bluuebunny/crossref_metadata_2025_split huggingface dataset:
Redox cofactors insertion in prokaryotic molybdoenzymes occurs via a conserved folding mechanism
Authors: Arias-Cartin Rodrigo , Ceccaldi Pierre , Schoepp-Cothenet Barbara , Frick Klaudia , Blanc Jean-Michel , Guigliarelli Bruno , Walburger Anne , Grimaldi Stéphane , Friedrich Thorsten , Receveur-Brechot Véronique , Magalon Axel 
Published: November 2016

AbstractA major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. This holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. This large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (Mo/W-bisPGD) and Fe/S clusters. Here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational changes accompanying Mo/W-bisPGD and Fe/S cofactors insertion. Identified conformational changes are shown to be essential for recognition of the dedicated chaperone involved in cofactors insertion. A solvent-exposed salt bridge is shown to play a key role in enzyme folding after cofactors insertion. Furthermore, this salt bridge is shown to be strictly conserved within this prokaryotic molybdoenzyme family as deduced from a phylogenetic analysis issued from 3D structure-guided multiple sequence alignment. A biochemical analysis with a distantly-related member of the family, respiratory complex I, confirmed the critical importance of the salt bridge for folding. Overall, our results point to a conserved cofactors insertion mechanism within the Mo/W-bisPGD family.
Expanding and exploring the diversity of phytoplasmas from lucerne (Medicago sativa)
Authors: Gopurenko David , Fletcher Murray J. , Liu Jian , Gurr Geoff M. 
Published: November 2016

AbstractPhytoplasmas are a group of insect-vectored bacteria responsible for disease in many plant species worldwide. Among the crop species affected is the economically valuable forage species lucerne. Here we provide comprehensive molecular evidence for infection in multiple lucerne plants by a phytoplasma not previously known from this plant species. This phytoplasma had a >99% genetic similarity to an unclassified 16S rRNA subgroup previously reported as Stylosanthes little leaf from Stylosanthes spp. and was genetically and symptomatically distinct from a co-occurring but less common 16SrIIA group phytoplasma. Neighbour-joining analyses with publicly available sequence data confirmed the presence of two distinct phytoplasma lineages in the plant population. No PCR detections were made among 38 individuals of 12 co-occurring weed species. Sequence analysis revealed that all nine PCR detections from among 106 individuals of five Hemiptera insect species from the site, three of which had previously been reported as likely vectors, were false positives. This study demonstrates the importance of sequencing to complement PCR detection and avoid potentially inaccurate conclusions regarding vectors, highlights that sampling over a wide spatio-temporal scale is important for vector and alternative host studies, and extends to eight the number of phytoplasma 16 Sr groups known from lucerne.
Drought rapidly diminishes the large net CO2 uptake in 2011 over semi-arid Australia
Authors: Ma Xuanlong , Huete Alfredo , Cleverly James , Eamus Derek , Chevallier Frédéric , Joiner Joanna , Poulter Benjamin , Zhang Yongguang , Guanter Luis , Meyer Wayne , Xie Zunyi , Ponce-Campos Guillermo 
Published: November 2016

AbstractEach year, terrestrial ecosystems absorb more than a quarter of the anthropogenic carbon emissions, termed as land carbon sink. An exceptionally large land carbon sink anomaly was recorded in 2011, of which more than half was attributed to Australia. However, the persistence and spatially attribution of this carbon sink remain largely unknown. Here we conducted an observation-based study to characterize the Australian land carbon sink through the novel coupling of satellite retrievals of atmospheric CO2 and photosynthesis and in-situ flux tower measures. We show the 2010–11 carbon sink was primarily ascribed to savannas and grasslands. When all biomes were normalized by rainfall, shrublands however, were most efficient in absorbing carbon. We found the 2010–11 net CO2 uptake was highly transient with rapid dissipation through drought. The size of the 2010–11 carbon sink over Australia (0.97 Pg) was reduced to 0.48 Pg in 2011–12, and was nearly eliminated in 2012–13 (0.08 Pg). We further report evidence of an earlier 2000–01 large net CO2 uptake, demonstrating a repetitive nature of this land carbon sink. Given a significant increasing trend in extreme wet year precipitation over Australia, we suggest that carbon sink episodes will exert greater future impacts on global carbon cycle.
A universal synthetic route to carbon nanotube/transition metal oxide nano-composites for lithium ion batteries and electrochemical capacitors
Authors: Zhou Han , Zhang Lusi , Zhang Dongyang , Chen Shuangqiang , Coxon Paul R. , He Xiong , Coto Mike , Kim Hyun-Kyung , Xi Kai , Ding Shujiang 
Published: November 2016

