bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition
Authors: Fang Jian , Cheng Jingdong , Wang Jiaolong , Zhang Qiao , Liu Mengjie , Gong Rui , Wang Ping , Zhang Xiaodan , Feng Yangyang , Lan Wenxian , Gong Zhou , Tang Chun , Wong Jiemin , Yang Huirong , Cao Chunyang , Xu Yanhui 
Published: April 2016

AbstractUHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD–PHD. The Spacer also facilitates UHRF1–DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD–PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1.
Balancing surface adsorption and diffusion of lithium-polysulfides on nonconductive oxides for lithium–sulfur battery design
Authors: Tao Xinyong , Wang Jianguo , Liu Chong , Wang Haotian , Yao Hongbin , Zheng Guangyuan , Seh Zhi Wei , Cai Qiuxia , Li Weiyang , Zhou Guangmin , Zu Chenxi , Cui Yi 
Published: April 2016

AbstractLithium–sulfur batteries have attracted attention due to their six-fold specific energy compared with conventional lithium-ion batteries. Dissolution of lithium polysulfides, volume expansion of sulfur and uncontrollable deposition of lithium sulfide are three of the main challenges for this technology. State-of-the-art sulfur cathodes based on metal-oxide nanostructures can suppress the shuttle-effect and enable controlled lithium sulfide deposition. However, a clear mechanistic understanding and corresponding selection criteria for the oxides are still lacking. Herein, various nonconductive metal-oxide nanoparticle-decorated carbon flakes are synthesized via a facile biotemplating method. The cathodes based on magnesium oxide, cerium oxide and lanthanum oxide show enhanced cycling performance. Adsorption experiments and theoretical calculations reveal that polysulfide capture by the oxides is via monolayered chemisorption. Moreover, we show that better surface diffusion leads to higher deposition efficiency of sulfide species on electrodes. Hence, oxide selection is proposed to balance optimization between sulfide-adsorption and diffusion on the oxides.
Sialylation converts arthritogenic IgG into inhibitors of collagen-induced arthritis
Authors: Ohmi Yuhsuke , Ise Wataru , Harazono Akira , Takakura Daisuke , Fukuyama Hidehiro , Baba Yoshihiro , Narazaki Masashi , Shoda Hirofumi , Takahashi Nobunori , Ohkawa Yuki , Ji Shuting , Sugiyama Fumihiro , Fujio Keishi , Kumanogoh Atsushi , Yamamoto Kazuhiko , Kawasaki Nana , Kurosaki Tomohiro , Takahashi Yoshimasa , Furukawa Koichi 
Published: April 2016

AbstractRheumatoid arthritis (RA)-associated IgG antibodies such as anti-citrullinated protein antibodies (ACPAs) have diverse glycosylation variants; however, key sugar chains modulating the arthritogenic activity of IgG remain to be clarified. Here, we show that reduced sialylation is a common feature of RA-associated IgG in humans and in mouse models of arthritis. Genetically blocking sialylation in activated B cells results in exacerbation of joint inflammation in a collagen-induced arthritis (CIA) model. On the other hand, artificial sialylation of anti-type II collagen antibodies, including ACPAs, not only attenuates arthritogenic activity, but also suppresses the development of CIA in the antibody-infused mice, whereas sialylation of other IgG does not prevent CIA. Thus, our data demonstrate that sialylation levels control the arthritogenicity of RA-associated IgG, presenting a potential target for antigen-specific immunotherapy.
Airway bacteria drive a progressive COPD-like phenotype in mice with polymeric immunoglobulin receptor deficiency
Authors: Richmond Bradley W. , Brucker Robert M. , Han Wei , Du Rui-Hong , Zhang Yongqin , Cheng Dong-Sheng , Gleaves Linda , Abdolrasulnia Rasul , Polosukhina Dina , Clark Peter E. , Bordenstein Seth R. , Blackwell Timothy S. , Polosukhin Vasiliy V. 
Published: April 2016

