Energy spectrum of cascades generated by muons in Baksan underground scintillation telescope

Spectrum of cascades generated by cosmic ray muons underground is presented. The mean zenith angle of the muon arrival is theta=35 deg the depth approx. 1000 hg/sq cm. In cascades energy range 700 GeV the measured spectrum is in agreement with the sea-level integral muon spectrum index gamma=3.0. Some decrease of this exponent has been found in the range 4000 Gev

Angular distribution of muons produced by cosmic ray neutrinos in rock

Measurement of the upgoing muons flux, produced by cosmic ray neutrinos is aiming at: (1) search for neutrino oscillation; (2); search for extraterrestrial neutrinos from local sources; and (3); search for any hypothetical neutral penetrating radiation different from neutrinos. Experimental data of the Baksan underground telescope on intensity of upward muons for three years of living time, was analyzed having in mind mainly neutrino oscillation

Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features

IntroductionT-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens. While a large number of TCR sequences specific to different antigenic peptides are known to date, the structural data describing the conformation and contacting residues for TCR-peptide-MHC complexes is relatively limited. In the present study we aim to extend and analyze the set of available structures by performing highly accurate template-based modeling of these complexes using TCR sequences with known specificity. MethodsIdentification of CDR3 sequences and their further clustering, based on available spatial structures, V- and J-genes of corresponding T-cell receptors, and epitopes, was performed using the VDJdb database. Modeling of the selected CDR3 loops was conducted using a stepwise introduction of single amino acid substitutions to the template PDB structures, followed by optimization of the TCR-peptide-MHC contacting interface using the Rosetta package applications. Statistical analysis and recursive feature elimination procedures were carried out on computed energy values and properties of contacting amino acid residues between CDR3 loops and peptides, using R.ResultsUsing the set of 29 complex templates (including a template with SARS-CoV-2 antigen) and 732 specificity records, we built a database of 1585 model structures carrying substitutions in either TCRα or TCRβ chains with some models representing the result of different mutation pathways for the same final structure. This database allowed us to analyze features of amino acid contacts in TCR - peptide interfaces that govern antigen recognition preferences and interpret these interactions in terms of physicochemical properties of interacting residues.ConclusionOur results provide a methodology for creating high-quality TCR-peptide-MHC models for antigens of interest that can be utilized to predict TCR specificity

Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis

BACKGROUND: Within the family of green fluorescent protein (GFP) homologs, one can mark two main groups, specifically, fluorescent proteins (FPs) and non-fluorescent or chromoproteins (CPs). Structural background of differences between FPs and CPs are poorly understood to date. RESULTS: Here, we applied site-directed and random mutagenesis in order to to transform CP into FP and vice versa. A purple chromoprotein asCP (asFP595) from Anemonia sulcata and a red fluorescent protein DsRed from Discosoma sp. were selected as representatives of CPs and FPs, respectively. For asCP, some substitutions at positions 148 and 165 (numbering in accordance to GFP) were found to dramatically increase quantum yield of red fluorescence. For DsRed, substitutions at positions 148, 165, 167, and 203 significantly decreased fluorescence intensity, so that the spectral characteristics of these mutants became more close to those of CPs. Finally, a practically non-fluorescent mutant DsRed-NF was generated. This mutant carried four amino acid substitutions, specifically, S148C, I165N, K167M, and S203A. DsRed-NF possessed a high extinction coefficient and an extremely low quantum yield (< 0.001). These spectral characteristics allow one to regard DsRed-NF as a true chromoprotein. CONCLUSIONS: We located a novel point in asCP sequence (position 165) mutations at which can result in red fluorescence appearance. Probably, this finding could be applied onto other CPs to generate red and far-red fluorescent mutants. A possibility to transform an FP into CP was demonstrated. Key role of residues adjacent to chromophore's phenolic ring in fluorescent/non-fluorescent states determination was revealed

Primary chemical composition from simultaneous recording of muons induced cascades and accompanying muon group underground

A new method to estimate the mean atomic number of primary cosmic rays in energy range 10 to the 3rd power to 10 to the 5th power Gev/nucleon is suggested. The Baksan underground scintillation telescope data are used for this analysis. The results of 7500 h run of this experiment are presented

Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity

T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5’D2-RS – 3’D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response

Flux profile scanners for scattered high-energy electrons

The paper describes the design and performance of flux integrating Cherenkov scanners with air-core reflecting light guides used in a high-energy, high-flux electron scattering experiment at the Stanford Linear Accelerator Center. The scanners were highly radiation resistant and provided a good signal to background ratio leading to very good spatial resolution of the scattered electron flux profile scans.Comment: 22 pages, 17 figure

Unique Electron Polarimeter Analyzing Power Comparison and Precision Spin-Based Energy Measurement

Precision measurements of the relative analyzing powers of five electron beam polarimeters, based on Compton, Moller, and Mott scattering, have been performed using the CEBAF accelerator at the Thomas Jefferson National Accelerator Facility ( Jefferson Laboratory). A Wien filter in the 100 keV beam line of the injector was used to vary the electron spin orientation exiting the injector. High statistical precision measurements of the scattering asymmetry as a function of the spin orientation were made with each polarimeter. Since each polarimeter receives beam with the same magnitude of polarization, these asymmetry measurements permit a high statistical precision comparison of the relative analyzing powers of the five polarimeters. This is the first time a precise comparison of the analyzing powers of Compton, Moller, and Mott scattering polarimeters has been made. Statistically significant disagreements among the values of the beam polarization calculated from the asymmetry measurements made with each polarimeter reveal either errors in the values of the analyzing power or failure to correctly include all systematic effects. The measurements reported here represent a first step toward understanding the systematic effects of these electron polarimeters. Such studies are necessary to realize high absolute accuracy (ca. 1%) electron polarization measurements, as required for some parity violation measurements planned at Jefferson Laboratory. Finally, a comparison of the value of the spin orientation exiting the injector that provides maximum longitudinal polarization in each experimental hall leads to an independent and very precise ( better than 10-4) absolute measurement of the final electron beam energy