Pan-genome of three genera

Here is another example of using Circos diagrams to visualize biological data. This time it is the concept of bacterial pan-genome.

These days sequencing become very cheap and data on bacterial genomes accumulates particularly fast. As of today GeneBank contains information on 131801 bacterial genomes, but thousands more are sequenced every day without being published. Faced with such load of information in their hands researches were able to look deeper in intra-species genome organisation. Having so many genomes allows you to ask questions like, what part of genome common for particular species? What composition of those common features makes a species?

Compared to animals, bacterial genomes are more dynamic as a result of horizontal gene transfer (HGT) between individual cells. Often HGT appears between different strains of same species, but sometimes can go even further, passing genes to other taxonomic groups (families and classes).

 If we take, for example, a genus of bacteria (doesn't matter which) and compare all genomes we have on the global scale there will be three areas. Some areas of genomes are unique, because they usually found only in a few species of the genus. These unique areas often are result of HTG and might find more similarity with species from other genera or even family. Other areas, called variable, are common for almost all species in the genus, but prone to mutation. Finally the third group of regions are specific to particular taxonomic group. These areas called core genome. Both variable and core genome regions make a pan-genome. Pan-genome regions create a signature, typical genome for particular species or genus. Genome that is shared among all members of particular taxon.

In the outer circle green shows core areas in pan-genomes of three genera. Those genes that are shared among more than 90% of all strains used in the analysis.

Second circle is called GC% content. Which basically means what percentage GC bases in particular gene. This matters because genomes that make up a genus usually have similar GC%. In this case for example, Arcobacter usually has 27%, similar to Campylobacter. In the diagram threshold is set to 28% GC and everything over it highlighted red (in light blue area). You can see that Helicobacter has different GC% from other two. It doesn't it somthing wrong, it's just different.

Another important point of GC% graph it allow to see foreign elements. If some genes or genome regions have GC% content significantly different from rest of the genome, it most likely appeared there recently through HGT. If you look at Helicobacter diagram you can easily see that some regions of GC% are not colored red. More interestingly if you look at pan-genome diagram above, you wont find green or grey stripes. These are most likely candidates for Unique regions.


How virulence factors related to pan-genome.

Figure caption: Connection and distribution of virulence factors between pan-genomes of three genera based on all available complete genome sequences. Outer circle 1 showing region similarity ranging 90-100% (indicated in dark green bars) to 80-90% and 70-80% (indicated in light green and gray bars).  Circle 2 shows GC content where upper (indicated in light blue) and lower (light red) boundaries set to 40% and 20%, respectively.  Circle 3 shows histogram of the distribution frequency of variable and core genes where Red bars indicate genes shared by number of strains to each particular cluster, whereas Blue bars represent heterogeneity of number of strains to that cluster. Circle 4 shows virulence, antibiotic resistance and toxin genes identified in pan-genomes of each genus. GenBank identifiers (GIs) from virulence factor database (VFDB) (black), Comprehensive Antibiotic Resistance Database (CARD) (green) and Toxin-antitoxin database (TADB) (blue). IDs shown in Red are connected by lines (in the center) where connecting lines in the center link to the IDs found in pan-genomes of three genera showing homologous virulence factor (blue), antibiotic resistance (green) and toxin (purple) genes.

Trascriptome analysis of programmed cell death in Cryphonectria parasitica

This is the first post in series dedicated to my research and project I'm involved in. Also, I'm going to bring here some analysis work I'm doing just to myself. To find out more follow the tags #myresearch and #myanalysis.

This time I'll bring an example of how to use Circos tool to visualize genomic and transcriptomics data. This tool is visually very appealing, but more you put on the graph less useful it becomes.

Before we start I want to introduce one basic concept from mycology, barrage. On figure below barrage shown by arrows and compatible strains' interactions shown by arrowheads.

