bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery
Authors: Jaroentomeechai Thapakorn , Stark Jessica C. , Natarajan Aravind , Glasscock Cameron J. , Yates Laura E. , Hsu Karen J. , Mrksich Milan , Jewett Michael C. , DeLisa Matthew P. 
Published: July 2018

AbstractThe emerging discipline of bacterial glycoengineering has made it possible to produce designer glycans and glycoconjugates for use as vaccines and therapeutics. Unfortunately, cell-based production of homogeneous glycoproteins remains a significant challenge due to cell viability constraints and the inability to control glycosylation components at precise ratios in vivo. To address these challenges, we describe a novel cell-free glycoprotein synthesis (CFGpS) technology that seamlessly integrates protein biosynthesis with asparagine-linked protein glycosylation. This technology leverages a glyco-optimized Escherichia coli strain to source cell extracts that are selectively enriched with glycosylation components, including oligosaccharyltransferases (OSTs) and lipid-linked oligosaccharides (LLOs). The resulting extracts enable a one-pot reaction scheme for efficient and site-specific glycosylation of target proteins. The CFGpS platform is highly modular, allowing the use of multiple distinct OSTs and structurally diverse LLOs. As such, we anticipate CFGpS will facilitate fundamental understanding in glycoscience and make possible applications in on demand biomanufacturing of glycoproteins.
Collapse and rescue of cooperation in evolving dynamic networks
Authors: Akçay Erol 
Published: July 2018

AbstractThe evolutionary dynamics of social traits depend crucially on the social structure of a population. The effects of social structure on social behaviors are well-studied, but relatively little is known about how social structure itself coevolves with social traits. Here, I study such coevolution with a simple yet realistic model of within-group social structure where social connections are either inherited from a parent or made randomly. I show that cooperation evolves when individuals make few random connections, but the presence of cooperation selects for increased rates of random connections, which leads to its collapse. Inherent costs of social connections can prevent this negative feedback, but these costs can negate some or all of the aggregate benefits of cooperation. Exogenously maintained social inheritance can mitigate the latter problem and allow cooperation to increase the average fitness of a population. These results illustrate how coevolutionary dynamics can constrain the long-term persistence of cooperation.
Characterization of a ripening-related transcription factor FcNAC1 from Fragaria chiloensis fruit
Authors: Carrasco-Orellana C. , Stappung Y. , Mendez-Yañez A. , Allan A. C. , Espley R. V. , Plunkett B. J. , Moya-Leon M. A. , Herrera R. 
Published: July 2018

AbstractFragaria chiloensis is a strawberry endemic from Chile with attractive white-pink fruit, pleasant aroma and taste. However, this fruit has a limited post-harvest period due to fast softening. Several transcription factors (TFs) are involved in the regulation of fruit ripening, and members of the NAC family have been implicated in cell wall remodeling. FcNAC1 was isolated from F. chiloensis fruit, coding a protein of 332 amino acid residues and displaying a characteristic NAC domain at the N terminus. FcNAC1 protein showed nuclear localization. An increase in transcript level was observed during ripening. A sequence of 1488 bp of FcNAC1 promoter was obtained. In silico analysis identified cis elements able to respond to some hormones and Secondary wall NAC binding elements (SNBE), and responding to auxin and ABA. A structural model of FcNAC1 provided evidence for interaction with DNA sequences containing SNBE, while a dual luciferase assay confirmed the transcriptional activation by FcNAC1 of the promoter of FcPL, a gene involved in cell wall remodeling in F. chiloensis fruit. The results suggest the participation of FcNAC1 during ripening development of strawberry fruit, by regulating pectin metabolism during softening.
Structural basis for cross-reactivity and conformation fluctuation of the major beech pollen allergen Fag s 1
Authors: Moraes Adolfo H. , Asam Claudia , Almeida Fabio C. L. , Wallner Michael , Ferreira Fatima , Valente Ana Paula 
Published: July 2018

