bluuebunny/crossref_metadata_2025 huggingface dataset:
Linearisable nonlinear partial differential equations in multidimensions
Authors: Dimakos M. , Fokas A. S.
Published: January 2015

We show that the complexification of the independent variables of a given partial differential equation (PDE) provides a straightforward approach for both unifying certain large classes of PDEs, as well as generating new classes of linearisable PDEs in multidimensions. For example, by complexifying the Burgers equation, which is a linearisable PDE in 1 + 1, i.e., an evolution equation in one spatial dimension, it is possible to construct a linearisable PDE in N + 1, i.e., an evolution PDE in N > 1 spatial dimensions. Among these equations in 2 + 1 are certain linearisable PDEs which have been recently introduced in the literature.
Spin and charge transport in double-junction Fe/MgO/GaAs/MgO/Fe heterostructures
Authors: Wolski S. , Szczepański T. , Dugaev V. K. , Barnaś J. , Landgraf B. , Slobodskyy T. , Hansen W.
Published: January 2015

We present theoretical and experimental results on tunneling current in single Fe/MgO/GaAs and double Fe/MgO/GaAs/MgO/Fe tunnel junctions. The charge and spin currents are calculated as a function of external voltage for different sets of parameters characterizing the semiconducting GaAs layer. Transport characteristics of a single Fe/MgO/GaAs junction reveal typical diode as well as spin diode features. The results of numerical calculations are compared with current-voltage characteristics measured experimentally for double tunnel junction structures, and a satisfactory agreement of the theoretical and experimental results has been achieved.
Can insulating gaseous layers provide a dielectric barrier discharge effect?
Authors: Guerra-Garcia Carmen , Martinez-Sanchez Manuel
Published: January 2015

This letter reports observations of the breakdown characteristics of helium/nitrogen parallel jets when AC voltage was applied across them. Below a certain voltage level, the plasma emission was fully confined to the helium stream as in a traditional dielectric barrier discharge, where the role of the dielectric was played by an insulating gas barrier (nitrogen as compared to helium). The discharge had characteristics of self-organized patterns. Some differences to traditional solid dielectrics are discussed.
Surface plasmon wave plates
Authors: Djalalian-Assl Amir , Cadusch Jasper J. , Teo Zhi Qin , Davis Timothy J. , Roberts Ann
Published: January 2015

Here, we investigate both numerically and experimentally, the polarization conversion capabilities of a rectangular array of holes with two unequal orthogonal periodicities. We show that it is possible to tune the periodicities in such a way that the transmitted light is circularly polarized for a nominated wavelength, λCPL, when the structure is illuminated with appropriately oriented linearly polarized light at normal incidence. A device was fabricated and experiments confirmed that a degree of circular polarization of 0.89 could be achieved at the resonant wavelength.
Simulation and characterization of a laterally-driven inertial micro-switch
Authors: Chen Wenguo , Wang Yang , Wang Huiying , Wang Yan , Ding Guifu , Yang Zhuoqing , Wang Hong , Zhao Xiaolin
Published: January 2015

A laterally-driven inertial micro-switch was designed and fabricated using surface micromachining technology. The dynamic response process was simulated by ANSYS software, which revealed the vibration process of movable electrode when the proof mass is shocked by acceleration in sensitive direction. The test results of fabricated inertial micro-switches with and without anti-shock beams indicated that the contact process of micro-switch with anti-shock beams is more reliable than the one without anti-shock beams. The test results indicated that three contact signals had been observed in the contact process of the inertial switch without anti-shock beams, and only one contact signal in the inertial switch with anti-shock beams, which demonstrated that the anti-shock beams can effectively constrain the vibration in non-sensitive direction.
Experiments on adjustable magnetic metamaterials applied in megahertz wireless power transmission
Authors: Zhang Yingyi , Tang Houjun , Yao Chen , Li Yuncheng , Xiao Siyu
Published: January 2015

Over the past few years, various metamaterials have been designed and applied in antenna systems. In this paper, a new structure of magnetic metamaterials is proposed for megahertz wireless power transmission, which can be manually adjusted to work at a variable frequency ranging from 10∼30 Mhz. The S parameters, resonant frequency, effective permeability of metamaterials are computed for analysis. The different substrates and layouts of metamaterial slab are also numerically evaluated by full-wave simulation. The specific magnetic metamaterial slabs with 17.6 MHz are fabricated and experimentally verified by the network analyzer. Finally, these slabs are applied in a more practical two-coil coupling system to evaluate their performance enhancement.
Developmental Improvement and Age-Related Decline in Unfamiliar Face Matching
Authors: Megreya Ahmed M , Bindemann Markus
Published: January 2015

Age-related changes have been documented widely in studies of face recognition and eyewitness identification. However, it is not clear whether these changes arise from general developmental differences in memory or occur specifically during the perceptual processing of faces. We report two experiments to track such perceptual changes using a 1-in-10 (experiment 1) and 1-in-1 (experiment 2) matching task for unfamiliar faces. Both experiments showed improvements in face matching during childhood and adult-like accuracy levels by adolescence. In addition, face-matching performance declined in adults of the age of 65 years. These findings indicate that developmental improvements and aging-related differences in face processing arise from changes in the perceptual encoding of faces. A clear face inversion effect was also present in all age groups. This indicates that those age-related changes in face matching reflect a quantitative effect, whereby typical face processes are engaged but do not operate at the best-possible level. These data suggest that part of the problem of eyewitness identification in children and elderly persons might reflect impairments in the perceptual processing of unfamiliar faces.
Facial Cosmetics Have Little Effect on Attractiveness Judgments Compared with Identity
Authors: Jones Alex L , Kramer Robin S S
Published: January 2015

