Structural and biochemical characterization of human Schlafen 5

The Schlafen family belongs to the interferon-stimulated genes and its members are involved in cell cycle regulation, T cell quiescence, inhibition of viral replication, DNA-repair and tRNA processing. Here, we present the cryo-EM structure of full-length human Schlafen 5 (SLFN5) and the high-resolution crystal structure of the highly conserved N-terminal core domain. We show that the core domain does not resemble an ATPase-like fold and neither binds nor hydrolyzes ATP. SLFN5 binds tRNA as well as single- and double-stranded DNA, suggesting a potential role in transcriptional regulation. Unlike rat Slfn13 or human SLFN11, human SLFN5 did not cleave tRNA. Based on the structure, we identified two residues in proximity to the zinc finger motif that decreased DNA binding when mutated. These results indicate that Schlafen proteins have divergent enzymatic functions and provide a structural platform for future biochemical and genetic studies

Implementation of GENFIT2 as an experiment independent track-fitting framework

The GENFIT toolkit, initially developed at the Technische Universitaet Muenchen, has been extended and modified to be more general and user-friendly. The new GENFIT, called GENFIT2, provides track representation, track-fitting algorithms and graphic visualization of tracks and detectors, and it can be used for any experiment that determines parameters of charged particle trajectories from spacial coordinate measurements. Based on general Kalman filter routines, it can perform extrapolations of track parameters and covariance matrices. It also provides interfaces to Millepede II for alignment purposes, and RAVE for the vertex finder. Results of an implementation of GENFIT2 in basf2 and PandaRoot software frameworks are presented here.Comment: 41 pages 24 figures, 1 table. Paper submitted to NI

The Full Event Interpretation -- An exclusive tagging algorithm for the Belle II experiment

The Full Event Interpretation is presented: a new exclusive tagging algorithm used by the high-energy physics experiment Belle II. The experimental setup of Belle II allows the precise measurement of otherwise inaccessible $B$ meson decay-modes. The Full Event Interpretation algorithm enables many of these measurements. The algorithm relies on machine learning to automatically identify plausible $B$ meson decay chains based on the data recorded by the detector. Compared to similar algorithms employed by previous experiments, the Full Event Interpretation provides a greater efficiency, yielding a larger effective sample size usable in the measurement.Comment: 11 pages, 7 figures, 1 tabl

The track finding algorithm of the Belle II vertex detectors

The Belle II experiment is a high energy multi purpose particle detector operated at the asymmetric e+e-- collier SuperKEKB in Tsukuba (Japan). In this work we describe the algorithm performing the pattern recognition for inner tracking detector which consists of two layers of pixel detectors and four layers of double sided silicon strip detectors arranged around the interaction region. The track finding algorithm will be used both during the High Level Trigger on-line track reconstruction and during the off-line full reconstruction. It must provide good efficiency down to momenta as low as 50 MeV/c where material effects are sizeable even in an extremely thin detector as the VXD. In addition it has to be able to cope with the high occupancy of the Belle II detectors due to the background. The underlying concept of the track finding algorithm, as well as details of the implementation are outlined. The algorithm is proven to run with good performance on simulated Y (4S) â\u86\u92 BB events with an efficiency for reconstructing tracks of above 90% over a wide range of momentum

Structural mechanism of extranucleosomal DNA readout by the INO80 complex

The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo–electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes