Protein conformational transitions form the molecular basis of many cellular processes, such as signal transduction and membrane traffic. However, in many cases, little is known about their ...structural dynamics. Here we have used dynamic single-molecule fluorescence to study at high time resolution, conformational transitions of syntaxin 1, a soluble N-ethylmaleimide-sensitive factor attachment protein receptors protein essential for exocytotic membrane fusion. Sets of syntaxin double mutants were randomly labeled with a mix of donor and acceptor dye and their fluorescence resonance energy transfer was measured. For each set, all fluorescence information was recorded simultaneously with high time resolution, providing detailed information on distances and dynamics that were used to create structural models. We found that free syntaxin switches between an inactive closed and an active open configuration with a relaxation time of 0.8 ms, explaining why regulatory proteins are needed to arrest the protein in one conformational state.
The South Pole, which hosts the IceCube Neutrino Observatory, has a complete and around-the-clock exposure to the Galactic Center. Hence, it is an ideal location to search for gamma rays of PeV ...energy coming from the Galactic Center. However, it is hard to detect air showers initiated by these gamma rays using cosmic-ray particle detectors due to the low elevation of the Galactic Center. The use of antennas to measure the radio footprint of these air showers will help in this case, and would allow for a 24/7 operation time. So far, only air showers with energies well above
10
16
eV have been detected with the radio technique. Thus, the energy threshold has to be lowered for the detection of gamma-ray showers of PeV energy. This can be achieved by optimizing the frequency band in order to obtain a higher level of signal-to-noise ratio. With such an approach, PeV gamma-ray showers with high inclination can be measured at the South Pole.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We present an improved method for the precise reconstruction of cosmic-ray air showers above 1017 eV with sparse radio arrays. The method is based on the comparison of measured pulses to predictions ...for radio pulse shapes by CoREAS simulations. We applied our method to the data of Tunka-Rex, a 1 km2 radio array in Siberia operating in the frequency band of 30–80 MHz. Tunka-Rex is triggered by the air-Cherenkov detector Tunka-133 and by scintillators (Tunka-Grande). The instrument collects air-shower data since 2012. The present paper describes an updated data analysis of Tunka-Rex and details of the new method applied. After quality cuts, when Tunka-Rex reaches its full efficiency, the energy resolution of about 10% given by the new method has reached the limit of systematic uncertainties due to the calibration uncertainty and shower-to-shower fluctuations. At the same time the shower maximum reconstruction has improved compared to the previous method based on the slope of the lateral distribution and reaches a precision of better than 35 g/cm2. We also define conditions of the measurements at which the shower maximum resolution of Tunka-Rex reaches a value of 25 g/cm2 and becomes competitive to optical detectors. To check and validate our reconstruction and efficiency cuts we compare individual events to the reconstruction of Tunka-133. Furthermore, we compare the mean of the shower maximum as a function of primary energy to the measurements of other experiments.
N‐Glycans direct protein function, stability, folding and targeting, and influence immunogenicity. While most glycosidases that process N‐glycans cleave a single sugar residue at a time, enzymes from ...glycoside hydrolase family 99 are endo‐acting enzymes that cleave within complex N‐glycans. Eukaryotic Golgi endo‐1,2‐α‐mannosidase cleaves glucose‐substituted mannose within immature glucosylated high‐mannose N‐glycans in the secretory pathway. Certain bacteria within the human gut microbiota produce endo‐1,2‐α‐mannanase, which cleaves related structures within fungal mannan, as part of nutrient acquisition. An unconventional mechanism of catalysis was proposed for enzymes of this family, hinted at by crystal structures of imino/azasugars complexed within the active site. Based on this mechanism, we developed the synthesis of two glycosides bearing a spiro‐epoxide at C‐2 as electrophilic trap, to covalently bind a mechanistically important, conserved GH99 catalytic residue. The spiro‐epoxyglycosides are equipped with a fluorescent tag, and following incubation with recombinant enzyme, allow concentration, time and pH dependent visualization of the bound enzyme using gel electrophoresis.
Eukaryotic endomannosidase from glycosyl hydrolase family 99 (GH99) is involved in the processing of immature N‐linked glycans, whereas bacterial GH99 endomannanase orthologs hydrolyze high‐mannose oligosaccharides. Based on the proposed unusual hydrolytic mechanism of these enzymes, two fluorescent spiro‐epoxyglycosides were synthesized and we show that these compounds function as activity‐based probes for these enzymes.
