julilili42/papers huggingface dataset:
Biochemical characterization of the tandem HAMP domain from Natronomonas pharaonis as an intraprotein signal transducer
2014-05-23

Available structures of HAMP domains suggest rotation as one potential mechanism in intraprotein signal transduction. It has been proposed that in poly‐ HAMP modules the signal sign is inverted with each additional HAMP . We examined signal transduction through the HAMP tandem domain from the phototaxis transducer of the halophilic archaeon N atronomonas pharaonis in membrane‐bound chimeras consisting of the E scherichia coli chemotaxis receptor for serine, T sr, as an input and the mycobacterial adenylyl cyclase R v3645 as an output domain, i.e. the basic chimera was ‘ T sr– N p HAMP tandem– R v3645 cyclase’. Neither of the N p HAMP units alone nor the N p HAMP tandem transduced a serine signal. After five targeted point mutations in the first α‐helix of N p HAMP 1 , the non‐functional N p HAMP modules combined into a functional HAMP tandem. 1 m m serine significantly inhibited cyclase activity (−35%; IC 50 = 30 μ m ) in disagreement with the structure‐based predictions. Surprisingly, replacement of N p AS 1 1 in the tandem by the respective AS 1 from HAMP T sr resulted in signal inversion, i.e. serine activated cyclase (+129%; EC 50 = 10 μ m ). Examination of 48 mutants of AS 1 1 in the HAMP tandem including two residues of a putative N ‐terminal control cable identified five residues in N p AS 1 1 which probably define different ground states of the output domain and thus affect the sign of signal output. The data question the predicted HAMP rotation as the predominant mechanism of intraprotein signal transduction and point to as yet unrecognized conformational motions of HAMP domains in intraprotein signaling.
Public health impact and cost-effectiveness of intranasal live attenuated influenza vaccination of children in Germany
2014-05-24

In 2011, intranasally administered live attenuated influenza vaccine (LAIV) was approved in the EU for prophylaxis of seasonal influenza in 2-17-year-old children. Our objective was to estimate the potential epidemiological impact and cost-effectiveness of an LAIV-based extension of the influenza vaccination programme to healthy children in Germany. An age-structured dynamic model of influenza transmission was developed and combined with a decision-tree to evaluate different vaccination strategies in the German health care system. Model inputs were based on published literature or were derived by expert consulting using the Delphi technique. Unit costs were drawn from German sources. Under base-case assumptions, annual routine vaccination of children aged 2-17 years with LAIV assuming an uptake of 50% would prevent, across all ages, 16 million cases of symptomatic influenza, over 600,000 cases of acute otitis media, nearly 130,000 cases of community-acquired pneumonia, nearly 1.7 million prescriptions of antibiotics and over 165,000 hospitalisations over 10 years. The discounted incremental cost-effectiveness ratio was <euro> 1,228 per quality-adjusted life year gained from a broad third-party payer perspective (including reimbursed direct costs and specific transfer payments), when compared with the current strategy of vaccinating primarily risk groups with the conventional trivalent inactivated vaccine. Inclusion of patient co-payments and indirect costs in terms of productivity losses resulted in discounted 10-year cost savings of <euro> 3.4 billion. In conclusion, adopting universal influenza immunisation of healthy children and adolescents would lead to a substantial reduction in influenza-associated disease at a reasonable cost to the German statutory health insurance system. On the basis of the epidemiological and health economic simulation results, a recommendation of introducing annual routine influenza vaccination of children 2-17 years of age might be taken into consideration.
AP5Z1/SPG4 8 frequency in autosomal recessive and sporadic spastic paraplegia
2014-05-25

