bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel Electric Responsive Columnar Liquid Crystals based on Perylene Tetra sec-alkyl Ester Derivatives
Authors: Wang Lei , Cui Qing , Chen Xiao-Fang , Li Yang , Li Zheng-Qiang , Wang Dong , Yang Huai
Published: May 2013

A series of novel perylene tetra sec-alkyl ester compounds were successfully designed and synthesised. The photophysical properties were investigated and the UV absorption and fluorescence emission spectra displayed a mirror-image relationship. The compound PS8 showed the highest fluorescent quantum yield, while the fluorescence of PS8 was quenched in the aggregated state in mixed solvents. Moreover, the electrochemical properties of the perylene derivatives were studied to determine the molecules’ highest occupied molecular orbital and lowest unoccupied molecular orbital levels by cyclic voltammetry. The most important result was that PS8 exhibited a columnar phase at room temperature and was responsive to an electric field. PS8 could perpendicularly orient to an applied electric field. In addition, highly oriented face-on alignment was achieved on indium tin oxide-covered glass by thermal annealing.
Innovative grassland management systems for environmental and livelihood benefits
Authors: Kemp David R. , Guodong Han , Xiangyang Hou , Michalk David L. , Fujiang Hou , Jianping Wu , Yingjun Zhang
Published: May 2013

Grasslands occupy 40% of the world’s land surface (excluding Antarctica and Greenland) and support diverse groups, from traditional extensive nomadic to intense livestock-production systems. Population pressures mean that many of these grasslands are in a degraded state, particularly in less-productive areas of developing countries, affecting not only productivity but also vital environmental services such as hydrology, biodiversity, and carbon cycles; livestock condition is often poor and household incomes are at or below poverty levels. The challenge is to optimize management practices that result in “win-win” outcomes for grasslands, the environment, and households. A case study is discussed from northwestern China, where it has been possible to reduce animal numbers considerably by using an energy-balance/market-based approach while improving household incomes, providing conditions within which grassland recovery is possible. This bottom-up approach was supported by informing and working with the six layers of government in China to build appropriate policies. Further policy implications are considered. Additional gains in grassland rehabilitation could be fostered through targeted environmental payment schemes. Other aspects of the livestock production system that can be modified are discussed. This work built a strategy that has implications for many other grassland areas around the world where common problems apply.
Green Revolution research saved an estimated 18 to 27 million hectares from being brought into agricultural production
Authors: Stevenson James R. , Villoria Nelson , Byerlee Derek , Kelley Timothy , Maredia Mywish
Published: May 2013

New estimates of the impacts of germplasm improvement in the major staple crops between 1965 and 2004 on global land-cover change are presented, based on simulations carried out using a global economic model (Global Trade Analysis Project Agro-Ecological Zone), a multicommodity, multiregional computable general equilibrium model linked to a global spatially explicit database on land use. We estimate the impact of removing the gains in cereal productivity attributed to the widespread adoption of improved varieties in developing countries. Here, several different effects—higher yields, lower prices, higher land rents, and trade effects—have been incorporated in a single model of the impact of Green Revolution research (and subsequent advances in yields from crop germplasm improvement) on land-cover change. Our results generally support the Borlaug hypothesis that increases in cereal yields as a result of widespread adoption of improved crop germplasm have saved natural ecosystems from being converted to agriculture. However, this relationship is complex, and the net effect is of a much smaller magnitude than Borlaug proposed. We estimate that the total crop area in 2004 would have been between 17.9 and 26.7 million hectares larger in a world that had not benefited from crop germplasm improvement since 1965. Of these hectares, 12.0–17.7 million would have been in developing countries, displacing pastures and resulting in an estimated 2 million hectares of additional deforestation. However, the negative impacts of higher food prices on poverty and hunger under this scenario would likely have dwarfed the welfare effects of agricultural expansion.
Mass spectrometry-based metabolomics of single yeast cells
Authors: Ibáñez Alfredo J. , Fagerer Stephan R. , Schmidt Anna Mareike , Urban Pawel L. , Jefimovs Konstantins , Geiger Philipp , Dechant Reinhard , Heinemann Matthias , Zenobi Renato
Published: May 2013

Single-cell level measurements are necessary to characterize the intrinsic biological variability in a population of cells. In this study, we demonstrate that, with the microarrays for mass spectrometry platform, we are able to observe this variability. We monitor environmentally (2-deoxy-
d
-glucose) and genetically (ΔPFK2) perturbed
Saccharomyces cerevisiae
cells at the single-cell, few-cell, and population levels. Correlation plots between metabolites from the glycolytic pathway, as well as with the observed ATP/ADP ratio as a measure of cellular energy charge, give biological insight that is not accessible from population-level metabolomic data.
Human frontal lobes are not relatively large
Authors: Barton Robert A. , Venditti Chris
Published: May 2013

One of the most pervasive assumptions about human brain evolution is that it involved relative enlargement of the frontal lobes. We show that this assumption is without foundation. Analysis of five independent data sets using correctly scaled measures and phylogenetic methods reveals that the size of human frontal lobes, and of specific frontal regions, is as expected relative to the size of other brain structures. Recent claims for relative enlargement of human frontal white matter volume, and for relative enlargement shared by all great apes, seem to be mistaken. Furthermore, using a recently developed method for detecting shifts in evolutionary rates, we find that the rate of change in relative frontal cortex volume along the phylogenetic branch leading to humans was unremarkable and that other branches showed significantly faster rates of change. Although absolute and proportional frontal region size increased rapidly in humans, this change was tightly correlated with corresponding size increases in other areas and whole brain size, and with decreases in frontal neuron densities. The search for the neural basis of human cognitive uniqueness should therefore focus less on the frontal lobes in isolation and more on distributed neural networks.
Murine leukemia virus glycosylated Gag blocks apolipoprotein B editing complex 3 and cytosolic sensor access to the reverse transcription complex
Authors: Stavrou Spyridon , Nitta Takayuki , Kotla Swathi , Ha Dat , Nagashima Kunio , Rein Alan R. , Fan Hung , Ross Susan R.
Published: May 2013