The vast majority of women in modern societies use facial cosmetics, which modify facial cues to attractiveness. However, the size of this increase remains unclear—how much more attractive are individuals after an application of cosmetics? Here, we utilised a ‘new statistics' approach, calculating the effect size of cosmetics on attractiveness using a within-subjects design, and compared this with the effect size due to identity—that is, the inherent differences in attractiveness between people. Women were photographed with and without cosmetics, and these images were rated for attractiveness by a second group of participants. The proportion of variance in attractiveness explained by identity was much greater than the variance within models due to cosmetics. This result was unchanged after statistically controlling for the perceived amount of cosmetics that each model used. Although cosmetics increase attractiveness, the effect is small, and the benefits of cosmetics may be inflated in everyday thinking.
Synthesis of Novel Triazole-Containing Phosphonate Polymers
Authors: Dolan Ciarán , Naysmith Briar , Hinkley Simon F. R. , Sims Ian M. , Brimble Margaret A. , Williams David E. , Jin Jianyong
Published: January 2015

The objective of this research was to develop novel phosphonate-containing polymers as they remain a relatively under researched area of polymer chemistry. Herein, we report the synthesis and characterization of 2-(1-(2-(diethoxyphosphoryl)ethyl)-1H-1,2,3-triazol-4-yl)ethyl acrylate (M1) and diethyl (2-(4-(2-acrylamidoethyl)-1H-1,2,3-triazol-1-yl)ethyl)phosphonate (M2) monomers using the copper-catalyzed azide–alkyne cycloaddition (CuAAC) ‘click’ reaction, and their subsequent polymerization via both uncontrolled and reversible addition–fragmentation chain transfer (RAFT) polymerization techniques yielding phosphonate polymers (P1–P4).
Multi-elemental scanning transmission X-ray microscopy–near edge X-ray absorption fine structure spectroscopy assessment of organo–mineral associations in soils from reduced environments
Authors: Chen Chunmei , Sparks Donald L.
Published: January 2015

Environmental context Organo–mineral associations represent a fundamental process for stabilising organic carbon in soils. In this study, we employed scanning transmission X-ray microscopy–near edge X-ray absorption fine structure (STXM-NEXAFS) spectroscopy at C, Al and Si K-edges as well as Ca and Fe L-edges to conduct submicrometre-level investigations of the associations of C with mineral components in soils from reduced environments. This study provides the first insights into organo–mineral associations in reduced environments and shows progress towards examining, at the submicrometre level, compositional chemistry and associative interactions between organic matter and soil mineral components. Abstract Organo–mineral associations represent a fundamental process for stabilising organic carbon (OC) in soils. However, direct investigation of organo–mineral associations has been hampered by a lack of methods that can simultaneously characterise organic matter (OM) and soil minerals, and most investigations have focussed only on well drained soils. In this study, we employed scanning transmission X-ray microscopy–near edge X-ray absorption fine structure (STXM-NEXAFS) spectroscopy at C, Al and Si K-edges as well as Ca and Fe L-edges to conduct submicrometre-level investigations of the associations of C with mineral components in soils from reduced environments. Soils were collected from a forest footslope that is periodically poorly drained as well as a waterlogged wetland. OM was coated on mineral particles as thin films. Part of the mineral surface did not show detectable OM coverage with OC loadings of ≥1.3mg C m–2 determined for the clay fractions from these soils. C was not preferentially associated with Fe oxides in the footslope soil. A generally good C–Ca association was found in the anoxic wetland soil, which is free of Fe oxides. It was demonstrated for the first time that OM composition varied spatially at the submicrometre scale in the reduced soils free of Fe oxides. The composition of OM in the organo–mineral interface in the anoxic environments was highly complex and composed of aromatic, phenolic, aliphatic, carboxyl, carboxylamide and O-alkyl C functional groups. There was no consistent pattern for the association of certain types of organics with specific mineral components in both soils. The anoxic conditions resulted in the reduction of Fe in the aluminosilicates. This study provides the first insights into organo–mineral associations in reduced environments.
Degradation of oxytetracycline in the aquatic environment: a proposed steady state kinetic model that takes into account hydrolysis, photolysis, microbial degradation and adsorption by colloidal and sediment particles
Authors: Zaranyika Mark F. , Dzomba Pamhidzai , Kugara Jameson
Published: January 2015