Hereditary spastic paraplegias (HSP) constitute a rare and highly heterogeneous group of neurodegenerative disorders, defined clinically by progressive lower limb spasticity and pyramidal weakness. Autosomal recessive HSP as well as sporadic cases present a significant diagnostic challenge. Mutations in AP5Z1, a gene playing a role in intracellular membrane trafficking, have been recently reported to be associated with spastic paraplegia type 48 (SPG48). Our objective was to determine the relative frequency and clinical relevance of AP5Z1 mutations in a large cohort of 127 HSP patients. We applied a targeted next-generation sequencing approach to analyze all coding exons of the AP5Z1 gene. With the output of high-quality reads and a mean coverage of 51-fold, we demonstrated a robust detection of variants. One 43-year-old female with sporadic complicated paraplegia showed two heterozygous nonsynonymous variants of unknown significance (VUS3; p.[R292W];[(T756I)]). Thus, AP5Z1 gene mutations are rare, at least in Europeans. Due to its low frequency, systematic genetic testing for AP5Z1 mutations is not recommended until larger studies are performed to add further evidence. Our findings demonstrate that amplicon-based deep sequencing is technically feasible and allows a compact molecular characterization of multiple HSP patients with high accuracy.
Vagus nerve controls resolution and pro-resolving mediators of inflammation
2014-05-26

Resolution of inflammation is now recognized as a biosynthetically active process involving pro-resolving mediators. Here, we show in zymosan-initiated peritoneal inflammation that the vagus nerve regulates local expression of netrin-1, an axonal guidance molecule that activates resolution, and that vagotomy reduced local pro-resolving mediators, thereby delaying resolution. In netrin-1+/− mice, resolvin D1 (RvD1) was less effective in reducing neutrophil influx promoting resolution of peritonitis compared with Ntn1+/+. Netrin-1 shortened the resolution interval, decreasing exudate neutrophils, reducing proinflammatory mediators, and stimulating the production of resolvins, protectins, and lipoxins. Human monocytes incubated with netrin-1 produced proresolving mediators, including resolvins and lipoxins. Netrin-1 and RvD1 displayed bidirectional activation in that they stimulated each other’s expression and enhanced efferocytosis. These results indicate that the vagus nerve regulates both netrin-1 and pro-resolving lipid mediators, which act in a bidirectional fashion to stimulate resolution, and provide evidence for a novel mechanism for local neuronal control of resolution.
In Vitro Reconstitution of a Cellular Phase‐Transition Process that Involves the mRNA Decapping Machinery
2014-05-26

Abstract In eukaryotic cells, components of the 5′ to 3′ mRNA degradation machinery can undergo a rapid phase transition. The resulting cytoplasmic foci are referred to as processing bodies (P‐bodies). The molecular details of the self‐aggregation process are, however, largely undetermined. Herein, we use a bottom‐up approach that combines NMR spectroscopy, isothermal titration calorimetry, X‐ray crystallography, and fluorescence microscopy to probe if mRNA degradation factors can undergo phase transitions in vitro. We show that the Schizosaccharomyces pombe Dcp2 mRNA decapping enzyme, its prime activator Dcp1, and the scaffolding proteins Edc3 and Pdc1 are sufficient to reconstitute a phase‐separation process. Intermolecular interactions between the Edc3 LSm domain and at least 10 helical leucine‐rich motifs in Dcp2 and Pdc1 build the core of the interaction network. We show that blocking of these interactions interferes with the clustering behavior, both in vitro and in vivo.
MASC – a small Remotely Piloted Aircraft (RPA) for wind energy research
2014-05-27

Abstract. Originally designed for atmospheric boundary layer research, the MASC (Multipurpose Airborne Sensor Carrier) RPA (Remotely Piloted Aircraft, also known as Unmanned Aerial Vehicle, UAV) is capable of making in-situ measurements of temperature, humidity and wind in high resolution and precision. The autopilot system ROCS (Research Onboard Computer System) enables the aircraft to fly pre-defined routes between waypoints at constant altitude and airspeed. The system manages to operate in wind speeds up to 15 m s−1 safely. It is shown that a MASC can fly as close as one rotor diameter upstream and downstream of running wind turbines at these wind speeds and take valuable data of incoming flow and wake. The flexible operation of an RPA at the size of a MASC can be a major advantage of the system compared to tower measurements and remote sensing in wind energy research. In the project "Lidar Complex" comparisons of RPA measurements with lidar systems and tower measurements are carried out at two different test sites. First results, including turbulence and wake measurements, from a campaign in autumn 2013 are presented.
Accessing the Transverse Dynamics and Polarization of Gluons inside the Proton at the LHC
2014-05-27

