bluuebunny/crossref_metadata_2025_split huggingface dataset:
The aged lymphoid tissue environment fails to support naïve T cell homeostasis
Authors: Becklund Bryan R. , Purton Jared F. , Ramsey Chris , Favre Stéphanie , Vogt Tobias K. , Martin Christopher E. , Spasova Darina S. , Sarkisyan Gor , LeRoy Eric , Tan Joyce T. , Wahlus Heidi , Bondi-Boyd Brea , Luther Sanjiv A. , Surh Charles D. 
Published: August 2016

AbstractAging is associated with a gradual loss of naïve T cells and a reciprocal increase in the proportion of memory T cells. While reduced thymic output is important, age-dependent changes in factors supporting naïve T cells homeostasis may also be involved. Indeed, we noted a dramatic decrease in the ability of aged mice to support survival and homeostatic proliferation of naïve T cells. The defect was not due to a reduction in IL-7 expression, but from a combination of changes in the secondary lymphoid environment that impaired naïve T cell entry and access to key survival factors. We observed an age-related shift in the expression of homing chemokines and structural deterioration of the stromal network in T cell zones. Treatment with IL-7/mAb complexes can restore naïve T cell homeostatic proliferation in aged mice. Our data suggests that homeostatic mechanisms that support the naïve T cell pool deteriorate with age.
Disruption of dmc1 Produces Abnormal Sperm in Medaka (Oryzias latipes)
Authors: Chen Ji , Cui Xiaojuan , Jia Shaoting , Luo Daji , Cao Mengxi , Zhang Yunsheng , Hu Hongling , Huang Kaiyao , Zhu Zuoyan , Hu Wei 
Published: August 2016

AbstractDMC1 is a recombinase that is essential for meiotic synapsis. Experiments in extensive species of eukaryotes have indicated the independent role of DMC1 in repairing double strand breaks (DSBs) produced during meiosis I. Mutation of dmc1 in mice and human often leads to obstacles in spermatogenesis and male sterility. Here, we report on the disruption of dmc1 in male medaka (Oryzias latipes). Synapsis was disturbed in the mutant medaka testis nuclei, as observed in mice and other organisms. Unexpectedly, the mutant medaka could produce a few sperm and, although most of these had multiple tail or multiple head malformations, some of them could swim and few of them even had insemination ability. Our transcriptome analysis showed that there was not a remarkable change in the expression of most of the genes involved in the pathways associated with the meiotic DNA repair and flagella assembly. Our results provided an indication of the accessory mechanisms that might be involved in the repair of DSBs during meiosis. In a species besides humans, we provided evidence that disorders in meiosis recombination might lead to the malformation of sperm.
ATF3 controls proliferation of osteoclast precursor and bone remodeling
Authors: Fukasawa Kazuya , Park Gyujin , Iezaki Takashi , Horie Tetsuhiro , Kanayama Takashi , Ozaki Kakeru , Onishi Yuki , Takahata Yoshifumi , Yoneda Yukio , Takarada Takeshi , Kitajima Shigetaka , Vacher Jean , Hinoi Eiichi 
Published: August 2016

AbstractBone homeostasis is maintained by the sophisticated coupled actions of bone-resorbing osteoclasts and bone-forming osteoblasts. Here we identify activating transcription factor 3 (ATF3) as a pivotal transcription factor for the regulation of bone resorption and bone remodeling under a pathological condition through modulating the proliferation of osteoclast precursors. The osteoclast precursor-specific deletion of ATF3 in mice led to the prevention of receptor activator of nuclear factor-κB (RANK) ligand (RANKL)-induced bone resorption and bone loss, although neither bone volume nor osteoclastic parameter were markedly altered in these knockout mice under the physiological condition. RANKL-dependent osteoclastogenesis was impaired in vitro in ATF3-deleted bone marrow macrophages (BMM). Mechanistically, the deficiency of ATF3 impaired the RANKL-induced transient increase in cell proliferation of osteoclast precursors in bone marrow in vivo as well as of BMM in vitro. Moreover, ATF3 regulated cyclin D1 mRNA expression though modulating activator protein-1-dependent transcription in the osteoclast precursor and the introduction of cyclin D1 significantly rescued the impairment of osteoclastogenesis in ATF3-deleted BMM. Therefore, these findings suggest that ATF3 could have a pivotal role in osteoclastogenesis and bone homeostasis though modulating cell proliferation under pathological conditions, thereby providing a target for bone diseases.
Deformation behavior of metallic glasses with shear band like atomic structure: a molecular dynamics study
Authors: Zhong C. , Zhang H. , Cao Q. P. , Wang X. D. , Zhang D. X. , Ramamurty U. , Jiang J. Z. 
Published: August 2016

AbstractMolecular dynamics simulations were employed to investigate the plastic deformation within the shear bands in three different metallic glasses (MGs). To mimic shear bands, MG specimens were first deformed until flow localization occurs, and then the volume of the material within the localized regions was extracted and replicated. Homogeneous deformation that is independent of the size of the specimen was observed in specimens with shear band like structure, even at a temperature that is far below the glass transition temperature. Structural relaxation and rapid cooling were employed to examine the effect of free volume content on the deformation behavior. This was followed by detailed atomic structure analyses, employing the concepts of Voronoi polyhedra and “liquid-like” regions that contain high fraction of sub-atomic size open volumes. Results suggest that the total fraction of atoms in liquid-like regions is a key parameter that controls the plastic deformation in MGs. These are discussed in the context of reported experimental results and possible strategies for synthesizing monolithic amorphous materials that can accommodate large tensile plasticity are suggested.
Systematic Quantification of GPCR/cAMP-Controlled Protein Kinase A
Interactions
Authors: Torres-Quesada O. , Röck R. , Stefan E. 
Published: August 2016

AbstractThe diffusible second messenger cyclic AMP (cAMP) originates from multiple G
protein-coupled receptor (GPCR) cascades activating the intracellular key
effector protein kinase A (PKA). Spatially and temporally restricted cAMP-fluxes
are directly sensed by macromolecular PKA complexes. The consequences are
alterations of molecular interactions, which lead to activation of
compartmentalized PKA phosphotransferase activities, regulating a vast array of
cellular functions. To decode cell-type and cell-compartment specific PKA
functions, the spatio-temporal dynamics of small molecule:protein interactions,
protein:protein interactions (PPIs), cAMP-mobilization, and phosphotransferase
activities need to be determined directly in the appropriate cellular context. A
collection of cell-based reporters has been developed to either visualize or
quantitatively measure kinase activities or PKA complex formation/dissociation.
In this review, we list a collection of unimolecular and bimolecular PKA
biosensors, followed by the specification of the modular design of a
Renilla luciferase based protein-fragment complementation assay (PCA)
platform for measuring PKA network interactions. We discuss the application
spectrum of the PCA reporter to identify, quantify, and dissect dynamic and
transient PKA complexes downstream of specific GPCR activities. We specify the
implementation of a PCA PKA platform to systematically quantify the concurrent
involvement of receptor-cAMP signaling, post-translational modifications, and
kinase subunit mutations/perturbations in PKA activation. The systematic
quantification of transient PKA network interactions will contribute to a better
understanding how GPCR-recognized input signals are streamlined through the
compartmentalized and cAMP-interacting PKA signalosome.
“Beyond this ignorant present”: the poverty of historicism in Macbeth
Authors: Heffernan Julián Jiménez 
Published: August 2016

AbstractAlthoughMacbethis notstricto sensua history play, its dominant concern with the paralogisms of time forces the reader to reconsider its relationship with history. Moreover, the scarcely noted fact that the debate for and against historicism—encouraged by thinkers like Hegel, Lukács, Strauss, Aron or Popper—tends to capitalize on the hermeneutic affordances of a play likeMacbeth, brings the historical (perhaps historicist) provocation of the play all the more sharply into focus. Self-validating prophecy emerges, in this reconsideration, as the pivotal, paralogic speech act in a play that reads like a parody of verification. By exposing the logical complicity between providentialist prophecy and historicist interpretation, this article contends that Shakespeare obtained, inMacbeth, ironic-critical distance from contemporary historiographic teleology, and that he thus sheltered himself in advance from the progressive-moralist, at bottom apocalyptic, arrogance of neo-historicist critics like Stephen Greenblatt or Richard Wilson. In the final analysis,Macbethgets the last word, one no oracular predictive or postdictive consummation is able to efface. This article is published as part of a collection to commemorate the 400th anniversary of William Shakespeare’s death.
Emerging single-phase state in small manganite nanodisks
Authors: Shao Jian , Liu Hao , Zhang Kai , Yu Yang , Yu Weichao , Lin Hanxuan , Niu Jiebin , Du Kai , Kou Yunfang , Wei Wengang , Lan Fanli , Zhu Yinyan , Wang Wenbin , Xiao Jiang , Yin Lifeng , Plummer E. W. , Shen Jian 
Published: August 2016

Significance
Electronic phase separation (EPS) is a common phenomenon in complex oxides systems. However, little is known regarding how EPS responds when the size of the system is smaller than the characteristic size of EPS. This issue is not only important for understanding the physical origin of EPS but also for oxides device applications in which oxides have to be fabricated into small-sized structures. Our work on manganites shows a surprising transition from the EPS state to a single phase state when the spatial size of the system is smaller than the characteristic length scale of EPS. This observation paves a way to manipulate EPS, which is potentially useful for oxides electronic and spintronic device applications.
Major neurotransmitter systems in dorsal hippocampus and basolateral amygdala control social recognition memory
Authors: Garrido Zinn Carolina , Clairis Nicolas , Silva Cavalcante Lorena Evelyn , Furini Cristiane Regina Guerino , de Carvalho Myskiw Jociane , Izquierdo Ivan 
Published: August 2016

Significance
The hippocampus and basolateral amygdala—modulated by β-noradrenergic, D1/D5 dopaminergic, and H2-histaminergic receptors—control memory processing of many memories, but their role in social recognition memory (SRM) has been little studied. SRM is fundamental for the establishment of social relationships and, consequently, for the formation and stability of social groups. The social deficits of psychiatric disorders, such as autism and schizophrenia, are believed to be caused by alterations in SRM processing by the hippocampus and amygdala. Here we examine the involvement of the hippocampus and basolateral amygdala—and β-noradrenergic, D1/D5 dopaminergic, and H2-histaminergic receptors therein—in SRM consolidation. The results suggest an important and complex modulation of this process, which may help to elucidate the basis of inappropriate social behavior in psychiatric patients.
Unveiling the early-stage anatomy of a protocluster hub with ALMA
Authors: Henshaw J. D. , Jiménez-Serra I. , Longmore S. N. , Caselli P. , Pineda J. E. , Avison A. , Barnes A. T. , Tan J. C. , Fontani F. 
Published: August 2016

Abstract
High-mass stars shape the interstellar medium in galaxies, and yet, largely because the initial conditions are poorly constrained, we do not know how they form. One possibility is that high-mass stars and star clusters form at the junction of filamentary networks, referred to as ‘hubs’. In this Letter we present the complex anatomy of a protocluster hub within an Infrared Dark Cloud (IRDC), G035.39−00.33, believed to be in an early phase of its evolution. We use high-angular resolution ({θmaj, θmin} = {1.4 arcsec, 0.8 arcsec} ∼ {0.02 pc, 0.01 pc}) and high-sensitivity (0.2 mJy beam−1; ∼0.2 Mȯ) 1.07 mm dust continuum observations from the Atacama Large Millimeter Array (ALMA) to identify a network of narrow, 0.028 ± 0.005 pc wide, filamentary structures. These are a factor of ≳3 narrower than the proposed ‘quasi-universal’ ∼0.1 pc width of interstellar filaments. Additionally, 28 compact objects are reported, spanning a mass range 0.3 Mȯ &lt; Mc &lt; 10.4 Mȯ. This indicates that at least some low-mass objects are forming coevally with more massive counterparts. Comparing to the popular ‘bead-on-a-string’ analogy, the protocluster hub is poorly represented by a monolithic clump embedded within a single filament. Instead, it comprises multiple intra-hub filaments, each of which retains its integrity as an independent structure and possesses its own embedded core population.
Genome-wide biases in the rate and molecular spectrum of spontaneous mutations inVibrio choleraeandVibrio fischeri
Authors: Dillon Marcus M. , Sung Way , Sebra Robert , Lynch Michael , Cooper Vaughn S. 
Published: August 2016

ABSTRACTThe vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera,Vibrio cholerae. Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of twoVibriospecies, the low-GC% squid symbiontV. fischeriand the pathogenV. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-typeV. fischeriandV. choleraehave among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10−3/genome/generation.V. fischeriandV. choleraehave distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates ofVibriospecies correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.
Hydroxycinnamoyltransferases Involved in the Accumulation of Caffeic Acid Esters in Gametophytes and Sporophytes of Equisetum arvense
Authors: Hohlfeld M. , Veit M. , Strack D. 
Published: August 2016

Abstract
Four hydroxycinnamoyltransferases from Equisetum arvense L. were studied that catalyze the formation of mono-O-caffeoyl-meso-tartrate, di-O-caffeoyl-meso-tartrate, 5-O-caffeoylshikimate (dactylifrate), and 5-O-caffeoylquinate (chlorogenate). The enzymes were classified as coenzyme A (CoA)-ester-dependent acyltransferases (EC 2.3.1), i.e. hydroxycinnamoyl-CoA:meso-tartrate hydroxycinnamoyltransferase (CTT), hydroxycinnamoyl-CoA:caf-feoyl-meso-tartrate hydroxycinnamoyltransferase (CCT), hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (CST), and hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase. The CTT, CCT, and CST were partially purified and separated from E. arvense gametophytes by hydrophobic interaction chromatography on Fractogel TSK Butyl-650 followed by molecular exclusion on fast protein liquid chromatography-Superdex-75 with 87-, 62-, and 130- fold enrichments and 12, 8, and 11% yields, respectively. The enzyme activities obtained with caffeoyl-CoA were 95 (CTT), 74 (CCT), and 200 [mu]kat (CST) kg-1 protein. The apparent native relative molecular weight values were found to be approximately 45,000 (CTT), 52,000 (CCT), and 50,000 (CST). Each enzyme showed highest activities at pH 7.5, the CCT and CST in Tris-HCl (1.2 and 1.0 M) and the CTT in imidazole-HCl (1.25 M). Enzyme activities were stimulated more than 3-fold by 100 mM ascorbate. The apparent energies of activation (kilojoules mol-1) were calculated to be 56 (CTT), 69 (CST), and 76 (CCT). The enzymes accepted cinnamoyl-CoA and various hydroxycinnamoyl-CoAs. The time course of the transferase activities along with that of a fourth one, hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase, and the pattern of product accumulation were determined during a 1-year growth period of the E. arvense sporophytes.
Plasma Membrane Na+ Transport in a Salt-Tolerant Charophyte (Isotopic Fluxes, Electrophysiology, and Thermodynamics in Plants Adapted to Saltwater and Freshwater)
Authors: Kiegle E. A. , Bisson M. A. 
Published: August 2016

Abstract
In salt-tolerant Chara longifolia, enhanced Na+ efflux plays an important role in maintaining low cytoplasmic Na+. When it is cultured in fresh water (FW), C. longifolia has a higher Na+ efflux than the obligate FW Chara corallina, although pH dependence and inhibitor profiles are similar for both species (J. Whittington and M.A. Bisson [1994] J Exp Bot 45: 657–665). When it is cultured in saltwater, C. longifolia has a Na+ efflux of 264 [plus or minus] 14 nmol m-2 s-1 at pH 7, 13 times higher than FW-adapted cultures and 31 times higher than C. corallina. As in FW-adapted plants, efflux is highest at pH 5, but pH dependence is less steep and more linear in cells adapted to saltwater. In plants of both species from FW cultures, Na+ efflux is inhibited by Li+ at pH 5 but not at pH 7 or 9, whereas in the salt-adapted C. longifolia, Li+ inhibits Na+ efflux at pH 7 and 9 but not at pH 5. Amiloride inhibits Na+ efflux in salt-adapted cells but not in FW cells. We conclude that a new type of Na+ efflux system is induced in salt-adapted plants, although both systems have characteristics suggestive of a Na+/H+ antiport. In all cases, a 1:1 Na+/H+ antiport would have sufficient energy to maintain the cytoplasmic Na+ activities measured at pH 5 and 7 but not at pH 9, which suggests that another efflux system must be operating at pH 9.
Autophagy in Tobacco Suspension-Cultured Cells in Response to Sucrose Starvation
Authors: Moriyasu Y. , Ohsumi Y. 
Published: August 2016

Abstract
The response of tobacco (Nicotiana tabacum) suspension-cultured cells (BY-2) to nutrient starvation was investigated. When the cells that were grown in Murashige-Skoog medium containing 3% (w/v) sucrose were transferred to the same medium without sucrose, 30 to 45% of the intracellular proteins were degraded in 2 d. An analysis with sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that proteins were degraded nonselectively. With the same treatment, protease activity in the cell, which was measured at pH 5.0 using fluorescein thiocarbamoyl-casein as a substrate, increased 3- to 7-fold after 1 d. When the cysteine protease inhibitor (2S,3S)-trans-epoxysuccinyl-L-leucylamido-3-methyl-butane (10 [mu]M) was present in the starvation medium, both the protein degradation and the increase in the protease activity were effectively inhibited. Light microscopy analysis showed that many small spherical bodies accumulated in the perinuclear region of the cytosol 8 h after the start of the inhibitor treatment. These bodies were shown to be membrane-bound vesicles of 1 to 6 [mu]m in diameter that contained several particles. Quinacrine stained these vesicles and the central vacuole; thus, both organelles are acidic compartments. Cytochemical enzyme analysis using 1-naphthylphosphate and β-glycerophosphate as substrates showed that these vesicles contained an acid phosphatase(s). We suggest that these vesicles contribute to cellular protein degradation stimulated under sucrose starvation conditions.
Membrane-Delimited Phosphorylation Enables the Activation of the Outward-Rectifying K Channels in Motor Cell Protoplasts of Samanea saman
Authors: Moran N. 
Published: August 2016

Abstract
Outward-rectifying K channels activated by membrane depolarization (Kout or KD channels) control K+ efflux from plant cells. To find out to what extent phosphorylation is required for the activity of these channels, the patch-clamp method was applied to protoplasts from the legume Samanea saman in both whole-cell and isolated-patch configurations. In the absence of either Mg2+ or ATP in the “cytosolic” solution, the KD channel activity declined completely within 15 min. This decline could be reversed in excised, inside-out patches by restoring MgATP (1 mM) to the cytoplasmic side of the membrane. Mg2+ (1 mM) plus 5[prime]-adenylylimidodiphosphate (1 mM), a nonhydrolyzable ATP analog, did not substitute for ATP. Mg2+ (1 mM) plus adenosine 5[prime]-O-(3-thiotriphosphate) (25 to &lt;100 [mu]M), an irreversibly thiophosphorylating ATP analog, sustained channel activity irreversibly. 1–(5-IsoquinolinesulphonyI)-2- methylpiperazine (100 [mu]M), a broad-range kinase inhibitor, blocked the activity of KD channels in the presence of MgATP. These results strongly suggest that the activation of the outward-rectifying K channels by depolarization depends critically on phosphorylation by a kinase tightly associated with the KD channel.
Predicting Light Acclimation in Cyanobacteria from Nonphotochemical Quenching of Photosystem II Fluorescence, Which Reflects State Transitions in These Organisms
Authors: Campbell D. , Oquist G. 
Published: August 2016

Abstract
An important factor in photosynthetic ecophysiology is the light regime that a photobiont is acclimated to exploit. In a wide range of cyanobacteria and cyano-lichens, the easily measured fluorescence parameters, coefficient of nonphotochemical quenching of photosystem II variable fluorescence (qN) and nonphotochemical quenching, decline to a minimum near the acclimated growth light intensity. This characteristic pattern predicts the integrated light regime to which populations are acclimated, information that is particularly useful for cyanobacteria or cyano-lichens from habitats with highly variable light intensities. qN reflects processes that compete with photosystem II photochemistry for absorbed excitation energy. In cyanobacteria, we find no evidence for energy-dependent quenching mechanisms, which are the predominant components of qN in higher plants. Instead, in cyanobacteria, qN correlates closely with the excitation flow from the phycobilisome to photosystem I, indicating that qN reflects the state transition mechanism for equilibration of excitation from the phycobilisome to the two photosystems.