bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global strategy to mitigate the environmental impact of China’s ruminant consumption boom
Authors: Du Yuanyuan , Ge Ying , Ren Yuan , Fan Xing , Pan Kaixuan , Lin Linshan , Wu Xu , Min Yong , Meyerson Laura A. , Heino Mikko , Chang Scott X. , Liu Xiaozi , Mao Feng , Yang Guofu , Peng Changhui , Qu Zelong , Chang Jie , Didham Raphael K. 
Published: October 2018

AbstractRising demand for ruminant meat and dairy products in developing countries is expected to double anthropogenic greenhouse gas and ammonia emissions from livestock by 2050. Mitigation strategies are urgently needed to meet demand while minimizing environmental impacts. Here, we develop scenarios for mitigating emissions under local vs global supply policies using data from 308 livestock farms across mainland China, where emissions intensities are ~50% higher than those in developed nations. Intensification of domestic production and globalized expansion through increased trade result in reductions in global emissions by nearly 30% over a business-as-usual scenario, but at the expense of trading partners absorbing the associated negative externalities of environmental degradation. Only adoption of a mixed strategy combining global best-practice in sustainable intensification of domestic production, with increased green-source trading as a short-term coping strategy, can meet 2050 demand while minimizing the local and global environmental footprint of China’s ruminant consumption boom.
Dopamine–endocannabinoid interactions mediate spike-timing-dependent potentiation in the striatum
Authors: Xu Hao , Perez Sylvie , Cornil Amandine , Detraux Bérangère , Prokin Ilya , Cui Yihui , Degos Bertrand , Berry Hugues , de Kerchove d’Exaerde Alban , Venance Laurent 
Published: October 2018

AbstractDopamine modulates striatal synaptic plasticity, a key substrate for action selection and procedural learning. Thus, characterizing the repertoire of activity-dependent plasticity in striatum and its dependence on dopamine is of crucial importance. We recently unraveled a striatal spike-timing-dependent long-term potentiation (tLTP) mediated by endocannabinoids (eCBs) and induced with few spikes (~5–15). Whether this eCB-tLTP interacts with the dopaminergic system remains to be investigated. Here, we report that eCB-tLTP is impaired in a rodent model of Parkinson’s disease and rescued by L-DOPA. Dopamine controls eCB-tLTP via dopamine type-2 receptors (D2R) located presynaptically in cortical terminals. Dopamine–endocannabinoid interactions via D2R are required for the emergence of tLTP in response to few coincident pre- and post-synaptic spikes and control eCB-plasticity by modulating the long-term potentiation (LTP)/depression (LTD) thresholds. While usually considered as a depressing synaptic function, our results show that eCBs in the presence of dopamine constitute a versatile system underlying bidirectional plasticity implicated in basal ganglia pathophysiology.
Simple ruthenium-catalyzed reductive amination enables the synthesis of a broad range of primary amines
Authors: Senthamarai Thirusangumurugan , Murugesan Kathiravan , Schneidewind Jacob , Kalevaru Narayana V. , Baumann Wolfgang , Neumann Helfried , Kamer Paul C. J. , Beller Matthias , Jagadeesh Rajenahally V. 
Published: October 2018

AbstractThe production of primary benzylic and aliphatic amines, which represent essential feedstocks and key intermediates for valuable chemicals, life science molecules and materials, is of central importance. Here, we report the synthesis of this class of amines starting from carbonyl compounds and ammonia by Ru-catalyzed reductive amination using H2. Key to success for this synthesis is the use of a simple RuCl2(PPh3)3 catalyst that empowers the synthesis of >90 various linear and branched benzylic, heterocyclic, and aliphatic amines under industrially viable and scalable conditions. Applying this catalyst, −NH2 moiety has been introduced in functionalized and structurally diverse compounds, steroid derivatives and pharmaceuticals. Noteworthy, the synthetic utility of this Ru-catalyzed amination protocol has been demonstrated by upscaling the reactions up to 10 gram-scale syntheses. Furthermore, in situ NMR studies were performed for the identification of active catalytic species. Based on these studies a mechanism for Ru-catalyzed reductive amination is proposed.
Pressure tuning of charge ordering in iron oxide
Authors: Ovsyannikov Sergey V. , Bykov Maxim , Bykova Elena , Glazyrin Konstantin , Manna Rudra Sekhar , Tsirlin Alexander A. , Cerantola Valerio , Kupenko Ilya , Kurnosov Alexander V. , Kantor Innokenty , Pakhomova Anna S. , Chuvashova Irina , Chumakov Aleksandr I. , Rüffer Rudolf , McCammon Catherine , Dubrovinsky Leonid S. 
Published: October 2018

