The aim of this study was to investigate if and how temporal context influences subjective affective responses to emotional images. To do so, we examined whether the subjective evaluation of a target image is influenced by the valence of its preceding image, and/or its overall position in a sequence of images. Furthermore, we assessed if these potentially confounding contextual effects can be moderated by a common procedural control: randomized stimulus presentation. Four groups of participants evaluated the same set of 120 pictures from the International Affective System (IAPS) presented in four different sequences. Our data reveal strong effects of both aspects of temporal context in all presentation sequences, modified only slightly in their nature and magnitude. Furthermore, this was true for both valence and arousal ratings. Subjective ratings of negative target images were influenced by temporal context most strongly across all sequences. We also observed important gender differences: females expressed greater sensitivity to temporal-context effects and design manipulations relative to males, especially for negative images. Our results have important implications for future emotion research that employs normative picture stimuli, and contributes to our understanding of context effects in general.
- Keywords
- assimilation effect, contrast effect, emotion, presentation sequence, temporal context,
- Publication type
- Journal Article MeSH
Plasmid pJW1 from Selenomonas ruminantium subsp. lactilytica strain JW13 has been cloned in Escherichia coli vector pBluescriptSK(-) and completely sequenced. The plasmid is only 1410 bp with an overall GC content of 42.2%. Computer analysis of sequence data revealed a single open reading frame (ORF1, 146 amino acids, MW 16,525.5 Da) encoding a putative replication protein which is similar to the Rep protein of Ruminobacter amylophilus plasmid pRAO1. ORF1 is followed by a long AT-rich (75%) region and a region abundant in direct and inverted repeats. Comparison of DNA sequences revealed the presence of a short (<250 bp) DNA segment which is highly conserved between several small S. ruminantium plasmids including pJDB21.
- MeSH
- DNA, Bacterial * MeSH
- Conserved Sequence * MeSH
- Molecular Sequence Data MeSH
- Plasmids * MeSH
- Amino Acid Sequence MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA methods MeSH
- Selenomonas genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA, Bacterial * MeSH
The accumulation of protein aggregates is toxic and linked to different diseases such as neurodegenerative disorders, but the role of the immune system to target and destroy aggregate-carrying cells is still relatively unknown. Here we show a substrate-specific presentation of antigenic peptides to the direct MHC class I pathway via autophagy. We observed no difference in presentation of peptides derived from the viral EBNA1 protein following suppression of autophagy by knocking down Atg5 and Atg12. However, the same knock down treatment suppressed the presentation from ovalbumin. Fusing the aggregate-prone poly-glutamine (PolyQ) to the ovalbumin had no effect on antigen presentation via autophagy. Interestingly, fusing the EBNA1-derived gly-ala repeat (GAr) sequence to ovalbumin rendered the presentation Atg5/12 independent. We also demonstrate that the relative levels of protein expression did not affect autophagy-mediated antigen presentation. These data suggest a substrate-dependent presentation of antigenic peptides for the MHC class I pathway via autophagy and indicate that the GAr of the EBNA1 illustrates a novel virus-mediated mechanism for immune evasion of autophagy-dependent antigen presentation.
- Keywords
- Autophagy, EBV-encoded EBNA1, MHC class I restricted antigen presentation, Protein aggregates,
- MeSH
- Antigens MeSH
- Autophagy MeSH
- Immune Evasion MeSH
- Histocompatibility Antigens Class I * MeSH
- Histocompatibility Antigens Class II metabolism MeSH
- Ovalbumin MeSH
- Antigen Presentation * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Antigens MeSH
- Histocompatibility Antigens Class I * MeSH
- Histocompatibility Antigens Class II MeSH
- Ovalbumin MeSH
Web Alignment Visualization Server contains a set of web-tools designed for quick generation of publication-quality color figures of multiple alignments of nucleotide or amino acids sequences. It can be used for identification of conserved regions and gaps within many sequences using only common web browsers. The server is accessible at http://wavis.img.cas.cz.
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
- MeSH
- Genetic Variation genetics MeSH
- Genomics * methods standards MeSH
- Heterochromatin genetics MeSH
- Humans MeSH
- Chromosomes, Human, Y * genetics MeSH
- Multigene Family genetics MeSH
- Genetics, Population MeSH
- Reference Standards MeSH
- DNA, Satellite genetics MeSH
- Segmental Duplications, Genomic genetics MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA * standards MeSH
- Tandem Repeat Sequences genetics MeSH
- Telomere genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- DAZ1 protein, human MeSH Browser
- Heterochromatin MeSH
- RBMY1A1 protein, human MeSH Browser
- DNA, Satellite MeSH
- TSPY1 protein, human MeSH Browser
Here we present the complete genome sequences of two TuRSV isolates. They are 90-100% identical in distinct genes, but reasonably less identical with RaMV isolates. Regarding the CPs, TuRSV and RaMV have an aa sequence identity of 72-74% among all isolates and the proposed cut-off level is 75%. For the proteinase-polymerase region, the average value between the two isolates of TuRSV and three isolates of RaMV is 79.8% and the cut-off level is 80%. At the moment, TuRSV and RaMV are the two identified species most closely related within the genus Comovirus.
