bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping
Authors: Müller Vilhelm , Rajer Fredrika , Frykholm Karolin , Nyberg Lena K. , Quaderi Saair , Fritzsche Joachim , Kristiansson Erik , Ambjörnsson Tobias , Sandegren Linus , Westerlund Fredrik 
Published: December 2016

AbstractBacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.
Biochemical and Structural Analysis of a Novel Esterase from Caulobacter crescentus related to Penicillin-Binding Protein (PBP)
Authors: Ryu Bum Han , Ngo Tri Duc , Yoo Wanki , Lee Sojeong , Kim Boo-Young , Lee Euijoo , Kim Kyeong Kyu , Kim T. Doohun 
Published: December 2016

AbstractConsidering that the prevalence of antibiotic-resistant pathogenic bacteria is largely increasing, a thorough understanding of penicillin-binding proteins (PBPs) is of great importance and crucial significance because this enzyme family is a main target of β-lactam-based antibiotics. In this work, combining biochemical and structural analysis, we present new findings that provide novel insights into PBPs. Here, a novel PBP homologue (CcEstA) from Caulobacter crescentus CB15 was characterized using native-PAGE, mass spectrometry, gel filtration, CD spectroscopy, fluorescence, reaction kinetics, and enzyme assays toward various substrates including nitrocefin. Furthermore, the crystal structure of CcEstA was determined at a 1.9 Å resolution. Structural analyses showed that CcEstA has two domains: a large α/β domain and a small α-helix domain. A nucleophilic serine (Ser68) residue is located in a hydrophobic groove between the two domains along with other catalytic residues (Lys71 and Try157). Two large flexible loops (UL and LL) of CcEstA are proposed to be involved in the binding of incoming substrates. In conclusion, CcEstA could be described as a paralog of the group that contains PBPs and β-lactamases. Therefore, this study could provide new structural and functional insights into the understanding this protein family.
Independent control of natural killer cell responsiveness and homeostasis at steady-state by CD11c+ dendritic cells
Authors: Luu Thuy Thanh , Ganesan Sridharan , Wagner Arnika Kathleen , Sarhan Dhifaf , Meinke Stephan , Garbi Natalio , Hämmerling Günter , Alici Evren , Kärre Klas , Chambers Benedict J. , Höglund Petter , Kadri Nadir 
Published: December 2016

AbstractDuring infection and inflammation, dendritic cells (DC) provide priming signals for natural killer (NK) cells via mechanisms distinct from their antigen processing and presentation functions. The influence of DC on resting NK cells, i.e. at steady-state, is less well studied. We here demonstrate that as early as 1 day after DC depletion, NK cells in naïve mice downregulated the NKG2D receptor and showed decreased constitutive phosphorylation of AKT and mTOR. Subsequently, apoptotic NK cells appeared in the spleen concomitant with reduced NK cell numbers. At 4 days after the onset of DC depletion, increased NK cell proliferation was seen in the spleen resulting in an accumulation of Ly49 receptor-negative NK cells. In parallel, NK cell responsiveness to ITAM-mediated triggering and cytokine stimulation dropped across maturation stages, suggestive of a functional deficiency independent from the homeostatic effect. A role for IL-15 in maintaining NK cell function was supported by a gene signature analysis of NK cell from DC-depleted mice as well as by in vivo DC transfer experiments. We propose that DC, by means of IL-15 transpresentation, are required to maintain not only homeostasis, but also function, at steady-state. These processes appear to be regulated independently from each other.
The complex nature of calcium cation interactions with phospholipid bilayers
Authors: Melcrová Adéla , Pokorna Sarka , Pullanchery Saranya , Kohagen Miriam , Jurkiewicz Piotr , Hof Martin , Jungwirth Pavel , Cremer Paul S. , Cwiklik Lukasz 
Published: December 2016

AbstractUnderstanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments. To gain additional atomic-level information, the experiments are complemented by molecular simulations that utilize an accurate force field for calcium ions with scaled charges effectively accounting for electronic polarization effects. We demonstrate that lipid membranes have substantial calcium-binding capacity, with several types of binding sites present. Significantly, the binding mode depends on calcium concentration with important implications for calcium buffering, synaptic plasticity, and protein-membrane association.
Changes in urinary metabolomic profile during relapsing renal vasculitis
Authors: Al-Ani Bahjat , Fitzpatrick Martin , Al-Nuaimi Hamad , Coughlan Alice M. , Hickey Fionnuala B. , Pusey Charles D. , Savage Caroline , Benton Christopher M. , O’Brien Eóin C. , O’Toole Declan , Mok Ken H. , Young Stephen P. , Little Mark A. 
Published: December 2016