AbstractWe report a simple synthetic approach to coaxially grow transition metal oxide (TMO) nanostructures on carbon nanotubes (CNT) with ready control of phase and morphology. A thin (~4 nm) sulfonated-polystyrene (SPS) pre-coating is essential for the deposition of transition metal based materials. This layer has abundant sulfonic groups (−SO3−) that can effectively attract Ni2+, Co2+, Zn2+ ions through electrostatic interaction and induce them via hydrolysis, dehydration and recrystallization to form coaxial (NiO, Co3O4, NiCoO2 and ZnCo2O4) shells and a nanosheet-like morphology around CNT. These structures possess a large active surface and enhanced structural robustness when used as electrode materials for lithium-ion batteries (LIBs) and electrochemical capacitors (ECs). As electrodes for LIBs, the ZnCo2O4@CNT material shows extremely stable cycling performance with a discharge capacity of 1068 mAh g−1 after 100 cycles at a current density of 400 mAg−1. For EC applications, the NiCoO2@CNT exhibits a high capacitance of 1360 Fg−1 at current densities of 10 Ag−1 after 3000 cycles and an overall capacitance loss of only 1.4%. These results demonstrate the potential of such hybrid materials meeting the crucial requirements of cycling stability and high rate capability for energy conversion and storage devices.
Dressed Photons Induced Resistance Oscillation and Zero Resistance in Arrayed Simple Harmonic Oscillators with No Impurity
Authors: Chang Chih-Chun , Chen Guang-Yin , Lin Lee 
Published: November 2016

AbstractWe investigate a system of an array of N simple harmonic oscillators (SHO) interacting with photons through QED interaction. As the energy of photon is around the spacing between SHO energy levels, energy gaps appear in the dispersion relation of the interacted (dressed) photons. This is quite different from the dispersion relation of free photons. Due to interactions between dressed photonic field and arrayed SHO, the photoresistance of this system shows oscillations and also drops to zero as irradiated by EM field of varying frequencies.
Fragmenting networks by targeting collective influencers at a mesoscopic level
Authors: Kobayashi Teruyoshi , Masuda Naoki 
Published: November 2016

AbstractA practical approach to protecting networks against epidemic processes such as spreading of infectious diseases, malware, and harmful viral information is to remove some influential nodes beforehand to fragment the network into small components. Because determining the optimal order to remove nodes is a computationally hard problem, various approximate algorithms have been proposed to efficiently fragment networks by sequential node removal. Morone and Makse proposed an algorithm employing the non-backtracking matrix of given networks, which outperforms various existing algorithms. In fact, many empirical networks have community structure, compromising the assumption of local tree-like structure on which the original algorithm is based. We develop an immunization algorithm by synergistically combining the Morone-Makse algorithm and coarse graining of the network in which we regard a community as a supernode. In this way, we aim to identify nodes that connect different communities at a reasonable computational cost. The proposed algorithm works more efficiently than the Morone-Makse and other algorithms on networks with community structure.
Apparent Power Law Scaling of Variable Range Hopping Conduction in Carbonized Polymer Nanofibers
Authors: Kim Kyung Ho , Lara-Avila Samuel , Kang Hojin , He Hans , Eklӧf Johnas , Hong Sung Ju , Park Min , Moth-Poulsen Kasper , Matsushita Satoshi , Akagi Kazuo , Kubatkin Sergey , Park Yung Woo 
Published: November 2016

AbstractWe induce dramatic changes in the structure of conducting polymer nanofibers by carbonization at 800 °C and compare charge transport properties between carbonized and pristine nanofibers. Despite the profound structural differences, both types of systems display power law dependence of current with voltage and temperature, and all measurements can be scaled into a single universal curve. We analyze our experimental data in the framework of variable range hopping and argue that this mechanism can explain transport properties of pristine polymer nanofibers as well.
Anatomical recovery of the spinal glutamatergic system following a complete spinal cord injury in lampreys
Authors: Fernández-López Blanca , Barreiro-Iglesias Antón , Rodicio María Celina 
Published: November 2016