AbstractFag s 1 is a member of the Pathogen Related protein family 10 (PR-10) and can elicit cross-reaction with IgE antibodies produced against the birch pollen allergen Bet v 1. The Nuclear Magnetic Resonance (NMR) structure of Fag s 1 is presented along with its dynamic properties. It shares 66% identity with Bet v 1 and exhibits the expected three α-helices and seven β-sheets arranged as a semi-beta barrel and exposing the residues mapped as the Bet v 1 IgE epitope. The structural dynamics of Fag s 1 were monitored on the fast and intermediate timescales, using relaxation rates. The complex dynamics of Fag s 1 are closely related to the internal cavity, and they modulate IgE and ligand binding.
First data of Neandertal bird and carnivore exploitation in the Cantabrian Region (Axlor; Barandiaran excavations; Dima, Biscay, Northern Iberian Peninsula)
Authors: Gómez-Olivencia Asier , Sala Nohemi , Núñez-Lahuerta Carmen , Sanchis Alfred , Arlegi Mikel , Rios-Garaizar Joseba 
Published: July 2018

AbstractNeandertals were top predators who basically relied on middle- to large-sized ungulates for dietary purposes, but there is growing evidence that supports their consumption of plants, leporids, tortoises, marine resources, carnivores and birds. The Iberian Peninsula has provided the most abundant record of bird exploitation for meat in Europe, starting in the Middle Pleistocene. However, the bird and carnivore exploitation record was hitherto limited to the Mediterranean area of the Iberian Peninsula. Here we present the first evidence of bird and carnivore exploitation by Neandertals in the Cantabrian region. We have found cut-marks in two golden eagles, one raven, one wolf and one lynx remain from the Mousterian levels of Axlor. The obtaining of meat was likely the primary purpose of the cut-marks on the golden eagle and lynx remains. Corvids, raptors, felids and canids in Axlor could have likely acted as commensals of the Neandertals, scavenging upon the carcasses left behind by these hunter-gatherers. This could have brought them closer to Neandertal groups who could have preyed upon them. These new results provide additional information on their dietary scope and indicate a more complex interaction between Neandertals and their environment.
Distinct Aqueous Humour Cytokine Profiles of Patients with Pachychoroid Neovasculopathy and Neovascular Age-related Macular Degeneration
Authors: Terao Nobuhiro , Koizumi Hideki , Kojima Kentaro , Yamagishi Tetsuya , Yamamoto Yuji , Yoshii Kengo , Kitazawa Koji , Hiraga Asako , Toda Munetoyo , Kinoshita Shigeru , Sotozono Chie , Hamuro Junji 
Published: July 2018

AbstractThis study investigated the pathophysiological features of pachychoroid neovasculopathy (PNV) and neovascular age-related macular degeneration (nAMD) by analysing and comparing cytokine profiles in aqueous humour (AH) collected from 18 PNV, 18 nAMD and 11 control patients. Responses to intravitreal injection of aflibercept were also analysed in the PNV and nAMD groups. In the PNV group, vascular endothelial growth factor (VEGF)-A was significantly lower than in the nAMD group (p = 0.03) but was almost identical to that in the control group (p = 0.86). The nAMD group showed positive correlations between interleukin (IL)-6 and IL-8 (r = 0.78, p < 0.001), IL-6 and monocyte chemoattractant protein (MCP)-1 (r = 0.68, p = 0.002) and IL-8 and MCP-1 (r = 0.68, p = 0.002). In the nAMD group, eyes with dry maculae one month after the first aflibercept injection showed significantly lower VEGF-A and placental growth factor (PlGF) at baseline than those with wet maculae (p = 0.02 for both). However, there was no significant difference between dry and wet maculae in the PNV group. The results suggest that angiogenic factors and proinflammatory cytokines may play the distinct roles in the pathogenesis of PNV and nAMD.
Angelica gigas Nakai and Decursin Downregulate Myc Expression to Promote Cell Death in B-cell Lymphoma
Authors: Kim Eungyoung , Nam Jehyun , Chang Woochul , Zulfugarov Ismayil S. , Okhlopkova Zhanna M. , Olennikov Daniil , Chirikova Nadezhda K. , Kim Sang-Woo 
Published: July 2018