AbstractCurrent biomarkers of renal disease in systemic vasculitis lack predictive value and are insensitive to early damage. To identify novel biomarkers of renal vasculitis flare, we analysed the longitudinal urinary metabolomic profile of a rat model of anti-neutrophil cytoplasmic antibody (ANCA) vasculitis. Wistar-Kyoto (WKY) rats were immunised with human myeloperoxidase (MPO). Urine was obtained at regular intervals for 181 days, after which relapse was induced by re-challenge with MPO. Urinary metabolites were assessed in an unbiased fashion using nuclear magnetic resonance (NMR) spectroscopy, and analysed using partial least squares discriminant analysis (PLS-DA) and partial least squares regression (PLS-R). At 56 days post-immunisation, we found that rats with vasculitis had a significantly different urinary metabolite profile than control animals; the observed PLS-DA clusters dissipated between 56 and 181 days, and re-emerged with relapse. The metabolites most altered in rats with active or relapsing vasculitis were trimethylamine N-oxide (TMAO), citrate and 2-oxoglutarate. Myo-inositol was also moderately predictive. The key urine metabolites identified in rats were confirmed in a large cohort of patients using liquid chromatography–mass spectrometry (LC-MS). Hypocitraturia and elevated urinary myo-inositol remained associated with active disease, with the urine myo-inositol:citrate ratio being tightly correlated with active renal vasculitis.
Neonicotinoid-induced impairment of odour coding in the honeybee
Authors: Andrione Mara , Vallortigara Giorgio , Antolini Renzo , Haase Albrecht 
Published: December 2016

AbstractExposure to neonicotinoid pesticides is considered one of the possible causes of honeybee (Apis mellifera) population decline. At sublethal doses, these chemicals have been shown to negatively affect a number of behaviours, including performance of olfactory learning and memory, due to their interference with acetylcholine signalling in the mushroom bodies. Here we provide evidence that neonicotinoids can affect odour coding upstream of the mushroom bodies, in the first odour processing centres of the honeybee brain, i.e. the antennal lobes (ALs). In particular, we investigated the effects of imidacloprid, the most common neonicotinoid, in the AL glomeruli via in vivo two-photon calcium imaging combined with pulsed odour stimulation. Following acute imidacloprid treatment, odour-evoked calcium response amplitude in single glomeruli decreases, and at the network level the representations of different odours are no longer separated. This demonstrates that, under neonicotinoid influence, olfactory information might reach the mushroom bodies in a form that is already incorrect. Thus, some of the impairments in olfactory learning and memory caused by neonicotinoids could, in fact, arise from the disruption in odor coding and olfactory discrimination ability of the honey bees.
Plant phenolic volatiles inhibit quorum sensing in pectobacteria and reduce their virulence by potential binding to ExpI and ExpR proteins
Authors: Joshi Janak Raj , Khazanov Netaly , Senderowitz Hanoch , Burdman Saul , Lipsky Alexander , Yedidia Iris 
Published: December 2016

AbstractQuorum sensing (QS) is a population density-dependent regulatory system in bacteria that couples gene expression to cell density through accumulation of diffusible signaling molecules. Pectobacteria are causal agents of soft rot disease in a range of economically important crops. They rely on QS to coordinate their main virulence factor, production of plant cell wall degrading enzymes (PCWDEs). Plants have evolved an array of antimicrobial compounds to anticipate and cope with pathogens, of which essential oils (EOs) are widely recognized. Here, volatile EOs, carvacrol and eugenol, were shown to specifically interfere with QS, the master regulator of virulence in pectobacteria, resulting in strong inhibition of QS genes, biofilm formation and PCWDEs, thereby leading to impaired infection. Accumulation of the signal molecule N-acylhomoserine lactone declined upon treatment with EOs, suggesting direct interaction of EOs with either homoserine lactone synthase (ExpI) or with the regulatory protein (ExpR). Homology models of both proteins were constructed and docking simulations were performed to test the above hypotheses. The resulting binding modes and docking scores of carvacrol and eugenol support potential binding to ExpI/ExpR, with stronger interactions than previously known inhibitors of both proteins. The results demonstrate the potential involvement of phytochemicals in the control of Pectobacterium.
Unique nonstructural proteins of Pneumonia Virus of Mice (PVM) promote degradation of interferon (IFN) pathway components and IFN-stimulated gene proteins
Authors: Dhar Jayeeta , Barik Sailen 
Published: December 2016