Environmental context Pollution of the aquatic environment by oxytetracycline can lead to microbial resistance thereby compromising the efficacy of current medication regimes. Adsorption by colloidal and sediment particles reduces the rate at which oxytetracycline degrades, whereas the longer the antimicrobial remains in the aquatic environment, the greater the danger of microbial resistance. There is need therefore for a fuller understanding of the kinetics of degradation of oxytetracycline in aquatic ecosystems before measures for mitigating pollution by the antimicrobial can be designed. Abstract The persistence of oxytetracycline in an aquatic microcosm and distilled water control experiments, was studied over a period of 90 days. An immediate 35% loss as a result of adsorption by the sediment was observed in the microcosm experiment soon after charging. Subsequently triphasic linear rates of oxytetracycline degradation were observed for both the water phase (3.1×10–2, 5.8×10–3 and 1×10–3µgg–1day–1) and sediment phase (4.8×10–2, 6.5×10–3 and 2×10–4µgg–1day–1). Degradation is attributed to photolysis and microbial degradation of the free oxytetracycline in solution, and microbial degradation of the colloidal and sediment particle adsorbed speciation forms. The distilled water control exhibited biphasic zero order kinetics attributed to hydrolysis (2×10–6µgg–1day–1) and microbial degradation (2.7×10–3µgg–1day–1) under dark conditions, and monophasic zero order kinetics attributed to photolysis (6.9×10–3µgg–1day–1) under sunlight exposure. A kinetic model that takes into account hydrolysis, photolysis, microbial degradation and adsorption of the antibiotic by colloidal and sediment particles, is presented to account for the monophasic, biphasic and triphasic zero order kinetics observed in the control and microcosm experiments. Possible remediation strategies for mitigating aquatic environments polluted by the antimicrobial are discussed.
Effects of grazing and climate warming on plant diversity, productivity and living state in the alpine rangelands and cultivated grasslands of the Qinghai-Tibetan Plateau
Authors: Zhang Yong , Gao Qingzhu , Dong Shikui , Liu Shiliang , Wang Xuexia , Su Xukun , Li Yuanyuan , Tang Lin , Wu Xiaoyu , Zhao Haidi
Published: January 2015

Overgrazing and climate warming may be important drivers of alpine rangeland degradation in the Qinghai-Tibetan Plateau (QTP). In this study, the effects of grazing and experimental warming on the vegetation of cultivated grasslands, alpine steppe and alpine meadows on the QTP were investigated. The three treatments were a control, a warming treatment and a grazing treatment and were replicated three times on each vegetation type. The warming treatment was applied using fibreglass open-top chambers and the grazing treatment was continuous grazing by yaks at a moderately high stocking rate. Both grazing and warming negatively affected vegetation cover. Grazing reduced vegetation height while warming increased vegetation height. Grazing increased but warming reduced plant diversity. Grazing decreased and warming increased the aboveground plant biomass. Grazing increased the preferred forage species in native rangelands (alpine steppe and alpine meadow), while warming increased the preferred forage species in the cultivated grassland. Grazing reduced the vegetation living state (VLS) of all three alpine grasslands by nearly 70%, while warming reduced the VLS of the cultivated grassland and the alpine steppe by 32% and 56%, respectively, and promoted the VLS of the alpine meadow by 20.5%. It was concluded that overgrazing was the main driver of change to the alpine grassland vegetation on the QTP. The findings suggest that grazing regimes should be adapted in order for them to be sustainable in a warmer future.
Spatial decoupling of soil nitrogen cycling in an arid chenopod pattern ground
Authors: Macdonald B. C. T. , Warneke S. , Maïson E. , McLachlan G. , Farrell M.
Published: January 2015

Patterned ground is a characteristic landscape form in arid zones across the globe and is caused by the redistribution of runoff. The vegetation is concentrated in groves, which receive runoff water from the bare soil surface of the intergroves. Despite many soil chemical and physical investigations, biogeochemical cycles are not described for this landscape form. This study focuses on the distinct features of the nitrogen (N) and carbon (C) cycle in intergrove and grove areas of chenopod pattern-ground soils of the Australian rangelands. The N concentration of grove soils is low compared with the intergrove soil because of a close link between the N cycle in the topsoil and the plant primary production. In grove soils, denitrification including emission of N2O dominated the N cycle, whereas in intergrove soils, abiotic N2O uptake is the sole fate of atmospheric N2O. The intergrove soils appear to be generally poor in bacterial quantity and diversity, and lacking denitrification by bacteria, which has an impact on the C cycle as well. Production of CO2 and consumption of CH4 were substantially lower than grove soils. There was partitioning of key biogeochemical processes between the intergrove and grove soils, which results in a spatially decoupled soil N and C cycle in arid chenopod, pattern-ground ecosystems.
PTPσ functions as a presynaptic receptor for the glypican-4/LRRTM4 complex and is essential for excitatory synaptic transmission
Authors: Ko Ji Seung , Pramanik Gopal , Um Ji Won , Shim Ji Seon , Lee Dongmin , Kim Kee Hun , Chung Gug-Young , Condomitti Giuseppe , Kim Ho Min , Kim Hyun , de Wit Joris , Park Kang-Sik , Tabuchi Katsuhiko , Ko Jaewon
Published: January 2015

Significance

This paper documents and systematically characterizes the molecular interactions of protein tyrosine phosphatase σ (PTPσ) with glypicans (GPCs). The identified interactions require heparan sulfate (HS), suggesting that GPCs are a major source of HS for PTPσ at excitatory synapses. Strikingly, we found that leucine-rich repeat transmembrane protein 4 (LRRTM4) induces presynaptic differentiation via the PTPσ/GPC interaction, suggesting that PTPσ may function as a coreceptor for GPCs in presynaptic neurons. More importantly, we found that HS-binding ability of PTPσ is critical for excitatory synaptic transmission. These results expand our previous understanding of how synaptic adhesion pathways regulate excitatory synapse development and shed light on GPCs/LRRTM4
trans
-synaptic signaling. Moreover, to our knowledge, this is the first study to document the physiological significance of HS in the presynaptic function of mammalian neurons.
Direct inhibition of oncogenic KRAS by hydrocarbon-stapled SOS1 helices
Authors: Leshchiner Elizaveta S. , Parkhitko Andrey , Bird Gregory H. , Luccarelli James , Bellairs Joseph A. , Escudero Silvia , Opoku-Nsiah Kwadwo , Godes Marina , Perrimon Norbert , Walensky Loren D.
Published: January 2015

