Biology subjects

Shcherbakova, A.

Publications and source records attributed to Shcherbakova, A..

4 recordsLinked to original sources

bioRxiv2026

Making the best of a sticky situation: Infection-mediated endothelial activation promotes new interactions with adhesins of the host-adapted Lyme disease spirochete

Lyme disease, caused by the spirochete Borrelia burgdorferi and closely related Lyme Borrelia, is the most prevalent tick-borne illness in the northern hemisphere. An important pathway for B. burgdorferi dissemination is its interaction with, and traversal of the vascular endothelium, a process that is not well understood and is mediated by spirochete surface adhesins. We show here that infection-induced activation of the endothelium in BALB/c mice results in new B. burgdorferi-endothelial interactions, indicating the presence of spirochete factors that interact specifically with activated endothelial cells. We show that these interactions are mediated by spirochetal surface proteins whose synthesis is dependent upon B. burgdorferi host adaptation. We used intravital microscopy and a functional gain approach to assess the binding of spirochetes that withstand the shear force of blood flow in post-capillary venules of living mice. We identified five previously undescribed, shear force-resistant adhesins that selectively mediate binding to activated endothelium (BBA66, P66, BBA36, BBA07 and DbpA) and interact with activation-induced endothelial surface changes. Two of these adhesins (P66 and DbpA) have been implicated in the spirochete extravasation process. We also identified seven previously undescribed shear force-resistant adhesins that target pre-activated endothelium (BBA04, BBK53, BBK07, BBA65, BB0844, ErpK and OspC). Three of these (BBK53, ErpK and OspC), display reduced binding to activated endothelium, a property that may facilitate the multi-step pathway of vascular transmigration. In particular, OspC has been previously implicated in spirochete extravasation. In summary, our results reveal a dynamic interaction network between the spirochete and the endothelium where the spirochete capitalizes on activation of the endothelium to establish new interactions and at the same time disrupt others. We propose that this scenario is part of a sequential interaction network leading to transendothelial migration of the spirochetes and subsequent tissue invasion. This work opens a new area of study focusing on eleven new adhesins described here and their vascular interactions and role in spirochete extravasation.

microbiology↗

bioRxiv2025

Generative design and construction of functional plasmids with a DNA language model

DNA language models offer a new paradigm for sequence design, yet their ability to generate functional genomic sequences remains underexplored. Plasmids act as a good testbed for evaluating DNA language model generation potential due to their simplicity and ease of construction. Here, we develop an end-to-end pipeline for generative design of Escherichia coli plasmid backbones, from large-scale data curation through fine-tuning, sampling, bioinformatic assessment, and candidate selection. A curated plasmid library was assembled from PlasmidScope and Addgene, and PlasmidGPT, a GPT-2-style DNA model, was fine-tuned on these corpora using circular-aware batching and random crops. Generations (1,000 per model) were produced under two prompting strategies: a minimal ATG seed to expose default tendencies, and a GFP cassette to enforce functional context. From 1000 generated synthetic plasmids, 16 candidates survived strict filtering and these were prioritised for wet-lab validation. Three shortlisted plasmids were synthesised and found to be functional, supporting growth, antibiotic resistance, and GFP expression in E. coli. These represent, to our knowledge, the first full AI-generated plasmids to be synthesised and validated in vivo. This work demonstrates that curated fine-tuning and prompt-aware generation enable DNA language models to progress from raw sequence sampling to experimentally testable plasmid designs. The approach offers a foundation for extending DNA design optimisation beyond E. coli, toward broader applications across engineering biology.

synthetic biology↗

bioRxiv2024

Designing minimal E. coli genomes using variational autoencoders

Designing minimal bacterial genomes remains a key challenge in synthetic biology. There is currently a lack of efficient tools for the rapid generation of streamlined bacterial genomes, limiting research in this area. Here, using a pangenome dataset for Escherichia coli, we show that variational autoencoders with modified loss functions can successfully create minimised genomes retaining the essential genes identified in the literature. We then sampled new genomes from our fitted model and performed computational validation using an E. coli whole-cell model. We found 6 out of 100 of the sampled genomes were viable in the computer model. These underwent a minimization routine starting from the MG1655 genome giving rise to six new minimal genomes with around a 40 % reduction in size. This study proposes a rapid, machine learning-based approach for bacterial sequence generation, that could accelerate the genomic design process.

synthetic biology↗

bioRxiv2024

Comparative framework and adaptation of ACME HS approach to single cell isolation from fresh-frozen endocrine tissues

Current scRNA-seq studies of solid tissues mostly rely on enzymatic dissociation of fresh samples or the fallback on nuclei isolation from frozen or partially fixed samples. However, due to the complex tissue organization or cell fragility, it could be challenging to apply these approaches to the sensitive endocrine tissues. That is, dissociating intact cells from such problematic fresh-frozen samples routinely collected by biobanks remains challenging. In this study, we adapted the acetic-methanol dissociation method - ACME High Salt (ACME HS) to effectively isolate intact single cells from fresh-frozen endocrine tumor samples, including adrenal gland neoplasms, thyroid carcinomas, and pituitary neuroendocrine tumors. We compared the ability of enzymatic, ACME HS, and nuclear isolation methods to preserve the integrity of major cell types and gene expression across 41 tissue samples of different origins. We demonstrated that ACME HS simultaneously dissociates and fixes cells, thus preserving morphology and a high RNA integrity number in problematic cell types. This finding renders the ACME HS dissociation method a valuable alternative in scRNA-seq protocols for challenging tissues where obtaining live cell suspension is difficult or impossible.

genomics↗