AbstractPneumonia Virus of Mice (PVM) is the only virus that shares the Pneumovirus genus of the Paramyxoviridae family with Respiratory Syncytial Virus (RSV). A deadly mouse pathogen, PVM has the potential to serve as a robust animal model of RSV infection, since human RSV does not fully replicate the human pathology in mice. Like RSV, PVM also encodes two nonstructural proteins that have been implicated to suppress the IFN pathway, but surprisingly, they exhibit no sequence similarity with their RSV equivalents. The molecular mechanism of PVM NS function, therefore, remains unknown. Here, we show that recombinant PVM NS proteins degrade the mouse counterparts of the IFN pathway components. Proteasomal degradation appears to be mediated by ubiquitination promoted by PVM NS proteins. Interestingly, NS proteins of PVM lowered the levels of several ISG (IFN-stimulated gene) proteins as well. These results provide a molecular foundation for the mechanisms by which PVM efficiently subverts the IFN response of the murine cell. They also reveal that in spite of their high sequence dissimilarity, the two pneumoviral NS proteins are functionally and mechanistically similar.
G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins
Authors: Mishra Subodh Kumar , Tawani Arpita , Mishra Amit , Kumar Amit 
Published: December 2016

AbstractNucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author’s name and techniques that were used to detect their interactions. G4IPDB also provides an efficient web-based “G-quadruplex predictor tool” that searches putative G-quadruplex forming sequences simultaneously in both sense and anti-sense strands of the query nucleotide sequence and provides the predicted G score. Studying the interaction between proteins and nucleic acids forming G-quadruplex structures could be of therapeutic significance for various diseases including cancer and neurological disease, therefore, having detail information about their interactions on a single platform would be helpful for the discovery and development of novel therapeutics. G4IPDB can be routinely updated (twice in year) and freely available on http://bsbe.iiti.ac.in/bsbe/ipdb/index.php.
Sailfish migrations connect productive coastal areas in the West Atlantic Ocean
Authors: Lam Chi Hin , Galuardi Benjamin , Mendillo Anthony , Chandler Emily , Lutcavage Molly E. 
Published: December 2016

AbstractIsla Mujeres, Mexico is home to one of the most well-known aggregations of sailfish. Despite its fisheries prominence, little is known about this sailfish assemblage, or its relationship to other aggregation sites in the western Atlantic. In January 2012, April 2013 and 2014, we deployed 34 popup satellite archival tags on sailfish in order to study their behavior, population connectivity and biophysical interactions. Sailfish were monitored for up to one year, and displayed (1) predominantly shelf associated activity (2) occupancy of the Yucatán Current near Isla Mujeres for up to five months and (3) subsequent dispersals from the Yucatán to productive coastal areas in the Gulf of Mexico, the Caribbean Sea and along the South American coast. Tagged sailfish occupied a median temperature of 26.4°C (interquartile range, IQR = 2.5 °C; range = 12.3–33.3 °C) and median depth of 4.4 m (IQR = 19 m; range = 0–452 m). Diel activity was present and individuals made distinctive descents before sunrise and sunset. Tracking missions of sufficient duration (~1 year) revealed previously undetected connectivity between western Atlantic sailfish fisheries and pelagic longline catches, and highlighted how fishery independent tagging can improve understanding of sailfish migrations and behavior for assessment and management.
Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold
Authors: Pavkov-Keller Tea , Strohmeier Gernot A. , Diepold Matthias , Peeters Wilco , Smeets Natascha , Schürmann Martin , Gruber Karl , Schwab Helmut , Steiner Kerstin 
Published: December 2016

AbstractTransaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. Here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (R)-amines as sole nitrogen source. While most of the candidate proteins were clearly assigned to known subgroups of the fold IV family of PLP-dependent enzymes by sequence analysis and characterisation of their substrate specificity, some of them did not fit to any of these groups. The structure of one of these enzymes from Curtobacterium pusillum, which can convert d-amino acids and various (R)-amines with high enantioselectivity, was solved at a resolution of 2.4 Å. It shows significant differences especially in the active site compared to other transaminases of the fold IV family and thus indicates the existence of a new subgroup within this family. Although the discovered transaminases were not able to convert ketones in a reasonable time frame, overall, the enrichment-based approach was successful, as we identified two amine transaminases, which convert (R)-amines with high enantioselectivity, and can be used for a kinetic resolution of 1-phenylethylamine and analogues to obtain the (S)-amines with e.e.s >99%.
Predicting missing links in complex networks based on common neighbors and distance
Authors: Yang Jinxuan , Zhang Xiao-Dong 
Published: December 2016

AbstractThe algorithms based on common neighbors metric to predict missing links in complex networks are very popular, but most of these algorithms do not account for missing links between nodes with no common neighbors. It is not accurate enough to reconstruct networks by using these methods in some cases especially when between nodes have less common neighbors. We proposed in this paper a new algorithm based on common neighbors and distance to improve accuracy of link prediction. Our proposed algorithm makes remarkable effect in predicting the missing links between nodes with no common neighbors and performs better than most existing currently used methods for a variety of real-world networks without increasing complexity.
Anti-Hu antibodies activate enteric and sensory neurons
Authors: Li Qin , Michel Klaus , Annahazi Anita , Demir Ihsan E. , Ceyhan Güralp O. , Zeller Florian , Komorowski Lars , Stöcker Winfried , Beyak Michael J. , Grundy David , Farrugia Gianrico , De Giorgio Roberto , Schemann Michael 
Published: December 2016

