bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional insights into the interaction and targeting hub TMD0 of the polypeptide transporter TAPL
Authors: Bock Christoph , Löhr Frank , Tumulka Franz , Reichel Katrin , Würz Julia , Hummer Gerhard , Schäfer Lars , Tampé Robert , Joseph Benesh , Bernhard Frank , Dötsch Volker , Abele Rupert 
Published: October 2018

AbstractThe ATP-binding cassette transporter TAPL translocates polypeptides from the cytosol into the lysosomal lumen. TAPL can be divided into two functional units: coreTAPL, active in ATP-dependent peptide translocation, and the N-terminal membrane spanning domain, TMD0, responsible for cellular localization and interaction with the lysosomal associated membrane proteins LAMP-1 and LAMP-2. Although the structure and function of ABC transporters were intensively analyzed in the past, the knowledge about accessory membrane embedded domains is limited. Therefore, we expressed the TMD0 of TAPL via a cell-free expression system and confirmed its correct folding by NMR and interaction studies. In cell as well as cell-free expressed TMD0 forms oligomers, which were assigned as dimers by PELDOR spectroscopy and static light scattering. By NMR spectroscopy of uniformly and selectively isotope labeled TMD0 we performed a complete backbone and partial side chain assignment. Accordingly, TMD0 has a four transmembrane helix topology with a short helical segment in a lysosomal loop. The topology of TMD0 was confirmed by paramagnetic relaxation enhancement with paramagnetic stearic acid as well as by nuclear Overhauser effects with c6-DHPC and cross-peaks with water.
Retinal vascular changes and aqueous humor cytokines changes after aflibercept intravitreal injection in treatment-naïve myopic choroidal neovascularization
Authors: Di Antonio Luca , Toto Lisa , Mastropasqua Alessandra , Brescia Lorenza , Erroi Emanuele , Lamolinara Alessia , Di Nicola Marta , Mastropasqua Leonardo 
Published: October 2018

AbstractThe aim of the study was to assess retinal vascular changes using optical coherence tomography angiography (OCTA) and aqueous humour changes of vascular endothelial growth factor (VEGF) and placental growth factor (PIGF) levels in treatment-naïve myopic choroidal neovascularization (mCNV) after aflibercept intravitreal injection. To explore the correlation between clinical and laboratory parameters. Fifteen eyes of 15 patients with treatment-naïve mCNV underwent 2 intravitreal injections of aflibercept. Main outcome measures were best corrected visual acuity (BCVA), central retinal thickness (CRT) and external limiting membrane (ELM) visualization at OCT, lesion area and leakage at fluorescein angiography (FA), OCTA flow area and selected area at baseline and after the injections. Analysis of VEGF and PlGF in the aqueous humor was performed before each injection in cases and prior to cataract surgery on 10 patients as included as controls. Median BCVA increased from 0.6 to 0.3 logMAR (p < 0.001); CRT decreased from 387.5 to 267 micron (p < 0.001); FA area from 0.8 to 0.5 mm2 and OCTA area from 0.9 to 0.5 mm2 (p = 0.005). PIGF values changed from 1.8 to 1.4 pg/ml (p = 0.019) and VEGF values from 3.4 to 0.5 pg/ml (p = 0.008). A significant correlation was found after treatment between PIGF levels and BCVA (rho = 0.006) and VEGF levels and BCVA (rho = 0.018); between PlGF and CRT (rho = 0.020), PlGF and ELM visualization (rho = 0.002) and PlGF and FA leakage (rho < 0.001). Our results showed a significant reduction of mCNV area after aflibercept in both FA and OCTA measurements; an improvement of BCVA, and a reduction of VEGF and PIGF levels related to inactivity of the disease.
Molecular mechanism of substrate selectivity of the arginine-agmatine Antiporter AdiC
Authors: Krammer Eva-Maria , Gibbons Andrew , Roos Goedele , Prévost Martine 
Published: October 2018