We argue that the study of heavy quarkonia, in particular that of Î¥, produced back to back with an isolated photon in pp collisions at the LHC is the best - and currently unique - way to access the distribution of both the transverse momentum and the polarization of the gluon in an unpolarized proton. These encode fundamental information on the dynamics of QCD. We derive analytical expressions for various transverse-momentum distributions that can be measured at the LHC and which allow for a direct extraction of the aforementioned quantities. To assess the feasibility of such measurements, we evaluate the expected yields and the relevant transverse-momentum distributions for different models of the gluon dynamics inside a proton. Â© 2014 American Physical Society.
Phenobarbital-Mediated Tumor Promotion in Transgenic Mice with Humanized CAR and PXR
2014-05-27

The nuclear receptors CAR (constitutive androstane receptor) and possibly PXR (pregnane X receptor) mediate the hepatic effects of phenobarbital (PB) and similar-acting compounds. Although PB is a potent nongenotoxic tumor promoter in rodent liver, epidemiological data from epilepsy patients treated with phenobarbital do not show a specific role of PB in human liver cancer risk. That points to species differences in the susceptibility to tumor promotion by PB, which might be attributed to divergent functions of the PB receptors CAR and PXR in mice and humans. In the present study, male transgenic mice expressing human CAR and PXR were used to detect possible differences between wild-type (WT) and humanized mice in their response to CAR activation in a tumor initiation/promotion experiment with a single injection of the tumor initiator N-nitrosodiethylamine preceding chronic PB treatment for 10 months. Analysis of liver tumor burden revealed that PB strongly promoted the outgrowth of hepatocellular adenoma driven by activated β-catenin in WT mice, whereas the tumor-promoting effect of PB was much less pronounced in the humanized group. In conclusion, the present findings demonstrate that human CAR and PXR support tumor promotion by PB in mouse liver, but to a significantly lesser extent than the WT murine receptors.
Preserved bioactivity and tunable release of a SDF1-GPVI bi-specific protein using photo-crosslinked PEGda hydrogels
2014-05-27

Chemokine-induced stem cell recruitment is a promising strategy for post myocardial infarction treatment. Injection of stromal cell-derived factor 1 (SDF1) has been shown to attract bone marrow-derived progenitor cells (BMPCs) from the blood that have the potential to differentiate into cardiovascular cells, which support angiogenesis, enabling the improvement of myocardial function. SDF1-GPVI bi-specific protein contains a glycoprotein VI (GPVI)-domain that serves as an anchor for collagen type I (Col I) and III, which are exposed in the wall of injured vasculature. In this study, we generated a cytocompatible hydrogel via photo-crosslinking of poly(ethylene glycol) diacrylate that serves as a reservoir for SDF1-GPVI. Controlled and sustained release of SDF1-GPVI was demonstrated over a period of 7 days. Release features were modifiable depending on the degree of the crosslinking density. Functionality of the GPVI-domain was investigated using a GPVI-binding ELISA to Col I. Activity of the SDF1-domain was tested for its CXCR4 binding potential. Preserved functionality of SDF1-GPVI bi-specific protein after photo-crosslinking and controllable release was successfully demonstrated in vitro supporting the implementation of this drug delivery system as a powerful tool for therapeutic protein delivery in the treatment of cardiovascular ischemic disease.
Additional resources and the default mode network: Evidence of increased connectivity and decreased white matter integrity in amyotrophic lateral sclerosis
2014-05-27

