Categories
Genomics News Research

A genetic basis for COVID susceptibility

A paper published yesterday supports a hypothesis that Richard Nichols and I made in March 2020. We published an article in The Conversation arguing that we need to know if someone’s chances of severe COVID symptoms are affected by their genes.

We suggested:

“It may be that just one or two genes are involved. Perhaps broken genes involved in the immune system or lung cell surfaces…It may be that there are thousands of genes involved. Perhaps a complex mix of genes involved in lung physiology, upper respiratory tract shape, and many other things we have never even thought of.”

Yesterday, the journal Science published a paper that begins to confirm this. It reports the discovery of broken immune system genes in some patients that have severe COVID symptoms.

The paper, titled “Inborn errors of type I IFN immunity in patients with life-threatening COVID-19” gives evidence that thirteen genes involved in the immune system have loss-of-function variants in a subset of patients with severe COVID symptoms.

An accompanying paper, titled “Auto-antibodies against type I IFNs in patients with life-threatening COVID-19” gives additional evidence that type I IFNs are critical to the body’s immune response to COVID. Impairment of their functioning leads to more severe symptoms in the patients they studied.

These studies are based on relatively small numbers of patients, and only studied a handful of genes that seemed likely from the outset to be involve in COVID immunity. If genome-wide association studies were conducted on large numbers of patients, as Richard Nichols and I suggested in March, we may discover that the 13 genes reported yesterday are just the tip of the iceberg.

Categories
Genomics News Research

Could we predict personal coronavirus risk from our DNA?

This article, co-authored with my colleague Prof. Richard Nichols, was published at The Conversation on 17th March 2020. Since then, Science has published a news article about efforts to do the type of studies that we advocated. NB. This is not about testing to see if we have coronavirus – this is about testing how badly affected we would be if we got it.

Coronavirus: sequencing the DNA of patients screened for coronavirus might save lives

Scientists should start sequencing the genomes of coronavirus patients. We should look for DNA differences between patients who are severely affected and those with mild symptoms. This could allow us to predict who else would be vulnerable and advise them to take precautions. We may be able to use this knowledge against the coronavirus epidemic before a vaccine is widely available.

Categories
Genomics Research

Lost elms of Kent

Mature elm trees in the English landscape are something I and many other have never seen. Dutch Elm Disease killed them all in the 1960s. Only the older generation can remember what we have lost. Browsing through some local photos from the 1930s this weekend, my eyes were opened to the size and grace of the elms that once existed. Here are some of those photos, from Capel, Kent. Beneath each one I show a picture of what the scenes look like today.

Categories
Research

How to lead a journal club

Getting together to discuss a published paper is a classic way of keeping on top of the literature and training students how to read it.

During my postgraduate studies I went to a journal club every week organised by my PhD supervisor. It was here that I learned how to read a scientific paper, and gained confidence in critiquing published studies. Now I run a journal club for my MSc students, and sometimes (but not often enough!) for my PhD students. Here are some tips I give my students before they lead a journal club meeting.

Categories
Genomics News Oak Research

PhD studentship: Genomics of oak trees and their microbiota

I have just advertised a new PhD studentship opportunity on FindAPhD.com. I am really excited about this project, and we have a huge amount on data already in hand for the new student to analyse. Here is the project description:

Categories
Genomics Research

“Abundant bioactivity” of random DNA sequences?

This blog was written for the Nature Ecology and Evolution Community where it is posted here.

Probing the claims of a recent study

Readers of this blog will be aware of the recent Nature Ecology and Evolution paper entitled “Random sequences are an abundant source of bioactive RNAs or peptides”. Rafik Neme, the first author, posted an engaging Behind the Paper blog here.

On a quick look, I thought the study might be the beginnings of the solution to the mystery of orphan genes. (I posted about orphan genes here a few months ago.) The paper appears to demonstrate that an unexpectedly high percentage of random 150 base-pair DNA sequences are functional when expressed in E. coli. If true, this would suggest that de novo gene evolution could occur easily from junk DNA.

Categories
News Research

Darwin’s abominable mystery

This blog was written for the Nature Ecology and Evolution Community where it is posted here

One of the hidden gems of Royal Botanic Gardens Kew is its library. I spent several happy hours there researching a recent letter to Nature Ecology and Evolution, published in June under the title “The deepening of Darwin’s abominable mystery“.

Categories
Ash Genomics Research

The evolutionary mystery of orphan genes

This blog was written for the Nature Ecology and Evolution Community where it is posted here.

Every newly sequenced genome contains genes with no traceable evolutionary descent – the ash genome was no exception

This week in Nature I and my co-authors published the ash tree genome. Within it we found 38,852 protein-coding genes. Of these one quarter (9,604) were unique to ash. On the basis of our research so far, I cannot suggest shared evolutionary ancestry for these genes with those in ten other plants we compared ash to: coffee, grape, loblolly pine, monkey flower, poplar, tomato, Amborella, Arabidopsis, barrel medic, and bladderwort. This is despite the fact that monkey flower and bladderwort are in the same taxonomic order (Lamiales) as ash.

Categories
Research

Phenotypic plasticity drives cichlid radiations?

This blog was first posted here at Nature Ecology & Evolution Community on 8 December 2016

Rapid convergent radiations and the Extended Evolutionary Synthesis

At the Royal Society last month, I was listening to proponents of the “extended evolutionary synthesis” (EES). Patrick Goymer has blogged this meeting for Nature Ecology & Evolution, and tweets from it can be found on Storify. The debates have rumbled on in the back of my mind since, especially the contention that phenotypic plasticity is too neglected in evolutionary biology. I was therefore fascinated to stumble upon a paper in press at Molecular Ecology which suggests an impressive case of phenotypic plasticity accelerating evolution. Ralf Schneider and Axel Meyer argue that rapid, convergent radiations of cichlid fish in East African Lakes have been greatly facilitated by morphological plasticity, and its fixation as regulatory networks degenerate. “The cichlids of Africa’s lakes impress us mightily with what evolution can do in a short space of time”, wrote Richard Dawkins in The Greatest Show on Earth (Bantam Press, 2009). Will these radiations become textbook examples of the EES in action?

Categories
Ash Genomics Oak Research

Telegraph article: British woodlands need diversity from around the world

This article was written for The Daily Telegraph and is published online here.

Foreign tree species are needed to help preserve Britain’s woodlands from disease, argues Dr Richard Buggs.

Trees in Britain do not have enough genetic diversity to cope with a global influx of pathogens.

As global trade introduces new pests and diseases, we face ecological and economic disaster as one after another tree species succumb to imported diseases.