characterized by overvaluation of shape/weight. This study examined the significance of overvaluation for BED using two complementary comparisons groups. Participants were 324 women who completed self‐report instruments as part of an Internet study. Analyses compared BMI, eating disorder (ED) features, and depressive levels in four groups: 123 overweight participants without ED, 47 BED participants who do not overvalue shape/weight, 101 BED participants who overvalue shape/weight, and 53 BN participants. Both BED groups had significantly greater ED psychopathology than the overweight group. Within BED, the group with overvaluation had significantly greater ED psychopathology and depressive levels despite no differences in binge eating. BED with overvaluation and BN groups differed little from each other but had significantly higher ED psychopathology and depressive levels than the other groups. Group differences existed despite similar age and BMI across the groups, as well as when controlling for group differences in depressive levels. These findings provide further support for the validity of BED and suggest that overvaluation of shape/weight, which provides important information about BED severity, warrants consideration as either a diagnostic specifier or as a dimensional severity rating. Although inclusion of overvaluation of shape/weight could be considered as a required criterion for BED, this would exclude a substantial proportion of BED patients with clinically significant problems.
Ab initio simulations of thermodynamic and chemical properties of detonation product mixtures
Authors: Maillet Jean-Bernard , Bourasseau Emeric
Published: August 2009

Thermodynamic and chemical properties of simple fluids N2, CO2, and H2O and their binary and ternary mixtures have been studied using density functional theory simulations in a high pressure and high temperature regime. We show that N2 and binary mixtures with N2 follow an ideal behavior over a large temperature and pressure range. On the contrary, the water molecule is observed to dissociate as either pressure or temperature increases. Dramatic consequences are observed when water is mixed with carbon dioxide at extreme conditions. Indeed, a new molecule is formed, CO3H2, and the thermodynamic behavior of the mixture strongly deviates from ideality. Chemistry occurring at extreme conditions is then discussed in the context of detonation product modeling.
Broadband, high dynamics and high resolution charge coupled device-based spectrometer in dynamic mode for multi-keV repetitive x-ray sources
Authors: Fourment C. , Arazam N. , Bonte C. , Caillaud T. , Descamps D. , Dorchies F. , Harmand M. , Hulin S. , Petit S. , Santos J. J.
Published: August 2009

We present a new operating mode, using a charged coupled device as dispersionless spectrometer dedicated to repetitive x-ray sources in the multi-keV domain. This enables to get spectra with high statistics in a short acquisition time and a way compatible with the operation of other diagnostics requiring accumulation. Several reconstruction algorithms for the spreading events are discussed, and a near Fano-limited resolution is demonstrated by using single pixel events. In this case, a method to take into account partial canceling of the events is presented. Experimental characterization and detailed modeling of the detector are performed, which allow to determine absolute number of photon with ±35% accuracy. Characterization of the 5–25 keV x rays emitted by a short pulse laser-produced plasma is reported, as well as their dependency with the atomic number, the laser duration, and energy.
Action potentials of HL-1 cells recorded with silicon nanowire transistors
Authors: Eschermann Jan Felix , Stockmann Regina , Hueske Martin , Vu Xuan Thang , Ingebrandt Sven , Offenhäusser Andreas
Published: August 2009

Silicon nanowire (NW) transistors were fabricated in a top-down process. These devices were used to record the extracellular potential of the spontaneous activity of cardiac muscle HL-1 cells. Their signals were measured by direct dc sampling of the drain current. An improved signal-to-noise ratio compared to planar field-effect devices was observed. Furthermore the signal shape was evaluated and could be associated to different membrane currents. With these experiments, a qualitative description of the properties of the cell-NW contact was obtained and the suitability of these sensors for electrophysiological measurements in vitro was demonstrated.
Formation and characterization of perpendicular mode Si ripples by glancing angle O2+ sputtering at room temperature
Authors: Mollick S. A. , Ghose D.
Published: August 2009

