Guest post on the University of Tartu blog

Communicating research to a wide audience that includes non-scientists is a tough but fun challenge. I recently gave it a go in a guest post on the UT blog:

http://blog.ut.ee/in-the-light-of-evolution/

Us humans are so generous with our genes, but how exactly?

There's been a lot of chatter in the blogo/twittershere this morning about contamination of genomes, which is something I'm rather interested in, simply because I use genomes from all sorts of organisms all the time and I've come across likely contaminants several times.

The sudden interest is down to two papers about human sequences in other genomes: "Abundant Human DNA Contamination Identified in Non-Primate Genome Databases" by Longo et al. in PLoS ONE and "Opportunity and Means: Horizontal Gene Transfer from the Human Host to a Bacterial Pathogen" by Anderson and Seifert in MBio.

Longo et al. found primate-specific repetitive elements in the genomes of many different non-primates, which they put down to contamination from us DNA-shedding humans during sequencing. Anderson and Seifert on the other hand found another element in human pathogen Neisseria gonorrhoeae, which they instead put down to horizontal gene transfer.

Can they both be right? On his blog, Mark Pallen suggests the Anderson and Seifert results might also be contamination, but the debate is ongoing, so check his blog post for the full story.

Some good thoughts about Tartu, the city of good thoughts

So far I haven't blogged about Tartu or Estonia, although I fully intended to when I started writing the blog. So OK, no time like the present.

Tartu town square

"City of good thoughts" is the official nickname of Tartu, and I guess it's supposed to conjure some impression of optimistic musings that might be inspired by the city, or maybe it's referring to the noble academic thoughts that are being spawned in the university. Maybe both. Anyway, Tartu has plenty of quirks, but on the whole I have good, positive thoughts about the place. So that's what this post will be about.

Tartu University main building. Lots of good thoughts going on inside, I'm sure. Though mostly administrative thoughts in this particular building. 

I moved from the UK in 2008 and spent two years working in Uppsala, Sweden. That happens to be where I am right now incidentally, since my partner Vasya has some work on at the uni here. Although it was a bumpy ride in Uppsala and I initially, unfairly blamed the country for that, over time I mentally separated the country from the stresses, and I grew to realise that I actually love Sweden, and would not mind ending up here. The country is beautiful, the quality of life is good and the language is learnable. I also have good friends here. So, I'd got used to Sweden, and I was a bit apprehensive about moving to Tartu to be honest... no mountains or coasts nearby, dreadful food (I'd visited Vasya several times and experienced some food horrors) and a frighteningly difficult language. I was expecting ex-soviet dreariness. But, after only 5 months living there, it really feels like home, unexpectedly so. And I wasn't hugely looking forward to leaving. 

What helps feeling settled of course is having a job you enjoy and being with your loved one in a cosy home. I have all of those, which are after all the main things that influence happiness in life (so I heard somewhere), and so I'm very content.

Our apartment in September (you can spot Vasya playing guitar on the balcony)...

...and just a couple of months later (too cold for outdoor serenades)

But home life and work life aren't the only things about Tartu that I like. Here are a few other things:

1. It's just so different. It's really not like Britain, and though I'm proud to be British, I feel like I know my homeland pretty well, and it's an adventure trying on a strange country for size. And Estonia really can be very strange, and therefore funny. Maybe it's my taste in surreal humour...

This slightly terrifying merry-go-round appears every christmas. That's my British mate Ady, riding the filter-feeder pig.

Last christmas a miniature galleon also suddenly appeared in town.

2. There are plenty of pubs. I'm a Brit. I just love pubs. I also appreciate that there is no state monopoly on alcohol and ridiculous alcohol buying hours like there are in Sweden.

3. Eating out in good restaurants is affordable. OK, so the food is so-so at best in the majority of places, but other places are fab, particularly the French place 'Crepe', The Italian place 'La Dolce Vita' and... I've forgotten its name, but the Georgian place. The Indian place Asian Chef is supposed to be great too, but we haven't tried it yet. By the by, here's a link a great blog on Tartu restaurants.

4. It's rustic. Most things are made from wood. Houses, utensils, stuff like that. I like that. Maybe because my dad is a retired woodwork teacher. Souvenirs are genuine handicrafts, wood and wool. We have an open fire at home, and we get trailer-loads of wood delivered that we stack in our wood shed. It's so far from the stark, institution-like apartment blocks of Sweden. Snuggling by the fire when it's snowing outside is heaven!