Pathogenic retroviruses have evolved multiple means for evading host restriction factors such as apolipoprotein B editing complex (APOBEC3) proteins. Here, we show that murine leukemia virus (MLV) has a unique means of counteracting APOBEC3 and other cytosolic sensors of viral nucleic acid. Using virus isolated from infected WT and APOBEC3 KO mice, we demonstrate that the MLV glycosylated Gag protein (glyco-Gag) enhances viral core stability. Moreover, in vitro endogenous reverse transcription reactions of the glyco-Gag mutant virus were substantially inhibited compared with WT virus, but only in the presence of APOBEC3. Thus, glyco-Gag rendered the reverse transcription complex in the viral core resistant to APOBEC3. Glyco-Gag in the virion also rendered MLV resistant to other cytosolic sensors of viral reverse transcription products in newly infected cells. Strikingly, glyco-Gag mutant virus reverted to glyco-Gag–containing virus only in WT and not APOBEC3 KO mice, indicating that counteracting APOBEC3 is the major function of glyco-Gag. Thus, in contrast to the HIV viral infectivity factor protein, which prevents APOBEC3 packaging in the virion, the MLV glyco-Gag protein uses a unique mechanism to counteract the antiviral action of APOBEC3 in vivo—namely, protecting the reverse transcription complex in viral cores from APOBEC3. These data suggest that capsid integrity may play a critical role in virus resistance to intrinsic cellular antiviral resistance factors that act at the early stages of infection.
Cyclophilin 20-3 relays a 12-oxo-phytodienoic acid signal during stress responsive regulation of cellular redox homeostasis
Authors: Park Sang-Wook , Li Wei , Viehhauser Andrea , He Bin , Kim Soonok , Nilsson Anders K. , Andersson Mats X. , Kittle Joshua D. , Ambavaram Madana M. R. , Luan Sheng , Esker Alan R. , Tholl Dorothea , Cimini Daniela , Ellerström Mats , Coaker Gitta , Mitchell Thomas K. , Pereira Andy , Dietz Karl-Josef , Lawrence Christopher B.
Published: May 2013

The jasmonate family of phytohormones plays central roles in plant development and stress acclimation. However, the architecture of their signaling circuits remains largely unknown. Here we describe a jasmonate family binding protein, cyclophilin 20-3 (CYP20-3), which regulates stress-responsive cellular redox homeostasis. (+)-12-oxo-phytodienoic acid (OPDA) binding promotes CYP20-3 to form a complex with serine acetyltransferase 1, which triggers the formation of a hetero-oligomeric cysteine synthase complex with
O
-acetylserine(thiol)lyase B in chloroplasts. The cysteine synthase complex formation then activates sulfur assimilation that leads to increased levels of thiol metabolites and the buildup of cellular reduction potential. The enhanced redox capacity in turn coordinates the expression of a subset of OPDA-responsive genes. Thus, we conclude that CYP20-3 is a key effector protein that links OPDA signaling to amino acid biosynthesis and cellular redox homeostasis in stress responses.
Molecular evolution of peptidergic signaling systems in bilaterians
Authors: Mirabeau Olivier , Joly Jean-Stéphane
Published: May 2013

Significance

Peptides and their specific receptors form molecular peptidergic systems (PSs) that are essential components of neuronal communication in the animal brain. Many PSs have been characterized in insects and mammals but their precise evolutionary relationship is not fully understood. We interrogated genomic sequence databases and used phylogenetic reconstruction tools to show that a large fraction of human PSs were already present in the last common ancestor of flies, mollusks, urchins, and mammals. Our analysis provides a comprehensive view of animal PSs that will pave the way for comparative studies leading to a better understanding of animal physiology and behavior.
Reinstatement of nicotine seeking is mediated by glutamatergic plasticity
Authors: Gipson Cassandra D. , Reissner Kathryn J. , Kupchik Yonatan M. , Smith Alexander C. W. , Stankeviciute Neringa , Hensley-Simon Megan E. , Kalivas Peter W.
Published: May 2013