AbstractLampreys recover locomotion following a spinal cord injury (SCI). Glutamate is necessary to initiate and control locomotion and recent data suggest a crucial role for intraspinal neurons in functional recovery following SCI. We aimed to determine whether, in lampreys, axotomized spinal glutamatergic neurons, which lose glutamate immunoreactivity immediately after SCI, recover it later on and to study the long-term evolution and anatomical recovery of the spinal glutamatergic system after SCI. We used glutamate immunoreactivity to study changes in the glutamatergic system, tract-tracing to label axotomized neurons and TUNEL labelling to study cell death. Transections of the cord were made at the level of the fifth gill. TUNEL experiments indicated that cell death is a minor contributor to the initial loss of glutamate immunoreactivity. At least some of the axotomized neurons lose glutamate immunoreactivity, survive and recover glutamate immunoreactivity 1 week post-lesion (wpl). We observed a progressive increase in the number of glutamatergic neurons/processes until an almost complete anatomical recovery at 10 wpl. Among all the glutamatergic populations, the population of cerebrospinal fluid-contacting cells is the only one that never recovers. Our results indicate that full recovery of the glutamatergic system is not necessary for the restoration of function in lampreys.
Atomic Resolution Interfacial Structure of Lead-free Ferroelectric K0.5Na0.5NbO3 Thin films Deposited on SrTiO3
Authors: Li Chao , Wang Lingyan , Wang Zhao , Yang Yaodong , Ren Wei , Yang Guang 
Published: November 2016

AbstractOxide interface engineering has attracted considerable attention since the discovery of its exotic properties induced by lattice strain, dislocation and composition change at the interface. In this paper, the atomic resolution structure and composition of the interface between the lead-free piezoelectric (K0.5Na0.5)NbO3 (KNN) thin films and single-crystalline SrTiO3 substrate were investigated by means of scanning transmission electron microscopy (STEM) combining with electron energy loss spectroscopy (EELS). A sharp epitaxial interface was observed to be a monolayer composed of Nb and Ti cations with a ratio of 3/1. The First-Principles Calculations indicated the interface monolayer showed different electronic structure and played the vital role in the asymmetric charge distribution of KNN thin films near the interface. We also observed the gradual relaxation process for the relatively large lattice strains near the KNN/STO interface, which remarks a good structure modulation behavior of KNN thin films via strain engineering.
An evolutionary conserved interaction between the Gcm transcription factor and the SF1 nuclear receptor in the female reproductive system
Authors: Cattenoz Pierre B. , Delaporte Claude , Bazzi Wael , Giangrande Angela 
Published: November 2016

AbstractNR5A1 is essential for the development and for the function of steroid producing glands of the reproductive system. Moreover, its misregulation is associated with endometriosis, which is the first cause of infertility in women. Hr39, the Drosophila ortholog of NR5A1, is expressed and required in the secretory cells of the spermatheca, the female exocrine gland that ensures fertility by secreting substances that attract and capacitate the spermatozoids. We here identify a direct regulator of Hr39 in the spermatheca: the Gcm transcription factor. Furthermore, lack of Gcm prevents the production of the secretory cells and leads to female sterility in Drosophila. Hr39 regulation by Gcm seems conserved in mammals and involves the modification of the DNA methylation profile of mNr5a1. This study identifies a new molecular pathway in female reproductive system development and suggests a role for hGCM in the progression of reproductive tract diseases in humans.
Improving landscape inference by integrating heterogeneous data in the inverse Ising problem
Authors: Barrat-Charlaix Pierre , Figliuzzi Matteo , Weigt Martin 
Published: November 2016

AbstractThe inverse Ising problem and its generalizations to Potts and continuous spin models have recently attracted much attention thanks to their successful applications in the statistical modeling of biological data. In the standard setting, the parameters of an Ising model (couplings and fields) are inferred using a sample of equilibrium configurations drawn from the Boltzmann distribution. However, in the context of biological applications, quantitative information for a limited number of microscopic spins configurations has recently become available. In this paper, we extend the usual setting of the inverse Ising model by developing an integrative approach combining the equilibrium sample with (possibly noisy) measurements of the energy performed for a number of arbitrary configurations. Using simulated data, we show that our integrative approach outperforms standard inference based only on the equilibrium sample or the energy measurements, including error correction of noisy energy measurements. As a biological proof-of-concept application, we show that mutational fitness landscapes in proteins can be better described when combining evolutionary sequence data with complementary structural information about mutant sequences.
Nicotinic and opioid receptor regulation of striatal dopamine D2-receptor mediated transmission
Authors: Mamaligas Aphroditi A. , Cai Yuan , Ford Christopher P. 
Published: November 2016