In a nutshell barrage or incompatibility reaction is a form of innate immune response that causes two genetically distinct fungal strains reject each other. In fungal world most of interactions between strains happen through hyphal fusion or anastomosis. If all immune signals check and no disagreement found two strains fuse and continue to exist as a single individual. But if immune response triggered, two strains form a barrage, a separation wall made out of dead cells. Barrage separates two strains restricting exchange of genetic material. It gives us a glimpse into early evolution of sexual reproduction and immunity. Basically saying if we too different from each other genetically direct exchange of genes may cause more damage than good, so lets have sex instead.

Circular diagram below shows genes differentially expressed in C. parasitica during incompatibility reaction.

This diagram allows to see overall picture of how C. parasitica genes (red dots) behave in relation to genome map. Plus you can compare them to genes of P. anserina (purple) and N. crassa (green) in similar reaction. Not particularly informative, but you certainly can take something out of it.

First of all C. parasitica  has much more upregulated genes (pink area) than other two fungi. Also there are transcriptionally inert areas of genome, showing no gene activation. And finally lack of correlation in expression rate between three species. Basically red dots do not appear together with purple and green, showing different or no expression at all.

Figure caption: Gene differential expression (DE) shown on C. parasitica genome map (11 largest scaffolds).
Diagrams from outside to inside: Black lines show genome map of 11 scaffolds, each tick mark corresponds to 100,000 bp. Inside the outer black lines, blue marks indicate previously annotated genes on JGI C. parasitica genome portal and orange marks indicate novel genes. Novel genes are transcripts which demonstrated detectable level of expression in areas of genome previously not annotated on genome portal. First circle shows expressed genes, and second circle shows DE genes during barrage. Interior to this are C. parasitica gene IDs of DE genes where black IDs indicate genes differentially expressed during barrage only in C. parasitica, green and purple IDs indicate that orthologs of those genes are DE during Heterokaryon Incompatibility (HI) in N. crassa and P. anserina respectively. The inner-most pink, grey and blue bands show plots of individual genes expression. The Y axis indicates genes differential expression in log2 scale. Y axis pink colour indicates upregulated (y> 2), blue – downregulated (y< -2) and grey (2>y>-2) indicate non-DE genes. Red dots indicate C. parasitica genes, green and purple dots indicate DE orthologs during HI in N. crassa and P. anserina respectively.

Painkillers

Article on opioid epidemics.
While it is really an issue, problem do seems to be a bit overblown.
In these kind of cases I blame how in western countries journalists like first hand experience.
You can never find a report in press generally describing an issue. Informing you on overall matter. It is always have to be accompanied by interviews with real simple folks who got  into it.
Of course it gives the problem a human face, something to relate to. But often it creates biases. As people tend to believe testimonies more than to careful analysis.

MH17

History

V.V. Shulgin is a person with very interesting history. He was Russian nationalist, monarchist, constitutional monarchy advocate  and one of the members of white movement (called white as opposed to red,old Russia anti-bolshevik movement). Was a member of all sessions of Duma (first Russian parliament). He was among those who accepted abdication of Nicholas II.

So, conservative, nationalist and one who was fighting communists, after all in 1920 wrote this (highlights are mine):

...our ideas jumped over forefront...they (bolsheviks) rebuild Russian army... It might be terrible to acknowledge that, but it's what it is... Bolsheviks raised the Flag of United Russia... Communist International appeared as weapon... to expand Russia's territory...and Moscow power... no one can deny, russian language again rules over 1/6 of the world and all that in the name of Communist International... bolsheviks: 1) rebuilding Russian army; 2) restoring Russian borders... 3) preparing the return of Russia's Tsar.

Valuable lesson here: Some people may appear wise and insightful, by just being narrow minded. It just happens sometimes that time steps on the same tracks with your narrow point of view. Never for long, though.

Cambodia

Some thoughts about Cambodia.
Money

That was tough experience converting between Riel and USD. And I think they should ban using dollars. It makes everything more expensive. I mean most stuff costs $1, because it's hard to split it further without using local money. Like in Thailand, $1 is about 60 baht. So you can conveniently split dollar at least by 6.

