bluuebunny/crossref_metadata_2025_split huggingface dataset:
Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations
Authors: Goldschmidt Felix , Regoes Roland R , Johnson David R 
Published: May 2017

Abstract
Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.
Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1
Authors: Ou Xiuyuan , Guan Hongxin , Qin Bo , Mu Zhixia , Wojdyla Justyna A. , Wang Meitian , Dominguez Samuel R. , Qian Zhaohui , Cui Sheng 
Published: May 2017

AbstractHuman coronavirus (CoV) HKU1 is a pathogen causing acute respiratory illnesses and so far little is known about its biology. HKU1 virus uses its S1 subunit C-terminal domain (CTD) and not the N-terminal domain like other lineage A β-CoVs to bind to its yet unknown human receptor. Here we present the crystal structure of HKU1 CTD at 1.9 Å resolution. The structure consists of three subdomains: core, insertion and subdomain-1 (SD-1). While the structure of the core and SD-1 subdomains of HKU1 are highly similar to those of other β-CoVs, the insertion subdomain adopts a novel fold, which is largely invisible in the cryo-EM structure of the HKU1 S trimer. We identify five residues in the insertion subdomain that are critical for binding of neutralizing antibodies and two residues essential for receptor binding. Our study contributes to a better understanding of entry, immunity and evolution of CoV S proteins.
Molecular basis for PrimPol recruitment to replication forks by RPA
Authors: Guilliam Thomas A. , Brissett Nigel C. , Ehlinger Aaron , Keen Benjamin A. , Kolesar Peter , Taylor Elaine M. , Bailey Laura J. , Lindsay Howard D. , Chazin Walter J. , Doherty Aidan J. 
Published: May 2017

AbstractDNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multifunctional replicative enzyme called primase–polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA. Using biophysical and crystallographic approaches, we identify that PrimPol possesses two RPA-binding motifs and ascertained the key residues required for these interactions. We demonstrate that one of these motifs is critical for PrimPol’s recruitment to stalled replication forks in vivo. In addition, biochemical analysis reveals that RPA serves to stimulate the primase activity of PrimPol. Together, these findings provide significant molecular insights into PrimPol’s mode of recruitment to stalled forks to facilitate repriming and restart.
Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus
Authors: Kotecha Abhay , Wang Quan , Dong Xianchi , Ilca Serban L. , Ondiviela Marina , Zihe Rao , Seago Julian , Charleston Bryan , Fry Elizabeth E. , Abrescia Nicola G. A. , Springer Timothy A. , Huiskonen Juha T. , Stuart David I. 
Published: May 2017

AbstractFoot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine–glycine–aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role.
Covalently linked dengue virus envelope glycoprotein dimers reduce exposure of the immunodominant fusion loop epitope
Authors: Rouvinski Alexander , Dejnirattisai Wanwisa , Guardado-Calvo Pablo , Vaney Marie-Christine , Sharma Arvind , Duquerroy Stéphane , Supasa Piyada , Wongwiwat Wiyada , Haouz Ahmed , Barba-Spaeth Giovanna , Mongkolsapaya Juthathip , Rey Félix A. , Screaton Gavin R. 
Published: May 2017

AbstractA problem in the search for an efficient vaccine against dengue virus is the immunodominance of the fusion loop epitope (FLE), a segment of the envelope protein E that is buried at the interface of the E dimers coating mature viral particles. Anti-FLE antibodies are broadly cross-reactive but poorly neutralizing, displaying a strong infection enhancing potential. FLE exposure takes place via dynamic ‘breathing’ of E dimers at the virion surface. In contrast, antibodies targeting the E dimer epitope (EDE), readily exposed at the E dimer interface over the region of the conserved fusion loop, are very potent and broadly neutralizing. We here engineer E dimers locked by inter-subunit disulfide bonds, and show by X-ray crystallography and by binding to a panel of human antibodies that these engineered dimers do not expose the FLE, while retaining the EDE exposure. These locked dimers are strong immunogen candidates for a next-generation vaccine.
Engaging and disengaging recurrent inhibition coincides with sensing and unsensing of a sensory stimulus
Authors: Saha Debajit , Sun Wensheng , Li Chao , Nizampatnam Srinath , Padovano William , Chen Zhengdao , Chen Alex , Altan Ege , Lo Ray , Barbour Dennis L. , Raman Baranidharan 
Published: May 2017