Significance

KRAS is one of the most prevalent and vicious oncogenic proteins, yet no drugs are available to inhibit its pathologic activity in patients. We report that KRAS-targeting stapled peptides, modeled after the native son of sevenless 1 (SOS1) helical domain, engage wild-type and clinically relevant KRAS mutant proteins with nanomolar affinity. To our knowledge, these compounds represent the highest affinity and broadest spectrum binders of KRAS mutants reported to date. The stapled peptides disrupt the SOS1/KRAS protein interaction and directly inhibit nucleotide association to wild-type and mutant KRAS proteins. We correlate functional binding activity with SAH-SOS1 cytotoxicity across a 13-member panel of KRAS-driven cancer cells and demonstrate sequence- and dose-dependent inhibition of the ERK-MAP kinase phosphosignaling cascade downstream of KRAS in vitro and in vivo.
Functional capacities of human IgM memory B cells in early inflammatory responses and secondary germinal center reactions
Authors: Seifert Marc , Przekopowitz Martina , Taudien Sarah , Lollies Anna , Ronge Viola , Drees Britta , Lindemann Monika , Hillen Uwe , Engler Harald , Singer Bernhard B. , Küppers Ralf
Published: January 2015

Significance

Human IgM+IgD+CD27+B lymphocytes represent a large subpopulation of the human B-cell pool, but their generation is debated and their immunological functions are poorly understood. This work shows that these lymphocytes possess typical memory B-cell expression patterns, enabling them to differentiate rapidly into plasma cells upon restimulation. Moreover, we reveal unique features of these IgM memory B cells, their potential to reenter germinal center reactions, and their specific interaction with immunomodulatory neutrophils in early inflammatory responses. Thus, key characteristics and functions of a major human B-cell subset are elucidated.
Quinary structure modulates protein stability in cells
Authors: Monteith William B. , Cohen Rachel D. , Smith Austin E. , Guzman-Cisneros Emilio , Pielak Gary J.
Published: January 2015

Significance

Globular proteins perform many of the chemical reactions required for life. The prevailing model of globular protein structure, which is based on studies in dilute solutions, emphasizes the requirement for a well-packed hydrophobic interior, but minimizes the importance of the exterior, provided it is hydrophilic. We demonstrate that the exterior plays a significant role when a globular protein is studied under physiologically relevant conditions. By changing a surface residue we show that attractive interactions between the protein surface and the cytosol modulate the stability of the protein, even though the change has a negligible effect in dilute solution. Recognizing and quantifying such intracellular interactions will aid in understanding and manipulating the biological role of proteins.
RETRACTED: Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses
Authors: Cox Jennifer E. , McClure Lydia V. , Goga Andrei , Sullivan Christopher S.
Published: January 2015

Diverse viruses encode regulatory RNAs called microRNAs (miRNAs). Despite much progress, the functions of the majority of viral miRNAs remain unknown. Most previous studies have used biochemical methods to uncover targets of viral miRNAs, but it is unclear what fraction of these targets is functionally important. Here, we apply an alternative strategy based on the premise that assorted viral miRNAs will share functionality. Screening a library of >70 human viral miRNAs showed that three unrelated miRNAs from distantly related herpesviruses significantly inhibited IFN signaling. Strikingly, each of these miRNAs directly reduced expression of the cyclic AMP-responsive element-binding protein (CBP), which as part of the p300-CBP complex, mediates IFN signaling. We show that both 5′ and 3′ derivatives from Epstein–Barr virus (EBV) encoded miR-BART-18 precursor miRNA (pre-miRNA) and the orthologous pre-miRNA from Rhesus lymphocryptovirus contribute to reducing IFN signaling. Thus, through both convergent and divergent evolutionary mechanisms, varied herpesviral miRNAs share the ability to decrease IFN signaling. Restoring miR-BART-18 to cells infected with an EBV miRNA mutant conveyed a cellular growth advantage upon IFN treatment, and relevant miRNAs from other herpesviruses were able to complement this activity. Blocking miR-BART-18 function in an EBV
+
tumor cell line renders cells more susceptible to IFN-mediated effects. These findings provide a mechanism that can at least partially explain the resistance of some EBV-associated tumors to IFN therapy. Our work suggests that similar pan-viral-miRNA functional-based screening strategies are warranted for determining relevant activities of other viral miRNAs.
Sound representation in higher language areas during language generation
Authors: Magrassi Lorenzo , Aromataris Giuseppe , Cabrini Alessandro , Annovazzi-Lodi Valerio , Moro Andrea
Published: January 2015

Significance

The results of our experiments show that a special representation of sound is actually exploited by the brain during language generation, even in the absence of speech. Taking advantage of data collected during neurosurgical operations on awake patients, here we cross-correlated the cortical activity in the frontal and temporal language areas of a person reading aloud or mentally with the envelope of the sound of the corresponding utterances. In both cases, cortical activity and the envelope of the sound of the utterances were significantly correlated. This suggests that in hearing people, sound representation deeply informs generation of linguistic expressions at a much higher level than previously thought. This may help in designing new strategies to help people with language disorders such as aphasia.
Optically driven translational and rotational motions of microrod particles in a nematic liquid crystal
Authors: Eremin Alexey , Hirankittiwong Pemika , Chattham Nattaporn , Nádasi Hajnalka , Stannarius Ralf , Limtrakul Jumras , Haba Osamu , Yonetake Koichiro , Takezoe Hideo
Published: January 2015