Nicotine abuse and addiction is a major health liability. Nicotine, an active alkaloid in tobacco, is self-administered by animals and produces cellular adaptations in brain regions associated with drug reward, such as the nucleus accumbens. However, it is unknown whether, akin to illicit drugs of abuse such as cocaine or heroin, the adaptations endure and contribute to the propensity to relapse after discontinuing nicotine use. Using a rat model of cue-induced relapse, we made morphological and electrophysiological measures of synaptic plasticity, as well as quantified glutamate overflow, in the accumbens after 2 wk of withdrawal with extinction training. We found an enduring basal increase in dendritic spine head diameter and in the ratio of AMPA to NMDA currents in accumbens spiny neurons compared with yoked saline animals at 2 wk after the last nicotine self-administration session. This synaptic potentiation was associated with an increase in both AMPA (GluA1) and NMDA (GluN2A and GluN2B) receptor subunits, and a reduction in the glutamate transporter-1 (GLT-1). When nicotine seeking was reinstated by presentation of conditioned cues, there were parallel increases in behavioral responding, extracellular glutamate, and further increases in dendritic spine head diameter and ratio of AMPA to NMDA currents within 15 min. These findings suggest that targeting glutamate transmission might inhibit cue-induced nicotine seeking. In support of this hypothesis, we found that pharmacological inhibition of GluN2A with 3-Chloro-4-fluoro-N-[4-[[2-(phenylcarbonyl)hydrazino]carbonyl]benzyl]benzenesulfonamide (TCN-201) or GluN2B with ifenprodil abolished reinstated nicotine seeking. These results indicate that up-regulated GluN2A, GluN2B, and rapid synaptic potentiation in the accumbens contribute to cue-induced relapse to nicotine use.
Mannodendrimers prevent acute lung inflammation by inhibiting neutrophil recruitment
Authors: Blattes Emilyne , Vercellone Alain , Eutamène Hélène , Turrin Cédric-Olivier , Théodorou Vassilia , Majoral Jean-Pierre , Caminade Anne-Marie , Prandi Jacques , Nigou Jérôme , Puzo Germain
Published: May 2013

Mycobacterium tuberculosismannose-capped lipoarabinomannan inhibits the release of proinflammatory cytokines by LPS-stimulated human dendritic cells (DCs) via targeting the C-type lectin receptor DC-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN). With the aim of mimicking the bioactive supramolecular structure of mannose-capped lipoarabinomannan, we designed and synthesized a set of poly(phosphorhydrazone) dendrimers grafted with mannose units, called mannodendrimers, that differed by size and the number and length of their (α1→2)-oligommanoside caps. A third-generation dendrimer bearing 48 trimannoside caps (3T) and a fourth-generation dendrimer bearing 96 dimannosides (4D) displayed the highest binding avidity for DC-SIGN. Moreover, these dendrimers inhibited proinflammatory cytokines, including TNF-α, production by LPS-stimulated DCs in a DC-SIGN–dependent fashion. Finally, in a model of acute lung inflammation in which mice were exposed to aerosolized LPS,per osadministration of 3T mannodendrimer was found to significantly reduce neutrophil influx via targeting the DC-SIGN murine homolog SIGN-related 1. The 3T mannodendrimer therefore represents an innovative fully synthetic compound for the treatment of lung inflammatory diseases.
Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers
Authors: Rakowska Paulina D. , Jiang Haibo , Ray Santanu , Pyne Alice , Lamarre Baptiste , Carr Matthew , Judge Peter J. , Ravi Jascindra , M. Gerling Ulla I. , Koksch Beate , Martyna Glenn J. , Hoogenboom Bart W. , Watts Anthony , Crain Jason , Grovenor Chris R. M. , Ryadnov Maxim G.
Published: May 2013

Antimicrobial peptides are postulated to disrupt microbial phospholipid membranes. The prevailing molecular model is based on the formation of stable or transient pores although the direct observation of the fundamental processes is lacking. By combining rational peptide design with topographical (atomic force microscopy) and chemical (nanoscale secondary ion mass spectrometry) imaging on the same samples, we show that pores formed by antimicrobial peptides in supported lipid bilayers are not necessarily limited to a particular diameter, nor they are transient, but can expand laterally at the nano-to-micrometer scale to the point of complete membrane disintegration. The results offer a mechanistic basis for membrane poration as a generic physicochemical process of cooperative and continuous peptide recruitment in the available phospholipid matrix.
Palmitoylation-dependent CDKL5–PSD-95 interaction regulates synaptic targeting of CDKL5 and dendritic spine development
Authors: Zhu Yong-Chuan , Li Dan , Wang Lu , Lu Bin , Zheng Jing , Zhao Shi-Lin , Zeng Rong , Xiong Zhi-Qi
Published: May 2013

The X-linked gene cyclin-dependent kinase-like 5 (
CDKL5
) is mutated in severe neurodevelopmental disorders, including some forms of atypical Rett syndrome, but the function and regulation of CDKL5 protein in neurons remain to be elucidated. Here, we show that CDKL5 binds to the scaffolding protein postsynaptic density (PSD)-95, and that this binding promotes the targeting of CDKL5 to excitatory synapses. Interestingly, this binding is not constitutive, but governed by palmitate cycling on PSD-95. Furthermore, pathogenic mutations that truncate the C-terminal tail of CDKL5 diminish its binding to PSD-95 and synaptic accumulation. Importantly, down-regulation of CDKL5 by RNA interference (RNAi) or interference with the CDKL5–PSD-95 interaction inhibits dendritic spine formation and growth. These results demonstrate a critical role of the palmitoylation-dependent CDKL5–PSD-95 interaction in localizing CDKL5 to synapses for normal spine development and suggest that disruption of this interaction by pathogenic mutations may be implicated in the pathogenesis of CDKL5-related disorders.
Perineuronal nets protect fast-spiking interneurons against oxidative stress
Authors: Cabungcal Jan-Harry , Steullet Pascal , Morishita Hirofumi , Kraftsik Rudolf , Cuenod Michel , Hensch Takao K. , Do Kim Q.
Published: May 2013