AbstractIgG of type 1 anti-neuronal nuclear antibody (ANNA-1, anti-Hu) specificity is a serological marker of paraneoplastic neurological autoimmunity (including enteric/autonomic) usually related to small-cell lung carcinoma. We show here that IgG isolated from such sera and also affinity-purified anti-HuD label enteric neurons and cause an immediate spike discharge in enteric and visceral sensory neurons. Both labelling and activation of enteric neurons was prevented by preincubation with the HuD antigen. Activation of enteric neurons was inhibited by the nicotinic receptor antagonists hexamethonium and dihydro-β-erythroidine and reduced by the P2X antagonist pyridoxal phosphate-6-azo (benzene-2,4-disulfonic acid (PPADS) but not by the 5-HT3 antagonist tropisetron or the N-type Ca-channel blocker ω-Conotoxin GVIA. Ca++ imaging experiments confirmed activation of enteric neurons but not enteric glia. These findings demonstrate a direct excitatory action of ANNA-1, in particular anti-HuD, on visceral sensory and enteric neurons, which involves nicotinic and P2X receptors. The results provide evidence for a novel link between nerve activation and symptom generation in patients with antibody-mediated gut dysfunction.
Phase-to-intensity conversion of magnonic spin currents and application to the design of a majority gate
Authors: Brächer T. , Heussner F. , Pirro P. , Meyer T. , Fischer T. , Geilen M. , Heinz B. , Lägel B. , Serga A. A. , Hillebrands B. 
Published: December 2016

AbstractMagnonic spin currents in the form of spin waves and their quanta, magnons, are a promising candidate for a new generation of wave-based logic devices beyond CMOS, where information is encoded in the phase of travelling spin-wave packets. The direct readout of this phase on a chip is of vital importance to couple magnonic circuits to conventional CMOS electronics. Here, we present the conversion of the spin-wave phase into a spin-wave intensity by local non-adiabatic parallel pumping in a microstructure. This conversion takes place within the spin-wave system itself and the resulting spin-wave intensity can be conveniently transformed into a DC voltage. We also demonstrate how the phase-to-intensity conversion can be used to extract the majority information from an all-magnonic majority gate. This conversion method promises a convenient readout of the magnon phase in future magnon-based devices.
Deep sequencing of transcriptome profiling of GSTM2 knock-down in swine testis cells
Authors: Lv Yuqi , Jin Yi , Zhou Yongqiang , Jin Jianjun , Ma Zhenfa , Ren Zhuqing 
Published: December 2016

AbstractGlutathione-S-transferases mu 2 (GSTM2), a kind of important Phase II antioxidant enzyme of eukaryotes, is degraded by nonsense mediated mRNA decay due to a C27T substitution in the fifth exon of pigs. As a reproductive performance-related gene,GSTM2is involved in embryo implantation, whereas, functional deficiency ofGSTM2induces pre- or post-natal death in piglets potentially. To have some insight into the role ofGSTM2in embryo development, high throughput RNA sequencing is performed using the swine testis cells (ST) with the deletion ofGSTM2. Some embryo development-related genes are observed from a total of 242 differentially expressed genes, includingSTAT1, SRC, IL-8, DUSPfamily,CCLfamily and integrin family.GSTM2affects expression ofSRC, OPN,andSLCs. GSTM2 suppresses phosphorylation of STAT1 by binding to STAT1. In addition, as an important transcription factor,STAT1regulates expression of uterus receptive-related genes includingCCLs, IRF9, IFITs, MXs, and OAS. The present study provides evidence to molecular mechanism ofGSTM2modulating embryo development.
Magnetising inductance of multiple‐output flyback dc–dc convertor for discontinuous‐conduction mode
Authors: Ayachit Agasthya , Reatti Alberto , Kazimierczuk Marian K. 
Published: December 2016

This study presents the following: (i) detailed derivation of the expressions for the maximum value of the magnetising inductance of the ideal and lossy two‐output flyback dc–dc convertor operating in discontinuous‐conduction mode, (ii) a method to appropriately select the duty cycle for the metal–oxide–semiconductor field‐effect transistor based on the rated output dc voltages of the two stages, and (iii) a design approach for a three‐winding transformer with a gapped core used in the two‐output flyback convertor. The expressions derived and the proposed design technique can be extended to flyback convertors with more than two output stages with equal or unequal load voltages. A universal power supply (ac line adapter) employing a flyback dc–dc convertor with output voltages 15 and 32 V, supplying a rated output current of 0.563 and 0.533 A, and operating at a switching frequency of 85 kHz is designed using the proposed methodology. Simulation and experimental results are presented to validate the theoretical predictions.