Glucocerebrosidase (GBA), a lysosomal retaining β‐d‐glucosidase, has recently been shown to hydrolyze β‐d‐xylosides and to transxylosylate cholesterol. Genetic defects in GBA cause the lysosomal ...storage disorder Gaucher disease (GD), and also constitute a risk factor for developing Parkinson's disease. GBA and other retaining glycosidases can be selectively visualized by activity‐based protein profiling (ABPP) using fluorescent probes composed of a cyclophellitol scaffold having a configuration tailored to the targeted glycosidase family. GBA processes β‐d‐xylosides in addition to β‐d‐glucosides, this in contrast to the other two mammalian cellular retaining β‐d‐glucosidases, GBA2 and GBA3. Here we show that the xylopyranose preference also holds up for covalent inhibitors: xylose‐configured cyclophellitol and cyclophellitol aziridines selectively react with GBA over GBA2 and GBA3 in vitro and in vivo, and that the xylose‐configured cyclophellitol is more potent and more selective for GBA than the classical GBA inhibitor, conduritol B‐epoxide (CBE). Both xylose‐configured cyclophellitol and cyclophellitol aziridine cause accumulation of glucosylsphingosine in zebrafish embryo, a characteristic hallmark of GD, and we conclude that these compounds are well suited for creating such chemically induced GD models.
New selective GBA inhibitor: We show that the β‐d‐xylose configured epoxide and aziridine are potent selective inhibitors towards GBA in vitro and in vivo, and their selectivity and inhibitory effect towards GBA are superior to the widely used GBA inhibitor Conduritol B‐epoxide (CBE).
KASCADE and KASCADE-Grande were multi-detector installations to measure individual air showers of cosmic rays at ultra-high energy. Based on data sets measured by KASCADE and KASCADE-Grande, 90% C.L. ...upper limits to the flux of gamma-rays in the primary cosmic ray flux are determined in an energy range of eV. The analysis is performed by selecting air showers with a low muon content as expected for gamma-ray-induced showers compared to air showers induced by energetic nuclei. The best upper limit of the fraction of gamma-rays to the total cosmic ray flux is obtained at eV with . Translated to an absolute gamma-ray flux this sets constraints on some fundamental astrophysical models, such as the distance of sources for at least one of the IceCube neutrino excess models.
The ‘KASCADE Cosmic ray Data Centre’ is a web portal (
https://kcdc.ikp.kit.edu
), where the data of the astroparticle physics experiment KASCADE-Grande are made available for the interested public. ...The KASCADE experiment was a large-area detector for the measurement of high-energy cosmic rays via the detection of extensive air showers. The multi-detector installations KASCADE and its extension KASCADE-Grande stopped the active data acquisition in 2013 after more than 20 years of data taking. In several updates since our first release in 2013 with KCDC we provide the public measured and reconstructed parameters of more than 433 million air showers. In addition, KCDC provides meta data information and documentation to enable a user outside the community of experts to perform their own data analysis. Simulation data from three different high energy interaction models have been made available as well as a compilation of measured and published spectra from various experiments. In addition, detailed educational examples shall encourage high-school students and early stage researchers to learn about astroparticle physics, cosmic radiation as well as the handling of Big Data and about the sustainable and public provision of scientific data.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Accumulation of mitochondrial DNA deletions is observed especially in dopaminergic neurons of the substantia nigra during ageing and even more in Parkinson's disease. The resulting mitochondrial ...dysfunction is suspected to play an important role in neurodegeneration. However, the molecular mechanisms involved in the preferential generation of mitochondrial DNA deletions in dopaminergic neurons are still unknown. To study this phenomenon, we developed novel polymerase chain reaction strategies to detect distinct mitochondrial DNA deletions and monitor their accumulation patterns. Applying these approaches in in vitro and in vivo models, we show that catecholamine metabolism drives the generation and accumulation of these mitochondrial DNA mutations. As in humans, age-related accumulation of mitochondrial DNA deletions is most prominent in dopaminergic areas of mouse brain and even higher in the catecholaminergic adrenal medulla. Dopamine treatment of terminally differentiated neuroblastoma cells, as well as stimulation of dopamine turnover in mice over-expressing monoamine oxidase B both induce multiple mitochondrial DNA deletions. Our results thus identify catecholamine metabolism as the driving force behind mitochondrial DNA deletions, probably being an important factor in the ageing-associated degeneration of dopaminergic neurons.
We present the results of the search for large-scale anisotropies in the arrival directions of cosmic rays performed with the KASCADE-Grande experiment at energies higher than eV. To eliminate ...spurious anisotropies due to atmospheric or instrumental effects we apply the east-west method. We show, using the solar time distribution of the number of counts, that this technique allow us to remove correctly the count variations not associated to real anisotropies. By applying the east-west method we obtain the distribution of number of counts in intervals of 20 minutes of sidereal time. This distribution is then analyzed by searching for a dipole component; the significance of the amplitude of the first harmonic is 3.5 , therefore, we derive its upper limit. The phase of the first harmonic is determined with an error of a few hours and is in agreement with the measurements obtained in the 1014 < E < 2 × 1015 eV energy range by the EAS-TOP, IceCube, and IceTop experiments. This supports the hypothesis of a change of the phase of the first harmonic at energies greater than ∼2 × 1014 eV.
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