AbstractA Verwey-type charge-ordering transition in magnetite at 120 K leads to the formation of linear units of three iron ions with one shared electron, called trimerons. The recently-discovered iron pentoxide (Fe4O5) comprising mixed-valent iron cations at octahedral chains, demonstrates another unusual charge-ordering transition at 150 K involving competing formation of iron trimerons and dimerons. Here, we experimentally show that applied pressure can tune the charge-ordering pattern in Fe4O5 and strongly affect the ordering temperature. We report two charge-ordered phases, the first of which may comprise both dimeron and trimeron units, whereas, the second exhibits an overall dimerization involving both the octahedral and trigonal-prismatic chains of iron in the crystal structure. We link the dramatic change in the charge-ordering pattern in the second phase to redistribution of electrons between the octahedral and prismatic iron chains, and propose that the average oxidation state of the iron cations can pre-determine a charge-ordering pattern.
Formation of the β-barrel assembly machinery complex in lipid bilayers as seen by solid-state NMR
Authors: Pinto Cecilia , Mance Deni , Sinnige Tessa , Daniëls Mark , Weingarth Markus , Baldus Marc 
Published: October 2018

AbstractThe β-barrel assembly machinery (BAM) is a pentameric complex (BamA–E), which catalyzes the essential process of β-barrel protein insertion into the outer membrane of E. coli. Thus far, a detailed understanding of the insertion mechanism has been elusive but recent results suggest that local protein motion, in addition to the surrounding membrane environment, may be of critical relevance. We have devised a high-sensitivity solid-state NMR approach to directly probe protein motion and the structural changes associated with BAM complex assembly in lipid bilayers. Our results reveal how essential BamA domains, such as the interface formed by the polypeptide transport associated domains P4 and P5 become stabilized after complex formation and suggest that BamA β-barrel opening and P5 reorientation is directly related to complex formation in membranes. Both the lateral gate, as well as P5, exhibit local dynamics, a property that could play an integral role in substrate recognition and insertion.
ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup
Authors: Chan Chang S. , Laddha Saurabh V. , Lewis Peter W. , Koletsky Matthew S. , Robzyk Kenneth , Da Silva Edaise , Torres Paula J. , Untch Brian R. , Li Janet , Bose Promita , Chan Timothy A. , Klimstra David S. , Allis C. David , Tang Laura H. 
Published: October 2018

AbstractThe commonly mutated genes in pancreatic neuroendocrine tumors (PanNETs) are ATRX, DAXX, and MEN1. We genotyped 64 PanNETs and found 58% carry ATRX, DAXX, and MEN1 mutations (A-D-M mutant PanNETs) and this correlates with a worse clinical outcome than tumors carrying the wild-type alleles of all three genes (A-D-M WT PanNETs). We performed RNA sequencing and DNA-methylation analysis to reveal two distinct subgroups with one consisting entirely of A-D-M mutant PanNETs. Two genes differentiating A-D-M mutant from A-D-M WT PanNETs were high ARX and low PDX1 gene expression with PDX1 promoter hyper-methylation in the A-D-M mutant PanNETs. Moreover, A-D-M mutant PanNETs had a gene expression signature related to that of alpha-cells (FDR q-value < 0.009) of pancreatic islets including increased expression of HNF1A and its transcriptional target genes. This gene expression profile suggests that A-D-M mutant PanNETs originate from or transdifferentiate into a distinct cell type similar to alpha cells.
Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice
Authors: Wu Yongzhen , Zhao Shuangshuang , Li Xianran , Zhang Bosen , Jiang Liyun , Tang Yanyan , Zhao Jie , Ma Xin , Cai Hongwei , Sun Chuanqing , Tan Lubin 
Published: October 2018