AbstractEven simple sensory stimuli evoke neural responses that are dynamic and complex. Are the temporally patterned neural activities important for controlling the behavioral output? Here, we investigated this issue. Our results reveal that in the insect antennal lobe, due to circuit interactions, distinct neural ensembles are activated during and immediately following the termination of every odorant. Such non-overlapping response patterns are not observed even when the stimulus intensity or identities were changed. In addition, we find that ON and OFF ensemble neural activities differ in their ability to recruit recurrent inhibition, entrain field-potential oscillations and more importantly in their relevance to behaviour (initiate versus reset conditioned responses). Notably, we find that a strikingly similar strategy is also used for encoding sound onsets and offsets in the marmoset auditory cortex. In sum, our results suggest a general approach where recurrent inhibition is associated with stimulus ‘recognition’ and ‘derecognition’.
Pseudoexfoliation syndrome-associated genetic variants affect transcription factor binding and alternative splicing of LOXL1
Authors: Pasutto Francesca , Zenkel Matthias , Hoja Ursula , Berner Daniel , Uebe Steffen , Ferrazzi Fulvia , Schödel Johannes , Liravi Panah , Ozaki Mineo , Paoli Daniela , Frezzotti Paolo , Mizoguchi Takanori , Nakano Satoko , Kubota Toshiaki , Manabe Shinichi , Salvi Erika , Manunta Paolo , Cusi Daniele , Gieger Christian , Wichmann Heinz-Erich , Aung Tin , Khor Chiea Chuen , Kruse Friedrich E. , Reis André , Schlötzer-Schrehardt Ursula 
Published: May 2017

AbstractAlthough lysyl oxidase-like 1 (LOXL1) is known as the principal genetic risk factor for pseudoexfoliation (PEX) syndrome, a major cause of glaucoma and cardiovascular complications, no functional variants have been identified to date. Here, we conduct a genome-wide association scan on 771 German PEX patients and 1,350 controls, followed by independent testing of associated variants in Italian and Japanese data sets. We focus on a 3.5-kb four-component polymorphic locus positioned spanning introns 1 and 2 of LOXL1 with enhancer-like chromatin features. We find that the rs11638944:C>G transversion exerts a cis-acting effect on the expression levels of LOXL1, mediated by differential binding of the transcription factor RXRα (retinoid X receptor alpha) and by modulating alternative splicing of LOXL1, eventually leading to reduced levels of LOXL1 mRNA in cells and tissues of risk allele carriers. These findings uncover a functional mechanism by which common noncoding variants influence LOXL1 expression.
Top predators constrain mesopredator distributions
Authors: Newsome Thomas M. , Greenville Aaron C. , Ćirović Duško , Dickman Christopher R. , Johnson Chris N. , Krofel Miha , Letnic Mike , Ripple William J. , Ritchie Euan G. , Stoyanov Stoyan , Wirsing Aaron J. 
Published: May 2017

AbstractTop predators can suppress mesopredators by killing them, competing for resources and instilling fear, but it is unclear how suppression of mesopredators varies with the distribution and abundance of top predators at large spatial scales and among different ecological contexts. We suggest that suppression of mesopredators will be strongest where top predators occur at high densities over large areas. These conditions are more likely to occur in the core than on the margins of top predator ranges. We propose the Enemy Constraint Hypothesis, which predicts weakened top-down effects on mesopredators towards the edge of top predators’ ranges. Using bounty data from North America, Europe and Australia we show that the effects of top predators on mesopredators increase from the margin towards the core of their ranges, as predicted. Continuing global contraction of top predator ranges could promote further release of mesopredator populations, altering ecosystem structure and contributing to biodiversity loss.
An engineered high affinity Fbs1 carbohydrate binding protein for selective capture of N-glycans and N-glycopeptides
Authors: Chen Minyong , Shi Xiaofeng , Duke Rebecca M. , Ruse Cristian I. , Dai Nan , Taron Christopher H. , Samuelson James C. 
Published: May 2017

AbstractA method for selective and comprehensive enrichment of N-linked glycopeptides was developed to facilitate detection of micro-heterogeneity of N-glycosylation. The method takes advantage of the inherent properties of Fbs1, which functions within the ubiquitin-mediated degradation system to recognize the common core pentasaccharide motif (Man3GlcNAc2) of N-linked glycoproteins. We show that Fbs1 is able to bind diverse types of N-linked glycomolecules; however, wild-type Fbs1 preferentially binds high-mannose-containing glycans. We identified Fbs1 variants through mutagenesis and plasmid display selection, which possess higher affinity and improved recovery of complex N-glycomolecules. In particular, we demonstrate that the Fbs1 GYR variant may be employed for substantially unbiased enrichment of N-linked glycopeptides from human serum. Most importantly, this highly efficient N-glycopeptide enrichment method enables the simultaneous determination of N-glycan composition and N-glycosites with a deeper coverage (compared to lectin enrichment) and improves large-scale N-glycoproteomics studies due to greatly reduced sample complexity.
Electronic evidence of temperature-induced Lifshitz transition and topological nature in ZrTe5
Authors: Zhang Yan , Wang Chenlu , Yu Li , Liu Guodong , Liang Aiji , Huang Jianwei , Nie Simin , Sun Xuan , Zhang Yuxiao , Shen Bing , Liu Jing , Weng Hongming , Zhao Lingxiao , Chen Genfu , Jia Xiaowen , Hu Cheng , Ding Ying , Zhao Wenjuan , Gao Qiang , Li Cong , He Shaolong , Zhao Lin , Zhang Fengfeng , Zhang Shenjin , Yang Feng , Wang Zhimin , Peng Qinjun , Dai Xi , Fang Zhong , Xu Zuyan , Chen Chuangtian , Zhou X. J. 
Published: May 2017

