Journal: bioRxiv

Article Title: Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer

doi: 10.1101/2023.02.15.528699

Figure Lengend Snippet: a) Line graph of PepCalMix peptides to assess the linearity measured by dia-PASEF mode in timsTOF mass spectrometer. b) Bar plots of total quantities of all 20 PepCalMix peptides observed with ESI, CS ion sources at 25 fmol injection amount at 40 μL /min and 1 μL /min respectively, and with VIP-HESI source at 25 & 800 fmol injection amounts at 40 μL /min. Keeping the concentration of the eluting peak height constant (25 fmol for 1 μL = CS, 800 fmol for 40 μL for VIP-HESI), the response of VIP-HESI is even increased by 30% and a slightly higher peak response using the VIP-HESI source is observed. The error bars indicate the variability within three replicates represented as the standard error of the mean at the log2 scale. These are calculated as the ratio of the standard deviation of the peptide intensities observed with each source setup replicate to the square root of the sample size ( n = 3). c) Extracted Ion Chromatogram (XIC) plots of a single precursor IGNEQGVSR.2 representing each source setup, colored by MS2 fragment intensity observed per measurement, as per the injection amount and flow rates.

Article Snippet: Sample-specific PepCalMix library was generated against the PepCalMix peptide FASTA sequence using the Spectronaut 17.0.221202.55965 (Biognosys) with the same setting described above.

Techniques: Data-independent acquisition, Mass Spectrometry, Injection, Concentration Assay, Standard Deviation

Journal: F1000Research

Article Title: RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction

doi: 10.12688/f1000research.52350.2

Figure Lengend Snippet: A . Job launcher screen (Run tab). The user only needs to upload the nucleotide sequences in FASTA format and select the model to be used based on the evolutionary close related species. B . Results web page screen. General report containing the list of coding and non-coding sequences in a dynamic table, in which the user can search for a particular sequence or filter only those coding or non-coding RNAs by using a free text form that will filter the results in the table dynamically. The user can download the complete table in tabular format and two FASTA files containing the set of coding and non-coding RNAs separately.

Article Snippet: All sequences in FASTA format with their respective Ensemble identifiers can be retrieved at RNAmining website ( https://rnamining.integrativebioinformatics.me/download ).

Techniques: Sequencing

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: eLife

Article Title: Genetically incorporated crosslinkers reveal NleE attenuates host autophagy dependent on PSMD10

doi: 10.7554/eLife.69047

Figure Lengend Snippet: ( A ) PSMD10 interacts with ATG10 and ATG12 in living cells. Shown are immunoblots of anti-Flag immunoprecipitates (Flag IP) and total cell lysates (Input). ( B, C ) Photocrosslinking experiments map of the PSMD10 interaction surface with ATG7. Residues X replaced by DiZPK are indicated in the upper row. ( D ) Three to five ankyrin repeats of PSMD10 are indispensable for interacting with ATG12. Shown are immunoblots of anti-Flag immunoprecipitates (Flag IP) and total cell lysates (Input). ( E, F ) The PSMD10 C4S mutation destroyed its interaction with ATG7 ( E ) and ATG10 ( F ). Figure 7—figure supplement 1—source data 1. Original western blot files for .

Article Snippet: Gene ( Homo sapiens ) , ATG12 , National Center for Biotechnology Information , Gene ID: 9140.

Techniques: Western Blot, Mutagenesis

Journal: eLife

Article Title: Genetically incorporated crosslinkers reveal NleE attenuates host autophagy dependent on PSMD10

doi: 10.7554/eLife.69047

Figure Lengend Snippet: ( A ) The N-terminus of PSMD10 is indispensable for interacting with ATG7 and ATG10. Shown are immunoblots of anti-Flag immunoprecipitates (Flag IP) and total cell lysates (Input). ( B ) Deletion of the PSMD10 N-terminus does not affect its interaction with ATG12. ( C ) The PSMD10 C4S mutant failed to enhance LPS and starve-induced autophagy in PSMD10 KO cells. Scale bars, 10 μm. ( D ) ATG7 and LC3 were not colocalized in PSMD10 KO cells expressing the PSMD10 C4S mutant. Representative images are shown. Scale bars, 10 μm. ( E, F ) Stabilized PSMD10 C4S homodimers restore its interaction with ATG7 in living cells. Shown are immunoblots of anti-Flag immunoprecipitates (Flag IP) and total cell lysates (Input). PSMD10 C4S homodimers stabilized by chemical crosslinking ( E ) and disulfide bonds ( F ). ( G ) The stabilized PSMD10 C4S homodimer functions in enhancing autophagy in PSMD10 KO cells. Scale bars, 10 μm. ( H ) NleE attenuates host autophagy in a PSMD10 homodimer-dependent manner. The PSMD10 C11S mutant, but not the PSMD10 C4S mutant, rescued the NleE functions in regulating host autophagy in PSMD10 KO cells. Scale bars, 10 μm. Figure 7—source data 1. Original western blot files for .

Article Snippet: Gene ( Homo sapiens ) , ATG12 , National Center for Biotechnology Information , Gene ID: 9140.

Techniques: Western Blot, Mutagenesis, Expressing

Journal: eLife

Article Title: Genetically incorporated crosslinkers reveal NleE attenuates host autophagy dependent on PSMD10

doi: 10.7554/eLife.69047

Figure Lengend Snippet:

Article Snippet: Gene ( Homo sapiens ) , ATG12 , National Center for Biotechnology Information , Gene ID: 9140.

Techniques: Western Blot, Immunofluorescence, Recombinant, Isolation, Enzyme-linked Immunosorbent Assay, In Vitro, Methylation, Software

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: