bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cool-Season Weed Control Using Ammonium Nonanoate and Cultivation in Organic Vidalia® Sweet Onion Production
Authors: Johnson W. Carroll , Luo Xuelin 
Published: November 2017

AbstractAmmonium nonanoate is registered for weed control in certified organic cropping systems and may be useful to control cool-season weeds in organic Vidalia® sweet onion production. Ammonium nonanoate combined with tine-weeder cultivation was evaluated for weed control in organic onion in Georgia. There were no statistical interactions between main effects of herbicides and cultivation with a tine weeder for cool-season weed control and onion yield, indicating that ammonium nonanoate does not improve weed control compared with cultivation. Ammonium nonanoate at 4% and 6% did not adequately control weeds and onion yields were reduced. Ammonium nonanoate at 8% and 10% controlled cutleaf evening-primrose and lesser swinecress equal to the standard of d-limonene (14%), but the degree of control did not consistently protect onion yields from losses due to weeds. These results are in agreement with previous studies using clove oil and pelargonic acid. There is no advantage to using ammonium nonanoate for cool-season weed control in organic Vidalia® sweet onion production.
The molecular basis of phosphite and hypophosphite recognition by ABC-transporters
Authors: Bisson Claudine , Adams Nathan B. P. , Stevenson Ben , Brindley Amanda A. , Polyviou Despo , Bibby Thomas S. , Baker Patrick J. , Hunter C. Neil , Hitchcock Andrew 
Published: November 2017

AbstractInorganic phosphate is the major bioavailable form of the essential nutrient phosphorus. However, the concentration of phosphate in most natural habitats is low enough to limit microbial growth. Under phosphate-depleted conditions some bacteria utilise phosphite and hypophosphite as alternative sources of phosphorus, but the molecular basis of reduced phosphorus acquisition from the environment is not fully understood. Here, we present crystal structures and ligand binding affinities of periplasmic binding proteins from bacterial phosphite and hypophosphite ATP-binding cassette transporters. We reveal that phosphite and hypophosphite specificity results from a combination of steric selection and the presence of a P-H…π interaction between the ligand and a conserved aromatic residue in the ligand-binding pocket. The characterisation of high affinity and specific transporters has implications for the marine phosphorus redox cycle, and might aid the use of phosphite as an alternative phosphorus source in biotechnological, industrial and agricultural applications.
An extracellular matrix-related prognostic and predictive indicator for early-stage non-small cell lung cancer
Authors: LIM Su Bin , TAN Swee Jin , LIM Wan-Teck , LIM Chwee Teck 
Published: November 2017

AbstractThe prognosis and prediction of adjuvant chemotherapy (ACT) response in early-stage non-small cell lung cancer (NSCLC) patients remain poor in this era of personalized medicine. We hypothesize that extracellular matrix (ECM)-associated components could be potential markers for better diagnosis and prognosis due to their differential expression in 1,943 primary NSCLC tumors as compared to 303 normal lung tissues. Here we develop a 29-gene ECM-related prognostic and predictive indicator (EPPI). We validate a robust performance of the EPPI risk scoring system in multiple independent data sets, comprising a total of 2,071 early-stage NSCLC tumors. Patients are stratified according to the universal cutoff score based on the EPPI when applied in the clinical setting; the low-risk group has significantly better survival outcome. The functional EPPI gene set represents a potential genomic tool to improve patient selection in early-stage NSCLC to further derive the best benefits of ACT and prevent unnecessary treatment or ACT-associated morbidity.
Glucocorticoid-induced phosphorylation by CDK9 modulates the coactivator functions of transcriptional cofactor GRIP1 in macrophages
Authors: Rollins David A. , Kharlyngdoh Joubert B. , Coppo Maddalena , Tharmalingam Bowranigan , Mimouna Sanda , Guo Ziyi , Sacta Maria A. , Pufall Miles A. , Fisher Robert P. , Hu Xiaoyu , Chinenov Yurii , Rogatsky Inez 
Published: November 2017