AbstractThe arginine-agmatine antiporter (AdiC) is a component of an acid resistance system developed by enteric bacteria to resist gastric acidity. In order to avoid neutral proton antiport, the monovalent form of arginine, about as abundant as its divalent form under acidic conditions, should be selectively bound by AdiC for transport into the cytosol. In this study, we shed light on the mechanism through which AdiC distinguishes Arg+ from Arg2+ of arginine by investigating the binding of both forms in addition to that of divalent agmatine, using a combination of molecular dynamics simulations with molecular and quantum mechanics calculations. We show that AdiC indeed preferentially binds Arg+. The weaker binding of divalent compounds results mostly from their greater tendency to remain hydrated than Arg+. Our data suggests that the binding of Arg+ promotes the deprotonation of Glu208, a gating residue, which in turn reinforces its interactions with AdiC, leading to longer residence times of Arg+ in the binding site. Although the total electric charge of the ligand appears to be the determinant factor in the discrimination process, two local interactions formed with Trp293, another gating residue of the binding site, also contribute to the selection mechanism: a cation-π interaction with the guanidinium group of Arg+ and an anion-π interaction involving Glu208.
Near theoretical ultra-high magnetic performance of rare-earth nanomagnets via the synergetic combination of calcium-reduction and chemoselective dissolution
Authors: Lee Jimin , Hwang Tae-Yeon , Cho Hong-Baek , Kim Jongryoul , Choa Yong-Ho 
Published: October 2018

AbstractRare earth permanent magnets with superior magnetic performance have been generally synthesized through many chemical methods incorporating calcium thermal reduction. However, a large challenge still exists with regard to the removal of remaining reductants, byproducts, and trace impurities generated during the purifying process, which serve as inhibiting intermediates, inducing productivity and purity losses, and a reduction in magnetic properties. Nevertheless, the importance of a post-calciothermic reduction process has never been seriously investigated. Here, we introduce a novel approach for the synthesis of a highly pure samarium-cobalt (Sm-Co) rare earth nanomagnet with near theoretical ultra-high magnetic performance via consecutive calcium-assisted reduction and chemoselective dissolution. The chemoselective dissolution effect of various solution mixtures was evaluated by the purity, surface microstructure, and magnetic characteristics of the Sm-Co. As a result, NH4Cl/methanol solution mixture was only capable of selectively rinsing out impurities without damaging Sm-Co. Furthermore, treatment with NH4Cl led to substantially improved magnetic properties over 95.5% of the Ms for bulk Sm-Co. The mechanisms with regard to the enhanced phase-purity and magnetic performance were fully elucidated based on analytical results and statistical thermodynamics parameters. We further demonstrated the potential application of chemoselective dissolution to other intermetallic magnets.
Off-axis rotor in Enterococcus hirae V-ATPase visualized by Zernike phase plate single-particle cryo-electron microscopy
Authors: Tsunoda Jun , Song Chihong , Imai Fabiana Lica , Takagi Junichi , Ueno Hiroshi , Murata Takeshi , Iino Ryota , Murata Kazuyoshi 
Published: October 2018

AbstractEhV-ATPase is an ATP-driven Na+ pump in the eubacteria Enterococcus hirae (Eh). Here, we present the first entire structure of detergent-solubilized EhV-ATPase by single-particle cryo-electron microscopy (cryo-EM) using Zernike phase plate. The cryo-EM map dominantly showed one of three catalytic conformations in this rotary enzyme. To further stabilize the originally heterogeneous structure caused by the ATP hydrolysis states of the V1-ATPases, a peptide epitope tag system was adopted, in which the inserted peptide epitope sequence interfered with rotation of the central rotor by binding the Fab. As a result, the map unexpectedly showed another catalytic conformation of EhV-ATPase. Interestingly, these two conformations identified with and without Fab conversely coincided with those of the minor state 2 and the major state 1 of Thermus thermophilus V/A-ATPase, respectively. The most prominent feature in EhV-ATPase was the off-axis rotor, where the cytoplasmic V1 domain was connected to the transmembrane Vo domain through the off-axis central rotor. Furthermore, compared to the structure of ATP synthases, the larger size of the interface between the transmembrane a-subunit and c-ring of EhV-ATPase would be more advantageous for active ion pumping.
Cardiac regeneration following cryoinjury in the adult zebrafish targets a maturation-specific biomechanical remodeling program
Authors: Yu Joseph K. , Sarathchandra Padmini , Chester Adrian , Yacoub Magdi , Brand Thomas , Butcher Jonathan T. 
Published: October 2018

