Biology subjects

Gates, A.

Publications and source records attributed to Gates, A..

3 recordsLinked to original sources

bioRxiv2025

Cross-linking mass spectrometry for structure analysis of the intrinsically disordered Tau and phosphorylated Tau protein

We present a novel method for analyzing the folding of intrinsically disordered proteins (IDPs), such as Tau and phosphorylated Tau (pTau), in solution. Using cross-linking mass spectrometry combined with a new downstream analysis framework, we construct weighted interaction networks from cross-link-derived residue pairs without relying on predefined secondary structure assumptions. Structural differences between protein conformations are quantified by comparing the organization of loop structures within their cross-link networks. Validation with bovine serum albumin (BSA) in native and denatured states shows that at least 500 cross-links--requiring 5-10 replicate measurements--are needed for reliable detection of structural divergence. Leave-one-out analysis confirms that structural transitions are global, highlighting the importance of comprehensive cross-link datasets. The coverage of unique cross-links was evaluated using accumulation curves from randomized permutations. Saturation levels were found to be 9.7%, 5.0%, and 6.2% of the total 528 and 10,731 possible cross-links after 30, 84, and 62 technical replicates, respectively, for myoglobin, native BSA, and denatured BSA. For Tau and pTau, coverage reached 10.8% and 5.5% of the upper limit (8,256). Finally, applying our structural analysis to Tau and pTau during arachidonic acid-induced aggregation revealed distinct patterns of structural evolution between the two proteins.

biochemistry↗

bioRxiv2025

AI-Based Detection of Coliform Colonies Using CNN Transfer Learning for Application to Cultured Plate Analysis in Water Quality Research

Pathogenic bacterial contamination of water poses a severe public health risk, particularly in settings with limited laboratory resources. We propose a two-stage artificial intelligence (AI) pipeline for automated detection and classification of coliform colonies on agar plates. In the first stage, a YOLOv8-based detector localizes colonies on full-plate images, eliminating the need for manual annotation. In the second stage, detected colony patches are classified using a convolutional neural network (CNN) trained via transfer learning, where models are first pretrained on a diverse public bacterial colony dataset and subsequently fine-tuned on coliform-specific classification tasks. Across both in-house and public datasets, transfer learning consistently improves classification performance relative to training from scratch. The complete pipeline processes each plate in under five seconds and outperforms classical feature-based baselines, including Histogram of Oriented Gradients, Local Binary Patterns, and Haralick descriptors with conventional classifiers. These results demonstrate the potential of a modular, low-cost AI framework for scalable and accessible microbiological analysis, with future work targeting color-aware models and on-device inference for field deployment.

microbiology↗

bioRxiv2024

In vitro biofilm formation only partially predicts beneficial Pseudomonas fluorescens protection against rhizosphere pathogens

Plant roots form associations with both beneficial and pathogenic soil microorganisms. While members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a robust biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas fluorescens WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen P. fluorescens N2C3 and confers robust protection against P. fluorescens N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. fluorescens WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased levels of biofilm on an abiotic surface, respectively. We found that while the P. fluorescens WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants, including those involved in large adhesion protein (Lap) biosynthesis, flagellin biosynthesis and O-antigen biosynthesis, lost protection against P. fluorescens N2C3. We found that the inability of P. fluorescens WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.

microbiology↗