AbstractThe glucocorticoid (GC) receptor (GR) suppresses inflammation by activating anti-inflammatory and repressing pro-inflammatory genes. GR-interacting protein-1 (GRIP1) is a GR corepressor in macrophages, however, whether GRIP1 mediates GR-activated transcription, and what dictates its coactivator versus corepressor properties is unknown. Here we report that GRIP1 loss in macrophages attenuates glucocorticoid induction of several anti-inflammatory targets, and that GC treatment of quiescent macrophages globally directs GRIP1 toward GR binding sites dominated by palindromic GC response elements (GRE), suggesting a non-redundant GRIP1 function as a GR coactivator. Interestingly, GRIP1 is phosphorylated at an N-terminal serine cluster by cyclin-dependent kinase-9 (CDK9), which is recruited into GC-induced GR:GRIP1:CDK9 hetero-complexes, producing distinct GRE-specific GRIP1 phospho-isoforms. Phosphorylation potentiates GRIP1 coactivator but, remarkably, not its corepressor properties. Consistently, phospho-GRIP1 and CDK9 are not detected at GR transrepression sites near pro-inflammatory genes. Thus, GR restricts actions of its own coregulator via CDK9-mediated phosphorylation to a subset of anti-inflammatory genes.
Receptor-binding loops in alphacoronavirus adaptation and evolution
Authors: Wong Alan H. M. , Tomlinson Aidan C. A. , Zhou Dongxia , Satkunarajah Malathy , Chen Kevin , Sharon Chetna , Desforges Marc , Talbot Pierre J. , Rini James M. 
Published: November 2017

AbstractRNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop–receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding.
Skyrmion dynamics in a frustrated ferromagnetic film and current-induced helicity locking-unlocking transition
Authors: Zhang Xichao , Xia Jing , Zhou Yan , Liu Xiaoxi , Zhang Han , Ezawa Motohiko 
Published: November 2017

AbstractThe helicity-orbital coupling is an intriguing feature of magnetic skyrmions in frustrated magnets. Here we explore the skyrmion dynamics in a frustrated magnet based on the J1-J2-J3 classical Heisenberg model explicitly by including the dipole-dipole interaction. The skyrmion energy acquires a helicity dependence due to the dipole-dipole interaction, resulting in the current-induced translational motion with a fixed helicity. The lowest-energy states are the degenerate Bloch-type states, which can be used for building the binary memory. By increasing the driving current, the helicity locking-unlocking transition occurs, where the translational motion changes to the rotational motion. Furthermore, we demonstrate that two skyrmions can spontaneously form a bound state. The separation of the bound state forced by a driving current is also studied. In addition, we show the annihilation of a pair of skyrmion and antiskyrmion. Our results reveal the distinctive frustrated skyrmions may enable viable applications in topological magnetism.
Ultrafast non-radiative dynamics of atomically thin MoSe2
Authors: Lin Ming-Fu , Kochat Vidya , Krishnamoorthy Aravind , Bassman Oftelie Lindsay , Weninger Clemens , Zheng Qiang , Zhang Xiang , Apte Amey , Tiwary Chandra Sekhar , Shen Xiaozhe , Li Renkai , Kalia Rajiv , Ajayan Pulickel , Nakano Aiichiro , Vashishta Priya , Shimojo Fuyuki , Wang Xijie , Fritz David M. , Bergmann Uwe 
Published: November 2017

AbstractPhoto-induced non-radiative energy dissipation is a potential pathway to induce structural-phase transitions in two-dimensional materials. For advancing this field, a quantitative understanding of real-time atomic motion and lattice temperature is required. However, this understanding has been incomplete due to a lack of suitable experimental techniques. Here, we use ultrafast electron diffraction to directly probe the subpicosecond conversion of photoenergy to lattice vibrations in a model bilayered semiconductor, molybdenum diselenide. We find that when creating a high charge carrier density, the energy is efficiently transferred to the lattice within one picosecond. First-principles nonadiabatic quantum molecular dynamics simulations reproduce the observed ultrafast increase in lattice temperature and the corresponding conversion of photoenergy to lattice vibrations. Nonadiabatic quantum simulations further suggest that a softening of vibrational modes in the excited state is involved in efficient and rapid energy transfer between the electronic system and the lattice.
Cryo-EM structure of Saccharomyces cerevisiae target of rapamycin complex 2
Authors: Karuppasamy Manikandan , Kusmider Beata , Oliveira Taiana M. , Gaubitz Christl , Prouteau Manoel , Loewith Robbie , Schaffitzel Christiane 
Published: November 2017