AbstractCardiac regeneration post-injury is a tantalizing feature of many lower vertebrates such as fishes and urodeles, but absent in adult humans. Restoration of pumping function is a key endpoint of cardiac regeneration, but very little is known about the biomechanical remodeling process. Here, we quantify and compare the evolution of cellular composition and mechanical stiffness of the zebrafish ventricular myocardium during maturation and following cryoinjury during regeneration to better understand the dynamics of biomechanical remodeling during these two processes. With increasing age, normal myocardial trabecular density and cardiomyocyte fraction increased, while non-myocyte cell fractions decreased. Cell density remained constant during maturation. Cardiomyocyte sarcomeres shortened to a minimum reached at 7.5 months of age, but lengthened with additional age. Concomitantly, ventricular wall stiffness increased up until 7.5 months before plateauing with additional age. Endothelial, myofibroblast/smooth muscle, and cardiomyocyte cell fractions were disrupted following cryoinjury, but were progressively restored to age-specific natural norms by 35 days post infarct (DPI). Infarcted myocardium stiffened immediately following cryoinjury and was a 100-fold greater than non-infarcted tissue by 3 DPI. By 14 DPI, stiffness of the infarcted myocardium had fallen below that of 0 DPI and had completely normalized by 35 DPI. Interestingly, cardiomyocyte sarcomere length increased until 14 DPI, but subsequently shortened to lengths below age-specific natural norms, indicating recovery from a volume overloaded condition. These observations are consistent with the view that regenerating myocardium requires biomechanical stimulation (e.g. strain) to rescue from a volume overloaded condition. Intriguingly, the biomechanical progression of the infarcted adult myocardial wall mirrors that of normal remodeling during aging. The biomechanical progression of the infarcted myocardium targets the values of age-specific norms despite a large divergence in initial conditions. These findings identify a novel biomechanical control of heart regeneration that may orchestrate cellular and tissue level remodeling responses.
Imaging acoustic sources through scattering media by using a correlation full-matrix filter
Authors: Rui Wei , Tao Chao , Liu Xiaojun 
Published: October 2018

AbstractIn the inhomogeneous medium, acoustic scattering is always a fundamental challenge for photoacoustic imaging. We implement a correlation full-matrix filter (CFMF) combing with a time reversal operator to improve the imaging quality of acoustic sources in complex media. The correlation full-matrix filtering process extracts the direct wave component from the detected signal and preserve all the useful information at the same time. A location factor is considered in the time reversal operator to compensate for the image distortion and false contrast caused by the limited-view detection. The numerical simulations demonstrate that the proposed approach can perform good imaging quality with the higher image signal-noise ratio and better resolution in an acoustic scattering environment. This scheme might be applied to improve the photoacoustic imaging for inhomogeneous biological tissues.
Locus Coeruleus as a vigilance centre for active inspiration and expiration in rats
Authors: Magalhães Karolyne S. , Spiller Pedro F. , da Silva Melina P. , Kuntze Luciana B. , Paton Julian F. R. , Machado Benedito H. , Moraes Davi J. A. 
Published: October 2018

AbstractAt rest, inspiration is an active process while expiration is passive. However, high chemical drive (hypercapnia or hypoxia) activates central and peripheral chemoreceptors triggering reflex increases in inspiration and active expiration. The Locus Coeruleus contains noradrenergic neurons (A6 neurons) that increase their firing frequency when exposed to hypercapnia and hypoxia. Using recently developed neuronal hyperpolarising technology in conscious rats, we tested the hypothesis that A6 neurons are a part of a vigilance centre for controlling breathing under high chemical drive and that this includes recruitment of active inspiration and expiration in readiness for flight or fight. Pharmacogenetic inhibition of A6 neurons was without effect on resting and on peripheral chemoreceptors-evoked inspiratory, expiratory and ventilatory responses. On the other hand, the number of sighs evoked by systemic hypoxia was reduced. In the absence of peripheral chemoreceptors, inhibition of A6 neurons during hypercapnia did not affect sighing, but reduced both the magnitude and incidence of active expiration, and the frequency and amplitude of inspiration. These changes reduced pulmonary ventilation. Our data indicated that A6 neurons exert a CO2-dependent modulation of expiratory drive. The data also demonstrate that A6 neurons contribute to the CO2-evoked increases in the inspiratory motor output and hypoxia-evoked sighing.
Clinical characteristics of patients with laboratory-confirmed influenza A(H1N1)pdm09 during the 2013/2014 and 2015/2016 clade 6B/6B.1/6B.2-predominant outbreaks
Authors: Hsieh Yu-Chia , Tsao Kuo-Chien , Huang Ching-Tai , Chang Kuang-Yi , Huang Yhu-Chering , Gong Yu-Nong 
Published: October 2018

