Journal: bioRxiv

Article Title: Stochastic variation in surface protein expression diversifies Trypanosoma cruzi infection

doi: 10.1101/2025.04.07.647584

Figure Lengend Snippet: A) Diagram of the YSD screen with sera from Chagas disease patients or healthy individuals. Sera was incubated with the YSD library expressing T. cruzi antigens on the surface and enriched using magnetic-activated cell sorting (MACS). After three rounds of enrichment, the library DNAs were sequenced using Oxford nanopore technology to identify enriched sequences compared to the initial non-enriched library or the library enriched with sera from healthy individuals. B) PCA plot of each sequencing replicate (dots) by each enrichment condition. The experiment was performed in three biological replicates. C) Volcano plot shows YSD screen analysis comparing MGF proteins enriched with ChD patients’ or healthy individuals’ antibodies. ChD or healthy enriched libraries were first compared to non-enriched libraries, and non-significant hits were removed. Only MGF proteins are shown. D) Diagram of T. cruzi TS on top. Not all TSs have FRIP, Asp boxes, or SAPA repeats. All contain VTV motifs. Each motif’s amino acid (aa) sequences are indicated, and x means any aa. The heatmap (bottom graph) displays the location of antibody binding to the TSs identified in the YSD screen, as mapped using nanopore sequencing. TS sequence lengths were normalized from 1-100 for visualization. On the right, sequence comparison of 30 TSs with antibodies reacting at their N-terminus (grey bar). Sequence alignment of aa 30 to 130. The first 30 aa represent predicted signal peptides removed for the analysis. The percentage of identity between all 30 sequences was obtained, and their correlation was analyzed and plotted. E) The heat map displays the locations of antibody binding sites on mucins, MASPs, DGF-1, and GP63, which were identified in the YSD screen and mapped using nanopore sequencing. Protein sequences were normalized to a range of 1-100 for visualization. Experiments were performed in three biological replicates.

Article Snippet: Briefly, Oxford nanopore sequence .fasta files were aligned to the genome using minimap2.

Techniques: Incubation, Expressing, FACS, Sequencing, Binding Assay, Nanopore Sequencing, Comparison

Journal: PLoS ONE

Article Title: Structural Differences between Human Proteins and Aero- and Microbial Allergens Define Allergenicity

doi: 10.1371/journal.pone.0040552

Figure Lengend Snippet: The percent identity levels between human proteins (x-axis) a representative helminth ( B. malayi , A ), protozoan ( P. falciparum , B ) and fungus ( C. albicans , C ) protein (y-axis). Correlations were evaluated by Spearman rank test. Each dot represents one allergen and the squared-dot at the origin of the axis represents allergens that had neither homologues in humans nor in the microbes: (A) n = 222, (B) n = 247 and (C) n = 210 allergens.

Article Snippet: Fasta files with translated CDS annotated protein sequences for Brugia malayi , Loa loa and Wuchereria bancrofti (all version 1) were downloaded from the Broad Institute ( http://www.broadinstitute.org/annotation/genome/filarial_worms/MultiDownloads.html ), Schistosoma mansoni fasta file (version GeneDB v 4.0 h) was downloaded from Sanger Institute ( ftp://ftp.sanger.ac.uk/pub/pathogens/ ), Plasmodium falciparum (PlasmoDB 6.4) from Plasmodb ( http://plasmodb.org/common/downloads/ ), Trypanosoma cruzi CL Brener (TriTrypDB-2.2) and Leishmania major Friedlin (TriTrypDB-2.2) from Tritrypdb ( http://tritrypdb.org/common/downloads/ ), Toxoplasma gondii ME-49 (ToxoDB 6.0) from Toxobd ( http://toxodb.org/common/downloads/ ).

Techniques:

Journal: Evolutionary Bioinformatics Online

Article Title: REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

doi:

Figure Lengend Snippet: REFGEN conversion of FASTA files for use in phylogenetic programs. A) Snapshot of CPN60 alignment. Sequences are derived from GenBank and the DOE JGI Phytophthora ramorum databases (please note although the DOE JGI sequence does not confirm to the long identification line format it is accommodated by REFGEN). All CPN60 sequences are curtailed after the first 70 amino acid positions for the purpose of this figure. Note the long database identifier lines given to each sequence. B) Screenshot of REFGEN formatting options. C) Output from REFGEN, with sequence labels now compatible with all phylogenetic programs and ready for analysis.

Article Snippet: REFGEN will then output a FASTA sequence file with the new shortened names (REFGEN IDs) that are compatible with all phylogenetic analysis programs.

Techniques: Derivative Assay, Sequencing

Journal: Horticulture Research

Article Title: OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data

doi: 10.1093/hr/uhad195

Figure Lengend Snippet: Formats, descriptions, and sample applications for input or output data files

Article Snippet: , Sequence FASTA format , Sequence FASTA format uses (.fasta, .fna, .fa) as the file suffix. It’s a text format for representing either nucleotide (DNA/RNA) sequences or amino acid (protein) sequences. , RevCom, LongMSA, SeqsTranslate, etc..

Techniques: Sequencing, Mutagenesis, Expressing, Mass Spectrometry, Generated