A hallmark of schizophrenia pathophysiology is the dysfunction of cortical inhibitory GABA neurons expressing parvalbumin, which are essential for coordinating neuronal synchrony during various sensory and cognitive tasks. The high metabolic requirements of these fast-spiking cells may render them susceptible to redox dysregulation and oxidative stress. Using mice carrying a genetic redox imbalance, we demonstrate that extracellular perineuronal nets, which constitute a specialized polyanionic matrix enwrapping most of these interneurons as they mature, play a critical role in the protection against oxidative stress. These nets limit the effect of genetically impaired antioxidant systems and/or excessive reactive oxygen species produced by severe environmental insults. We observe an inverse relationship between the robustness of the perineuronal nets around parvalbumin cells and the degree of intracellular oxidative stress they display. Enzymatic degradation of the perineuronal nets renders mature parvalbumin cells and fast rhythmic neuronal synchrony more susceptible to oxidative stress. In parallel, parvalbumin cells enwrapped with mature perineuronal nets are better protected than immature parvalbumin cells surrounded by less-condensed perineuronal nets. Although the perineuronal nets act as a protective shield, they are also themselves sensitive to excess oxidative stress. The protection might therefore reflect a balance between the oxidative burden on perineuronal net degradation and the capacity of the system to maintain the nets. Abnormal perineuronal nets, as observed in the postmortem patient brain, may thus underlie the vulnerability and functional impairment of pivotal inhibitory circuits in schizophrenia.
RETRACTED: Dominant suppression of inflammation by glycan-hydrolyzed IgG
Authors: Nandakumar Kutty Selva , Collin Mattias , Happonen Kaisa E. , Croxford Allyson M. , Lundström Susanna L. , Zubarev Roman A. , Rowley Merrill J. , Blom Anna M. , Holmdahl Rikard
Published: May 2013

A unique anti-inflammatory property of IgG, independent of antigen specificity, is described. IgG with modification of the heavy-chain glycan on asparagine 297 by the streptococcal enzyme endo-β-
N
-acetylglucosaminidase (EndoS) induced a dominant suppression of immune complex (IC)-mediated inflammation, such as arthritis, through destabilization of local ICs by fragment crystallizable–fragment crystallizable (Fc-Fc) interactions. Small amounts (250 µg) of EndoS-hydrolyzed IgG were sufficient to inhibit arthritis in mice and most effective during the formation of ICs in the target tissue. The presence of EndoS-hydrolyzed IgG disrupted larger IC lattice formation both in vitro and in vivo, as visualized with anti-C3b staining. Neither complement binding in vitro nor antigen–antibody binding per se was affected.
Early hominin auditory ossicles from South Africa
Authors: Quam Rolf M. , de Ruiter Darryl J. , Masali Melchiorre , Arsuaga Juan-Luis , Martínez Ignacio , Moggi-Cecchi Jacopo
Published: May 2013

The middle ear ossicles are only rarely preserved in fossil hominins. Here, we report the discovery of a complete ossicular chain (malleus, incus, and stapes) ofParanthropus robustusas well as additional ear ossicles fromAustralopithecus africanus. The malleus in both early hominin taxa is clearly human-like in the proportions of the manubrium and corpus, whereas the incus and stapes resemble African and Asian great apes more closely. A deep phylogenetic origin is proposed for the derived malleus morphology, and this may represent one of the earliest human-like features to appear in the fossil record. The anatomical differences found in the early hominin incus and stapes, along with other aspects of the outer, middle, and inner ear, are consistent with the suggestion of different auditory capacities in these early hominin taxa compared with modern humans.
PRMT5 modulates the metabolic response to fasting signals
Authors: Tsai Wen-Wei , Niessen Sherry , Goebel Naomi , Yates John R. , Guccione Ernesto , Montminy Marc
Published: May 2013

Under fasting conditions, increases in circulating glucagon maintain glucose balance by promoting hepatic gluconeogenesis. Triggering of the cAMP pathway stimulates gluconeogenic gene expression through the PKA-mediated phosphorylation of the cAMP response element binding (CREB) protein and via the dephosphorylation of the latent cytoplasmic CREB regulated transcriptional coactivator 2 (CRTC2). CREB and CRTC2 activities are increased in insulin resistance, in which they promote hyperglycemia because of constitutive induction of the gluconeogenic program. The extent to which CREB and CRTC2 are coordinately up-regulated in response to glucagon, however, remains unclear. Here we show that, following its activation, CRTC2 enhances CREB phosphorylation through an association with the protein arginine methyltransferase 5 (PRMT5). In turn, PRMT5 was found to stimulate CREB phosphorylation via increases in histone H3 Arg2 methylation that enhanced chromatin accessibility at gluconeogenic promoters. Because depletion of PRMT5 lowers hepatic glucose production and gluconeogenic gene expression, these results demonstrate how a chromatin-modifying enzyme regulates a metabolic program through epigenetic changes that impact the phosphorylation of a transcription factor in response to hormonal stimuli.
Transformation of polarized epithelial cells by apical mistrafficking of epiregulin
Authors: Singh Bhuminder , Bogatcheva Galina , Washington Mary Kay , Coffey Robert J.
Published: May 2013

Establishment and maintenance of apico-basolateral trafficking pathways are critical to epithelial homeostasis. Loss of polarity and trafficking fidelity are thought to occur as a consequence of transformation; however, here we report that selective mistrafficking of the epidermal growth factor receptor (EGFR) ligand epiregulin (EREG) from the basolateral to the apical cell surface drives transformation. Normally, EREG is preferentially delivered to the basolateral surface of polarized Madin-Darby canine kidney cells. EREG basolateral trafficking is regulated by a conserved tyrosine-based basolateral sorting motif in its cytoplasmic domain (YXXΦ: Y
156
ERV). Both Y156 and V159 are required for basolateral sorting of EREG, because Y156A and V159G substitutions redirect EREG to the apical cell surface. We also show that basolateral sorting of EREG is adaptor protein 1B–independent. Apical mistrafficking of EREG has a distinctive phenotype. In contrast to transient EGFR tyrosine phosphorylation after basolateral EREG stimulation, apical EREG leads to prolonged EGFR tyrosine phosphorylation, which may be related, at least in part, to a lack of negative regulatory Y1045 phosphorylation and subsequent ubiquitylation. Notably, Madin-Darby canine kidney cells stably expressing apically mistrafficked EREG form significantly larger, hyperproliferative, poorly differentiated, and locally invasive tumors in nude mice compared with WT EREG-expressing cells.
Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids
Authors: Kamphorst Jurre J. , Cross Justin R. , Fan Jing , de Stanchina Elisa , Mathew Robin , White Eileen P. , Thompson Craig B. , Rabinowitz Joshua D.
Published: May 2013