AbstractImproving the yield by modifying plant architecture was a key step during crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 in Asian cultivated rice (Oryza sativa), which is closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene, harbors a tandem repeat of seven zinc-finger genes. Three of these genes regulate the plant architecture, suggesting that the deletion also promoted the critical transition from the prostrate growth and low yield of wild rice (O. rufipogon) to the erect growth and high yield of Asian cultivated rice. We refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Further, a similar but independent 113-kb deletion is detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, eliminating a tandem repeat of zinc-finger genes, may have been involved in the parallel domestication of plant architecture in Asian and African rice.
Time units for learning involving maintenance of system-wide cFos expression in neuronal assemblies
Authors: Chowdhury Ananya , Caroni Pico 
Published: October 2018

AbstractRepeated experiences may be integrated in succession during a learning process, or they may be combined as a whole within dedicated time windows to possibly promote quality control. Here we show that in Pavlovian, incremental and incidental learning, related information acquired within time windows of 5 h is combined to determine what mice learn. Trials required for learning had to occur within 5 h, when learning-related shared cues could produce association and interference. Upon acquisition, cFos expression was elevated during 5 h throughout specific system-wide neuronal assemblies. Time window function depended on network activity and cFos expression. Local cFos activity was required for distant assembly recruitment through network activity and distant BDNF. Activation of learning-related cFos assemblies was sufficient and necessary for time window function. Therefore, learning processes consist of dedicated 5 h time windows (time units for learning), involving maintenance of system-wide neuronal assemblies through network activity and cFos expression.
ATR/Chk1 signaling induces autophagy through sumoylated RhoB-mediated lysosomal translocation of TSC2 after DNA damage
Authors: Liu Mingdong , Zeng Taoling , Zhang Xin , Liu Chunyan , Wu Zhihui , Yao Luming , Xie Changchuan , Xia Hui , Lin Qi , Xie Liping , Zhou Dawang , Deng Xianming , Chan Hong-Lin , Zhao Tong-Jin , Wang Hong-Rui 
Published: October 2018

AbstractDNA damage can induce autophagy; however, the underlying mechanism remains largely unknown. Here we report that DNA damage leads to autophagy through ATR/Chk1/RhoB-mediated lysosomal recruitment of TSC complex and subsequent mTORC1 inhibition. DNA damage caused by ultraviolet light (UV) or alkylating agent methyl methanesulphonate (MMS) results in phosphorylation of small GTPase RhoB by Chk1. Phosphorylation of RhoB enhances its interaction with the TSC2, and promotes its sumoylation by PIAS1, which is required for RhoB/TSC complex to translocate to lysosomes. As a result, mTORC1 is inhibited, and autophagy is activated. Knockout of RhoB severely attenuates lysosomal translocation of TSC complex and the DNA damage-induced autophagy. Reintroducing wild-type but not sumoylation-resistant RhoB into RhoB−/− cells restores the onset of autophagy. Hence, our study identifies a molecular mechanism for translocation of TSC complex to lysosomes in response to DNA damage, which depends on ATR/Chk1-mediated RhoB phosphorylation and sumoylation.
A comprehensive overview of genomic imprinting in breast and its deregulation in cancer
Authors: Goovaerts Tine , Steyaert Sandra , Vandenbussche Chari A. , Galle Jeroen , Thas Olivier , Van Criekinge Wim , De Meyer Tim 
Published: October 2018

