159 research outputs found
The C-Terminal Domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC Is a Lectin-Like Carbohydrate Binding Module
The D-arabinan-containing polymers arabinogalactan (AG) and lipoarabinomannan (LAM) are essential components of the unique cell envelope of the pathogen Mycobacterium tuberculosis. Biosynthesis of AG and LAM involves a series of membrane-embedded arabinofuranosyl (Araf) transferases whose structures are largely uncharacterised, despite the fact that several of them are pharmacological targets of ethambutol, a frontline drug in tuberculosis therapy. Herein, we present the crystal structure of the C-terminal hydrophilic domain of the ethambutol-sensitive Araf transferase M. tuberculosis EmbC, which is essential for LAM synthesis. The structure of the C-terminal domain of EmbC (EmbCCT) encompasses two sub-domains of different folds, of which subdomain II shows distinct similarity to lectin-like carbohydrate-binding modules (CBM). Co-crystallisation with a cell wall-derived di-arabinoside acceptor analogue and structural comparison with ligand-bound CBMs suggest that EmbCCT contains two separate carbohydrate binding sites, associated with subdomains I and II, respectively. Single-residue substitution of conserved tryptophan residues (Trp868, Trp985) at these respective sites inhibited EmbC-catalysed extension of LAM. The same substitutions differentially abrogated binding of di- and penta-arabinofuranoside acceptor analogues to EmbCCT, linking the loss of activity to compromised acceptor substrate binding, indicating the presence of two separate carbohydrate binding sites, and demonstrating that subdomain II indeed functions as a carbohydrate-binding module. This work provides the first step towards unravelling the structure and function of a GT-C-type glycosyltransferase that is essential in M. tuberculosis. Author Summary Top Tuberculosis (TB), an infectious disease caused by the bacillus Mycobacterium tuberculosis, burdens large swaths of the world population. Treatment of active TB typically requires administration of an antibiotic cocktail over several months that includes the drug ethambutol. This front line compound inhibits a set of arabinosyltransferase enzymes, called EmbA, EmbB and EmbC, which are critical for the synthesis of arabinan, a vital polysaccharide in the pathogen's unique cell envelope. How precisely ethambutol inhibits arabinosyltransferase activity is not clear, in part because structural information of its pharmacological targets has been elusive. Here, we report the high-resolution structure of the C-terminal domain of the ethambutol-target EmbC, a 390-amino acid fragment responsible for acceptor substrate recognition. Combining the X-ray crystallographic analysis with structural comparisons, site-directed mutagenesis, activity and ligand binding assays, we identified two regions in the C-terminal domain of EmbC that are capable of binding acceptor substrate mimics and are critical for activity of the full-length enzyme. Our results begin to define structure-function relationships in a family of structurally uncharacterised membrane-embedded glycosyltransferases, which are an important target for tuberculosis therapy
Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains
We describe the complete synthesis, assembly, debugging, and characterization of a synthetic 404,963 bp chromosome, synIX (synthetic chromosome IX). Combined chromosome construction methods were used to synthesize and integrate its left arm (synIXL) into a strain containing previously described synIXR. We identified and resolved a bug affecting expression of EST3, a crucial gene for telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains, we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. Both steps of this chromosome substitution method were efficient. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these chromosomes. </p
Convolutional Neural Networks Applied to Neutrino Events in a Liquid Argon Time Projection Chamber
We present several studies of convolutional neural networks applied to data
coming from the MicroBooNE detector, a liquid argon time projection chamber
(LArTPC). The algorithms studied include the classification of single particle
images, the localization of single particle and neutrino interactions in an
image, and the detection of a simulated neutrino event overlaid with cosmic ray
backgrounds taken from real detector data. These studies demonstrate the
potential of convolutional neural networks for particle identification or event
detection on simulated neutrino interactions. We also address technical issues
that arise when applying this technique to data from a large LArTPC at or near
ground level
A Proposal for a Three Detector Short-Baseline Neutrino Oscillation Program in the Fermilab Booster Neutrino Beam
A Short-Baseline Neutrino (SBN) physics program of three LAr-TPC detectors
located along the Booster Neutrino Beam (BNB) at Fermilab is presented. This
new SBN Program will deliver a rich and compelling physics opportunity,
including the ability to resolve a class of experimental anomalies in neutrino
physics and to perform the most sensitive search to date for sterile neutrinos
at the eV mass-scale through both appearance and disappearance oscillation
channels. Using data sets of 6.6e20 protons on target (P.O.T.) in the LAr1-ND
and ICARUS T600 detectors plus 13.2e20 P.O.T. in the MicroBooNE detector, we
estimate that a search for muon neutrino to electron neutrino appearance can be
performed with ~5 sigma sensitivity for the LSND allowed (99% C.L.) parameter
region. In this proposal for the SBN Program, we describe the physics analysis,
the conceptual design of the LAr1-ND detector, the design and refurbishment of
the T600 detector, the necessary infrastructure required to execute the
program, and a possible reconfiguration of the BNB target and horn system to
improve its performance for oscillation searches.Comment: 209 pages, 129 figure
Determination of muon momentum in the MicroBooNE LArTPC using an improved model of multiple Coulomb scattering
We discuss a technique for measuring a charged particle's momentum by means
of multiple Coulomb scattering (MCS) in the MicroBooNE liquid argon time
projection chamber (LArTPC). This method does not require the full particle
ionization track to be contained inside of the detector volume as other track
momentum reconstruction methods do (range-based momentum reconstruction and
calorimetric momentum reconstruction). We motivate use of this technique,
describe a tuning of the underlying phenomenological formula, quantify its
performance on fully contained beam-neutrino-induced muon tracks both in
simulation and in data, and quantify its performance on exiting muon tracks in
simulation. Using simulation, we have shown that the standard Highland formula
should be re-tuned specifically for scattering in liquid argon, which
significantly improves the bias and resolution of the momentum measurement.