Significance

This paper addresses light-driven dynamic motions of microrods suspended in a liquid crystal (LC) host. The results presented in this paper advance molecular-assisted manipulations of colloidal particles and their assemblies, which is a key concept for smart microdevices, using their interplay with the topology of the nematic director field. Almost all previous studies on colloids in LC (except some work by Yamamoto et al.) have dealt with the observation and analysis of defect structures around colloid particle(s) with fixed anchoring conditions. Herein we use a photoactive surfactant, which enables control of the LC anchoring by light irradiation. The induced reversible anchoring transition is accompanied by a reorientation of the rods and/or their translational motion.
Differential regulation of the Hippo pathway by adherens junctions and apical–basal cell polarity modules
Authors: Yang Chih-Chao , Graves Hillary K. , Moya Ivan M. , Tao Chunyao , Hamaratoglu Fisun , Gladden Andrew B. , Halder Georg
Published: January 2015

Significance

The control of organ growth involves cell–cell communication that is mediated by signal transduction pathways. The Hippo signaling pathway has emerged as an essential regulator of organ size in
Drosophila
and mammals, and defects in Hippo signaling drive cancer progression. An important unresolved question in the growth control field is, How is the Hippo pathway regulated? Recent reports show that adherens junctions and cell polarity complexes regulate the Hippo pathway, but controversy exists about the mechanisms involved. Here we report that in
Drosophila
and in mammalian cells, adherens junctions and basolateral polarity complexes regulate the Hippo pathway independently of each other. These results thus deepen our knowledge of this important growth control and tumor suppressor pathway.
Flagella-independent surface motility in
Salmonella enterica
serovar Typhimurium
Authors: Park Sun-Yang , Pontes Mauricio H. , Groisman Eduardo A.
Published: January 2015

Significance

We identified a form of surface motility in the bacterium
Salmonella enterica
serovar Typhimurium that is activated in low Mg
2+
by PhoP/PhoQ, a regulatory system that hinders flagella expression and activity. PhoP furthers motility by promoting expression of the
pagM
gene, which specifies a small protein of unknown function, and also of two other genes that create the cytosolic conditions necessary for full
pagM
expression. Low Mg
2+
-promoted motility is a group behavior exclusive to a subset of
S. enterica
serovars harboring a particular allele of
pagM
. The
pagM
gene is present in nonfunctional allelic forms in certain
S. enterica
serovars and rarely found outside the genus
Salmonella
. Not required for virulence, PagM-mediated motility helps survival outside animal hosts.
Identification of plant compounds that disrupt the insect juvenile hormone receptor complex
Authors: Lee Seok-Hee , Oh Hyun-Woo , Fang Ying , An Saes-Byeol , Park Doo-Sang , Song Hyuk-Hwan , Oh Sei-Ryang , Kim Soo-Young , Kim Seonghyun , Kim Namjung , Raikhel Alexander S. , Je Yeon Ho , Shin Sang Woon
Published: January 2015

Significance

Juvenile hormone (JH) plays key roles in insect development, reproduction, and many other physiological functions. Because JH is specific to insects, it has been investigated for use as pest control. Although compounds that mimic the action of JH (JH analogues/agonists) are efficient, they have a limited scope of application. Development of potent compounds counteracting JH action (JH antagonists) would find a wider range of control applications. However, thus far, such JH antagonists have not been developed. Here, we report on the discovery of potent JH antagonists in plants, which represents an innate resistance mechanism of plants against insect herbivores. These newly discovered plant JH antagonist compounds could be used as the starting material for developing novel insecticides.
Anti-vascular endothelial growth factor treatment normalizes tuberculosis granuloma vasculature and improves small molecule delivery
Authors: Datta Meenal , Via Laura E. , Kamoun Walid S. , Liu Chong , Chen Wei , Seano Giorgio , Weiner Danielle M. , Schimel Daniel , England Kathleen , Martin John D. , Gao Xing , Xu Lei , Barry Clifton E. , Jain Rakesh K.
Published: January 2015

Significance

Tuberculosis (TB) is the second most lethal pathogen worldwide. Pulmonary granulomas are a hallmark of this disease. By discovering similarities between granulomas and solid cancerous tumors, we identified a novel therapeutic target for TB, the abnormal granuloma-associated vasculature that contributes to the abnormal granuloma microenvironment. We then asked if we could “normalize” granuloma vasculature by blocking VEGF signaling, an approach originally shown to enhance cancer treatment. Our results demonstrate that bevacizumab, a widely prescribed anti-VEGF antibody for cancer and eye diseases, is able to create more structurally and functionally normal granuloma vasculature and improve the delivery of a low-molecular-weight tracer. This effect suggests that vascular normalization in combination with anti-TB drugs has the potential to enhance treatment in patients with TB.
Evolution of herbivory in Drosophilidae linked to loss of behaviors, antennal responses, odorant receptors, and ancestral diet
Authors: Goldman-Huertas Benjamin , Mitchell Robert F. , Lapoint Richard T. , Faucher Cécile P. , Hildebrand John G. , Whiteman Noah K.
Published: January 2015