Cancer cell growth requires fatty acids to replicate cellular membranes. The kinase Akt is known to up-regulate fatty acid synthesis and desaturation, which is carried out by the oxygen-consuming enzyme stearoyl-CoA desaturase (SCD)1. We used
13
C tracers and lipidomics to probe fatty acid metabolism, including desaturation, as a function of oncogene expression and oxygen availability. During hypoxia, flux from glucose to acetyl-CoA decreases, and the fractional contribution of glutamine to fatty acid synthesis increases. In addition, we find that hypoxic cells bypass de novo lipogenesis, and thus, both the need for acetyl-CoA and the oxygen-dependent SCD1-reaction, by scavenging serum fatty acids. The preferred substrates for scavenging are phospholipids with one fatty acid tail (lysophospholipids). Hypoxic reprogramming of de novo lipogenesis can be reproduced in normoxic cells by Ras activation. This renders Ras-driven cells, both in culture and in allografts, resistant to SCD1 inhibition. Thus, a mechanism by which oncogenic Ras confers metabolic robustness is through lipid scavenging.
Building the Islamic State: The Draft Constitution of 1979 Reconsidered
Authors: Randjbar-Daemi Siavush
Published: May 2013

The early drafts of the constitution of 1979 have represented a crucial moment in the creation of the post-revolutionary Iranian state. This article makes use of primary sources of the time and recently revealed material in order to provide a systematic analysis of the events which led to the production of the key versions of the draft constitution and the reaction to them by the multitude of political movements which were then active. The aim of this study is to clarify events and processes which have been left unexplored by the existing academic literature.
CD47 fusion protein targets CD172a+ cells in Crohn’s disease and dampens the production of IL-1β and TNF
Authors: Baba Nobuyasu , Van Vu Quang , Wakahara Keiko , Rubio Manuel , Fortin Geneviève , Panzini Benoît , Soucy Geneviève , Wassef Ramses , Richard Carole , Tamaz Raja , Lahaie Raymond , Bernard Edmond-Jean , Caussignac Yves , Leduc Raymond , Lougnarath Rasmy , Bergeron Carole , Racicot Marc-André , Bergeron Fanny , Panzini Marie-Andrée , Demetter Pieter , Franchimont Denis , Schäkel Knut , Weckbecker Gisbert , Kolbinger Frank , Heusser Christoph , Huber Thomas , Welzenbach Karl , Sarfati Marika
Published: May 2013

In mice, the transfer of CD172a+ (SIRP-α) dendritic cells (DCs) elicits T cell–driven colitis, whereas treatment with CD47-Fc protein, a CD172a-binding agent, confers protection. The aim of this study was to elucidate the nature and functional properties of human CD172a+ DCs in chronic intestinal inflammation. Here, we show that CD172a+CD11c+ cells accumulate in the mesenteric lymph nodes (mLNs) and inflamed intestinal mucosa in patients with Crohn’s disease (CD). These cells are distinct from resident DCs and may coexpress markers typically associated with monocyte-derived inflammatory DCs such as CD14 and/or DC-SIGN, E-Cadherin, and/or CX3CR1. Spontaneous IL-1β and TNF production by HLA-DR+ cells in CD tissues is restricted to those expressing CD172a. An avidity-improved CD47 fusion protein (CD47-Var1) suppresses the release of a wide array of inflammatory cytokines by CD172a+ cells, which may include HLA-DR−CD172a+ neutrophils, in inflamed colonic explant cultures and impairs the ability of HLA-DR+CD172a+ cells to activate memory Th17 but not Th1 responses in mLNs. In conclusion, targeting CD172a+ cells may represent novel therapeutic perspectives for patients with CD.
Voltage-dependent processes in the electroneutral amino acid exchanger ASCT2
Authors: Zander Catherine B. , Albers Thomas , Grewer Christof
Published: May 2013

Neutral amino acid exchange by the alanine serine cysteine transporter (ASCT)2 was reported to be electroneutral and coupled to the cotransport of one Na+ ion. The cotransported sodium ion carries positive charge. Therefore, it is possible that amino acid exchange is voltage dependent. However, little information is available on the electrical properties of the ASCT2 amino acid transport process. Here, we have used a combination of experimental and computational approaches to determine the details of the amino acid exchange mechanism of ASCT2. The [Na+] dependence of ASCT2-associated currents indicates that the Na+/amino acid stoichiometry is at least 2:1, with at least one sodium ion binding to the amino acid–free apo form of the transporter. When the substrate and two Na+ ions are bound, the valence of the transport domain is +0.81. Consistently, voltage steps applied to ASCT2 in the fully loaded configuration elicit transient currents that decay on a millisecond time scale. Alanine concentration jumps at the extracellular side of the membrane are followed by inwardly directed transient currents, indicative of translocation of net positive charge during exchange. Molecular dynamics simulations are consistent with these results and point to a sequential binding process in which one or two modulatory Na+ ions bind with high affinity to the empty transporter, followed by binding of the amino acid substrate and the subsequent binding of a final Na+ ion. Overall, our results are consistent with voltage-dependent amino acid exchange occurring on a millisecond time scale, the kinetics of which we predict with simulations. Despite some differences, transport mechanism and interaction with Na+ appear to be highly conserved between ASCT2 and the other members of the solute carrier 1 family, which transport acidic amino acids.
A biased intruder in a dense quiescent medium: looking beyond the force–velocity relation
Authors: Bénichou Olivier , Illien Pierre , Mejía-Monasterio Carlos , Oshanin Gleb
Published: May 2013