AbstractAngelica gigas Nakai (AGN) is an oriental traditional medicine to treat anemia, dysmenorrhea, and migraine. However, its anti-lymphoma effect is yet to be tested. Here, we demonstrated that AGN and its major component decursin target Myc to suppress lymphomagenesis in vitro and in vivo. AGN inhibited cell viability in multiple B lymphoma cells, while sparing normal splenocytes and bone marrow cells. Increased cleaved PARP level and caspase 3/7 activity and the repression of survival-promoting AKT/mTOR and MAPK pathways downstream of BCR, were responsible for the pro-apoptotic effects of AGN. We found that Myc, a prominent downstream target of these signaling pathways, contributes to AGN-induced cell death. Moreover, co-treatment with AGN and a Myc inhibitor, JQ1 or 10058-F4 yielded synergistic cytotoxic activities against cancer cells with markedly reduced Myc expression. AGN downregulated Myc expression and suppressed tumorigenesis in Eμ-myc transgenic mice. The proapoptotic activities of AGN were recapitulated by decursin, indicating that the anti-tumor effect of AGN was mainly caused by decursin. These findings suggest that AGN and decursin possess potent anti-lymphoma activity, and combination therapies with AGN/decursin and a Myc inhibitor to target Myc more efficiently could be a valuable avenue to explore in the treatment of B-cell lymphoma.
Effect of ABCB1 genetic polymorphisms on the transport of rivaroxaban in HEK293 recombinant cell lines
Authors: Sennesael Anne-Laure , Panin Nadtha , Vancraeynest Christelle , Pochet Lionel , Spinewine Anne , Haufroid Vincent , Elens Laure 
Published: July 2018

AbstractDirect oral anticoagulants (DOAC) are substrates for the ABCB1 transporter (also called P-glycoprotein), an active efflux pump. ABCB1 polymorphisms have been previously reported to influence the pharmacokinetics of several drugs such as immunosuppressants and tyrosine kinase inhibitors. Recently, in vivo studies have suggested that genetic variants might contribute to the inter-individual variability in DOAC plasma concentrations. Therefore, we evaluated the in vitro effect of the most common coding ABCB1 single nucleotide polymorphisms (SNP), 1236 C > T-2677G > T-3435C > T, and the coding ABCB1 1199 G > A SNP on the transport activity towards rivaroxaban. HEK293 cells were transfected to overexpress the ABCB1 wild-type (1236C-2677G-3435C, 1199 G) or variant proteins (1236C-2677G-3435T, 1236T-2677T-3435T or 1199 A). ABCB1 expression decreased the intracellular accumulation of rivaroxaban, when compared to control cells. This confirms the involvement of ABCB1 in the active transport of rivaroxaban. However, the ABCB1 1236 C > T-2677G > T-3435C > T and 1199 G > A SNPs had no significant influence on the intracellular accumulation of rivaroxaban when compared to the wild-type protein. These results suggest that the ABCB1 coding SNPs investigated in the present study are unlikely to contribute to the inter-individual variability in rivaroxaban plasma concentrations.
Effects of gadolinium on cardiac mechanosensitivity in whole isolated swine hearts
Authors: Zhang Hanyu , Walcott Gregory P. , Rogers Jack M. 
Published: July 2018

AbstractMechanical stimulation can elicit electrical activation of the heart. This mechanosensitivity can start life-threatening arrhythmias (commotio cordis) or terminate them (precordial thump). Mechanosensitivity may also be involved in arrhythmogenesis in other settings. Stretch-activated ion channels (SACs) are thought to be important in mechanosensitivity and a number of agents that block them have been identified. Such agents could potentially be used as tools in experimental investigation of mechanosensitivity. However, studies using them in intact-heart preparations have yielded inconsistent results. In the present study, we used isolated, perfused hearts from 25–35 kg pigs and a computer-controlled device that repeatably delivered focal mechanical stimuli. The concentration-dependent ability of the SAC blocker gadolinium to suppress mechanical activation was assessed by the success rate of mechanical stimulation and by the delay between successful mechanical stimulation and electrical activation. In six hearts, perfusate was recirculated. In an additional six hearts, perfusate was not recirculated to prevent gadolinium from forming complexes with metabolic waste and possibly precipitating. Gadolinium did not suppress mechanically-induced activation. Although gadolinium has been shown to be an effective SAC blocker in isolated cells, using it to probe the role of mechanical stimulation in whole heart preparations should be done with great caution.
Targeting a Reticulocyte Binding Protein and Duffy Binding Protein to Inhibit Reticulocyte Invasion by Plasmodium vivax
Authors: Gupta Sonal , Singh Shailja , Popovici Jean , Roesch Camille , Shakri Ahmed Rushdi , Guillotte-Blisnick Micheline , Huon Christèle , Menard Didier , Chitnis Chetan E. 
Published: July 2018