AbstractA novel pandemic influenza A(H1N1)pdm09 virus emerged in 2009 globally, and it continues to circulate in humans. The National Influenza Surveillance Network in Taiwan identified five A(H1N1)pdm09-predominant seasons, representing the 2009/2010, 2010/2011, 2012/2013, 2013/2014, and 2015/2016 outbreaks from 2009 to 2016. Independently, a retrospective cohort study (which enrolled 639 infected patients during the five seasons) was conducted at Chang Gung Memorial Hospital to explore the risk factors associated with influenza A(H1N1)pdm09-related complications. A phylogenetic analysis of hemagglutinin (HA) sequences showed that the circulating A(H1N1)pdm09 virus belonged to clades 1, 2, and 8 in 2009/2010; clades 3, 4, 5, and 7 in 2010/2011; clades 7 and 6C in 2012/2013; clades 6B in 2013/2014; and 6B/6B.1/6B.2 in 2015/2016. Compared to individuals infected in non-6B/6B.1/6B.2 seasons (2009/2010, 2010/2011, and 2012/2013), those infected in 6B/6B.1/6B.2 seasons (2013/2014 and 2015/2016) were at higher risk for influenza-related complications (adjusted odds ratio [aOR]: 1.6, 95% confidence interval [CI]: 1.0–2.8), pneumonia (aOR: 1.78, 95% CI: 1.04–3.04), mechanical ventilation (aOR: 2.6, 95% CI: 1.2–5.6), and acute respiratory distress syndrome (aOR: 5.5, 95% CI: 1.9–15.9). For the increased severity of infection during the influenza A(H1N1)pdm09 clade 6B/6B.1/6B.2 seasons, aspects related to the antigenic change of A(H1N1)pdm09 virus, immune response of the host, and environmental factors required further investigation.
Sensitivity to near-future CO2 conditions in marine crabs depends on their compensatory capacities for salinity change
Authors: Whiteley Nia M. , Suckling Coleen C. , Ciotti Benjamin J. , Brown James , McCarthy Ian D. , Gimenez Luis , Hauton Chris 
Published: October 2018

AbstractMarine crabs inhabit shallow coastal/estuarine habitats particularly sensitive to climate change, and yet we know very little about the diversity of their responses to environmental change. We report the effects of a rarely studied, but increasingly prevalent, combination of environmental factors, that of near-futurepCO2(~1000 µatm) and a physiologically relevant 20% reduction in salinity. We focused on two crab species with differing abilities to cope with natural salinity change, and revealed via physiological and molecular studies that salinity had an overriding effect on ion exchange in the osmoregulating shore crab,Carcinus maenas. This species was unaffected by elevated CO2, and was able to hyper-osmoregulate and maintain haemolymph pH homeostasis for at least one year. By contrast, the commercially important edible crab,Cancer pagurus, an osmoconformer, had limited ion-transporting capacities, which were unresponsive to dilute seawater. Elevated CO2disrupted haemolymph pH homeostasis, but there was some respite in dilute seawater due to a salinity-induced metabolic alkalosis (increase in HCO3−at constantpCO2). Ultimately,Cancer paguruswas poorly equipped to compensate for change, and exposures were limited to 9 months. Failure to understand the full spectrum of species-related vulnerabilities could lead to erroneous predictions of the impacts of a changing marine climate.
Modelling Dolphin Distribution to Inform Future Spatial Conservation Decisions in a Marine Protected Area
Authors: Passadore Cecilia , Möller Luciana M. , Diaz-Aguirre Fernando , Parra Guido J. 
Published: October 2018

AbstractAs marine predators experience increasing anthropogenic pressures, there is an urgent need to understand their distribution and their drivers to inform spatial conservation planning. We used an ensemble modelling approach to investigate the spatio-temporal distribution of southern Australian bottlenose dolphins (Tursiopscf.australis) in relation to a variety of ecogeographical and anthropogenic variables in Coffin Bay, Thorny Passage Marine Park, South Australia. Further, we evaluated the overlap between current spatial management measures and important dolphin habitat. Dolphins showed no distinct seasonal shifts in distribution patterns. Models of the entire study area indicate that zones of high probability of dolphin occurrence were located mainly within the inner area of Coffin Bay. In the inner area, zones with high probability of dolphin occurrence were associated with shallow waters (2–4 m and 7–10 m) and located within 1,000 m from land and 2,500 m from oyster farms. The multi-modal response curve of depth in the models likely shows how the different dolphin communities in Coffin Bay occupy different embayments characterized by distinct depth patterns. The majority of areas of high (>0.6) probability of dolphin occurrence are outside sanctuary zones where multiple human activities are allowed. The inner area of Coffin Bay is an important area of year-round habitat suitability for dolphins. Our results can inform future spatial conservation decisions and improve protection of important dolphin habitat.
Bacterial and archaeal community structures in perennial cave ice
Authors: Itcus Corina , Pascu Madalina D. , Lavin Paris , Perşoiu Aurel , Iancu Lavinia , Purcarea Cristina 
Published: October 2018