In amyotrophic lateral sclerosis (ALS), cognition is affected. Cortical atrophy in frontal and temporal areas has been associated with the cognitive profile of patients. Additionally, reduced metabolic turnover and regional cerebral blood flow in frontal areas indicative of reduced neural activity have been reported for ALS. We hypothesize that functional connectivity in non-task associated functional default mode network (DMN) is associated with cognitive profile and white matter integrity. This study focused on specific cognitive tasks known to be impaired in ALS such as verbal fluency and attention, and the relationship with functional connectivity in the DMN and white matter integrity. Nine patients and 11 controls were measured with an extensive neuropsychological battery. Resting-state functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) data were acquired. Results showed that ALS patients performed significantly worse in attention and verbal fluency task. Patients showed increased functional connectivity in parahippocampal and parietal areas of the non-task associated DMN compared to controls. The more pronounced the cognitive deficits, the stronger the increase in functional connectivity in those areas. White matter integrity was reduced in frontal areas in the patients. In conclusion, increased connectivity in the DMN in parahippocampal and parietal areas might represent recruitment of accessory brain regions to compensate for dysfunctional frontal networks.
Boryl Azides in 1,3-Dipolar Cycloadditions
2014-05-27

The 1,3-dipolar cycloaddition reaction of boron azides with alkynes has been investigated experimentally and computationally. At room temperature pinBN3 (pin = pinacolato) reacts with the strained triple bond of cyclooctyne with formation of an oligomeric boryl triazole. Alcoholysis of the oligomer yields the parent 4,5,6,7,8,9-hexahydro-2H-cyclooctatriazole, which could be characterized as a hydrate by X-ray crystallography. A computational analysis of the reaction of tri- and tetracoordinate boron azides R2BN3 (R = H, Me, pin, cat; cat = catecholato) and IMe·H2BN3 (IMe = 2,6-dimethylimidazole-2-ylidene) reveals significant differences in the reactivity depending on the coordination number: tricoordinate boron azides behave as type II 1,3-dipoles, while the tetracoordinate IMe·H2BN3 is an electron-rich 1,3-dipole (type I) that strongly prefers reactions with electron-poor alkynes.
Combination therapy for carbapenem-resistant Gram-negative bacteria
2014-05-28

Carbapenem-resistant Gram-negative bacteria (CR-GNB) represent an increasing hazard in healthcare settings. A central question concerning the treatment of invasive infections caused by CR-GNB involves the use of combination therapy. Potential advantages of combination therapy include improved efficacy due to synergy, while the disadvantages include adverse events and increased antibiotic use with a potential drive towards resistance. Several observational studies have examined whether combination therapy offers an advantage over colistin/polymyxin monotherapy. We highlight the inherent limitations of these studies related to their observational design and sample size to show why they do not at present provide an answer to the question of combination versus monotherapy. This distinction is important to guide clinical practice until solid evidence has been obtained and to enable the recruitment of patients into randomized controlled trials. A few randomized controlled trials examining specific combinations have recently been completed or are ongoing. Currently, however, there is no evidence-based support for most combination therapies against CR-GNB, including colistin/carbapenem combination therapy.
Dative or Not Dative?
2014-05-28

Is a meatball an animal praline? The authors of the Essay Dative Bonds in Main‐Group Compounds: A Case for Fewer Arrows! respond to the criticism of Gernot Frenking and correct one point in their original Essay.
Enhanced Orai1 and STIM1 expression as well as store operated Ca2+ entry in therapy resistant ovary carcinoma cells
2014-05-28

Mechanisms underlying therapy resistance of tumor cells include protein kinase Akt. Putative Akt targets include store-operated Ca(2+)-entry (SOCE) accomplished by pore forming ion channel unit Orai1 and its regulator STIM1. We explored whether therapy resistant (A2780cis) differ from therapy sensitive (A2780) ovary carcinoma cells in Akt, Orai1, and STIM1 expression, Ca(2+)-signaling and cell survival following cisplatin (100 μM) treatment. Transcript levels were quantified with RT-PCR, protein abundance with Western blotting, cytosolic Ca(2+)-activity ([Ca(2+)]i) with Fura-2-fluorescence, SOCE from increase of [Ca(2+)]i following Ca(2+)-readdition after Ca(2+)-store depletion, and apoptosis utilizing flow cytometry. Transcript levels of Orai1 and STIM1, protein expression of Orai1, STIM1, and phosphorylated Akt, as well as SOCE were significantly higher in A2780cis than A2780 cells. SOCE was decreased by Akt inhibitor III (SH-6, 10 μM) in A2780cis but not A2780 cells and decreased in both cell lines by Orai1 inhibitor 2-aminoethoxydiphenyl borate (2-ABP, 50 μM). Phosphatidylserine exposure and late apoptosis following cisplatin treatment were significantly lower in A2780cis than A2780 cells, a difference virtually abolished by SH-6 or 2-ABP. In conclusion, Orai1/STIM1 expression and function are increased in therapy resistant ovary carcinoma cells, a property at least in part due to enhanced Akt activity and contributing to therapy resistance in those cells.
Improving Site‐Directed RNA Editing In Vitro and in Cell Culture by Chemical Modification of the GuideRNA
2014-05-28