We study the dynamics of a biased intruder (BI) pulled by a constant force F through a dense molecular crowding environment modelled as a lattice gas of unbiased, randomly moving hard-core particles. Going beyond the usual analysis of the force–velocity relation (FVR), we focus on the behaviour of the higher moments of the BI vector displacement R

n
at time n (the FVR is just the first moment) in the leading order in the density ρ0 of vacancies (O(ρ0)). We prove that in infinite 2D systems the probability distribution P(R

n
) converges to a Gaussian as n → ∞, despite the fact that the BI drives the system into a non-equilibrium steady state with a non-homogeneous spatial distribution of the lattice gas particles. We show that in infinite 2D systems the variance

of the distribution P(R

n
) along the direction of the bias grows (weakly) super-diffusively:

. In the direction perpendicular to the bias, the variance

. The coefficients ν1 and ν2, which we determine exactly for arbitrary bias in O(ρ0), mirror the interplay between the bias, vacancy-controlled transport and the back-flow effects of the medium on the BI. We observe that ν1 ∼ |F|2 for small bias, which signifies that the super-diffusive behaviour emerges beyond the linear-response approximation. We present analytical arguments showing that such an anomalous, field-induced broadening of fluctuations is dramatically enhanced in confined, quasi-1D geometries—infinite 2D stripes and 3D capillaries. We argue that in such systems,

exhibits a strongly super-diffusive behaviour,

. Monte Carlo simulations confirm our analytical results.
On isomorphisms of certain functors for Cherednik algebras
Authors: Losev Ivan
Published: May 2013

Bezrukavnikov and Etingof introduced some functors between the categories

O

\mathcal {O}

for rational Cherednik algebras. Namely, they defined two induction functors

I
n
d

b

,

i
n
d

λ

\mathrm {Ind}_b, \mathrm {ind}_\lambda

and two restriction functors

R
e
s

b

,

r
e
s

λ

\mathrm {Res}_b,\mathrm {res}_\lambda

. They conjectured that one has functor isomorphisms
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="normal upper I normal n normal d Subscript b Baseline approximately-equals normal i normal n normal d Subscript lamda Baseline comma normal upper R normal e normal s Subscript b Baseline approximately-equals normal r normal e normal s Subscript lamda Baseline">

I
n
d

b

≅

i
n
d

λ

,

R
e
s

b

≅

r
e
s

λ

\mathrm {Ind}_b\cong \mathrm {ind}_\lambda , \mathrm {Res}_b\cong \mathrm {res}_\lambda

. The goal of this paper is to prove this conjecture.
Migration of saithe (Pollachius virens) in the Northeast Atlantic
Authors: Homrum Eydna í , Hansen Bogi , Jónsson Sigurður Þór , Michalsen Kathrine , Burgos Julian , Righton David , Steingrund Petur , Jakobsen Tore , Mouritsen Rógvi , Hátún Hjálmar , Armannsson Hlynur , Joensen Jákup Sverri
Published: May 2013

Homrum, E. í, Hansen, B., Jónsson, S. Þ., Michalsen, K., Burgos, J., Righton, D., Steingrund, P., Jakobsen, T., Mouritsen, R., Hátún, H., Armannsson, H., and Joensen, J. S. 2013. Migration of saithe (Pollachius virens) in the Northeast Atlantic. – ICES Journal of Marine Science, 70: 782–792. Saithe (Pollachius virens) stocks in the Northeast Atlantic intermingle as a result of migration among stock areas. The extent of migration has been poorly quantified. Here, we estimate measures of the migration based on existing tagging data from Icelandic, Faroese and Continental (Scotland, North Sea and Norway) waters. Saithe tagged in Icelandic waters were seldom caught outside Icelandic waters (<1% of tag returns), whereas 42% of adult saithe tagged in Faroese waters were recaptured outside Faroese waters. Of adult saithe tagged in Norwegian waters 6.6% were recaptured outside Continental waters. In broad terms, there was a net migration of saithe towards Icelandic waters. The distance between tagging and recapture increased with increasing size and age, with saithe tagged in Norwegian waters moving the longest distances. The results demonstrate significant, but variable, migration rates of adult saithe in the Northeast Atlantic. More detailed studies are needed to clarify the mechanisms behind the migration and what causes the differences among the areas.
Evaluating effectiveness of time/area closures, quotas/caps, and fleet communications to reduce fisheries bycatch
Authors: O'Keefe Catherine E. , Cadrin Steven X. , Stokesbury Kevin D. E.
Published: May 2013