AbstractIn addition to dopamine neuron firing, cholinergic interneurons (ChIs) regulate dopamine release in the striatum via presynaptic nicotinic receptors (nAChRs) on dopamine axon terminals. Synchronous activity of ChIs is necessary to evoke dopamine release through this pathway. The frequency-dependence of disynaptic nicotinic modulation has led to the hypothesis that nAChRs act as a high-pass filter in the dopaminergic microcircuit. Here, we used optogenetics to selectively stimulate either ChIs or dopamine terminals directly in the striatum. To measure the functional consequence of dopamine release, D2-receptor synaptic activity was assessed via virally overexpressed potassium channels (GIRK2) in medium spiny neurons (MSNs). We found that nicotinic-mediated dopamine release was blunted at higher frequencies because nAChRs exhibit prolonged desensitization after a single pulse of synchronous ChI activity. However, when dopamine neurons alone were stimulated, nAChRs had no effect at any frequency. We further assessed how opioid receptors modulate these two mechanisms of release. Bath application of the κ opioid receptor agonist U69593 decreased D2-receptor activation through both pathways, whereas the μ opioid receptor agonist DAMGO decreased D2-receptor activity only as a result of cholinergic-mediated dopamine release. Thus the release of dopamine can be independently modulated when driven by either dopamine neurons or cholinergic interneurons.
Acupuncture and Moxibustion have Different Effects on Fatigue by Regulating the Autonomic Nervous System: A Pilot Controlled Clinical Trial
Authors: Shu Qing , Wang Hua , Litscher Daniela , Wu Song , Chen Li , Gaischek Ingrid , Wang Lu , He Wenjuan , Zhou Huanjiao , Litscher Gerhard , Liang Fengxia 
Published: November 2016

AbstractIn order to investigate the different effects of acupuncture and moxibustion on chronic fatigue syndrome (CFS) and alterations in the autonomic nervous system by measuring heart rate variability (HRV). Forty-five participants were recruited and randomly divided into 3 groups using a randomization schedule. The control group (CG, n = 15) and the acupuncture group (AG, n = 15) were treated by manipulation acupuncture, and the moxibustion group (MG, n = 15) was treated by indirect moxibustion. Primary outcomes were the scores of the Fatigue Assessment Instrument (FAI). Secondary outcomes were the HRV parameters which can reflect activity of the autonomic nervous system. This trial considered both instantaneous changes and long-term effectiveness. FAI scores decreased after the 4th and 10th treatments in the 3 groups. The decrease in FAI in the MG was greater than that in the AG. Acupuncture was more effective in instantaneous changes of HRV and moxibustion in long-term aspects. Both acupuncture and moxibustion improved fatigue in CFS patients, but moxibustion was more effective. The possible mechanism of the intervention may be through activation of the vagus nerve. Moxibustion was more effective than acupuncture in long-term treatment of CFS.
Coastal leatherback turtles reveal conservation hotspot
Authors: Robinson Nathan J. , Morreale Stephen J. , Nel Ronel , Paladino Frank V. 
Published: November 2016

AbstractPrevious studies have shown that the world’s largest reptile – the leatherback turtle Dermochelys coriacea – conducts flexible foraging migrations that can cover thousands of kilometres between nesting sites and distant foraging areas. The vast distances that may be travelled by migrating leatherback turtles have greatly complicated conservation efforts for this species worldwide. However, we demonstrate, using a combination of satellite telemetry and stable isotope analysis, that approximately half of the nesting leatherbacks from an important rookery in South Africa do not migrate to distant foraging areas, but rather, forage in the coastal waters of the nearby Mozambique Channel. Moreover, this coastal cohort appears to remain resident year-round in shallow waters (<50 m depth) in a relatively fixed area. Stable isotope analyses further indicate that the Mozambique Channel also hosts large numbers of loggerhead turtles Caretta caretta. The rare presence of a resident coastal aggregation of leatherback turtles not only presents a unique opportunity for conservation, but alongside the presence of loggerhead turtles and other endangered marine megafauna in the Mozambique Channel, highlights the importance of this area as a marine biodiversity hotspot.
AM fungi patchiness and the clonal growth of Glechoma hederacea in heterogeneous environments
Authors: Vannier Nathan , Bittebiere Anne-Kristel , Vandenkoornhuyse Philippe , Mony Cendrine 
Published: November 2016