The September arrival of our wood for the winter! We've had to get another load delivered since then.

A cute, rustic cobbled street

Wooden houses come in large size too

5. It's semi-Russian. Vasya is Russian by birth, Belorussian by passport, and so I'm curious about Eastern cultures. Again, very different to Britain.

6. The snowy winters. I love snow. Our Estonian friend Arvi is "sick of this white shit", but I can't get enough of it. Hmm maybe that will all change when we buy a car though...

"Snoooooowwwww!"

7.  The people. We know some great people in Tartu, including Vasya's and my boss Tanel, who we call the Godfather. That's less in the scary mafia way, and more in the wish-granting fairy godmother kind of way.

So those are the main things! Oh also, there's the fact that Tallinn isn't too far away, and it's beautiful.

Tallinn at Christmas

Tallin city walls

So there you go!

Pic from www.visittartu.com

RNA is so passé. Mitochondrial ribosomes ditch rRNA in favour of protein

Mitochondria are the energy-producing organelles of eukaryotes that evolved from a endosymbiotic bacterial ancestor, probably before the divergence of all known eukaryotes. They retain a minimal genome, which in humans amounts to just 37 genes: 13 for components of respiratory complexes and 24 for translation (22 transfer (t) RNAs and 2 ribosomal (r) RNAs).

Translation is pretty bizarre in mitochondria, and very different among different eukaryotic lineages in terms of mRNA features and involvement of protein factors. Vasya has covered some peculiarities of mitochondrial information processing in his blog posts here, here and here. I want to touch upon another part of it: rRNA reduction and replacement with protein.

The mammalian mitochondrial ribosome is bigger than that of its bacterial counterpart, however it contains less RNA, with the remainder of its mass being made up of ribosomal proteins (RBPs) that are encoded in the nucleus and post-translationally targeted to mitochondria. The extra RBPs that have evolved to replace the RNA tend to have no recognisable homologues in prokaryotic or eukaryotic cytoplasmic proteomes, and are evolving faster than cytoplasmic RBPs (O'Brien, 2002). 

Nematode ribosomes are even more striking in their rRNA loss, as you can see from the figure below, and are even more protein-rich (Watanabe, 2010; Zhao et al., 2005).

Figure and caption from WATANABE, K. (2010): Three-dimensional models for large mt ribosomal RNA (gray) from mammalian (middle) and C. elegans (right) mitochondria, based on the crystal structure of a bacterial 50S subunit108) (left). The outline shows an edge line of the crystal structure of the 50S subunit from the crown view. Some functional rRNA domains are colored: red, P loop; blue, A loop; green, S/R loop; light blue, L2 binding helix (H66). The topological orientation of the ribosomal protein is based on the model for the mammalian mt ribosome.

So why is this happening? Maybe this replacement of RNA with protein is a part of the ongoing transition from the RNA world into the protein world. But why is this replacement so pronounced in mitochondria? I wonder whether instead, it might be linked to RNA stability within the unique mitochondrial environment. Only very few mRNAs are present in mitochondria. For most of the proteins required there, the mRNA and proteins are made elsewhere in the cell and only then targeted to mitochondria. Perhaps mitochondrial chemistry isn't RNA-friendly, and it's beneficial for the cell to cut it down wherever possible and replace with more stable protein. I'm intrigued, but really not sure about this, and couldn't find any references to back up the idea, so I'd be grateful for any comments or links to references that any readers may have!

O'Brien TW (2002). Evolution of a protein-rich mitochondrial ribosome: implications for human genetic disease. Gene, 286 (1), 73-9 PMID: 11943462

WATANABE, K. (2010). Unique features of animal mitochondrial translation systems Proceedings of the Japan Academy, Series B, 86 (1), 11-39 DOI: 10.2183/pjab.86.11

Zhao F, Ohtsuki T, Yamada K, Yoshinari S, Kita K, Watanabe Y, & Watanabe K (2005). Isolation and physiochemical properties of protein-rich nematode mitochondrial ribosomes. Biochemistry, 44 (25), 9232-7 PMID: 15966747

I love snowboarding

Vasya and I are back in Uppsala, Sweden for while, and Sweden in February means snowboarding! Here is me at Romme Alpin yesterday, boarding, falling and boarding again.

It was so good to be in the fresh mountain air after a week of working at home, and it was beautiful weather. Simply a perfect day on the mountain! And next weekend, we'll go back to Romme for my other winter sport love: downhill skiing!