Significance

The evolution of herbivory in animals is rare but has resulted in major adaptive radiations. Its rarity suggests that there are barriers to colonization of plants. Behavioral adaptations, involving host plant finding, are likely the first to evolve during the transition to herbivory. A recently evolved herbivorous fly species was derived from yeast-feeding ancestors. This herbivorous fly, unlike its yeast-feeding relatives, lost attraction to yeast volatiles, the ability to detect yeast volatiles, and three genes that encode olfactory receptors critical for detecting yeast volatiles inDrosophila melanogaster. Loss-of-function mutations may play a role in the transition to herbivory in insects, which account for nearly 25% of all species of life.
Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes
Authors: Cai Yizhi , Agmon Neta , Choi Woo Jin , Ubide Alba , Stracquadanio Giovanni , Caravelli Katrina , Hao Haiping , Bader Joel S. , Boeke Jef D.
Published: January 2015

Significance

The advance of biotechnology opens up greater possibilities of bioterror and bioerror. Here, we propose multiplexed safeguard switches rooted in the development of foundational genomic, regulatory, and metabolic technologies. Safeguard switches can be regulated by submicromolar small molecule(s) and combined in a modular fashion. The resulting safeguard strains show high fitness and low reversion rates. Moreover, two distinct classes of safeguard switches are orthogonal, providing a potential fail-safe mechanism. The safeguard technologies provide a practical and generic approach to containing engineered microbes within defined laboratory and/or industrial environments, and can in principle be used in the field as well.
Structural and biochemical studies of HCMV gH/gL/gO and Pentamer reveal mutually exclusive cell entry complexes
Authors: Ciferri Claudio , Chandramouli Sumana , Donnarumma Danilo , Nikitin Pavel A. , Cianfrocco Michael A. , Gerrein Rachel , Feire Adam L. , Barnett Susan W. , Lilja Anders E. , Rappuoli Rino , Norais Nathalie , Settembre Ethan C. , Carfi Andrea
Published: January 2015

Significance

Human cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and in fetuses after congenital infection. gH/gL/gO and Pentamer are targets for neutralizing antibodies. We show that gO and UL128/UL130/UL131A bind to the same site on gH/gL through formation of a disulfide bond with gL-Cys144. The alternative use of this binding site by either gO or the ULs may provide a mechanism for cell tropism modulation. Our analysis reveals that gH/gL antigenic sites are conserved among gH/gL, gH/gL/gO, and Pentamer, whereas gH/gL/gO- and Pentamer-specific neutralizing antibody-binding sites are located in the gH/gL N terminus protrusion that contains the gO and the UL subunits. These data support the development of vaccines and antibody therapeutics against HCMV.
Invasive breast cancer reprograms early myeloid differentiation in the bone marrow to generate immunosuppressive neutrophils
Authors: Casbon Amy-Jo , Reynaud Damien , Park Chanhyuk , Khuc Emily , Gan Dennis D. , Schepers Koen , Passegué Emmanuelle , Werb Zena
Published: January 2015

Significance

We show that tumor reprogramming of hematopoiesis in bone marrow occurs at the onset of malignant conversion and results in systemic expansion of circulating activated neutrophils that preferentially accumulate in lungs. Our data are, to our knowledge, the first to show that activation and not inhibition of myeloid differentiation is responsible for expansion and activity of T cell-suppressive myeloid cells; a tumor-derived factor targets the immature hematopoietic compartment to drive myeloid expansion; granulocyte-colony stimulating factor (G-CSF) is the only hematopoietic growth factor to increase in serum during early tumor development; prolonged G-CSF induces production of Rb1lowneutrophils and not short-term mobilization; and G-CSF acts in a cell intrinsic manner to expand multipotent progenitors to increase production of tumor-derived Ly6G+neutrophils.
CTCF-binding elements 1 and 2 in the
Igh
intergenic control region cooperatively regulate V(D)J recombination
Authors: Lin Sherry G. , Guo Chunguang , Su Arthur , Zhang Yu , Alt Frederick W.
Published: January 2015

Significance

Mice and humans generate diverse antibody repertoires through a genomic rearrangement process termed “V(D)J recombination” that assembles genetic regions that encode antigen-binding portions of antibodies by cutting and pasting together different combinations of V, D, and J gene segments. V(D)J recombination is strictly controlled to ensure generating a sufficiently large antibody repertoire to recognize any pathogen encountered and to minimize generation of self-reactive antibodies. Across the large antibody heavy-chain locus, V(D)J recombination regulation depends on a small control region, intergenic control region 1 (IGCR1), containing two CCCTC-binding factor–binding elements (CBEs) that bind a broadly expressed factor implicated in chromosomal looping. The current studies show that these two CBEs function cooperatively to mediate full IGCR1 functions and suggest a working model for how they do so.
Conscious and unconscious detection of semantic anomalies
Authors: Hannon Brenda
Published: January 2015