Beggars

People constantly begging for money almost everywhere. Victims of war, mothers with babies or children with big eyes. Striking thing was not that I never seen it before. I've seen lots of stuff like that back in Russia. It was that I haven't noticed anything like that in Thailand. Still mistery for me.
Sometimes it is interesting what things remind me about my motherland. When I talk with Chinese (esspessially mainland and HK) they remind me Russians by their lifestyle choices and maybe a bit of temperament. And now beggars in Cambodia.

Random thoughts

God created everything in 7 days. It's a biblical myth usually called 6 days creation. But we know that a day is one rotation of Earth around the sun. And according to the story Earth appears only on second "day", after the sun (light). So, considering that it should be called 5ish days creation.

Climate

This is interesting.

So apparently, Exxon accuses Rockefeller to plot a climate change conspiracy against them.

Interesting times indeed.

http://www.nytimes.com/2016/11/21/science/exxon-mobil-rockefellers-climate-change.html

Pronauns

Peterson is right that legislature on the subject of pronouns is bad idea. It is rather silly that I can butcher person's name, but must use right pronoun. But he's wrong about being so stubborn on his refusal to call people whatever way they want. At the beginning of term every teacher takes students list in his or her or zie or per class and establishes how students want to be called.

And I have the same issue as Peterson, having a hard time to remember students names. But if there is no law forcing me do so whole pronouns story doesn't make much difference. I can't remember names of 90% of students (well ok, people), but now in addition to that I won't be able to remember their pronouns. In most cases names I remember are students who perform well in class or ask a lot of questions. If student makes those efforts in class, I will make an effort to remember names, nicknames, pronouns etc. I feel it is feir enough. 

Mozart - Requiem

This is one those thing which staed with me since childhood.
An amazing piece of music from first minute till the last.
  

Russia

Putin threatens to suspended Plutonium treaty. He want US to withdraw forces from Eastern Europe and cancel sanctions against corrupt officials and ones related to annexation of Crimea. 

Considering that US recently cancelled negotiations with him on Syria issues it looks quite interesting. Basically, he's showing that he's wants new negotiations.

Putin clearly demonstrated in recent years that for him process of  negotiations and all this hassle with Americans on the global stage is more important than solving issues on the table. Basically for him longer it lasts the better. Americans realized it long time ago, but only recently started to be practical about it. They started to do the worst! They started to ignore him. And I think it is right thing to do. As one the main rules of internet says: "Don't feed the trolls!".

Biggest problem though, it is absolutely impossible to say what Putin's reaction will be. 

http://www.reuters.com/article/us-russia-usa-nuclear-idUSKCN1230YN

Trump support

Some good thoughts on Trump from Scott Aaronson.

Would Trump moderate his insane “policies” once elected?  I don’t know, but I’d say that electing someone who promises to ignore the rule of law, in the hope that they don’t really mean it, has one of the worst track records of any idea in human history. 

I think people support Trump for the same reason why second-graders support the class clown who calls the teacher a fart-brain to her face.  It’s not that the class literally agrees that the teacher’s cranium is filled with intestinal gases, or considers that an important question to raise.  It’s simply that the clown had the guts to stand up to this scolding authority figure who presumes to tell the class every day what they are and aren’t allowed to think.  (As far as I can tell, this has also been the central operating principle of right-wing shock artists over the decades, from Rush Limbaugh to Ann Coulter to Milo Yiannopoulos.)

[...] 

The truth is, there’s a movement that’s very effectively wielded social media to remake the public face of progressive activism—to the point where today, progressivism could strike an outside observer as being less about stopping climate change, raising the minimum wage, or investing in public transit than simply about ruining the lives of Brendan Eich and Matt Taylor and Tim Hunt and Erika Christakis and Dongle Guy and Elevator Guy and anyone else who tells the wrong joke, wears the wrong shirt, or sends the wrong email.  It strikes me that this movement never understood the extent to which progressive social values were already winning, with no need for this sort of vindictiveness.  It’s insisted instead on treating its vanquished culture-war enemies as shortsightedly as the Allies treated the Germans at Versailles.

