Biology subjects

Li, z.

Publications and source records attributed to Li, z..

3 recordsLinked to original sources

bioRxiv2026

Proteome-Scale Mining and Multi-Objective Prioritization of Encrypted Antimicrobial Peptides with Experimental Validation

Encrypted antimicrobial peptides (eAMPs) are bioactive fragments embedded within larger proteins and represent an underexplored source of antimicrobial candidates. We developed a multi-layer proteome-mining framework to identify and prioritise eAMPs from 95%-identity-reduced protein sets derived from 265 high-quality bacterial genomes. Three complementary, layer-specific extraction strategies targeting protein termini, internal cleavage sites, and cationic hotspots yielded 29,251,180 unique peptide candidates. Dual AMP prediction with AMP-scanner v2 and Macrel reduced this space to 3,249,772 consensus candidates. Downstream prioritisation followed two complementary routes: a low-haemolysis branch focused on selectivity-oriented candidates and a high-activity branch that retained predicted haemolytic sequences as mechanistic comparators. Structure prediction and review were performed for 185 candidates, and 18 entered Tier-1 developability, novelty, and membrane-activity assessment. Three sequence-matched representatives were selected for experimental evaluation. Molecular-dynamics simulations supported water-phase stability of GEAMP_71c139393ac596b5 and deep anionic-membrane insertion by GEAMP_12ffb5d589c8cb1b. In replicated colony-count assays against Escherichia coli and Staphylococcus aureus, all three peptides showed concentration-dependent activity over 8-128 uM. GEAMP_12ffb5d589c8cb1b was the most active, producing 1.52- and 2.27-log10 reductions, respectively, at 128 uM relative to the matched 8 uM condition. Together, these results establish a sequence-traceable workflow linking proteome-scale eAMP discovery with structural prioritisation and experimental activity assessment.

bioinformatics↗

bioRxiv2026

Genome-context-aware discovery of antibacterial peptides from bacterial small open reading frames

Small open reading frames (sORFs) are a potentially rich, yet error-prone, source of antimicrobial-peptide (AMP) candidates: short sequences are readily prioritized by AMP classifiers but may derive from incomplete gene calls. We developed a genome-context-aware discovery workflow that separates AMP-like sequence properties from evidence for a complete, recurrent coding locus. From 649,653 RefSeq assemblies representing 327 clinically relevant bacterial species, species-aware clustering and length filtering yielded 4,442,548 representative 10-100-aa sequences. AmpScanner v2, Macrel and AMPlify identified 585 non-haemolytic records supported by all three models. However, genome-context auditing of 11,918 mapped candidates showed that 529 of 536 mapped consensus candidates were supported exclusively by partial ORFs near contig termini. By contrast, 3,382 candidates had at least one complete non-edge occurrence; 1,069 recurred in [≥]2 assemblies and 251 in [≥]10 assemblies. We therefore assembled a 20-peptide panel through two explicitly labelled routes: sequence/structure-led selection (n=8) and genome-supported selection (n=12). Broth microdilution against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923 identified low-micromolar activity in both routes. CAND_04141, a recurrent complete non-edge candidate, had the strongest combined profile (MICs of 4 and 2 M, respectively), while CAND_07825 and CAND_04265 were also active at low micromolar concentrations. In plate-count MBC assays, all three advanced peptides achieved [≥]3-log10 reductions at 128 M. These findings show that high classifier agreement is not a substitute for genomic evidence and provide an auditable framework for prioritizing both synthetic AMP-like sequences and candidate genome-encoded peptides.

bioinformatics↗

bioRxiv2019

Characterization of aroma-active compounds in delicious apples juices by gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O) and odor activity value (OAV)

Volatile aroma compounds of delicious apple juice in three cultivars were obtained by gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O), and GC-flame photometric detection (FPD). Quantitatively, the major volatiles of the delicious apple juice were detected by GC-MS, such as esters, alcohols, aldehydes. In addition, GC-O and OAV were used to determine the aroma-active compounds in fruit. Amongst these compounds, ethyl 2-methylbutanoate (47-229), butyl 2-methylbutanoate (8-208), (E)-2-hexenal (25-120), butyl propanoate (14-54), methyl 2-methylbutanoate (28-41), ethyl hexanoate (4-32), ethyl butanoate (5-17) showed high OAVs in three delicious apple juices, which contributed greatly to the aroma of delicious apple juice. Beside those compounds, methanethiol (OAV: 1.1-1.6), dimethyl sulfide (OAV: 2.5-3.6), methional (OAV: 4.2-11.7) and 2-(methylthio)ethanol (OAV: 1.2-1.9) also presented relatively high OAVs. Finally, four compounds (ethyl 2-methylbutanoate, ethyl octanoate, ethyl butanoate and ethyl hexanoate) were selected to investigate the possible interactions occurring in the delicious apple juice. The resultants demonstrated that those aroma volatile compounds can decrease threshold of the solution to dissimilar degrees before and after their addition.

biochemistry↗