Biology subjects

Dallachiesa, D.

Publications and source records attributed to Dallachiesa, D..

2 recordsLinked to original sources

bioRxiv2025

ColabPCR: A validated Google Colaboratory Notebook for Reproducible and Precise Primer Design.

The Polymerase Chain Reaction (PCR) method often has a lower success rate when amplifying specific genomic regions in eukaryotic genomes. This is frequently due to the non-specific annealing of primers at various genomic locations. To address this issue, we created ColabPCR, a program specifically designed to optimize the selection and evaluation of primers for a defined genomic region. ColabPCR refines primer length and melting temperature parameters through the utilization of Primer3 software, and it quantifies the number of potential off-target binding regions within the target genome via BLASTn analysis. Furthermore, the program facilitates the integration of restriction enzyme recognition sites at the 5 termini of primers and provides a mechanism to confirm the absence of such sites within the intended amplification region. ColabPCR centralizes all these functionalities within a single interface, utilizing Google Colabs computational resources to ensure high performance and accessibility without requiring local software installation. We rigorously validated ColabPCR by designing primers for promoter and terminator regions within the Daucus carota (DCARv2, DH1v3) reference genome. Our findings unequivocally demonstrate significantly enhanced success rates, particularly when primers exhibiting off-target binding are excluded from the primer design process. In summary, ColabPCR offers a user-friendly and powerful solution that simplifies and enhances the primer design and evaluation workflow, leading to increased accuracy and success in molecular biology experiments.

bioinformatics↗

bioRxiv2023

Improved detection and phylogenetic analysis of plant proteins containing LysM domains.

Plants perceive N-acetyl-d-glucosamine-containing oligosaccharides that play a role in the interaction with bacteria and fungi, both pathogenic and symbiotic, through cell-surface receptors that belong to the Receptor-Like Kinase (RLK) or Receptor-Like Protein (RLP) families. Structurally characterised proteins from these families have been shown to contain a tight bundle of three LysM domains in their extracellular domain. However, the identification of LysM domains of RLK/Ps using sequence based methods has led to some ambiguity, as some proteins have been annotated with one or only two LysM domains. This missing annotation was likely produced by the failure of the LysM hidden Markov model (HMM) from the PFAM database to correctly identify some LysM domains in proteins of plant origin. In this work, we provide improved HMMs for LysM domain detection in plants, that were built from the structural alignment of manually curated LysM domain structures from PDB and AlphaFold. Furthermore, we evaluated different sets of ligand-specific HMMs that were able to correctly classify a limited set of fully characterised RLK/Ps by their ligand specificity. In contrast, the phylogenetic analysis of the extracellular region of RLK/Ps, or of their individual LysM domains, was unable to discriminate these proteins by their ligand specificity. The HMMs reported here will allow a more sensitive detection of plant proteins containing LysM domains and help improve their characterisation.

plant biology↗