Off-normal low energy ion beam sputtering of solid surfaces often leads to morphological instabilities resulting in the spontaneous formation of ripple structures in nanometer length scales. In the case of Si surfaces at ambient temperature, ripple formation is found to take place normally at lower incident angles with the wave vector parallel to the ion beam direction. The absence of ripple pattern on Si surface at larger angles is due to the dominance of ion beam polishing effect. We have shown that a gentle chemical roughening of the starting surface morphology can initiate ripple pattern under grazing incidence ion beam sputtering (θ>64° with respect to the surface normal), where the ripple wave vector is perpendicular to the ion beam direction. The characteristics of the perpendicular mode ripples are studied as a function of pristine surface roughness (2–30 nm) and projectile fluence (5×1016–1.5×1018 O atoms cm−2). The quality of the morphological structure is assessed from the analysis of ion induced topological defects.
Control of electric current by graphene edge structure engineering
Authors: Yamamoto Masayuki , Wakabayashi Katsunori
Published: August 2009

In graphene nanoribbon junctions, the nearly perfect transmission occurs in some junctions while the zero conductance dips due to antiresonance appear in others. We have classified the appearance of zero conductance dips for all combinations of ribbon and junction edge structures. These transport properties do not attribute to the whole junction structure but the partial corner edge structure, which indicates that one can control the electric current simply by cutting a part of nanoribbon edge. The ribbon width is expected to be narrower than 10 nm in order to observe the zero conductance dips at room temperature.
Processing route for size distribution narrowing of ion beam synthesized nanoclusters
Authors: Yuan C. W. , Boswell Cosima N. , Shin S. J. , Liao C. Y. , Guzman J. , Ager J. W. , Haller E. E. , Chrzan D. C.
Published: August 2009

Ion beam synthesis of nanocrystals is explored using a recently developed kinetic Monte Carlo model for the process. The model suggests that temperature can be used to engineer nanocrystal size distributions. Specifically, by initiating implants at low temperature and then ramping the temperature upward, one can both tune the average size of the nanocrystals and restrict size distribution widths to less than 20% of the average size.
Structural tunability in metamaterials
Authors: Lapine Mikhail , Powell David , Gorkunov Maxim , Shadrivov Ilya , Marqués Ricardo , Kivshar Yuri
Published: August 2009

We propose an efficient approach for tuning the transmission characteristics of metamaterials through a continuous adjustment of the lattice structure and confirm it experimentally in the microwave range. The concept is rather general and applicable to various metamaterials as long as the effective medium description is valid. The demonstrated continuous tuning of a metamaterial response is highly desirable for a number of emerging applications of metamaterials, including sensors, filters, and switches, realizable in a wide frequency range.
Second harmonic generation microscopic observations of a multiferroic BiFeO3 single crystal
Authors: Yokota Hiroko , Haumont Raphael , Kiat Jean-Michel , Matsuura Hiroto , Uesu Yoshiaki
Published: August 2009

Anisotropy of the optical second harmonic generation (SHG) in a multiferroic BiFeO3 single crystal is observed by an SHG microscope. Polarization dependences of SH intensities are measured in several polarization configurations of the incident and SH waves to determine the magnitude and sign of polar i-type SHG tensor components. To obtain proper values of these SHG tensors, the effects of the interference term and wave number mismatch are taken into account in these analyses. d24 component is 15 times larger than d32 and this result is essentially different from the thin film case.
Record pulsed power demonstration of a 2 μm GaSb-based optically pumped semiconductor laser grown lattice-mismatched on an AlAs/GaAs Bragg mirror and substrate
Authors: Yarborough J. M. , Lai Yi-Ying , Kaneda Yushi , Hader Jörg , Moloney Jerome V. , Rotter T. J. , Balakrishnan G. , Hains C. , Huffaker D. , Koch S. W. , Bedford R.
Published: August 2009

An optically pumped semiconductor laser resonant periodic gain structure, grown lattice-mismatched on an AlAs/GaAs Bragg mirror, exhibits a peak pulsed power of 70 W when pumped with a pulsed 1064 nm neodymium doped yttrium aluminum garnet laser.
Growth kinetics of CdTe colloidal nanocrystals
Authors: Ferreira D. Lourençoni , Silva F. Oliveira , Viol L. Cristina de Souza , Licínio P. , Valadares M. , Cury L. Alberto , Schiavon M. Antônio , Alves J. Luiz Aarestrup
Published: August 2009