AbstractGenomic imprinting plays an important role in growth and development. Loss of imprinting (LOI) has been found in cancer, yet systematic studies are impeded by data-analytical challenges. We developed a methodology to detect monoallelically expressed loci without requiring genotyping data, and applied it on The Cancer Genome Atlas (TCGA, discovery) and Genotype-Tissue expression project (GTEx, validation) breast tissue RNA-seq data. Here, we report the identification of 30 putatively imprinted genes in breast. In breast cancer (TCGA),HM13is featured by LOI and expression upregulation, which is linked to DNA demethylation. Other imprinted genes typically demonstrate lower expression in cancer, often associated with copy number variation and aberrant DNA methylation. Downregulation in cancer frequently leads to higher relative expression of the (imperfectly) silenced allele, yet this is not considered canonical LOI given the lack of (absolute) re-expression. In summary, our novel methodology highlights the massive deregulation of imprinting in breast cancer.
Subtomogram averaging of COPII assemblies reveals how coat organization dictates membrane shape
Authors: Hutchings Joshua , Stancheva Viktoriya , Miller Elizabeth A. , Zanetti Giulia 
Published: October 2018

AbstractEukaryotic cells employ membrane-bound carriers to transport cargo between compartments in a process essential to cell functionality. Carriers are generated by coat complexes that couple cargo capture to membrane deformation. The COPII coat mediates export from the endoplasmic reticulum by assembling in inner and outer layers, yielding carriers of variable shape and size that allow secretion of thousands of diverse cargo. Despite detailed understanding of COPII subunits, the molecular mechanisms of coat assembly and membrane deformation are unclear. Here we present a 4.9 Å cryo-tomography subtomogram averaging structure of in vitro-reconstituted membrane-bound inner coat. We show that the outer coat (Sec13–Sec31) bridges inner coat subunits (Sar1–Sec23–Sec24), promoting their assembly into a tight lattice. We directly visualize the membrane-embedded Sar1 amphipathic helix, revealing that lattice formation induces parallel helix insertions, yielding tubular curvature. We propose that regulators like the procollagen receptor TANGO1 modulate this mechanism to determine vesicle shape and size.
Blood meal-induced inhibition of vector-borne disease by transgenic microbiota
Authors: Shane Jackie L. , Grogan Christina L. , Cwalina Caroline , Lampe David J. 
Published: October 2018

AbstractVector-borne diseases are a substantial portion of the global disease burden; one of the deadliest of these is malaria. Vector control strategies have been hindered by mosquito and pathogen resistances, and population alteration approaches using transgenic mosquitos still have many hurdles to overcome before they can be implemented in the field. Here we report a paratransgenic control strategy in which the microbiota of Anopheles stephensi was engineered to produce an antiplasmodial effector causing the mosquito to become refractory to Plasmodium berghei. The midgut symbiont Asaia was used to conditionally express the antiplasmodial protein scorpine only when a blood meal was present. These blood meal inducible Asaia strains significantly inhibit pathogen infection, and display improved fitness compared to strains that constitutively express the antiplasmodial effector. This strategy may allow the antiplasmodial bacterial strains to survive and be transmitted through mosquito populations, creating an easily implemented and enduring vector control strategy.
ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB
Authors: Teng Yaqun , Yadav Tribhuwan , Duan Meihan , Tan Jun , Xiang Yufei , Gao Boya , Xu Jianquan , Liang Zhuobin , Liu Yang , Nakajima Satoshi , Shi Yi , Levine Arthur S. , Zou Lee , Lan Li 
Published: October 2018

AbstractActively transcribed regions of the genome are protected by transcription-coupled DNA repair mechanisms, including transcription-coupled homologous recombination (TC-HR). Here we used reactive oxygen species (ROS) to induce and characterize TC-HR at a transcribed locus in human cells. As canonical HR, TC-HR requires RAD51. However, the localization of RAD51 to damage sites during TC-HR does not require BRCA1 and BRCA2, but relies on RAD52 and Cockayne Syndrome Protein B (CSB). During TC-HR, RAD52 is recruited by CSB through an acidic domain. CSB in turn is recruited by R loops, which are strongly induced by ROS in transcribed regions. Notably, CSB displays a strong affinity for DNA:RNA hybrids in vitro, suggesting that it is a sensor of ROS-induced R loops. Thus, TC-HR is triggered by R loops, initiated by CSB, and carried out by the CSB-RAD52-RAD51 axis, establishing a BRCA1/2-independent alternative HR pathway protecting the transcribed genome.
Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism
Authors: Peek James , Lilic Mirjana , Montiel Daniel , Milshteyn Aleksandr , Woodworth Ian , Biggins John B. , Ternei Melinda A. , Calle Paula Y. , Danziger Michael , Warrier Thulasi , Saito Kohta , Braffman Nathaniel , Fay Allison , Glickman Michael S. , Darst Seth A. , Campbell Elizabeth A. , Brady Sean F. 
Published: October 2018

AbstractRifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5′-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.
Fractionalized excitations in the partially magnetized spin liquid candidate YbMgGaO4
Authors: Shen Yao , Li Yao-Dong , Walker H. C. , Steffens P. , Boehm M. , Zhang Xiaowen , Shen Shoudong , Wo Hongliang , Chen Gang , Zhao Jun 
Published: October 2018

AbstractQuantum spin liquids (QSLs) are exotic states of matter characterized by emergent gauge structures and fractionalized elementary excitations. The recently discovered triangular lattice antiferromagnet YbMgGaO4 is a promising QSL candidate, and the nature of its ground state is still under debate. Here we use neutron scattering to study the spin excitations in YbMgGaO4 under various magnetic fields. Our data reveal a dispersive spin excitation continuum with clear upper and lower excitation edges under a weak magnetic field (H = 2.5 T). Moreover, a spectral crossing emerges at the Γ point at the Zeeman-split energy. The corresponding redistribution of the spectral weight and its field-dependent evolution are consistent with the theoretical prediction based on the inter-band and intra-band spinon particle-hole excitations associated with the Zeeman-split spinon bands, implying the presence of fractionalized excitations and spinon Fermi surfaces in the partially magnetized QSL state in YbMgGaO4.
Galanin neurons in the ventrolateral preoptic area promote sleep and heat loss in mice
Authors: Kroeger Daniel , Absi Gianna , Gagliardi Celia , Bandaru Sathyajit S. , Madara Joseph C. , Ferrari Loris L. , Arrigoni Elda , Münzberg Heike , Scammell Thomas E. , Saper Clifford B. , Vetrivelan Ramalingam 
Published: October 2018

AbstractThe preoptic area (POA) is necessary for sleep, but the fundamental POA circuits have remained elusive. Previous studies showed that galanin (GAL)- and GABA-producing neurons in the ventrolateral preoptic nucleus (VLPO) express cFos after periods of increased sleep and innervate key wake-promoting regions. Although lesions in this region can produce insomnia, high frequency photostimulation of the POAGAL neurons was shown to paradoxically cause waking, not sleep. Here we report that photostimulation of VLPOGAL neurons in mice promotes sleep with low frequency stimulation (1–4 Hz), but causes conduction block and waking at frequencies above 8 Hz. Further, optogenetic inhibition reduces sleep. Chemogenetic activation of VLPOGAL neurons confirms the increase in sleep, and also reduces body temperature. In addition, chemogenetic activation of VLPOGAL neurons induces short-latency sleep in an animal model of insomnia. Collectively, these findings establish a causal role of VLPOGAL neurons in both sleep induction and heat loss.
Salt concentration and charging velocity determine ion charge storage mechanism in nanoporous supercapacitors
Authors: Prehal C. , Koczwara C. , Amenitsch H. , Presser V. , Paris O. 
Published: October 2018

Abstract
A fundamental understanding of ion charge storage in nanoporous electrodes is essential to improve the performance of supercapacitors or devices for capacitive desalination. Here, we employ in situ X-ray transmission measurements on activated carbon supercapacitors to study ion concentration changes during electrochemical operation. Whereas counter-ion adsorption was found to dominate at small electrolyte salt concentrations and slow cycling speed, ion replacement prevails for high molar concentrations and/or fast cycling. Chronoamperometry measurements reveal two distinct time regimes of ion concentration changes. In the first regime the supercapacitor is charged, and counter- and co-ion concentration changes align with ion replacement and partially co-ion expulsion. In the second regime, the electrode charge remains constant, but the total ion concentration increases. We conclude that the initial fast charge neutralization in nanoporous supercapacitor electrodes leads to a non-equilibrium ion configuration. The subsequent, charge-neutral equilibration slowly increases the total ion concentration towards counter-ion adsorption.