- MeSH
- Genome, Viral * MeSH
- Molecular Sequence Data MeSH
- Plant Diseases virology MeSH
- Gene Expression Regulation, Viral physiology MeSH
- Plant Viruses genetics MeSH
- Amino Acid Sequence MeSH
- Base Sequence MeSH
- Viral Proteins chemistry genetics metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Viral Proteins MeSH
Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
- MeSH
- Molecular Sequence Annotation MeSH
- Genome, Plant MeSH
- Genomics methods MeSH
- DNA, Intergenic MeSH
- Hordeum genetics MeSH
- Terminal Repeat Sequences MeSH
- Retroelements MeSH
- Sequence Analysis, DNA MeSH
- Computational Biology methods MeSH
- High-Throughput Nucleotide Sequencing methods MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA, Intergenic MeSH
- Retroelements MeSH
The field of mRNA translation has witnessed an impressive expansion in the last decade. The once standard model of translation initiation has undergone, and is still undergoing, a major overhaul, partly due to more recent technical advancements detailing, for example, initiation at non-AUG codons. However, some of the pioneering works in this area have come from immunology and more precisely from the field of antigen presentation to the major histocompatibility class I (MHC-I) pathway. Despite early innovative studies from the lab of Nilabh Shastri demonstrating alternative mRNA translation initiation as a source for MHC-I peptide substrates, the mRNA translation field did not include these into their models. It was not until the introduction of the ribo-sequence technique that the extent of non-canonical translation initiation became widely acknowledged. The detection of peptides on MHC-I molecules by CD8 + T cells is extremely sensitive, making this a superior model system for studying alternative mRNA translation initiation from specific mRNAs. In view of this, we give a brief history on alternative initiation from an immunology perspective and its fundamental role in allowing the immune system to distinguish self from non-self and at the same time pay tribute to the works of Nilabh Shastri.
- Keywords
- Antigen presentation, MHC class I pathway, mRNA translation initiation,
- MeSH
- CD8-Positive T-Lymphocytes immunology MeSH
- Humans MeSH
- RNA, Messenger genetics immunology MeSH
- Histocompatibility Antigens Class I genetics immunology MeSH
- Peptides genetics immunology MeSH
- Antigen Presentation genetics immunology MeSH
- Protein Biosynthesis genetics immunology MeSH
- Receptors for Activated C Kinase genetics immunology MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
- Names of Substances
- RNA, Messenger MeSH
- Histocompatibility Antigens Class I MeSH
- peptide I MeSH Browser
- Peptides MeSH
- Receptors for Activated C Kinase MeSH
Harmonic elastic constants of 3-11 bp duplex DNA fragments were evaluated using four 5 ns unrestrained molecular dynamics simulation trajectories of 17 bp duplexes with explicit inclusion of solvent and counterions. All simulations were carried out with the Cornell et al. force-field and particle mesh Ewald method for long-range electrostatic interactions. The elastic constants including anisotropic bending and all coupling terms were derived by analyzing the correlations of fluctuations of structural properties along the trajectories. The following sequences have been considered: homopolymer d(ApA)(n) and d(GpG)(n), and alternating d(GPC)(n) and d(APT)(n). The calculated values of elastic constants are in very good overall agreement with experimental values for random sequences. The atomic-resolution molecular dynamics approach, however, reveals a pronounced sequence-dependence of the stretching and torsional rigidity of DNA, while sequence-dependence of the bending rigidity is smaller for the sequences considered. The earlier predicted twist-bend coupling emerged as the most important cross-term for fragments shorter than one helical turn. The calculated hydrodynamic relaxation times suggest that damping of bending motions may play a role in molecular dynamics simulations of long DNA fragments. A comparison of elasticity calculations using global and local helicoidal analyses is reported. The calculations reveal the importance of the fragment length definition. The present work shows that large-scale molecular dynamics simulations represent a unique source of data to study various aspects of DNA elasticity including its sequence-dependence.
- MeSH
- Algorithms MeSH
- Anisotropy MeSH
- DNA chemistry genetics metabolism MeSH
- Nucleic Acid Conformation * MeSH
- Oligodeoxyribonucleotides chemistry genetics metabolism MeSH
- Base Pairing MeSH
- Computer Simulation MeSH
- Motion MeSH
- Elasticity MeSH
- Solvents MeSH
- Base Sequence MeSH
- Static Electricity MeSH
- Thermodynamics MeSH
- Water metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA MeSH
- Oligodeoxyribonucleotides MeSH
- Solvents MeSH
- Water MeSH
The complete genome sequence of a severe isolate of broad bean true mosaic virus (genus Comovirus, subfamily Comovirinae, family Secoviridae) is presented. Comparison of the amino acid sequences of the capsid proteins and the polymerase showed striking differences to other comoviruses and highest similarities to legume-infecting comoviruses. Red clover mottle virus was recognized as the most similar virus with amino acid sequence identities ranging from 43 to 67% for individual genes.
- MeSH
- Comovirus genetics MeSH
- Phylogeny MeSH
- Genome, Viral * MeSH
- Molecular Sequence Data MeSH
- RNA, Viral genetics MeSH
- Base Sequence MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- RNA, Viral MeSH