The growth kinetics of CdTe colloidal nanocrystals has been analyzed quantitatively by means of dynamic light scattering and photoluminescence measurements. The growth rates, size distributions, critical radii, and diffusion constants have been calculated in the framework of the Sugimoto theoretical model. A two-step diffusion-controlled growth regime has been proposed for the reported synthesis and a set of relations for the time evolution of the size distribution has been derived and discussed in the sense of the size distribution focusing concept.
Multiple conducting carriers generated in LaAlO3/SrTiO3 heterostructures
Authors: Seo S. S. A. , Marton Z. , Choi W. S. , Hassink G. W. J. , Blank D. H. A. , Hwang H. Y. , Noh T. W. , Egami T. , Lee H. N.
Published: August 2009

We have found that there is more than one type of conducting carriers generated in LaAlO3/SrTiO3 heterostructures by comparing the sheet carrier density and mobility from optical transmission spectroscopy with those from dc-transport measurements. When multiple types of carriers exist, optical characterization dominantly reflects the contribution from the high-density carriers whereas dc-transport measurements may exaggerate the contribution of the high-mobility carriers even though they are present at low density. Since the low-temperature mobility determined by dc-transport in the LaAlO3/SrTiO3 heterostructures is much higher than that extracted by optical method, we attribute the origin of high-mobility transport to the low-density conducting carriers.
Effect of gate orientation on dc characteristics of Si-doped, nonpolar AlGaN/GaN metal-oxide semiconductor high electron mobility transistors
Authors: Chang C. Y. , Wang Yu-Lin , Gila B. P. , Gerger A. P. , Pearton S. J. , Lo C. F. , Ren F. , Sun Q. , Zhang Yu. , Han J.
Published: August 2009

Sc 2 O 3 / AlGaN / GaN metal-oxide-semiconductor (MOS) high electron mobility transistors were fabricated on (112¯0) a-plane, Si-doped epitaxial layers grown by metal organic chemical vapor deposition on (1 1̱20) r-plane sapphire substrates. The gate finger direction was varied from parallel to the in-plane c-axis [0001] to the m-axis [1 01̱0] direction perpendicular to the observed striations in surface morphology. The [0001] gate devices show lower drain-source current, mobility, and transconductance than their [1 01̱0] counterparts, with a systematic dependence on gate finger direction. The symmetrical gate current-voltage characteristics and low gate current (∼3×10−9 A at ±5 V) confirm the effectiveness of the MOS gate, which is an attractive approach for these structures containing heavily Si-doped AlGaN.
The regulatory role of cell mechanics for migration of differentiating myeloid cells
Authors: Lautenschläger Franziska , Paschke Stephan , Schinkinger Stefan , Bruel Arlette , Beil Michael , Guck Jochen
Published: August 2009

Migration of cells is important for tissue maintenance, immune response, and often altered in disease. While biochemical aspects, including cell adhesion, have been studied in detail, much less is known about the role of the mechanical properties of cells. Previous measurement methods rely on contact with artificial surfaces, which can convolute the results. Here, we used a non-contact, microfluidic optical stretcher to study cell mechanics, isolated from other parameters, in the context of tissue infiltration by acute promyelocytic leukemia (APL) cells, which occurs during differentiation therapy with retinoic acid. Compliance measurements of APL cells reveal a significant softening during differentiation, with the mechanical properties of differentiated cells resembling those of normal neutrophils. To interfere with the migratory ability acquired with the softening, differentiated APL cells were exposed to paclitaxel, which stabilizes microtubules. This treatment does not alter compliance but reduces cell relaxation after cessation of mechanical stress six-fold, congruent with a significant reduction of motility. Our observations imply that the dynamical remodeling of cell shape required for tissue infiltration can be frustrated by stiffening the microtubular system. This link between the cytokeleton, cell mechanics, and motility suggests treatment options for pathologies relying on migration of cells, notably cancer metastasis.
Unexpected expression of α- and β-globin in mesencephalic dopaminergic neurons and glial cells
Authors: Biagioli Marta , Pinto Milena , Cesselli Daniela , Zaninello Marta , Lazarevic Dejan , Roncaglia Paola , Simone Roberto , Vlachouli Christina , Plessy Charles , Bertin Nicolas , Beltrami Antonio , Kobayashi Kazuto , Gallo Vittorio , Santoro Claudio , Ferrer Isidro , Rivella Stefano , Beltrami Carlo Alberto , Carninci Piero , Raviola Elio , Gustincich Stefano
Published: August 2009