When asked What superhero is associated with bats, Robin, the Penguin, Metropolis, Catwoman, the Riddler, the Joker, and Mr. Freeze? people frequently fail to notice the anomalous word Metropolis. The goals of this study were to determine whether detection of semantic anomalies, like Metropolis, is conscious or unconscious and whether this detection is immediate or delayed. To achieve these goals, participants answered anomalous and nonanomalous questions as their reading times for words were recorded. Comparisons between detected versus undetected anomalies revealed slower reading times for detected anomalies—a finding that suggests that people immediately and consciously detected anomalies. Further, comparisons between first and second words following undetected anomalies versus nonanomalous controls revealed some slower reading times for first and second words—a finding that suggests that people may have unconsciously detected anomalies but this detection was delayed. Taken together, these findings support the idea that when we are immediately aware of a semantic anomaly (i.e., immediate conscious detection) our language processes make immediate adjustments in order to reconcile contradictory information of anomalies with surrounding text; however, even when we are not consciously aware of semantic anomalies, our language processes still make these adjustments, although these adjustments are delayed (i.e., delayed unconscious detection).
Continuous visual properties of number influence the formation of novel symbolic representations
Authors: Merkley Rebecca , Scerif Gaia
Published: January 2015

Numerical symbols are thought to be mapped onto preexisting nonsymbolic representations of number. A growing body of evidence suggests that nonsymbolic numerical processing is significantly influenced by the associated visual properties of continuous quantity (e.g., surface area, density), but their role in the acquisition of novel symbols is unknown. Forty undergraduate students were trained to associate novel abstract symbols with numerical magnitudes. Half of the symbols were associated with nonsymbolic arrays in which total surface area and numerosity were correlated (“congruent”), and the other symbols were associated with arrays in which total surface area was equated across numerosities (“incongruent”). As numbers are represented in multiple formats (words, digits, nonsymbolic arrays), we also tested whether providing auditory nonword labels facilitated symbol learning. Following training, participants engaged in speeded comparisons of the newly learnt symbols. Comparisons were affected by the ratio between the numerosities associated with each symbol, a characteristic marker of numerical processing. Furthermore, comparisons were hardest for large-ratio comparisons of symbols associated with incongruent area and numerosity pairing during learning. In turn, these findings call for the further investigation of visual parameters on the development of numerical cognition.
Lack of the ubiquitin-editing enzyme A20 results in loss of hematopoietic stem cell quiescence
Authors: Nakagawa Masahiro Marshall , Thummar Keyur , Mandelbaum Jonathan , Pasqualucci Laura , Rathinam Chozha Vendan
Published: January 2015

A balance between quiescence and proliferation is critical for proper maintenance of the hematopoietic stem cell (HSC) pool. Although a lot is known about hematopoiesis, molecular mechanisms that control HSC quiescence remain largely unknown. The ubiquitin-editing enzyme A20 functions as a central regulator of inflammation and adaptive immunity. Here, we show that a deficiency of A20 in the hematopoietic system causes anemia, lymphopenia, and postnatal lethality. Lack of A20 in HSCs results in diminished pool size, impaired radioprotection, defective repopulation, and loss of quiescence. A20-deficient HSCs display increased IFN-γ signaling, caused by augmented NF-κB activation. Strikingly, deletion of both IFN-γ and A20 in hematopoietic cells results in partial rescue of the HSC phenotype. We anticipate that our experiments will facilitate the understanding of mechanisms through which A20-mediated inflammatory signals control HSC quiescence and functions.
Effects of Cultivars, Transplanting Patterns, Environment, and Their Interactions on Grain Quality of Japonica Rice
Authors: Liu Qihua , Wu Xiu , Ma Jiaqing , Xin Caiyun
Published: January 2015

With the increasing scarcity of rural labor, the rice transplanting pattern is encountering a shift from artificial transplanting (AT) to mechanical transplanting (MT) in numerous rice‐growing districts of China. The shift of transplanting patterns combined with altered growing environment during the grain‐filling stage in different years presumably affects rice quality. Nevertheless, related information is currently limited. This study investigated the effects of cultivars, transplanting patterns, environment, and their interactions on appearance, milling, eating, and nutritional qualities of four japonica rice varieties. The significant interactive effects of cultivars, environment, and transplanting patterns on almost all rice quality parameters (except Thr, Met, and Ile) were observed. Cultivars and environment were the main factors influencing rice appearance and milling and eating qualities. Cultivar was the primary factor affecting rice nutritional quality. Among all treatments, environment showed the strongest effect on percentage of chalky kernel, milled rice yield, peak viscosity, breakdown, setback, consistence, amylose, Glu, Tyr, and Met contents. However, Leu and Phe contents were unaffected by environment but only by cultivars and transplanting patterns. In addition to amylose and protein, Glu and Met contents were also involved in determining rice eating quality. Amino acid contents (except Cys, Tyr, and Met) were significantly negatively correlated with head rice yield, showing the function of amino acids in controlling rice milling quality. Percentage of chalky kernel as well as protein and almost all amino acid contents were significantly negatively correlated with the difference of maximum and minimum temperature (DMMT) and positively correlated with relative humidity (RH), whereas head rice yield did it reversely. Amylose content and setback were significantly negatively related to daily maximum temperature (DMAT), daily minimum temperature (DMIT), daily average temperature (DAT), and effective temperature accumulation (ETA). However, peak viscosity, breakdown, and consistence had contrary performances. According to these results, we can infer that DMMT and RH are important environmental factors affecting rice appearance, milling qualities, and nutritional qualities and that DMAT, DMIT, DAT, and ETA are key environmental factors influencing rice eating quality.
CD2-1, the C-Terminal Region of Flagellin, Modulates the Induction of Immune Responses in Rice
Authors: Katsuragi Yuya , Takai Ryota , Furukawa Takehito , Hirai Hiroyuki , Morimoto Takumi , Katayama Takara , Murakami Takahiko , Che Fang-Sik
Published: January 2015