AbstractThe topological materials have attracted much attention for their unique electronic structure and peculiar physical properties. ZrTe5 has host a long-standing puzzle on its anomalous transport properties manifested by its unusual resistivity peak and the reversal of the charge carrier type. It is also predicted that single-layer ZrTe5 is a two-dimensional topological insulator and there is possibly a topological phase transition in bulk ZrTe5. Here we report high-resolution laser-based angle-resolved photoemission measurements on the electronic structure and its detailed temperature evolution of ZrTe5. Our results provide direct electronic evidence on the temperature-induced Lifshitz transition, which gives a natural understanding on underlying origin of the resistivity anomaly in ZrTe5. In addition, we observe one-dimensional-like electronic features from the edges of the cracked ZrTe5 samples. Our observations indicate that ZrTe5 is a weak topological insulator and it exhibits a tendency to become a strong topological insulator when the layer distance is reduced.
Structural water engaged disordered vanadium oxide nanosheets for high capacity aqueous potassium-ion storage
Authors: Charles Daniel Scott , Feygenson Mikhail , Page Katharine , Neuefeind Joerg , Xu Wenqian , Teng Xiaowei 
Published: May 2017

AbstractAqueous electrochemical energy storage devices using potassium-ions as charge carriers are attractive due to their superior safety, lower cost and excellent transport properties compared to other alkali ions. However, the accommodation of potassium-ions with satisfactory capacity and cyclability is difficult because the large ionic radius of potassium-ions causes structural distortion and instabilities even in layered electrodes. Here we report that water induces structural rearrangements of the vanadium-oxygen octahedra and enhances stability of the highly disordered potassium-intercalated vanadium oxide nanosheets. The vanadium oxide nanosheets engaged by structural water achieves high capacity (183 mAh g−1 in half-cells at a scan rate of 5 mV s−1, corresponding to 0.89 charge per vanadium) and excellent cyclability (62.5 mAh g−1 in full cells after 5,000 cycles at 10 C). The promotional effects of structural water on the disordered vanadium oxide nanosheets will contribute to the exploration of disordered structures from earth-abundant elements for electrochemical energy storage.
Long-term mutual phase locking of picosecond pulse pairs generated by a semiconductor nanowire laser
Authors: Mayer B. , Regler A. , Sterzl S. , Stettner T. , Koblmüller G. , Kaniber M. , Lingnau B. , Lüdge K. , Finley J. J. 
Published: May 2017

AbstractThe ability to generate phase-stabilized trains of ultrafast laser pulses by mode-locking underpins photonics research in fields, such as precision metrology and spectroscopy. However, the complexity of conventional mode-locked laser systems has hindered their realization at the nanoscale. Here we demonstrate that GaAs-AlGaAs nanowire lasers are capable of emitting pairs of phase-locked picosecond laser pulses with a repetition frequency up to 200 GHz when subject to incoherent pulsed optical excitation. By probing the two-pulse interference spectra, we show that pulse pairs remain mutually coherent over timescales extending to 30 ps, much longer than the emitted laser pulse duration (≤3 ps). Simulations performed by solving the optical Bloch equations produce good quantitative agreement with experiments, revealing how the phase information is stored in the gain medium close to transparency. Our results open the way to phase locking of nanowires integrated onto photonic circuits, optical injection locking and applications, such as on-chip Ramsey comb spectroscopy.
Structural basis for perception of diverse chemical substances by T1r taste receptors
Authors: Nuemket Nipawan , Yasui Norihisa , Kusakabe Yuko , Nomura Yukiyo , Atsumi Nanako , Akiyama Shuji , Nango Eriko , Kato Yukinari , Kaneko Mika K. , Takagi Junichi , Hosotani Maiko , Yamashita Atsuko 
Published: May 2017