The mesencephalic dopaminergic (mDA) cell system is composed of two major groups of projecting cells in the
substantia nigra
(SN) (A9 neurons) and the ventral tegmental area (VTA) (A10 cells). A9 neurons form the nigrostriatal pathway and are involved in regulating voluntary movements and postural reflexes. Their selective degeneration leads to Parkinson's disease. Here, we report that gene expression analysis of A9 dopaminergic neurons (DA) identifies transcripts for α- and β-chains of hemoglobin (Hb). Globin immunoreactivity decorates the majority of A9 DA, a subpopulation of cortical and hippocampal astrocytes and mature oligodendrocytes. This pattern of expression was confirmed in different mouse strains and in rat and human. We show that Hb is expressed in the SN of human postmortem brain. By microarray analysis of dopaminergic cell lines overexpressing α- and β-globin chains, changes in genes involved in O
2
homeostasis and oxidative phopshorylation were observed, linking Hb expression to mitochondrial function. Our data suggest that the most famed oxygen-carrying globin is not exclusively restricted to the blood, but it may play a role in the normal physiology of the brain and neurodegenerative diseases.
An interference account of cue-independent forgetting in the no-think paradigm
Authors: Tomlinson Tracy D. , Huber David E. , Rieth Cory A. , Davelaar Eddy J.
Published: August 2009

Memory suppression is investigated with the no-think paradigm, which produces forgetting following repeated practice of not thinking about a memory [Anderson MC, Green C (2001)
Nature
410:366–369]. Because the forgotten item is not retrieved even when tested with an independent, semantically related cue, it has been assumed that this forgetting is due to an inhibition process. However, this conclusion is based on a single stage to recall, whereas global memory models, which produce forgetting through a process of interference, include both a sampling and a recovery stage to recall. By assuming that interference exists during recovery, these models can explain cue-independent forgetting. We tested several predictions of this interference explanation of cue-independent forgetting by modifying the think/no-think paradigm. We added a condition where participants quickly pressed enter rather than not thinking. We also manipulated initial memory strength and tested recognition memory. Most importantly, learning to quickly press enter produced as much cue-independent forgetting as no-think instructions. Demonstrating the adequacy of two-stage recall, a simple computational model (SAM-RI) simultaneously captured the original cue, independent cue, and recognition results.
Substrate binding site flexibility of the small heat shock protein molecular chaperones
Authors: Jaya Nomalie , Garcia Victor , Vierling Elizabeth
Published: August 2009

Small heat shock proteins (sHSPs) serve as a first line of defense against stress-induced cell damage by binding and maintaining denaturing proteins in a folding-competent state. In contrast to the well-defined substrate binding regions of ATP-dependent chaperones, interactions between sHSPs and substrates are poorly understood. Defining substrate-binding sites of sHSPs is key to understanding their cellular functions and to harnessing their aggregation-prevention properties for controlling damage due to stress and disease. We incorporated a photoactivatable cross-linker at 32 positions throughout a well-characterized sHSP, dodecameric PsHsp18.1 from pea, and identified direct interaction sites between sHSPs and substrates. Model substrates firefly luciferase and malate dehydrogenase form strong contacts with multiple residues in the sHSP N-terminal arm, demonstrating the importance of this flexible and evolutionary variable region in substrate binding. Within the conserved α-crystallin domain both substrates also bind the β-strand (β7) where mutations in human homologs result in inherited disease. Notably, these binding sites are poorly accessible in the sHSP atomic structure, consistent with major structural rearrangements being required for substrate binding. Detectable differences in the pattern of cross-linking intensity of the two substrates and the fact that substrates make contacts throughout the sHSP indicate that there is not a discrete substrate binding surface. Our results support a model in which the intrinsically-disordered N-terminal arm can present diverse geometries of interaction sites, which is likely critical for the ability of sHSPs to protect efficiently many different substrates.
A role for galanin in human and experimental inflammatory demyelination
Authors: Wraith David C. , Pope Robert , Butzkueven Helmut , Holder Heidi , Vanderplank Penny , Lowrey Pauline , Day Michael J. , Gundlach Andrew L. , Kilpatrick Trevor J. , Scolding Neil , Wynick David
Published: August 2009