Flagellin from the rice avirulent N1141 strain of Acidovorax avenae functions as a pathogen-associated molecular pattern (PAMP) and induces PAMP-triggered immunity (PTI) in rice. To study the recognition mechanism of flagellin in rice, we attempted to define one or more regions of the flagellin protein required to activate the PTI response. Based on domain classification, we produced four fragments of N1141 flagellin: N-terminal D0, D1. and D2 domains (ND0-2), N-terminal D2, D3, and C-terminal D2 domains (ND2-CD2), C-terminal D2, D1, and D0 domains (CD2-0), and C-terminal D2 and D1 domains (CD2-1). The C-terminal CD2-1 and CD2-0 fragments induced PTI responses in cultured rice cells. Synthetic flg22, which is sufficient to produce the flagellin response in Arabidopsis, and the N-terminal flagellin fragments containing flg22 region elicited very weak immune responses in rice. OsFLS2, the rice ortholog of AtFLS2, which mediates flg22 recognition, was not involved in CD2-0 or CD2-1 recognition in rice. In addition, CD2-0 triggered resistance to coinfection with pathogenic bacteria. Taken together, these data suggest that rice mainly recognizes flagellin CD2-1 by a receptor distinct from OsFLS2 and that this epitope recognition leads to PTI responses.
The VELVET Complex in the Gray Mold FungusBotrytis cinerea: Impact of BcLAE1 on Differentiation, Secondary Metabolism, and Virulence
Authors: Schumacher Julia , Simon Adeline , Cohrs Kim C. , Traeger Stefanie , Porquier Antoine , Dalmais Bérengère , Viaud Muriel , Tudzynski Bettina
Published: January 2015

Botrytis cinerea, the gray mold fungus, is an important plant pathogen. Field populations are characterized by variability with regard to morphology, the mode of reproduction (conidiation or sclerotia formation), the spectrum of secondary metabolites (SM), and virulence. Natural variation in bcvel1 encoding the ortholog of Aspergillus nidulans VeA, a member of the VELVET complex, was previously shown to affect light-dependent differentiation, the formation of oxalic acid (OA), and virulence. To gain broader insight into the B. cinerea VELVET complex, an ortholog of A. nidulans LaeA, BcLAE1, a putative interaction partner of BcVEL1, was studied. BcVEL1 but not its truncated versions interacts with BcLAE1 and BcVEL2 (VelB ortholog). In accordance with the expected common as well as specific functions of BcVEL1 and BcLAE1, the deletions of both genes result in similar though not identical phenotypes. Both mutants lost the ability to produce OA, to colonize the host tissue, and to form sclerotia. However, mutants differ with regard to aerial hyphae and conidia formation. Genome-wide expression analyses revealed that BcVEL1 and BcLAE1 have common and distinct target genes. Some of the genes that are underexpressed in both mutants, e.g., those encoding SM-related enzymes, proteases, and carbohydrate-active enzymes, may account for their reduced virulence.
Seasonal Variation in Populations of ‘Candidatus Liberibacter asiaticus’ in Citrus Trees in Paraná State, Brazil
Authors: Sauer Aline Vanessa , Zanutto Carlos Alexandre , Nocchi Paula Thais Requena , Machado Marcos Antonio , Bock Clive H. , Nunes William M. C.
Published: January 2015

Huanglongbing (HLB) is considered one of the most destructive diseases of citrus because the plants rapidly become unproductive, enter a decline, and eventually die. HLB is caused by the phloem-limited bacterium ‘Candidatus Liberibacter’ spp. The objective of this study was to evaluate seasonal variation of the in planta population of ‘Ca. Liberibacter asiaticus’ in the foliage of citrus trees in Brazil using real-time polymerase chain reaction (qPCR). Eleven plants (naturally infected, then screened) in the field with very mild and localized symptoms of HLB were confirmed to be ‘Ca. L. asiaticus’ infected by conventional PCR, and the canopies were divided into four quadrants. The bacterial population in the trees was tested on a monthly basis for up to 20 months by quantifying ‘Ca. L. asiaticus’ DNA using qPCR ‘Ca. L. asiaticus’-specific primers (As84F/As180R). The average cycle threshold (Ct) values, which relate to ‘Ca. L. asiaticus’ titer, were analyzed using a mixed model. Significant differences were observed in Ct values between seasons (F = 8.77, P = 0.0004), and abrupt changes were observed in Ct values in different quadrants of the trees. Autumn had the lowest Ct values, indicating the highest ‘Ca. L. asiaticus’ titer, and, thus, is considered the best period to detect ‘Ca. L. asiaticus’ infection in foliage of citrus trees in southern Brazil. In addition to the seasonal changes in Ct values, there was an initial decline in the Ct value in the months following initial detection, the rate of decline slowing with time. Concomitant with the increase of the bacterial population in the host, there was an increase in severity of HLB symptoms in the trees over time (Spearman’s rank correlation, r = −0.4083, P < 0.0001). The results identify the optimal season to sample foliage for ‘Ca. L. asiaticus’ in southern Brazil (autumn) and confirm the importance of sample timing to maximize detection of ‘Ca. L. asiaticus’ and, thus, contribute to the search for effective measures to manage HLB.