Category Archives: DNA and RNA

Walk through a cell

In 2022, Maritan et al. released the first ever macromolecular model of an entire cell. The cell in question is a bacterial cell from the genus Mycoplasma. If you’re a biologist, you likely know Mycoplasma as a common cell culture contaminant.

Now, through the work of app developer Timothy Davison, you can interactively explore this cell model from the comfort of your iPhone or Apple Vision Pro. Here are three reasons why I like CellWalk:

1. It’s pretty

The visuals of CellWalk are striking. The app offers a rich depiction of the cell, allowing the user to zoom from the whole cell to individual atoms. I spent a while clicking through each protein I could see to see if I could guess what it was or what it did. Zooming out, CellWalk offers a beautiful tripartite cross section of the cell, showing first the lipid membrane, then a colourful jumble-bag of all its cellular proteins, and then finally the spaghetti-like polynucleic acids.

Tripartite cross section of a Mycoplasma cell. Screengrab taken from the CellWalk app on my phone.
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An evolutionary lens for understanding cancer and its treatment

I recently found myself in the Oxford Blackwells’ Norrington Room browsing the shelves for some holiday reading. One book in particular caught my eye, a blend of evolution — a topic that has long interested me — and cancer biology, a topic I’m increasingly exposed to in immune repertoire analysis collaborations but on which I am assuredly “non-expert”!

Paperback cover of “The Cheating Cell” by Athene Aktipis.

The Cheating Cell by Athene Aktipis provides a theoretical framework for understanding cancer by considering it as a logical sequitor of the advent of successful multicellular life.

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The evolution, evolvability and engineering of gene regulatory DNA

Catching up on the literature is one of the highlights of my job as a scientist. True, sometimes you can be overwhelmed by the amount of information you don’t have; or wonder if we really need another paper showing that protein-ligand scoring functions don’t work. And yet, sometimes you find excellent research that you can’t but regard with a mixture of awe and envy. At a recent group meeting, I discussed one such paper from the research group of Aviv Regev at MIT, where the authors perform an impressive combination of computation and experiment to consider some basic questions in gene regulation and evolution. Here is why I think it’s excellent.

The authors are interested in promoters, small sequences of DNA that precede genes, which are known to regulate how frequently their partners will be expressed. In short, these promoters are binding sites for transcription factors, a family of proteins that in turn recruit RNA polymerase to transcribe DNA to RNA. In turn, albeit not directly, the rate of gene transcription determines the rate at which a protein is produced. If this sounds simple, however, that is where our understanding stops. The human genome encodes some 1.6k different transcription factors (~6-7% of protein-coding genes) and their underworkings are still not well-understood.

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New review on BCR/antibody repertoire analysis out in MAbs!

In our latest immunoinformatics review, OPIG has teamed up with experienced antibody consultant Dr. Anthony Rees to outline the evidence for BCR/antibody repertoire convergence on common epitopes post-pathogen exposure, and all the ways we can go about detecting it from repertoire gene sequencing data. We highlight the new advances in the repertoire functional analysis field, including the role for OPIG’s latest tools for structure-aware antibody analytics: Structural Annotation of AntiBody repertoires+ (SAAB+), Paratyping, Ab-Ligity, Repertoire Structural Profiling & Structural Profiling of Antibodies to Cluster by Epitope (‘SPACE’).

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RNA-Seq for dummies

RNA sequencing (RNA-Seq) is a powerful technique to study the transcriptome of an organism at a given moment. As its name suggests, RNA-Seq is sequencing the RNA molecules from the sample. But how are the samples prepared? Here I will present a summary of this process:

Disclaimer: This post is not a guide or protocol to perform RNA extraction for RNA-Seq. The objective giving an overview of the process, highlighting the most important steps. 

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