AbstractPlasmodium vivax merozoite invasion is restricted to Duffy positive reticulocytes. Merozoite interaction with the Duffy antigen is mediated by the P. vivax Duffy binding protein (PvDBP). The receptor-binding domain of PvDBP maps to an N-terminal cysteine-rich region referred to as region II (PvDBPII). In addition, a family of P. vivax reticulocyte binding proteins (PvRBPs) mediates interactions with reticulocyte receptors. The receptor binding domain of P. vivax reticulocyte binding protein 1a (PvRBP1a) maps to a 30 kD region (PvRBP1a30). Antibodies raised against recombinant PvRBP1a30 and PvDBPII recognize the native P. vivax antigens and inhibit their binding to host receptors. Rabbit IgG purified from sera raised against PvRBP1a30 and PvDBPII were tested individually and in combination for inhibition of reticulocyte invasion by P. vivax field isolates. While anti-PvDBPII rabbit IgG inhibits invasion, anti-PvRBP1a30 rabbit IgG does not show significant invasion inhibitory activity. Combining antibodies against PvDBPII and PvRBP1a30 also does not increase invasion inhibitory activity. These studies suggest that although PvRBP1a mediates reticulocyte invasion by P. vivax merozoites, it may not be useful to include PvRBP1a30 in a blood stage vaccine for P. vivax malaria. In contrast, these studies validate PvDBPII as a promising blood stage vaccine candidate for P. vivax malaria.
Multi-spectral optical imaging of the spatiotemporal dynamics of ionospheric intermittent turbulence
Authors: Chian Abraham C.-L. , Abalde José R. , Miranda Rodrigo A. , Borotto Felix A. , Hysell David L. , Rempel Erico L. , Ruffolo David 
Published: July 2018

AbstractEquatorial plasma depletions have significant impact on radio wave propagation in the upper atmosphere, causing rapid fluctuations in the power of radio signals used in telecommunication and GPS navigation, thus playing a crucial role in space weather impacts. Complex structuring and self-organization of equatorial plasma depletions involving bifurcation, connection, disconnection and reconnection are the signatures of nonlinear evolution of interchange instability and secondary instabilities, responsible for the generation of coherent structures and turbulence in the ionosphere. The aims of this paper are three-fold: (1) to report the first optical imaging of reconnection of equatorial plasma depletions in the South Atlantic Magnetic Anomaly, (2) to investigate the optical imaging of equatorial ionospheric intermittent turbulence, and (3) to compare nonlinear characteristics of optical imaging of equatorial plasma depletions for two different altitudes at same times. We show that the degree of spatiotemporal complexity of ionospheric intermittent turbulence can be quantified by nonlinear studies of optical images, confirming the duality of amplitude-phase synchronization in multiscale interactions. By decomposing the analyses into North-South and East-West directions we show that the degree of non-Gaussianity, intermittency and multifractality is stronger in the North-South direction, confirming the anisotropic nature of the interchange instability. In particular, by using simultaneous observation of multi-spectral all-sky emissions from two different heights we show that the degree of non-Gaussianity and intermittency in the bottomside F-region ionosphere is stronger than the peak F-region ionosphere. Our results are confirmed by two sets of observations on the nights of 28 September 2002 and 9 November 2002.
Differences between microhabitat and broad-scale patterns of niche evolution in terrestrial salamanders
Authors: Ficetola Gentile Francesco , Lunghi Enrico , Canedoli Claudia , Padoa-Schioppa Emilio , Pennati Roberta , Manenti Raoul 
Published: July 2018