AbstractMechanisms driving persistent airway inflammation in chronic obstructive pulmonary disease (COPD) are incompletely understood. As secretory immunoglobulin A (SIgA) deficiency in small airways has been reported in COPD patients, we hypothesized that immunobarrier dysfunction resulting from reduced SIgA contributes to chronic airway inflammation and disease progression. Here we show that polymeric immunoglobulin receptor-deficient (pIgR−/−) mice, which lack SIgA, spontaneously develop COPD-like pathology as they age. Progressive airway wall remodelling and emphysema in pIgR−/− mice are associated with an altered lung microbiome, bacterial invasion of the airway epithelium, NF-κB activation, leukocyte infiltration and increased expression of matrix metalloproteinase-12 and neutrophil elastase. Re-derivation of pIgR−/− mice in germ-free conditions or treatment with the anti-inflammatory phosphodiesterase-4 inhibitor roflumilast prevents COPD-like lung inflammation and remodelling. These findings show that pIgR/SIgA deficiency in the airways leads to persistent activation of innate immune responses to resident lung microbiota, driving progressive small airway remodelling and emphysema.
Generation of large coherent states by bang–bang control of a trapped-ion oscillator
Authors: Alonso J. , Leupold F. M. , Solèr Z. U. , Fadel M. , Marinelli M. , Keitch B. C. , Negnevitsky V. , Home J. P. 
Published: April 2016

AbstractFast control of quantum systems is essential to make use of quantum properties before they degrade by decoherence. This is important for quantum-enhanced information processing, as well as for pushing quantum systems towards the boundary between quantum and classical physics. ‘Bang–bang’ control attains the ultimate speed limit by making large changes to control fields much faster than the system can respond, but is often challenging to implement experimentally. Here we demonstrate bang–bang control of a trapped-ion oscillator using nanosecond switching of the trapping potentials. We perform controlled displacements with which we realize coherent states with up to 10,000 quanta of energy. We use these displaced states to verify the form of the ion-light interaction at high excitations far outside the usual regime of operation. These methods provide new possibilities for quantum-state manipulation and generation, alongside the potential for a significant increase in operational clock speed for trapped-ion quantum information processing.
Localisation and protein-protein interactions of the Helicobacter pylori taxis sensor TlpD and their connection to metabolic functions
Authors: Behrens Wiebke , Schweinitzer Tobias , McMurry Jonathan L. , Loewen Peter C. , Buettner Falk F.R. , Menz Sarah , Josenhans Christine 
Published: April 2016

AbstractThe Helicobacter pylori energy sensor TlpD determines tactic behaviour under low energy conditions and is important in vivo. We explored protein-protein interactions of TlpD and their impact on TlpD localisation and function. Pull-down of tagged TlpD identified protein interaction partners of TlpD, which included the chemotaxis histidine kinase CheAY2, the central metabolic enzyme aconitase (AcnB) and the detoxifying enzyme catalase (KatA). We confirmed that KatA and AcnB physically interact with TlpD. While the TlpD-dependent behavioural response appeared not influenced in the interactor mutants katA and acnB in steady-state behavioural assays, acetone carboxylase subunit (acxC) mutant behaviour was altered. TlpD was localised in a bipolar subcellular pattern in media of high energy. We observed a significant change in TlpD localisation towards the cell body in cheAY2-, catalase- or aconitase-deficient bacteria or in bacteria incubated under low energy conditions, including oxidative stress or respiratory inhibition. Inactivation of tlpD resulted in an increased sensitivity to iron limitation and oxidative stress and influenced the H. pylori transcriptome. Oxidative stress, iron limitation and overexpressing the iron-sulfur repair system nifSU altered TlpD-dependent behaviour. We propose that TlpD localisation is instructed by metabolic activity and protein interactions, and its sensory activity is linked to iron-sulfur cluster integrity.
Discovery of a small-molecule binder of the oncoprotein gankyrin that modulates gankyrin activity in the cell
Authors: Chattopadhyay Anasuya , O’Connor Cornelius J. , Zhang Fengzhi , Galvagnion Celine , Galloway Warren R. J. D. , Tan Yaw Sing , Stokes Jamie E. , Rahman Taufiq , Verma Chandra , Spring David R. , Itzhaki Laura S. 
Published: April 2016