The neuropeptide galanin is widely expressed by many differing subsets of neurons in the nervous system. There is a marked upregulation in the levels of the peptide in a variety of nerve injury models and in the basal forebrain of humans with Alzheimer's disease. Here we demonstrate that galanin expression is specifically and markedly upregulated in microglia both in multiple sclerosis (MS) lesions and shadow plaques. Galanin expression is also upregulated in the experimental autoimmune encephalomyelitis (EAE) model of MS, although solely in oligodendrocytes. To study whether the observed increase in expression of galanin in inflammatory demyelination might modulate disease activity, we applied the EAE model to a panel of galanin transgenic lines. Over-expression of galanin in transgenic mice (Gal-OE) abolishes disease in the EAE model, whilst loss-of-function mutations in galanin or galanin receptor-2 (GalR2) increase disease severity. The pronounced effects of altered endogenous galanin or GalR2 expression on EAE disease activity may reflect a direct neuroprotective effect of the neuropeptide via activation of GalR2, similar to that previously described in a number of neuronal injury paradigms. Irrespective of the mechanism(s) by which galanin alters EAE disease activity, our findings imply that galanin/GalR2 agonists may have future therapeutic implications for MS.
Protein quantification across hundreds of experimental conditions
Authors: Khan Zia , Bloom Joshua S. , Garcia Benjamin A. , Singh Mona , Kruglyak Leonid
Published: August 2009

Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.
Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2
Authors: Umitsu Masataka , Nishimasu Hiroshi , Noma Akiko , Suzuki Tsutomu , Ishitani Ryuichiro , Nureki Osamu
Published: August 2009

S
-adenosylmethionine (AdoMet) is a methyl donor used by a wide variety of methyltransferases, and it is also used as the source of an α-amino-α-carboxypropyl (“acp”) group by several enzymes. tRNA-yW synthesizing enzyme-2 (TYW2) is involved in the biogenesis of a hypermodified nucleotide, wybutosine (yW), and it catalyzes the transfer of the “acp” group from AdoMet to the C7 position of the imG-14 base, a yW precursor. This modified nucleoside yW is exclusively located at position 37 of eukaryotic tRNA
Phe
, and it ensures the anticodon-codon pairing on the ribosomal decoding site. Although this “acp” group has a significant role in preventing decoding frame shifts, the mechanism of the “acp” group transfer by TYW2 remains unresolved. Here we report the crystal structures and functional analyses of two archaeal homologs of TYW2 from
Pyrococcus horikoshii
and
Methanococcus jannaschii
. The in vitro mass spectrometric and radioisotope-labeling analyses confirmed that these archaeal TYW2 homologues have the same activity as yeast TYW2. The crystal structures verified that the archaeal TYW2 contains a canonical class-I methyltransferase (MTase) fold. However, their AdoMet-bound structures revealed distinctive AdoMet-binding modes, in which the “acp” group, instead of the methyl group, of AdoMet is directed to the substrate binding pocket. Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the “acp” group, and not the methyl group, from AdoMet to the nucleobase.
A DNA barcode for land plants
Authors:   CBOL Plant Working Group1, Hollingsworth Peter M. , Forrest Laura L. , Spouge John L. , Hajibabaei Mehrdad , Ratnasingham Sujeevan , van der Bank Michelle , Chase Mark W. , Cowan Robyn S. , Erickson David L. , Fazekas Aron J. , Graham Sean W. , James Karen E. , Kim Ki-Joong , Kress W. John , Schneider Harald , van AlphenStahl Jonathan , Barrett Spencer C.H. , van den Berg Cassio , Bogarin Diego , Burgess Kevin S. , Cameron Kenneth M. , Carine Mark , Chacón Juliana , Clark Alexandra , Clarkson James J. , Conrad Ferozah , Devey Dion S. , Ford Caroline S. , Hedderson Terry A.J. , Hollingsworth Michelle L. , Husband Brian C. , Kelly Laura J. , Kesanakurti Prasad R. , Kim Jung Sung , Kim Young-Dong , Lahaye Renaud , Lee Hae-Lim , Long David G. , Madriñán Santiago , Maurin Olivier , Meusnier Isabelle , Newmaster Steven G. , Park Chong-Wook , Percy Diana M. , Petersen Gitte , Richardson James E. , Salazar Gerardo A. , Savolainen Vincent , Seberg Ole , Wilkinson Michael J. , Yi Dong-Keun , Little Damon P.
Published: August 2009