AbstractThe taste receptor type 1 (T1r) family perceives ‘palatable’ tastes. These receptors function as T1r2-T1r3 and T1r1-T1r3 heterodimers to recognize a wide array of sweet and umami (savory) tastes in sugars and amino acids. Nonetheless, it is unclear how diverse tastes are recognized by so few receptors. Here we present crystal structures of the extracellular ligand-binding domains (LBDs), the taste recognition regions of the fish T1r2-T1r3 heterodimer, bound to different amino acids. The ligand-binding pocket in T1r2LBD is rich in aromatic residues, spacious and accommodates hydrated percepts. Biophysical studies show that this binding site is characterized by a broad yet discriminating chemical recognition, contributing for the particular trait of taste perception. In contrast, the analogous pocket in T1r3LBD is occupied by a rather loosely bound amino acid, suggesting that the T1r3 has an auxiliary role. Overall, we provide a structural basis for understanding the chemical perception of taste receptors.
Synergistic effects of influenza and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) can be eliminated by the use of influenza therapeutics: experimental evidence for the multi-hit hypothesis
Authors: Sadasivan Shankar , Sharp Bridgett , Schultz-Cherry Stacey , Smeyne Richard Jay 
Published: May 2017

AbstractCentral Nervous System inflammation has been implicated in neurodegenerative disorders including Parkinson’s disease (Ransohoff, Science 353: 777–783, 2016; Kannarkat et al. J. Parkinsons Dis. 3: 493–514, 2013). Here, we examined if the H1N1 influenza virus (Studahl et al. Drugs 73: 131–158, 2013) could synergize with the parkinsonian toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (Jackson-Lewis et al. in Mark LeDoux (ed) Movement Disorders: Genetics and Models: 287–306, Elsevier, 2015) to induce a greater microglial activation and loss of substantia nigra pars compacta dopaminergic neurons than either insult alone. H1N1-infected animals administered 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine exhibit a 20% greater loss of substantia nigra pars compacta dopaminergic neurons than occurs from the additive effects of H1N1 or 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine alone (p < 0.001). No synergistic effects were found in microglial activation. The synergistic dopaminergic neuron loss is eliminated by influenza vaccination or treatment with oseltamivir carboxylate. This work shows that multiple insults can induce synergistic effects; and even these small changes can be significant as it might allow one to cross a phenotypic disease threshold that would not occur from individual non-interacting exposures. Our observations also have important implications for public health, providing impetus for influenza vaccination or prompt treatment with anti-viral medications upon influenza diagnosis.
Combined magnetron sputtering and pulsed laser deposition of TiO
2
and BFCO thin films
Authors: Benetti D. , Nouar R. , Nechache R. , Pepin H. , Sarkissian A. , Rosei F. , MacLeod J. M. 
Published: May 2017

AbstractWe report the successful demonstration of a hybrid system that combines pulsed laser deposition (PLD) and magnetron sputtering (MS) to deposit high quality thin films. The PLD and MS simultaneously use the same target, leading to an enhanced deposition rate. The performance of this technique is demonstrated through the deposition of titanium dioxide and bismuth-based perovskite oxide Bi2FeCrO6 (BFCO) thin films on Si(100) and LaAlO3 (LAO) (100). These specific oxides were chosen due to their functionalities, such as multiferroic and photovoltaic properties (BFCO) and photocatalysis (TiO2). We compare films deposited by conventional PLD, MS and PLD combined with MS, and show that under all conditions the latter technique offers an increased deposition rate (+50%) and produces films denser (+20%) than those produced by MS or PLD alone, and without the large clusters found in the PLD-deposited films. Under optimized conditions, the hybrid technique produces films that are two times smoother than either technique alone.
Metabolomics biomarkers to predict acamprosate treatment response in alcohol-dependent subjects
Authors: Hinton David J. , Vázquez Marely Santiago , Geske Jennifer R. , Hitschfeld Mario J. , Ho Ada M. C. , Karpyak Victor M. , Biernacka Joanna M. , Choi Doo-Sup 
Published: May 2017

AbstractPrecision medicine for alcohol use disorder (AUD) allows optimal treatment of the right patient with the right drug at the right time. Here, we generated multivariable models incorporating clinical information and serum metabolite levels to predict acamprosate treatment response. The sample of 120 patients was randomly split into a training set (n = 80) and test set (n = 40) five independent times. Treatment response was defined as complete abstinence (no alcohol consumption during 3 months of acamprosate treatment) while nonresponse was defined as any alcohol consumption during this period. In each of the five training sets, we built a predictive model using a least absolute shrinkage and section operator (LASSO) penalized selection method and then evaluated the predictive performance of each model in the corresponding test set. The models predicted acamprosate treatment response with a mean sensitivity and specificity in the test sets of 0.83 and 0.31, respectively, suggesting our model performed well at predicting responders, but not non-responders (i.e. many non-responders were predicted to respond). Studies with larger sample sizes and additional biomarkers will expand the clinical utility of predictive algorithms for pharmaceutical response in AUD.