Designing effective bycatch mitigation programmes requires an understanding of the life histories of target and non-target species, interactions of fish and fishing gear, effects of spatial and temporal shifts in fishing effort, socio-economic impacts to the fishery, and incentives of fishery participants. The effects of mitigation measures (including fishing gear modification, time/area closures, bycatch quotas and caps, incentive programs, and fleet communication programs) have been evaluated with respect to reducing bycatch and discards. Less attention has been focused on evaluating unanticipated results related to shifts in fishing effort, changes in the size of non-target species caught, reduced catch of target species, and economic viability to fishing fleets. Time/area closures, bycatch quotas/caps, and fleet communication programmes were evaluated against a set of criteria to assess overall effectiveness in reducing bycatch without causing unintended biological and socio-economic impacts. The results suggest that wide-ranging studies of species' life histories, potential changes in fleet behaviour, and individual incentives are important for developing and implementing mitigation programmes. Combining a suite of mitigation techniques has been successful in meeting biological and socio-economic fisheries goals. Additionally, collaborative programmes that utilize the skill sets of fishers, scientists, and managers have increased effectiveness in meeting bycatch reduction objectives.
A Novel Spore Collection Device for Sampling Exposure Pathways: A Case Study of Puccinia psidii
Authors: Holliday J. L. , Jones S. A. , Simpson J. A. , Glen M. , Edwards J. , Robinson A. , Burgman M. A.
Published: May 2013

A device comprising a filter attached to a vacuum cleaner was purpose-built to sample rust spores from three potentially high-risk pathways in Australia: passengers, fresh flowers, and sea cargo. The proportion of spores recovered from eight surfaces comparable with those on each pathway (cotton, denim, roses, carnations, chrysanthemums, wood, plastic, and metal) was estimated in the laboratory. Spore recovery percentages were highest for denim clothing (61% Puccinia triticina Erikss. and 62% Uromycladium tepperianum) and lowest for carnations (4% P. triticina Erikss. and 5% U. tepperianum). Subsequently, the device was tested at several locations on the Central Coast of New South Wales, Australia, recently affected by a “myrtle rust” outbreak. Symptomatic and asymptomatic myrtle rust hosts, myrtle rust nonhosts, and inanimate objects (e.g., clothing and vehicles) were sampled in conjunction with the emergency response to the outbreak. A polymerase chain reaction (PCR) assay developed for P. psidii established the presence of myrtle rust, and visual inspections provided spore count estimations. All samples from symptomatic myrtle rust hosts produced positive PCR results and spore count estimations were generally much greater. Several samples from asymptomatic myrtle rust hosts, myrtle rust nonhosts, and inanimate objects also produced positive PCR results; however, there were discrepancies between PCR results and spore count estimations in some of these samples, all of which had <100 spores. This study highlights the utility of the device and analytical methodology, especially during the early stages of a disease outbreak when infection symptoms on plants and contamination on objects is not visible upon gross examination.
TWIN SISTER OF FT, GIGANTEA, and CONSTANS Have a Positive But Indirect Effect on Blue Light-Induced Stomatal Opening in Arabidopsis
Authors: Ando Eigo , Ohnishi Masato , Wang Yin , Matsushita Tomonao , Watanabe Aiko , Hayashi Yuki , Fujii Miho , Ma Jian Feng , Inoue Shin-ichiro , Kinoshita Toshinori
Published: May 2013

FLOWERING  LOCUS T (FT) is the major regulatory component controlling photoperiodic floral transition. It is expressed in guard cells and affects blue light-induced stomatal opening induced by the blue-light receptor phototropins phot1 and phot2. Roles for other flowering regulators in stomatal opening have yet to be determined. We show in Arabidopsis (Arabidopsis thaliana) that TWIN SISTER OF FT (TSF), CONSTANS (CO), and GIGANTEA (GI) provide a positive effect on stomatal opening. TSF, which is the closest homolog of FT, was transcribed in guard cells, and light-induced stomatal opening was repressed in tsf-1, a T-DNA insertion mutant of TSF. Overexpression of TSF in a phot1 phot2 mutant background gave a constitutive open-stomata phenotype. Then, we examined whether CO and GI, which are upstream regulators of FT and TSF in photoperiodic flowering, are involved in stomatal opening. Similar to TSF, light-induced stomatal opening was suppressed in the GI and CO mutants gi-1 and co-1. A constitutive open-stomata phenotype was observed in GI and CO overexpressors with accompanying changes in the transcription of both FT and TSF. In photoperiodic flowering, photoperiod is sensed by photoreceptors such as the cryptochromes cry1 and cry2. We examined stomatal phenotypes in a cry1 cry2 mutant and in CRY2 overexpressors. Light-induced stomatal opening was suppressed in cry1 cry2, and the transcription of FT and TSF was down-regulated. In contrast, the stomata in CRY2 overexpressors opened even in the dark, and FT and TSF transcription was up-regulated. We conclude that the photoperiodic flowering components TSF, GI, and CO positively affect stomatal opening.
Analysis of variant selection in friction-stir-processed high-strength low-alloy steels
Authors: Abbasi Majid , Nelson Tracy W. , Sorensen Carl D.
Published: May 2013

Variant selection in friction-stir-welded high-strength low-alloy steels has been studied using the electron backscatter diffraction and prior austenite (PA) reconstruction techniques described in previous papers. A hypothesis for variant selection has been proposed based on grain-boundary interfacial energy and misorientation. This study focuses on austenite 〈111〉 boundaries with a two-dimensional approach. Results indicate that variant selection is strongly dependent on misorientation. Certain PA misorientations produce combinations of variants that minimize the interfacial energies between a ferrite nucleus and a neighboring austenite grain, and between adjoining ferrite nuclei along the boundary between two PA grains. PA grains that exhibit a 60° 〈111〉 misorientation between them satisfy both these conditions for a combination of variants. These PA boundaries exhibit strong variant selection. As a result, the density of these boundary types influences the overall variant selection. Additionally, variant selection is more prevalent in small PA grains (<150 µm), which is probably a result of limited intragranular nucleation. Nearly all variants are present in larger PA grains.
Contrast enhancement of data measured with area detectors: a way to generalize the use of neutron diffraction for thin-film studies
Authors: Bataille Alexandre M. , Auvray Vincent , Gatel Christophe , Gukasov Arsen
Published: May 2013

