Lab news
Papers, Blog posts, news…
November 23, 2023 - Modesto Promoted to PPL (Associate Professor)
We are happy to share that our PI was promoted to “Profesor Permanente Laboral”, a permanent position in teaching and research. 🍾🍾
August 21, 2023 - New Paper Alert!
It took some time, but our new method for whole genome and metagenomes DNA amplification is just published in NAR Genomics and Bioinformatics: https://academic.oup.com/nargab/article/5/3/lqad073/7246555
\(\\\) This work was led by @CarlosDOC_, with the participation of @karmayoral from the lab. We were also very fortunate to be able to count on the collaboration of Dr. Conceiçao Egas from Biocant-CNC (Portugal).
In this work, we used the piPolB to develop new methods for whole genome and metagenome amplification (WGA). We used the piPolB in two different protocols: (1) piPolB MDA and (2) piMDA, with piPolB in combination with a Φ29 DNA polymerase (Φ29DNAP). In short, the second proved to be a great protocol, outperforming all previously available methods. In particular, our piMDA method (piPolB + Φ29DNAP) provides not only high DNA yield but also a very competent and unbiased coverage for sequences with high GC content, usually the Achilles heel of most MDA methods.
Along the way, we found that piPolB is capable of ab initio DNA synthesis, without DNA primers or templates. This activity has been described before for other polymerases, especially thermoresistant enzymes, but it is often neglected in the literature. Ab initio DNA synthesis by piPolB is negligible for optimized piMDA methods, but is of importance for piPolB solo amplifications. Ongoing work aims to understand how this spurious DNA synthesis is regulated and control it to developing improved piPolB-base MDA methodologies.
We have performed deep sequencing and a detailed comparison of non-amplified samples with samples that were amplified with piPolB MDA and piMDA, with and without a previous alkaline denaturation step. Additionally, we compared the piPolB-based methods with two commercially available kits based on Φ29DNAP, namely RepliG (Qiagen) for Random-Primers MDA and TruePrime (4BaseBio) for a primase-based MDA.
All in all, we can conclude that piMDA methods enable proficient WGA of a wide range of genomes for downstream applications, including those related to the study of microbiome diversity in different environments, especially in environments where high-GC microorganisms, such as halophiles or thermophiles, would predominate. In addition, our results suggest that piMDA has great potential for application in microbiome studies involving DNA amplification, such as those using single-cell metagenomics to reconstruct strain-resolved genomes of microbial communities at once, at the risk of missing poorly represented sequences with high GC content.
Finally, we would like to dedicate this work to the memory of Professor Margarita Salas, for her long and inspiring support in our careers and for her seminal contributions to the discovery of piPolB and the early development of this project.
June 15, 2023 - European patent application for piPolB granted!
The WIPO site publishes today the decision to grant the European Patent of piPolB, entitled “Primer-independent DNA polymerases and their use for DNA synthesis”, with ref. EP305029628.
May 29, 2023 - New Paper Alert
We are happy to share our new review on DNA polymerases for whole (meta)genome amplification: https://mdpi.com/1422-0067/24/11/9331 by @CarlosDOC_ and @mredrejo
Jul 23, 2022 - CIVIS Summer School: Bioinformatics for non bioinformaticians.
Modesto was one of the lectures in this great summer school @uni_tue, hosted by Profs. Thorsten Schmidt and Andre F. Martins.
Jul 27, 2020 - Pipolins provided an opportunity to study diversity and variability of self-replicative genetic mobile elements in circulating bacteria
Behind the paper in Nature Microbiology Community. Link