AbstractThe target of rapamycin (TOR) kinase assembles into two distinct multiprotein complexes, conserved across eukaryote evolution. In contrast to TOR complex 1 (TORC1), TORC2 kinase activity is not inhibited by the macrolide rapamycin. Here, we present the structure of Saccharomyces cerevisiae TORC2 determined by electron cryo-microscopy. TORC2 contains six subunits assembling into a 1.4 MDa rhombohedron. Tor2 and Lst8 form the common core of both TOR complexes. Avo3/Rictor is unique to TORC2, but interacts with the same HEAT repeats of Tor2 that are engaged by Kog1/Raptor in mammalian TORC1, explaining the mutual exclusivity of these two proteins. Density, which we conclude is Avo3, occludes the FKBP12-rapamycin-binding site of Tor2’s FRB domain rendering TORC2 rapamycin insensitive and recessing the kinase active site. Although mobile, Avo1/hSin1 further restricts access to the active site as its conserved-region-in-the-middle (CRIM) domain is positioned along an edge of the TORC2 active-site-cleft, consistent with a role for CRIM in substrate recruitment.
North Atlantic variability and its links to European climate over the last 3000 years
Authors: Moffa-Sánchez Paola , Hall Ian R. 
Published: November 2017

AbstractThe subpolar North Atlantic is a key location for the Earth’s climate system. In the Labrador Sea, intense winter air–sea heat exchange drives the formation of deep waters and the surface circulation of warm waters around the subpolar gyre. This process therefore has the ability to modulate the oceanic northward heat transport. Recent studies reveal decadal variability in the formation of Labrador Sea Water. Yet, crucially, its longer-term history and links with European climate remain limited. Here we present new decadally resolved marine proxy reconstructions, which suggest weakened Labrador Sea Water formation and gyre strength with similar timing to the centennial cold periods recorded in terrestrial climate archives and historical records over the last 3000 years. These new data support that subpolar North Atlantic circulation changes, likely forced by increased southward flow of Arctic waters, contributed to modulating the climate of Europe with important societal impacts as revealed in European history.
Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins
Authors: Li Yuli , Sun Xiaoqing , Hu Xiaoli , Xun Xiaogang , Zhang Jinbo , Guo Ximing , Jiao Wenqian , Zhang Lingling , Liu Weizhi , Wang Jing , Li Ji , Sun Yan , Miao Yan , Zhang Xiaokang , Cheng Taoran , Xu Guoliang , Fu Xiaoteng , Wang Yangfan , Yu Xinran , Huang Xiaoting , Lu Wei , Lv Jia , Mu Chuang , Wang Dawei , Li Xu , Xia Yu , Li Yajuan , Yang Zhihui , Wang Fengliang , Zhang Lu , Xing Qiang , Dou Huaiqian , Ning Xianhui , Dou Jinzhuang , Li Yangping , Kong Dexu , Liu Yaran , Jiang Zhi , Li Ruiqiang , Wang Shi , Bao Zhenmin 
Published: November 2017

AbstractBivalve molluscs are descendants of an early-Cambrian lineage superbly adapted to benthic filter feeding. Adaptations in form and behavior are well recognized, but the underlying molecular mechanisms are largely unknown. Here, we investigate the genome, various transcriptomes, and proteomes of the scallop Chlamys farreri, a semi-sessile bivalve with well-developed adductor muscle, sophisticated eyes, and remarkable neurotoxin resistance. The scallop’s large striated muscle is energy-dynamic but not fully differentiated from smooth muscle. Its eyes are supported by highly diverse, intronless opsins expanded by retroposition for broadened spectral sensitivity. Rapid byssal secretion is enabled by a specialized foot and multiple proteins including expanded tyrosinases. The scallop uses hepatopancreas to accumulate neurotoxins and kidney to transform to high-toxicity forms through expanded sulfotransferases, probably as deterrence against predation, while it achieves neurotoxin resistance through point mutations in sodium channels. These findings suggest that expansion and mutation of those genes may have profound effects on scallop’s phenotype and adaptation.
Ultrafast bridge planarization in donor-π-acceptor copolymers drives intramolecular charge transfer
Authors: Roy Palas , Jha Ajay , Yasarapudi Vineeth B. , Ram Thulasi , Puttaraju Boregowda , Patil Satish , Dasgupta Jyotishman 
Published: November 2017