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (
atpF–atpH
spacer,
matK
gene,
rbcL
gene,
rpoB
gene,
rpoC1
gene,
psbK–psbI
spacer, and
trnH–psbA
spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of
rbcL
+
matK
as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
Suppression of a pro-apoptotic K+channel as a mechanism for hepatitis C virus persistence
Authors: Mankouri Jamel , Dallas Mark L. , Hughes Mair E. , Griffin Stephen D. C. , Macdonald Andrew , Peers Chris , Harris Mark
Published: August 2009

An estimated 3% of the global population are infected with hepatitis C virus (HCV), and the majority of these individuals will develop chronic liver disease. As with other chronic viruses, establishment of persistent infection requires that HCV-infected cells must be refractory to a range of pro-apoptotic stimuli. In response to oxidative stress, amplification of an outward K+current mediated by the Kv2.1 channel, precedes the onset of apoptosis. We show here that in human hepatoma cells either infected with HCV or harboring an HCV subgenomic replicon, oxidative stress failed to initiate apoptosis via Kv2.1. The HCV NS5A protein mediated this effect by inhibiting oxidative stress-induced p38 MAPK phosphorylation of Kv2.1. The inhibition of a host cell K+channel by a viral protein is a hitherto undescribed viral anti-apoptotic mechanism and represents a potential target for antiviral therapy.
Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration
Authors: He Huawei , Yang Taehong , Terman Jonathan R. , Zhang Xuewu
Published: August 2009

Plexin cell surface receptors bind to semaphorin ligands and transduce signals for regulating neuronal axon guidance. The intracellular region of plexins is essential for signaling and contains a R-Ras/M-Ras GTPase activating protein (GAP) domain that is divided into two segments by a Rho GTPase-binding domain (RBD). The regulation mechanisms for plexin remain elusive, although it is known that activation requires both binding of semaphorin to the extracellular region and a Rho-family GTPase (Rac1 or Rnd1) to the RBD. Here we report the crystal structure of the plexin A3 intracellular region. The structure shows that the N- and C-terminal portions of the GAP homologous regions together form a GAP domain with an overall fold similar to other Ras GAPs. However, the plexin GAP domain adopts a closed conformation and cannot accommodate R-Ras/M-Ras in its substrate-binding site, providing a structural basis for the autoinhibited state of plexins. A comparison with the plexin B1 RBD/Rnd1 complex structure suggests that Rnd1 binding alone does not induce a conformational change in plexin, explaining the requirement of both semaphorin and a Rho GTPase for activation. The structure also identifies an N-terminal segment that is important for regulation. Both the N-terminal segment and the RBD make extensive interactions with the GAP domain, suggesting the presence of an allosteric network connecting these three domains that integrates semaphorin and Rho GTPase signals to activate the GAP. The importance of these interactions in plexin signaling is shown by both cell-based and in vivo axon guidance assays.
Thickness–radius relationship and spring constants of cholesterol helical ribbons
Authors: Khaykovich Boris , Kozlova Natalia , Choi Wonshik , Lomakin Aleksey , Hossain Chintan , Sung Yongjin , Dasari Ramachandra R. , Feld Michael S. , Benedek George B.
Published: August 2009