AbstractGankyrin is an ankyrin-repeat oncoprotein whose overexpression has been implicated in the development of many cancer types. Elevated gankyrin levels are linked to aberrant cellular events including enhanced degradation of tumour suppressor protein p53 and inhibition of gankyrin activity has therefore been identified as an attractive anticancer strategy. Gankyrin interacts with several partner proteins and a number of these protein-protein interactions (PPIs) are of relevance to cancer. Thus, molecules that bind the PPI interface of gankyrin and interrupt these interactions are of considerable interest. Herein, we report the discovery of a small molecule termed cjoc42 that is capable of binding to gankyrin. Cell-based experiments demonstrate that cjoc42 can inhibit gankyrin activity in a dose-dependent manner: cjoc42 prevents the decrease in p53 protein levels normally associated with high amounts of gankyrin and it restores p53-dependent transcription and sensitivity to DNA damage. The results represent the first evidence that gankyrin is a “druggable” target with small molecules.
A snail-eating snake recognizes prey handedness
Authors: Danaisawadi Patchara , Asami Takahiro , Ota Hidetoshi , Sutcharit Chirasak , Panha Somsak 
Published: April 2016

AbstractSpecialized predator-prey interactions can be a driving force for their coevolution. Southeast Asian snail-eating snakes (Pareas) have more teeth on the right mandible and specialize in predation on the clockwise-coiled (dextral) majority in shelled snails by soft-body extraction. Snails have countered the snakes’ dextral-predation by recurrent coil reversal, which generates diverse counterclockwise-coiled (sinistral) prey where Pareas snakes live. However, whether the snake predator in turn evolves any response to prey reversal is unknown. We show that Pareas carinatus living with abundant sinistrals avoids approaching or striking at a sinistral that is more difficult and costly to handle than a dextral. Whenever it strikes, however, the snake succeeds in predation by handling dextral and sinistral prey in reverse. In contrast, P. iwasakii with little access to sinistrals on small peripheral islands attempts and frequently misses capturing a given sinistral. Prey-handedness recognition should be advantageous for right-handed snail-eating snakes where frequently encountering sinistrals. Under dextral-predation by Pareas snakes, adaptive fixation of a prey population for a reversal gene instantaneously generates a sinistral species because interchiral mating is rarely possible. The novel warning, instead of sheltering, effect of sinistrality benefitting both predators and prey could further accelerate single-gene ecological speciation by left-right reversal.
Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof
Authors: Nolden T. , Pfaff F. , Nemitz S. , Freuling C. M. , Höper D. , Müller T. , Finke Stefan 
Published: April 2016

AbstractReverse genetics approaches are indispensable tools for proof of concepts in virus replication and pathogenesis. For negative strand RNA viruses (NSVs) the limited number of infectious cDNA clones represents a bottleneck as clones are often generated from cell culture adapted or attenuated viruses, with limited potential for pathogenesis research. We developed a system in which cDNA copies of complete NSV genomes were directly cloned into reverse genetics vectors by linear-to-linear RedE/T recombination. Rapid cloning of multiple rabies virus (RABV) full length genomes and identification of clones identical to field virus consensus sequence confirmed the approache’s reliability. Recombinant viruses were recovered from field virus cDNA clones. Similar growth kinetics of parental and recombinant viruses, preservation of field virus characters in cell type specific replication and virulence in the mouse model were confirmed. Reduced titers after reporter gene insertion indicated that the low level of field virus replication is affected by gene insertions. The flexibility of the strategy was demonstrated by cloning multiple copies of an orthobunyavirus L genome segment. This important step in reverse genetics technology development opens novel avenues for the analysis of virus variability combined with phenotypical characterization of recombinant viruses at a clonal level.
High mobility and high stability glassy metal-oxynitride materials and devices
Authors: Lee Eunha , Kim Taeho , Benayad Anass , Hur Jihyun , Park Gyeong-Su , Jeon Sanghun 
Published: April 2016