AbstractDonor-π-acceptor conjugated polymers form the material basis for high power conversion efficiencies in organic solar cells. Large dipole moment change upon photoexcitation via intramolecular charge transfer in donor-π-acceptor backbone is conjectured to facilitate efficient charge-carrier generation. However, the primary structural changes that drive ultrafast charge transfer step have remained elusive thereby limiting a rational structure-function correlation for such copolymers. Here we use structure-sensitive femtosecond stimulated Raman spectroscopy to demonstrate that π-bridge torsion forms the primary reaction coordinate for intramolecular charge transfer in donor-π-acceptor copolymers. Resonance-selective Raman snapshots of exciton relaxation reveal rich vibrational dynamics of the bridge modes associated with backbone planarization within 400 fs, leading to hot intramolecular charge transfer state formation while subsequent cooling dynamics of backbone-centric modes probe the charge transfer relaxation. Our work establishes a phenomenological gating role of bridge torsions in determining the fundamental timescale and energy of photogenerated carriers, and therefore opens up dynamics-based guidelines for fabricating energy-efficient organic photovoltaics.
The Aegilops tauschii genome reveals multiple impacts of transposons
Authors: Zhao Guangyao , Zou Cheng , Li Kui , Wang Kai , Li Tianbao , Gao Lifeng , Zhang Xiaoxia , Wang Hongjin , Yang Zujun , Liu Xu , Jiang Wenkai , Mao Long , Kong Xiuying , Jiao Yuannian , Jia Jizeng 
Published: November 2017

AbstractWheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time.
Aberrant perfusion and its connectivity within default mode network of first-episode drug-naïve schizophrenia patients and their unaffected first-degree relatives
Authors: Cui Long-Biao , Wang Liu-Xian , Tian Ping , Wang Hua-Ning , Cai Min , Guo Fan , Li Chen , Wu Yu-Jing , Qiao Peng-Gang , Xu Zi-Liang , Liu Lin , He Hong , Wu Wen-Jun , Xi Yi-Bin , Yin Hong 
Published: November 2017

AbstractNeural substrates behind schizophrenia (SZ) and its heritability mediated by brain function are largely unknown. Cerebral blood flow (CBF), as a biomarker of activation in the brain, reflects the neuronal metabolism, and is promisingly used to detect cerebral alteration thereby shedding light on the features of individuals at high genetic risk. We performed a cross-sectional functional magnetic resonance imaging (MRI) study enrolling 45 first-episode drug-naïve patients with SZ, 32 unaffected first-degree relatives of these patients, and 51 healthy controls (HCs). We examined CBF, CBF connectivity, and CBF topological properties. SZ patients showed increased CBF in the left medial superior frontal gyrus and right precuneus compared with HCs, and decreased CBF in the left middle temporal gyrus compared with their relatives. Furthermore, unaffected relatives revealed higher level of CBF pronounced in regions within default mode network (DMN). Both SZ patients and their relatives exhibited dysconnectivity patterns. Notably, as for the network properties, unaffected relatives were with an intermediate level between SZ patients and HCs in the local efficiency and global efficiency. Our findings demonstrate the aberrant CBF of areas within DMN and the CBF connectivity pattern might be a familial feature in the brain of first-episode SZ patients and their relatives.
Systems analysis of latent HIV reversal reveals altered stress kinase signaling and increased cell death in infected T cells
Authors: Fong Linda E. , Sulistijo Endah S. , Miller-Jensen Kathryn 
Published: November 2017