So yes, I do think that the bullying wing of the social-justice left bears at least some minor, indirect responsibility for the rise of Trump.  If you demonstrate enough times that even people who are trying to be decent will still get fired, jeered at, and publicly shamed over the tiniest ideological misstep, then eventually some of those who you’ve frightened might turn toward a demagogue who’s incapable of shame.

http://www.scottaaronson.com/blog/?p=2777

Biologist life

So, I was looking for concise (slim) gene ontology (GO) annotation.
Being concentrated on my writing I opened new browser tab and googled "GO slim".
I feel like that little girl who searched for "wet pussy".

BLM

Let's see if I understand it right.
Pride parade is an event which gather all kinds of people, which support all possible inclusiveness and equality you can only think of.
So blacklivesmatter decided to harass the very crowd they can find the most support from demanding to make Pride parade less inclusive.

Wild thoughts

In a world where mosquitoes sucking fat instead of blood, swamps would be full of rich and glamorous people and Siberia would be a resort.

Для истории

Пророчество:
Следующая война России будет с Казахстаном.

Cordyceps militaris

Browsing some fungus stuff today (some think that this is the only thing I do in my life) and found very interesting paper on Cordyceps militaris [2]. Fungus with very peculiar appearance and priced remedy in traditional Chinese medicine. It likes silkworms and rice (I feel we have so much in common).

As you can see on the picture this fungus producing it's fruiting bodies on infected pupa, what means the harvest is not too big. And when it comes to almost any traditional medicine, more rare it is more diseases it can cure. For this fungus list goes on and on, it is basically anti-everything [1]. So no surprise that market value comes to $10 000 per kilo. Good news for consumers here is that they didn't find any known genes of mycotoxins in the genome. So, at least it's harmless.

Very little is known about it's life cycle. Cordyceps infects pupas and can survive in soil to a certain degree and that's about it. They are proposed as teleomorphic stage for Metarhizium spp.  Peculiar thing is that Cordyceps is heterothallic, but it can produce fruiting bodies even when only one mating type is present. Problem though is that those fruiting bodies don't produce asci (on 3rd picture a and b).

1. Das, S. K., et al. (2010), 'Medicinal uses of the mushroom Cordyceps militaris: current state and prospects', Fitoterapia, 81 (8), 961-8.
2. Zheng, P., et al. (2011), 'Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine', Genome Biol, 12 (11), R116.

Story about M.

So, I asked M. (my supervisor) today that we need some "Items" in the lab. We try to look it up in the lab again and couldn't find any. Then he says:
M: Ok, stay here, don't go anywhere, I'll bring you one!
Me: Are you sure? I can help.
M: No, no! Just stay here! Don't go anywhere!

Then he brings it.
Me: Should I return it after I'm done!
M.: *relaxed* No, don't worry about it.
Me: But, to where?
M.:*pointing his finger up* Exactly!

Film

Those moments when you develop a film are amazing. I still remember them since I was a kid. And when this guy was taking out his film from rolls after processing it you can feel how wonderful it is.

Those moments are priceless. You spend whole the day developing films you brought from a trip, all those pictures taken months ago. And now they are ready and you can finally see them. You hold your breath and impassionately putting it against the light, trying to recognize familiar faces and scenes on those negatives.

And what now. You take a shot, look at the screen, say something like: "Blah!". And delete it.

I love digital photography and probably will never go back to the actual film. But I miss those days and especially those moments.

Cakes

So, when, say, bouncer not letting you inside a club, because he didn't like the way you look it feels bad, but people manage to deal with that. But it's not ok to refuse service when it comes to homophobic bakers and florists. Why?

My guess would be that when it comes to food people feel totally different about discrimination. 

Just try to feel following situations:

Phrase "I'm not letting you in coz you should dress better" feels offencive, sad and just wrong. 

But phrase "I'm not giving you that cake coz your dress is ugly!" sounds so inhumane and facist.