Daniela Barilla'

Protein layers protect #microbes from harsh environment and #viruses. A study of a sheath-forming #proteins revealed their huge diversity in #archaea and potential for involvement in cell interactions and lysis. @SGribaldo @ISMEJournal @ISME_microbes academic.oup.com/ismej/advance-…

biorxiv.org/content/10.110… BORGS - the large extrachromosomal elements of anaerobic methane-oxidizing archaea are likely viruses and have evolved genomic features similar to Giant Viruses!

» A widespread phage-encoded kinase enables evasion of multiple host antiphage defence systems | Nature Microbiology nature.com/articles/s4156…

Congrats to @DavidRcoMark on publishing his PhD work! @Tucker303 @MicrobioSoc Chromosome architecture as a determinant for biosynthetic diversity in Micromonospora - go.shr.lc/4fwg5HU

» DNAproDB: an updated database for the automated and interactive analysis of protein–DNA complexes | Nucleic Acids Research | Oxford Academic academic.oup.com/nar/advance-ar…

Why did some groups of genes get progressively closer on the chromosome  to ultimately form operons ? We addressed and quantified the role of gene multiplicity (strictly connected to the number of active replication forks in a cell) and metabolic homeostasis in this process.

New PhD position! Interested in using cutting-edge biophysics? 🔬Join @chillzaa, Dr Purba Mukherjee and I @UniOfYork to explore the mechanisms of genome replication in enteroviruses. 🧬 Apply now! 👇 tinyurl.com/573nctrh @DiMeN_DTP @YBRI_UoY @BiologyatYork @UoY_PET

🔥JOB ADVERT🔥 Looking for a postdoc to work on #machine_learning classification of #knots & #proteins and discovery of new topological invariants. Start by November 2025 Duration 2 years min Where: TAPLab @PhysAstroEd Generously funded by @LeverhulmeTrust Retweet pls ❤️

New from me and a huge cast of amazing bioimage analysts in @J_Cell_Sci - - "The crucial role of bioimage analysts in scientific research and publication" journals.biologists.com/jcs/article/13… . Hop into 🧵to learn more! (1/x)

AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic beta-solenoid structures for repeat proteins biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Tubulin-like proteins CetZ1 and CetZ2 coordinate cellular morphogenesis in the archaeon Haloferax volcanii biorxiv.org/cgi/content/sh… #biorxiv_micrbio

RepeatsDB in 2025: Expanding Annotations of Structured Tandem Repeat Proteins on AlphaFoldDB @NAR_Open • The 2025 update of RepeatsDB vastly expands the database’s coverage, adding over 34,000 new protein sequences from more than 2,000 species, representing a fifteenfold increase in structured tandem repeat proteins (STRPs) annotated. • Utilizing STRPsearch, an advanced structural alignment tool, RepeatsDB now offers more precise and rapid detection of repeat regions across both experimental PDB and AlphaFold structures. • New features include an enhanced user interface and a comprehensive statistics page, which allows users to explore data based on repeat classifications, improving the browsing and searching experience. • Community curation efforts have reviewed over 15,000 PDB structures, adding experimentally verified repeat regions and refining repeat classifications in collaboration with the Pfam and InterPro databases. • The dedicated Biocuration tool allows authenticated users to manually annotate or verify repeat predictions, streamlining the curation process and ensuring data accuracy across periodic updates. • RepeatsDB’s API has been optimized for scalability, now supporting a RESTful architecture with improved performance and pagination, making the data easily accessible for research and integration. • RepeatsDB is now a fundamental resource for researchers investigating protein repeats, contributing to fields such as molecular biology, structural bioinformatics, and therapeutic development. @AlexanderMonzon @BioComputingUP @ArriasPN 💻Code: repeatsdb.org 📜Paper: academic.oup.com/nar/advance-ar… #ProteinRepeats #Bioinformatics #AlphaFold #StructuralBiology #MolecularBiology #DatabaseUpdate

Excited to share our last collab paper in @NatureComms on the structure & interference mechanism of the mysterious 𝗧𝘆𝗽𝗲 𝗜𝗩-𝗔 𝗖𝗥𝗜𝗦𝗣𝗥-𝗖𝗮𝘀 system!! 🧬🚀 🔗nature.com/articles/s4146… 🧵 by @patrick_pausch below!

We have a post-doc opportunity for a molecular microbiologist available. Please contact directly for an informal discussion. jobs.ac.uk/job/DKH037/res…

Excited to share our first DNA-protein work! Thanks to @mahipal_ganji for collaboration and the encouragement to explore this system and @ARNABCHATERJE for the help during revision! Cryo-EM Reveals the Mechanism of DNA Compaction by Mycobacterium smegm... sciencedirect.com/science/articl…

Funded PhD available with us, @martllewellyn and James Cotton @UofGSii @UofGSBOHVM @WCIPGLASGOW to study genome replication and (in)stability across diverse kinetoplastids. Applications (via FindaPhD) taken from Nov 1st - Jan 12th. Enquiries welcome. tinyurl.com/mfz4yh3k

AlphaBridge: tools for the analysis of predicted macromolecular complexes biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

AlphaBridge: tools for the analysis of predicted macromolecular complexes • AlphaBridge introduces tools to analyze and visualize the interfaces between predicted macromolecular complexes using data from AlphaFold3. It processes the predicted interactions into intuitive diagrams and 3D models for easy interpretation. • The tool uses a novel “Predicted Merged Confidence” (PMC) matrix, which combines the Predicted Local Distance Difference Test (pLDDT) and Predicted Aligned Error (PAE) metrics to identify multi-component structural modules and binary interfaces with high confidence. • AlphaBridge uses graph-based community clustering to detect interaction motifs in biomolecular complexes, then visualizes these interactions as chord diagrams (“AlphaBridge diagrams”) to provide a clear and intuitive summary of predicted binding interfaces. • The tool allows researchers to evaluate the reliability of interactions in predicted protein-protein, protein-DNA, and protein-RNA complexes, offering a scoring and ranking system for predicted interfaces before detailed analysis. • By varying the cut-off for contact predictions, AlphaBridge can help distinguish between reliable and unreliable predictions, providing insights into physiological relevance. It was particularly useful for evaluating interactions in DNA mismatch repair proteins and RNA binding proteins. • The AlphaBridge webserver (alpha-bridge.eu) offers an interactive platform where users can upload AlphaFold3 prediction files, visualize the predicted 3D structures, and analyze contact interfaces through an integrated web viewer. • AlphaBridge enhances accessibility for both expert and non-expert users by combining multiple layers of information—contact links, prediction confidence, and visual representations—into one interactive diagram, simplifying the evaluation of complex predictions. @TassosPerrakis @rborza_ 💻Code: github.com/PDB-REDO/Alpha… 📜Paper: biorxiv.org/content/10.110…

» Genomic landscape of antiviral defense systems in prokaryotes and phages | bioRxiv biorxiv.org/content/10.110…

Un texto a modo de homenaje a nuestro compañero Manolo, que nos dejó inesperadamente en esta semana. Un magnífico científico, entusiasta y humanista que siempre estará en nuestro recuerdo. ➡️i.mtr.cool/wiugmggszh