AbstractViral latency remains the most significant obstacle to HIV eradication. Clinical strategies aim to purge the latent CD4+ T cell reservoir by activating viral expression to induce death, but are undercut by the inability to target latently infected cells. Here we explored the acute signaling response of latent HIV-infected CD4+ T cells to identify dynamic phosphorylation signatures that could be targeted for therapy. Stimulation with CD3/CD28, PMA/ionomycin, or latency reversing agents prostratin and SAHA, yielded increased phosphorylation of IκBα, ERK, p38, and JNK in HIV-infected cells across two in vitro latency models. Both latent infection and viral protein expression contributed to changes in perturbation-induced signaling. Data-driven statistical models calculated from the phosphorylation signatures successfully classified infected and uninfected cells and further identified signals that were functionally important for regulating cell death. Specifically, the stress kinase pathways p38 and JNK were modified in latently infected cells, and activation of p38 and JNK signaling by anisomycin resulted in increased cell death independent of HIV reactivation. Our findings suggest that altered phosphorylation signatures in infected T cells provide a novel strategy to more selectively target the latent reservoir to enhance eradication efforts.
Chemokines protect vascular smooth muscle cells from cell death induced by cyclic mechanical stretch
Authors: Zhao Jing , Nishimura Yuhei , Kimura Akihiko , Ozawa Kentaro , Kondo Toshikazu , Tanaka Toshio , Yoshizumi Masanori 
Published: November 2017

AbstractThe pulsatile nature of blood flow exposes vascular smooth muscle cells (VSMCs) in the vessel wall to cyclic mechanical stretch (CMS), which evokes VSMC proliferation, cell death, phenotypic switching, and migration, leading to vascular remodeling. These responses have been observed in many cardiovascular diseases; however, the underlying mechanisms remain unclear. We have revealed that CMS of rat aortic smooth muscle cells (RASMCs) causes JNK- and p38-dependent cell death and that a calcium channel blocker and angiotensin II receptor antagonist decreased the phosphorylation of JNK and p38 and subsequently decreased cell death by CMS. In the present study, we showed that the expression of Cxcl1 and Cx3cl1 was induced by CMS in a JNK-dependent manner. The expression of Cxcl1 was also induced in VSMCs by hypertension produced by abdominal aortic constriction (AAC). In addition, antagonists against the receptors for CXCL1 and CX3CL1 increased cell death, indicating that CXCL1 and CX3CL1 protect RASMCs from CMS-induced cell death. We also revealed that STAT1 is activated in RASMCs subjected to CMS. Taken together, these results indicate that CMS of VSMCs induces inflammation-related gene expression, including that of CXCL1 and CX3CL1, which may play important roles in the stress response against CMS caused by hypertension.
Identification of the Binding Sites on Rab5 and p110beta Phosphatidylinositol 3-kinase
Authors: Whitecross Dielle E. , Anderson Deborah H. 
Published: November 2017

AbstractRab5 is a small monomeric GTPase that mediates protein trafficking during endocytosis. Inactivation of Rab5 by GTP hydrolysis causes a conformational change that masks binding sites on its “switch regions” from downstream effectors. The p85 subunit of phosphatidylinositol 3-kinase (PI3K) is a GTPase activating protein (GAP) towards Rab5. Whereas p85 can bind with both Rab5-GTP and Rab5-GDP, the PI3K catalytic subunit p110β binds only Rab5-GTP, suggesting it interacts with the switch regions. Thus, the GAP functions of the catalytic arginine finger (from p85) and switch region stabilization (from p110β) may be provided by both proteins, acting together. To identify the Rab5 residues involved in binding p110β, residues in the Rab5 switch regions were mutated. A stabilized recombinant p110 protein, where the p85-iSH2 domain was fused to p110 (alpha or beta) was used in binding experiments. Eleven Rab5 mutants, including E80R and H83E, showed reduced p110β binding. The Rab5 binding site on p110β was also resolved through mutation of p110β in its Ras binding domain, and includes residues I234, E238 and Y244. This is a second region within p110β important for Rab5 binding. The Rab5-GTP:p110β interaction may be further elucidated through the characterization of these non-binding mutants in cells.