AbstractIn thin film technology, future semiconductor and display products with high performance, high density, large area, and ultra high definition with three-dimensional functionalities require high performance thin film transistors (TFTs) with high stability. Zinc oxynitride, a composite of zinc oxide and zinc nitride, has been conceded as a strong substitute to conventional semiconductor film such as silicon and indium gallium zinc oxide due to high mobility value. However, zinc oxynitride has been suffered from poor reproducibility due to relatively low binding energy of nitrogen with zinc, resulting in the instability of composition and its device performance. Here we performed post argon plasma process on zinc oxynitride film, forming nano-crystalline structure in stable amorphous matrix which hampers the reaction of oxygen with zinc. Therefore, material properties and device performance of zinc oxynitride are greatly enhanced, exhibiting robust compositional stability even exposure to air, uniform phase, high electron mobility, negligible fast transient charging and low noise characteristics. Furthermore, We expect high mobility and high stability zinc oxynitride customized by plasma process to be applicable to a broad range of semiconductor and display devices.
Optogenetic approaches addressing extracellular modulation of neural excitability
Authors: Ferenczi Emily A. , Vierock Johannes , Atsuta-Tsunoda Kyoko , Tsunoda Satoshi P. , Ramakrishnan Charu , Gorini Christopher , Thompson Kimberly , Lee Soo Yeun , Berndt Andre , Perry Chelsey , Minniberger Sonja , Vogt Arend , Mattis Joanna , Prakash Rohit , Delp Scott , Deisseroth Karl , Hegemann Peter 
Published: April 2016

AbstractThe extracellular ionic environment in neural tissue has the capacity to influence and be influenced by, natural bouts of neural activity. We employed optogenetic approaches to control and investigate these interactions within and between cells and across spatial scales. We began by developing a temporally precise means to study microdomain-scale interactions between extracellular protons and acid-sensing ion channels (ASICs). By coupling single-component proton-transporting optogenetic tools to ASICs to create two-component optogenetic constructs (TCOs), we found that acidification of the local extracellular membrane surface by a light-activated proton pump recruited a slow inward ASIC current, which required molecular proximity of the two components on the membrane. To elicit more global effects of activity modulation on ‘bystander’ neurons not under direct control, we used densely-expressed depolarizing (ChR2) or hyperpolarizing (eArch3.0, eNpHR3.0) tools to create a slow non-synaptic membrane current in bystander neurons, which matched the current direction seen in the directly modulated neurons. Extracellular protons played contributory role but were insufficient to explain the entire bystander effect, suggesting the recruitment of other mechanisms. Together, these findings present a new approach to the engineering of multicomponent optogenetic tools to manipulate ionic microdomains and probe the complex neuronal-extracellular space interactions that regulate neural excitability.
The resveratrol-enriched rice DJ526 boosts motor coordination and physical strength
Authors: Chung Hea-Jong , Sharma Satya Priya , Kim Hyeon-Jin , Baek So-Hyeon , Hong Seong-Tshool 
Published: April 2016

AbstractThe main objective of current genetic modifications in crops is to boost agricultural production or to develop GM crops with an improved nutrient profile by introducing a new trait to the plants. A GM crop surpassing the ability of the introduced genetic characteristics has not been developed yet. Here, we show that the resveratrol-enriched rice DJ526, a GM crop, has unexpectedly high beneficial health effects surpassing the introduced genetic characteristic of resveratrol synthetic ability. The synergistic effect of its innate and transgenic properties not only ameliorates age-related deterioration but also boosts motor coordination and physical strength during the aging process. The gene expression profiling analyses by DNA chip showed that the gene expression pattern of mice fed resveratrol-enriched rice DJ526 was very different from mice fed either resveratrol or Dongjin rice alone, respectively, modifying expression of genes related to aging regulation, cell differentiation, extracellular matrix, neurogenesis, or secretion.
Protein Repeats from First Principles
Authors: Turjanski Pablo , Parra R. Gonzalo , Espada Rocío , Becher Verónica , Ferreiro Diego U. 
Published: April 2016