With the tuned formula, we find agreement between data and simulation for
contained tracks, with a small bias in the momentum reconstruction and with
resolutions that vary as a function of track length, improving from about 10%
for the shortest (one meter long) tracks to 5% for longer (several meter)
tracks. For simulated exiting muons with at least one meter of track contained,
we find a similarly small bias, and a resolution which is less than 15% for
muons with momentum below 2 GeV/c. Above 2 GeV/c, results are given as a first
estimate of the MCS momentum measurement capabilities of MicroBooNE for high
momentum exiting tracks
Design and construction of the MicroBooNE Cosmic Ray Tagger system
The MicroBooNE detector utilizes a liquid argon time projection chamber
(LArTPC) with an 85 t active mass to study neutrino interactions along the
Booster Neutrino Beam (BNB) at Fermilab. With a deployment location near ground
level, the detector records many cosmic muon tracks in each beam-related
detector trigger that can be misidentified as signals of interest. To reduce
these cosmogenic backgrounds, we have designed and constructed a TPC-external
Cosmic Ray Tagger (CRT). This sub-system was developed by the Laboratory for
High Energy Physics (LHEP), Albert Einstein center for fundamental physics,
University of Bern. The system utilizes plastic scintillation modules to
provide precise time and position information for TPC-traversing particles.
Successful matching of TPC tracks and CRT data will allow us to reduce
cosmogenic background and better characterize the light collection system and
LArTPC data using cosmic muons. In this paper we describe the design and
installation of the MicroBooNE CRT system and provide an overview of a series
of tests done to verify the proper operation of the system and its components
during installation, commissioning, and physics data-taking
Ionization Electron Signal Processing in Single Phase LArTPCs II. Data/Simulation Comparison and Performance in MicroBooNE
The single-phase liquid argon time projection chamber (LArTPC) provides a
large amount of detailed information in the form of fine-grained drifted
ionization charge from particle traces. To fully utilize this information, the
deposited charge must be accurately extracted from the raw digitized waveforms
via a robust signal processing chain. Enabled by the ultra-low noise levels
associated with cryogenic electronics in the MicroBooNE detector, the precise
extraction of ionization charge from the induction wire planes in a
single-phase LArTPC is qualitatively demonstrated on MicroBooNE data with event
display images, and quantitatively demonstrated via waveform-level and
track-level metrics. Improved performance of induction plane calorimetry is
demonstrated through the agreement of extracted ionization charge measurements
across different wire planes for various event topologies. In addition to the
comprehensive waveform-level comparison of data and simulation, a calibration
of the cryogenic electronics response is presented and solutions to various
MicroBooNE-specific TPC issues are discussed. This work presents an important
improvement in LArTPC signal processing, the foundation of reconstruction and
therefore physics analyses in MicroBooNE.Comment: 54 pages, 36 figures; the first part of this work can be found at
arXiv:1802.0870
Measurement of the Inclusive Semi-electronic Branching Fraction
Using the angular correlation between the emitted in a decay and the emitted in the subsequent decay, we have measured the branching fraction for the
inclusive semi-electronic decay of the meson to be: {\cal B}(D^0
\rightarrow X e^+ \nu) = [6.64 \pm 0.18 (stat.) \pm 0.29 (syst.)] \%. The
result is based on 1.7 fb of collisions recorded by the CLEO II
detector located at the Cornell Electron Storage Ring (CESR). Combining the
analysis presented in this paper with previous CLEO results we find,
\frac{{\cal B} (D^0 \rightarrow X e^+ \nu)}
{{\cal B} (D^0 \rightarrow K^- \pi^+)}
= 1.684 \pm 0.056 (stat.) \pm 0.093(syst.) and
\frac{{\cal B}(D\rightarrow K^-e^+\nu)}
{{\cal B}(D\rightarrow Xe^+\nu)}
= 0.581 \pm 0.023 (stat.) \pm 0.028(syst.).
The difference between the inclusive rate and the sum of the measured
exclusive branching fractions (measured at CLEO and other experiments) is of the inclusive rate.Comment: Latex file, 33pages, 4 figures Submitted to PR
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