AbstractIce entrenched microcosm represents a vast reservoir of novel species and a proxy for past climate reconstitution. Among glacial ecosystems, ice caves represent one of the scarcely investigated frozen habitats. To characterize the microbial diversity of perennial ice from karst ecosystems, Roche 454 sequencing of 16S rRNA gene amplicons from the underground ice block of Scarisoara Ice Cave (Romania) was applied. The temporal distribution of bacterial and archaeal community structures from newly formed, 400, and 900 years old ice layers was surveyed and analyzed in relation with the age and geochemical composition of the ice substrate. The microbial content of cave ice layers varied from 3.3 104up to 7.5 105cells mL−1, with 59–78% viability. Pyrosequencing generated 273,102 reads for the five triplicate ice samples, which corresponded to 3,464 operational taxonomic units (OTUs). The distribution of the bacterial phyla in the perennial cave ice varied with age, organic content, and light exposure. Proteobacteria dominated the 1 and 900 years old organic rich ice deposits, while Actinobacteria was mostly found in 900 years old ice strata, and Firmicutes was best represented in 400 years old ice. Cyanobacteria and Chlorobi representatives were identified mainly from the ice block surface samples exposed to sunlight. Archaea was observed only in older ice strata, with a high incidence of Crenarchaeota and Thaumarchaeaota in the 400 years old ice, while Euryarchaeota dominated the 900 years old ice layers, with Methanomicrobia representing the predominant taxa. A large percentage (55.7%) of 16S rRNA gene amplicons corresponded to unidentified OTUs at genus or higher taxa levels, suggesting a greater undiscovered bacterial diversity in this glacial underground habitat. The prokaryotes distribution across the cave ice block revealed the presence of 99 phylotypes specific for different ice layers, in addition to the shared microbial community. Ice geochemistry represented an important factor that explained the microbial taxa distribution in the cave ice block, while the total organic carbon content had a direct impact on the cell density of the ice microcosm. Both bacterial and archaeal community structures appeared to be affected by climate variations during the ice formation, highlighting the cave ice microbiome as a source of putative paleoclimatic biomarkers. This report constitutes the first high-throughput sequencing study of the cave ice microbiome and its distribution across the perennial underground glacier of an alpine ice cave.
Investigation on the adsorption of phosphorus in all fractions from sediment by modified maifanite
Authors: Liu Zisen , Zhang Yi , Han Fan , Yan Pan , Liu Biyun , Zhou Qiaohong , Min Fenli , He Feng , Wu Zhenbin 
Published: October 2018

AbstractSediment phosphorus (P) removal is crucial for the control of eutrophication, and the in-situ adsorption is an essential technique. In this study, modified maifanite (MMF) prepared by acidification, alkalization, salinization, calcination and combined modifications, respectively, were first applied to treat sediment P. The morphology and microstructure of MMF samples were characterized by X-ray fluorescence (XRF), Fourier transform infrared (FTIR), X-ray diffraction (XRD), scanning electron microscope (SEM) and Brunauer-Emmett-Teller (BET). Various adsorption parameters were tested, such as dosage of maifanite, time, operation pH and temperature. The adsorption mechanisms were also investigated and discussed. Results showed that CMMF-H2.5-400 (2.5 mol/L H2SO4 and calcined at 400 °C) exhibited the highest P adsorption capacity. Thus, it was selected as the in-situ adsorbent material to control the internal P loading. Under the optimal conditions of dynamic experiments, the adsorption rates of TP, IP, OP, Fe/Al-P and Ca-P by CMMF-H2.5-400 were 37.22%, 44.41%, 25.54%, 26.09% and 60.34%, respectively. The adsorption mechanisms analysis revealed that the adsorption of P onto CMMF-H2.5-400 mainly by ligand exchange. Results of this work indicated that the modification treatment could improve the adsorption capacity of maifanite, and CMMF-H2.5-400 could be further applied to eutrophication treatment.