Using quantitative phase microscopy, we have discovered a quadratic relationship between the radius
R
and the thickness
t
of helical ribbons that form spontaneously in multicomponent cholesterol–surfactant mixtures. These helical ribbons may serve as mesoscopic springs to measure or to exert forces on nanoscale biological objects. The spring constants of these helices depend on their submicroscopic thickness. The quadratic relationship (
R
∝
t
2
) between radius and thickness is a consequence of the crystal structure of the ribbons and enables a determination of the spring constant of any of our helices solely in terms of its observable geometrical dimensions.
Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae
Authors: Luo M. C. , Deal K. R. , Akhunov E. D. , Akhunova A. R. , Anderson O. D. , Anderson J. A. , Blake N. , Clegg M. T. , Coleman-Derr D. , Conley E. J. , Crossman C. C. , Dubcovsky J. , Gill B. S. , Gu Y. Q. , Hadam J. , Heo H. Y. , Huo N. , Lazo G. , Ma Y. , Matthews D. E. , McGuire P. E. , Morrell P. L. , Qualset C. O. , Renfro J. , Tabanao D. , Talbert L. E. , Tian C. , Toleno D. M. , Warburton M. L. , You F. M. , Zhang W. , Dvorak J.
Published: August 2009

Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of
Aegilops tauschii
, the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and
Ae. tauschii
lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere–telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomere–telomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of
Ae. tauschii
genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern
Ae. tauschii
chromosomes but not in the vicinity of the ancient termini embedded in the
Ae. tauschii
chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere–telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated.
Attractivity for two-dimensional linear systems whose anti-diagonal coefficients are periodic
Authors: Sugie Jitsuro , Endo Ayano
Published: August 2009

This paper deals with the linear systemx′=A(t)x\mathbf {x}’ = A(t)\mathbf {x}withA(t)A(t)being a2×22\times 2matrix. The anti-diagonal components ofA(t)A(t)are assumed to be periodic, but the diagonal components are not necessarily periodic. Our concern is to establish sufficient conditions for the zero solution to be attractive. Floquet theory is of no use in solving our problem, because not all components are periodic. Another approach is adopted. Some simple examples are included to illustrate the main result.
Localizable operators and the construction of localized frames
Authors: Futamura Fumiko
Published: August 2009

We introduce the notion of localizable operators with respect to frames and prove the boundedness of such operators on families of Banach spaces. This generalizes previous results for specific operators, such as pseudodifferential operators on modulation spaces. We also use this notion to provide sufficient conditions for the construction of frames which have the localization property.
A direct proof of the theorem on formal functions
Authors: Sancho de Salas Fernando , Sancho de Salas Pedro
Published: August 2009

We give a direct and elementary proof of the theorem on formal functions by studying the behaviour of the Godement resolution of a sheaf of modules under completion. This proof also works in some non-noetherian cases.
Higher order embeddings of certain blow-ups of ℙ²
Authors: De Volder Cindy , Tutaj-Gasińska Halszka
Published: August 2009

Let

X
n

X_n

be the blow-up of the projective plane along

n
n

general points of a smooth cubic plane curve and let

L

\mathcal {L}

be the linear series of strict transforms of plane curves of degree

d
d

having multiplicity at least

m
i

m_i

at the

i
i

-th blown-up point. We prove that if

L

\mathcal {L}

is

k
k

-very ample, then

L

\mathcal {L}

is excellent and

L

⋅
(
−

K
n

)
≥
k
+
2

\mathcal {L}\cdot (-K_n) \geq k+2

. Then we give a numerical criterion for the

k
k

-very ampleness of excellent classes with

L

⋅
(
−

K
n

)
≥
k
+
2

\mathcal {L} \cdot (-K_n) \geq k+2

, which in many cases is a necessary and sufficient condition.