AbstractSome natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family.
Structural basis for the membrane association of ankyrinG via palmitoylation
Authors: Fujiwara Yuichiro , Kondo Hiroko X. , Shirota Matsuyuki , Kobayashi Megumi , Takeshita Kohei , Nakagawa Atsushi , Okamura Yasushi , Kinoshita Kengo 
Published: April 2016

AbstractBy clustering various ion channels and transporters, ankyrin-G (AnkG) configures the membrane-excitation platforms in neurons and cardiomyocytes. AnkG itself localizes to specific areas on the plasma membrane via s-palmitoylation of Cys. However, the structural mechanism by which AnkG anchors to the membrane is not understood. In this study, we solved the crystal structures of the reduced and oxidized forms of the AnkG s-palmitoylation domain and used multiple long-term coarse-grained molecular dynamics simulations to analyze their membrane association. Here we report that the membrane anchoring of AnkG was facilitated by s-palmitoylation, defining a stable binding interface on the lipid membrane and that AnkG without s-palmitoylation also preferred to stay near the membrane but did not have a unique binding interface. This suggests that AnkG in the juxtamembrane region is primed to accept lipid modification at Cys and once that happens AnkG constitutes a rigid structural base upon which a membrane-excitation platform can be assembled.
Controlling the Adhesion of Superhydrophobic Surfaces Using Electrolyte Jet Machining Techniques
Authors: Yang Xiaolong , Liu Xin , Lu Yao , Zhou Shining , Gao Mingqian , Song Jinlong , Xu Wenji 
Published: April 2016

AbstractPatterns with controllable adhesion on superhydrophobic areas have various biomedical and chemical applications. Electrolyte jet machining technique (EJM), an electrochemical machining method, was firstly exploited in constructing dimples with various profiles on the superhydrophobic Al alloy surface using different processing parameters. Sliding angles of water droplets on those dimples firstly increased and then stabilized at a certain value with the increase of the processing time or the applied voltages of the EJM, indicating that surfaces with different adhesion force could be obtained by regulating the processing parameters. The contact angle hysteresis and the adhesion force that restricts the droplet from sliding off were investigated through experiments. The results show that the adhesion force could be well described using the classical Furmidge equation. On account of this controllable adhesion force, water droplets could either be firmly pinned to the surface, forming various patterns or slide off at designed tilting angles at specified positions on a superhydrophobic surface. Such dimples on superhydrophopbic surfaces can be applied in water harvesting, biochemical analysis and lab-on-chip devices.
Evaluating the effectiveness of localized control strategies to curtail chikungunya
Authors: Ndeffo-Mbah Martial L. , Durham David P. , Skrip Laura A. , Nsoesie Elaine O. , Brownstein John S. , Fish Durland , Galvani Alison P. 
Published: April 2016

AbstractChikungunya, a re-emerging arbovirus transmitted to humans by Aedes aegypti and Ae. albopictus mosquitoes, causes debilitating disease characterized by an acute febrile phase and chronic joint pain. Chikungunya has recently spread to the island of St. Martin and subsequently throughout the Americas. The disease is now affecting 42 countries and territories throughout the Americas. While chikungunya is mainly a tropical disease, the recent introduction and subsequent spread of Ae. albopictus into temperate regions has increased the threat of chikungunya outbreaks beyond the tropics. Given that there are currently no vaccines or treatments for chikungunya, vector control remains the primary measure to curtail transmission. To investigate the effectiveness of a containment strategy that combines disease surveillance, localized vector control and transmission reduction measures, we developed a model of chikungunya transmission dynamics within a large residential neighborhood, explicitly accounting for human and mosquito movement. Our findings indicate that prompt targeted vector control efforts combined with measures to reduce transmission from symptomatic cases to mosquitoes may be highly effective approaches for controlling outbreaks of chikungunya, provided that sufficient detection of chikungunya cases can be achieved.