Abstract Adenosine‐to‐inosine deamination can be re‐addressed to user‐defined mRNAs by applying phosphothioate/2′‐methoxy‐modified guideRNAs. Dense chemical modification of the guideRNA clearly improves performance of the covalent conjugates inside the living cell. Furthermore, careful positioning of a few modifications controls editing selectivity in vitro and was exploited for the challenging repair of the Factor 5 Leiden missense mutation.
Diffusion and Dynamics of γ-Globulin in Crowded Aqueous Solutions
2014-05-28

Dynamics in protein solutions is essential for both protein function and cellular processes. The hierarchical complexity of global protein diffusion, side-chain diffusion, and microscopic motions of chemical groups renders a complete understanding challenging. We present results from quasi-elastic neutron scattering on protein solutions of γ-globulin over a wide range of volume fractions. Translational and rotational diffusion can be self-consistently separated from internal motions. The global diffusion is consistent with predictions for effective spheres even though the branched molecular shape differs considerably from a colloidal sphere. The internal motions are characterized both geometrically and dynamically, suggesting a picture of methyl rotations and restricted diffusion of side chains. We show that the advent of new neutron spectrometers allows the study of current questions including the coupling of intracellular dynamics and protein function.
Fairy wrasses perceive and respond to their deep red fluorescent coloration
2014-05-28

Fluorescence enables the display of wavelengths that are absent in the natural environment, offering the potential to generate conspicuous colour contrasts. The marine fairy wrasse Cirrhilabrus solorensis displays prominent fluorescence in the deep red range (650–700 nm). This is remarkable because marine fishes are generally assumed to have poor sensitivity in this part of the visual spectrum. Here, we investigated whether C. solorensis males can perceive the fluorescence featured in this species by testing whether the presence or absence of red fluorescence affects male–male interactions under exclusive blue illumination. Given that males respond aggressively towards mirror-image stimuli, we quantified agonistic behaviour against mirrors covered with filters that did or did not absorb long (i.e. red) wavelengths. Males showed significantly fewer agonistic responses when their fluorescent signal was masked, independent of brightness differences. Our results unequivocally show that C. solorensis can see its deep red fluorescent coloration and that this pattern affects male–male interactions. This is the first study to demonstrate that deep red fluorescent body coloration can be perceived and has behavioural significance in a reef fish.
Isolation, Expansion and Transplantation of Postnatal Murine Progenitor Cells of the Enteric Nervous System
2014-05-28

Neural stem or progenitor cells have been proposed to restore gastrointestinal function in patients suffering from congenital or acquired defects of the enteric nervous system. Various, mainly embryonic cell sources have been identified for this purpose. However, immunological and ethical issues make a postnatal cell based therapy desirable. We therefore evaluated and quantified the potential of progenitor cells of the postnatal murine enteric nervous system to give rise to neurons and glial cells in vitro. Electrophysiological analysis and BrdU uptake studies provided direct evidence that generated neurons derive from expanded cells in vitro. Transplantation of isolated and expanded postnatal progenitor cells into the distal colon of adult mice demonstrated cell survival for 12 weeks (end of study). Implanted cells migrated within the gut wall and differentiated into neurons and glial cells, both of which were shown to derive from proliferated cells by BrdU uptake. This study indicates that progenitor cells isolated from the postnatal enteric nervous system might have the potential to serve as a source for a cell based therapy for neurogastrointestinal motility disorders. However, further studies are necessary to provide evidence that the generated cells are capable to positively influence the motility of the diseased gastrointestinal tract.