History and aims

The LBD was founded in 2009, at the former Department of Signal Processing of Tampere University of Technology. Nowadays, we are in Arvo at the Faculty of Medicine and Health Technology of Tampere University. Initially, we used computational methods, such as stochastic models and simulators of genetic circuits. In 2011, we setup a laboratory to perform live single-cell microscopy, flow-cytometry and RNA-seq, among other. This made our work multi-disciplinary. A description of some past and current projects is available in Research.

Our aim is to understand the in vivo dynamics and regulatory mechanisms of bacterial gene networks in health and under stress, including antibiotic stresses. We combine measurements (RNA-seq, flow-cytometry, time-lapse microscopy, etc.) and new dynamic models from the nucleotide level, up to circuits with thousands of genes and interactions. We apply tailored methods of single-cell image and signal processing, stochastic and analytical models, RNA-seq data analysis, and synthetic gene engineering.

Recent highlights

• We are happy to receive our newest team member, for Ph.D. studies, Pooja Ravaria.

• Our paper on the dynamics of transcription in operons has just been published in Science Advances!! Congratulations to Rahul and all the other authors!!! LINK: https://www.science.org/doi/10.1126/sciadv.adl3570. 

• 14.2.2025 We have a new paper published! Ines Baptista led the project now published in PLoS Computational Biology! https://doi.org/10.1371/journal.pcbi.1012817. A few years ago, Vinodh Kandavalli found that a few genes of the YFP strain library were exhibiting bimodal single-cell distributions of gene expression. Such natural genes might become important in the future, for example to store information, respond to external signals, etc. Thus, Ines, Suchintak Dash, et al, studied them in detail, subject them to perturbations, made a stochastic model, etc. We learned about their behavior's robustness and the source of bimodality! Thanks also to Barry Sanders et al, for the wonderful collaboration.  

• 24.10.2024 Ines Baptista also completed her Ph.D.! Ines has made several original contributions to the lab, and we are very thankful for it. We wish her the best has she enters the next phase in her life.

• 20.9.2024 Suchintak Dash just completed his Ph.D.! We are also very happy to see him progress in his scientific career, moving to a lab that will further open his possibilities to have a wonderful career in Science. Best wishes to him. 

• 22.8.2024 We have a new paper in Biochemistry (ACS): https://pubs.acs.org/toc/bichaw/63/16! This work by V. Chauhan and I. Baptista et al, uses synthetic promoters in tandem formation to show that they produce less RNAs than expected due to collisions between RNAPs that cause premature fall-offs. The new strains and findings could be useful to research of bacterial gene expression and synthetic circuits.

• 7.8.2024. We are very happy to inform that our first synthetic gene library is available in AddGene: www.addgene.org/Andre_Sanches_Ribeiro/

• 31.5.2024. Our newest paper is now available in mSystems: https://doi.org/10.1128/msystems.00065-24! Produced by S Dash et al, the paper presents a library of fluorescent reporters of the global regulators of gene expression of E. coli. These reporters are not available in the largest strain libraries. Thus, the new strains should be useful to many researchers.

• 10.1.2023. We have published a YouTube video of our work on sigma factors (https://www.youtube.com/watch?v=NLVmPHD7TaY)

• 2.12.2022. The 4th LBD Webinar on Biosystems has arrived! We are very happy to see our former students and listen what everyone is working! Wonderful talks and new science. Thank you all!

• Aug 2022: Nucleic Acids Research has now also published an in-house work about genes' supercoiling sensitivity as a trigger for genome-wide cold-shock responses by E. coli. DOI: 10.1093/nar/gkac643.

This is our 3rd study using our new methodology of combining RNA-seq, flow-cytometry, databases, and stochastic models to discover natural response mechanisms to genome-wide stresses. We also explored the conservation of responsive genes and their DNA sequences.

• June 2022: We are thrilled to announce that Nucleic Acids Research has published one of our studies with several collaborators. 

This study provides direct empirical evidence that global topological and logic features of the gene network of E. coli affect its response to a genome wide stress. Our findings could contribute in the design of new models of complex transcriptional programs in large GRNs: DOI:10.1093/nar/gkac540.