A denoising method is reported for the treatment of neutron scattering data obtained with position-sensitive detectors, which enhances the information obtained from weak and very weak Bragg peaks. The core element of the method is the application of a Laplacian of Gaussian filter calculated using the parameters of the resolution of the instrument. This adaptation of well established image-processing techniques offers a very efficient way to denoise the data, as shown through the application of the reported method to a study of the magnetic Bragg peaks of a 300 nm-thick epitaxial Cr film. The procedure enhances the contrast by a factor of more than 35 and thus allows precise determination of the position of the integration mask. The large contrast enhancement also lowers the detection threshold of standard elastic neutron diffractometers down to the level usually available solely on optimized triple-axis spectrometers.
Determination of the distribution of elements with similar electron counts: a practical guide for resonant X-ray scattering
Authors: Welzmiller Simon , Urban Philipp , Fahrnbauer Felix , Erra Loredana , Oeckler Oliver
Published: May 2013

This article attempts to present straightforward and easy-to-understand guidelines for the determination of element distribution in compounds lacking X-ray scattering contrast because they have similar electron counts. Different sources of anomalous dispersion correction terms (especially Δf′ values) are compared with respect to their suitability, reliability and quality. Values from databases are compared with Δfvalues calculated from fluorescence spectra and those refined from single-crystal diffraction data, using both reference crystals without scattering contrast problems and crystals containing elements with similar electron counts. The number of data sets required to determine reliably the element distribution and the optimum wavelengths to be used are discussed. Joint multiple data set refinements are suitable for the refinement of multiply mixed occupancies of elements lacking scattering contrast. The most straightforward method of obtaining Δf′ values depends on the complexity of the problem to be solved and the precision required.
Determination of crystal symmetry for Bi4Ti3O12-based ferroelectrics by using electron diffraction
Authors: Ye Wanneng , Lu Chaojing , You Peng , Liang Kun , Zhou Yichun
Published: May 2013

In recent years, inconsistent space groups of monoclinicB1a1 and orthorhombicB2cbhave been reported for the room-temperature ferroelectric phases of both Bi4Ti3O12and lanthanide-substituted Bi4Ti3O12. In this article, the electron diffraction technique is employed to unambiguously clarify the crystal symmetries of ferroelectric Bi4Ti3O12and Bi3.15Nd0.85Ti3O12single crystals at room temperature. All the reflections observed from the two crystals match well with those derived fromB1a1, but the observed reflections 010, 030, {\overline 2}10 and {\overline 2}30 should be forbidden in the case ofB2cb. This fact indicates that both the ferroelectrics are of the space groupB1a1 rather thanB2cb, which is confirmed by convergent-beam electron diffraction observations. On the basis of the monoclinic space groupB1a1, the lattice parameters of both the ferroelectrics were calculated by the Rietveld refinement of powder X-ray diffraction data.
A geometrical approach for semi-automated crystal centering andin situX-ray diffraction data collection
Authors: Heidari Khajepour Mohammad Yaser , Lebrette Hugo , Vernede Xavier , Rogues Pierrick , Ferrer Jean-Luc
Published: May 2013

High-throughput protein crystallography projects pushed forward the development of automated crystallization platforms that are now commonly used. This created an urgent need for adapted and automated equipment for crystal analysis. However, first these crystals have to be harvested, cryo-protected and flash-cooled, operations that can fail or negatively impact on the crystal.In situX-ray diffraction analysis has become a valid alternative to these operations, and a growing number of users apply it for crystal screening and to solve structures. Nevertheless, even this shortcut may require a significant amount of beam time. In thisin situhigh-throughput approach, the centering of crystals relative to the beam represents the bottleneck in the analysis process. In this article, a new method to accelerate this process, by recording accurately the local geometry coordinates for each crystal in the crystallization plate, is presented. Subsequently, the crystallization plate can be presented to the X-ray beam by an automated plate-handling device, such as a six-axis robot arm, for an automated crystal centering in the beam,in situscreening or data collection. Here the preliminary results of such a semi-automated pipeline are reported for two distinct test proteins.
Structural study of Yb1–xTbxMnO3manganites: site occupancy and coexistence of hexagonal and orthorhombic phases
Authors: Bolívar Guarín Mónica Esperanza , Moreira Alexandre de Melo , Speziali Nivaldo Lúcio
Published: May 2013

Polycrystalline samples of mixed Yb1−xTbxMnO3(x= 0, 0.25, 0.50, 0.75 and 1) were prepared by a solid state reaction procedure. Detailed crystal structure studies were performed using X-ray diffraction data obtained at room temperature. The application of the Rietveld method confirmed the reported hexagonalP63cmand orthorhombicPnmaphases forx= 0 (YbMnO3) andx= 1 (TbMnO3), respectively. A single hexagonal phase was also observed forx= 0.25, while in the case ofx= 0.50 andx= 0.75 both phases coexist in the produced samples. Crystallographic parameters for the pure compounds are in agreement with those found in the literature. Changes in the lattice parameters, unit-cell volume, polyhedral distortions and tilting observed in the mixed compounds are explained as a function ofx. Sharing of Tb3+and Yb3+ions between different sites is discussed.