AbstractThe effect of AM fungi spatial distribution on individual plant development may determine the dynamics of the whole plant community. We investigated whether clonal plants display, like for other resources, a foraging or a specialization response, to adapt to the distribution of AM fungi. Two separate experiments were done to investigate the response of Glechoma hederacea to a heterogeneous distribution of a mixture of 3 AM fungi species, and the effects of each species on colonization and allocation traits. No specialization and a limited foraging response to the heterogeneous distribution of AM fungi was observed. An effect of the AM fungal species on plant mass allocation and ramet production, but not on spacer length, was detected. Two possible explanations are proposed: (i) the plant’s responses are buffered by differences in individual effects of the fungal species or their root colonization intensity. (ii) the initial heterogeneous distribution of AM fungi is perceived as homogeneous by the plant either by reduced physiological integration or due to the transfer of AM fungi propagules through the stolons. Microscopic and DNA sequencing analyses provided evidence of this transfer, thus demonstrating the role of stolons as dispersal vectors of AM fungi within the plant clonal network.
Boosting photoresponse in silicon metal-semiconductor-metal photodetector using semiconducting quantum dots
Authors: Biswas Chandan , Kim Yonghwan , Lee Young Hee 
Published: November 2016

AbstractSilicon based metal-semiconductor-metal (MSM) photodetectors have faster photogeneration and carrier collection across the metal-semiconductor Schottky contacts, and CMOS integratibility compared to conventional p-n junction photodetectors. However, its operations are limited by low photogeneration, inefficient carrier-separation, and low mobility. Here, we show a simple and highly effective approach for boosting Si MSM photodetector efficiency by uniformly decorating semiconducting CdSe quantum dots on Si channel (Si-QD). Significantly higher photocurrent on/off ratio was achieved up to over 500 compared to conventional Si MSM photodetector (on/off ratio ~5) by increasing photogeneration and improving carrier separation. Furthermore, a substrate-biasing technique invoked wide range of tunable photocurrent on/off ratio in Si-QD photodetector (ranging from 2.7 to 562) by applying suitable combinations of source-drain and substrate biasing conditions. Strong photogeneration and carrier separation were achieved by employing Stark effect into the Si-QD hybrid system. These results highlight a promising method for enhancing Si MSM photodetector efficiency more than 100 times and simultaneously compatible with current silicon technologies.
In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD
Authors: Martínez-Flores Irma , Pérez-Morales Deyanira , Sánchez-Pérez Mishael , Paredes Claudia C. , Collado-Vides Julio , Salgado Heladia , Bustamante Víctor H. 
Published: November 2016

AbstractA wide variety of Salmonella enterica serovars cause intestinal and systemic infections to humans and animals. Salmonella Patogenicity Island 1 (SPI-1) is a chromosomal region containing 39 genes that have crucial virulence roles. The AraC-like transcriptional regulator HilD, encoded in SPI-1, positively controls the expression of the SPI-1 genes, as well as of several other virulence genes located outside SPI-1. In this study, we applied a clustering method to the global gene expression data of S. enterica serovar Typhimurium from the COLOMBOS database; thus genes that show an expression pattern similar to that of SPI-1 genes were selected. This analysis revealed nine novel genes that are co-expressed with SPI-1, which are located in different chromosomal regions. Expression analyses and protein-DNA interaction assays showed regulation by HilD for six of these genes: gtgE, phoH, sinR, SL1263 (lpxR) and SL4247 were regulated directly, whereas SL1896 was regulated indirectly. Interestingly, phoH is an ancestral gene conserved in most of bacteria, whereas the other genes show characteristics of genes acquired by Salmonella. A role in virulence has been previously demonstrated for gtgE, lpxR and sinR. Our results further expand the regulon of HilD and thus identify novel possible Salmonella virulence genes.