AbstractThe extent to which closely related species share similar niches remains highly debated. Ecological niches are increasingly analysed by combining distribution records with broad-scale climatic variables, but interactions between species and their environment often occur at fine scales. The idea that macroscale analyses correctly represent fine-scale processes relies on the assumption that average climatic variables are meaningful predictors of processes determining species persistence, but tests of this hypothesis are scarce. We compared broad- and fine-scale (microhabitat) approaches by analyzing the niches of European plethodontid salamanders. Both the microhabitat and the macroecological approaches identified niche differences among species, but the correspondence between micro- and macroecological niches was weak. When exploring niche evolution, the macroecological approach suggested a close relationship between niche and phylogenetic history, but this relationship did not emerge in fine-scale analyses. The apparent pattern of niche evolution emerging in broad-scale analyses likely was the by-product of related species having closely adjacent ranges. The environment actually experienced by most of animals is more heterogeneous than what is apparent from macro-scale predictors, and a better combination between macroecological and fine-grained data may be a key to obtain robust ecological generalizations.
DNA Methylome Analysis of Saturated Aliphatic Aldehydes in Pulmonary Toxicity
Authors: Cho Yoon , Song Mi-Kyung , Kim Tae Sung , Ryu Jae-Chun 
Published: July 2018

AbstractRecent studies have investigated the epigenetic effects of environmental exposure to chemicals on human health. The associations of DNA methylation, environmental exposure and human diseases have been widely demonstrated. However, the use of gene methylation patterns as a predictive biomarker for exposure to environmental toxicants is relatively poorly understood. Here, we focused on low-molecular-weight saturated aliphatic aldehydes (LSAAs), which are important environmental risk factors in humans as major indoor air pollutants. Based on DNA methylation profiling in gene promoter regions, we analysed DNA methylation profiles following exposure of A549 cells to seven LSAAs (propanal, butanal, pentanal, hexanal, heptanal, octanal, and nonanal) to identify LSAA-characterized methylated sites and target genes, as well as to investigate whether exposure to LSAAs contributes to inducing of pulmonary toxicity. Additionally, by integrating DNA methylation and mRNA expression profile analyses, we identified core anti-correlated target genes. Gene ontology analysis of these target genes revealed several key biological processes. These findings suggest that alterations in DNA methylation by exposure to LSAAs provide novel epigenetic biomarkers for risk assessments. This DNA methylation-mRNA approach also reveals potential new mechanistic insights into the epigenetic actions of pulmonary toxicity.
Classification system of the tibiofibular syndesmosis blood supply and its clinical relevance
Authors: Mróz Izabela , Bachul Piotr J. , Tomaszewski Krzysztof A. , Bereza Tomasz , Gil Krzysztof , Walocha Jerzy A. , Pasternak Artur 
Published: July 2018

AbstractDue to the lack of anatomical studies concerning complexity of the tibiofibular syndesmosis blood supply, density of blood vessels with further organization of syndesmotic vascular variations is presented in clinically relevant classification system. The material for the study was obtained from cadaveric dissections. We dissected 50 human ankles observing different types of arterial blood supply. Our classification system is based on the vascular variations of the anterior aspect of tibiofibular syndesmosis and corresponds with vascular density. According to our study the mean vascular density of tibiofibular syndesmosis is relatively low (4.4%) and depends on the type of blood supply. The highest density was observed among ankles with complete vasculature and the lowest when lateral anterior malleolar artery was absent (5.8% vs. 3.5%, respectively). Awareness of various types of tibiofibular syndesmosis arterial blood supply is essential for orthopedic surgeons who operate in the ankle region and radiologists for the anatomic evaluation of this area. Knowledge about possible variations along with relatively low density of vessels may contribute to modification of treatment approach by the increase of the recommended time of syndesmotic screw stabilization in order to prevent healing complications.
Agulhas Current properties shape microbial community diversity and potential functionality
Authors: Phoma Sandra , Vikram Surendra , Jansson Janet K. , Ansorge Isabelle J. , Cowan Don A. , Van de Peer Yves , Makhalanyane Thulani P. 
Published: July 2018

AbstractUnderstanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.