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dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
Abstract Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation
TLDR
An online database dbCAN-seq is built to provide pre-computed CAZyme sequence and annotation data for 5,349 bacterial genomes and will become a valuable web resource for CAZYme research, with a focus complementary to dbCAN (automated CAzyme annotation server) and CAZs (CAZy family classification and reference database).
Landscape and Selection of Vaccine Epitopes in SARS-CoV-2
TLDR
This study combines computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2, and proposes a set of Sars-Cov-2 vaccine peptides for use in subsequent murine studies and clinical trials.
Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches
TLDR
A bioinformatics pipeline is developed to identify genomic loci containing Acr homologs and/or Aca Homologs by combining three computational approaches: homology, guilt-by-association, and self-targeting spacers to facilitate anti-CRISPR research.
The Transcriptional Regulator Hbx1 Affects the Expression of Thousands of Genes in the Aflatoxin-Producing Fungus Aspergillus flavus
TLDR
This study revealed that hbx1 affects the expression of other transcription factor genes involved in development, including the conidiation central regulatory pathway and flb genes, and has a broad effect on A. flavus gene expression.
Orphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity
TLDR
This study provides direct evidence to suggest that ORFans shared by more pathogens are more associated with pathogenicity-related genes and thus are more important targets for development of new diagnostic markers or therapeutic drugs for bacterial infectious diseases.
Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion
TLDR
Cell wall polysaccharide synthesis-related genes respond to osmotic stress in a manner that is similar to land plants, and three glycosyltransferase families were selected for in-depth phylogenetic analyses, which confirmed their presence in UTEX 1559.
Landscape and selection of vaccine epitopes in SARS-CoV-2
TLDR
The selection process and vaccine formulation are found to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes.
rmtA-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence in Aspergillus flavus
TLDR
Over 2000 genes that were rmtA-dependent, including over 200 transcription factor genes, as well as an uncharacterized secondary metabolite gene cluster possibly responsible for the synthesis of an epidithiodiketopiperazine-like compound are identified.
478 Translation of a therapeutic neoantigen vaccine workflow to SARS-CoV-2 vaccine development
TLDR
Adapting methods for predicting tumor-specific antigens, a set of peptide candidates with high overlap for T and B cell epitopes and broad haplotype population coverage are presented, with validation of immunogenicity in murine vaccine studies.
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