Sunday, November 11, 2018

Soviet Sci-Fi

Culture Trip made a good selection of soviet sci-fi movies. Here, I just want to keep it for reference and give little bit of my insight.

First group is movies I haven't seen and definitely want to see. Here we have Inquest of Pilot Pirx (1978) and Dead Man’s Letters (1986).
Pilot Pirx is base on Stanislav Lem's novel which is a good recommendation on its own. Second just seems appealing in terms of story setting.
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In second group is movies I've seen and would strongly recommend. Here are the products of late Soviet era, when censorship weakened.  Kin-Dza-Dza! (1986) is surrealistic and post-apocalyptic style movie with marvelous actors and well written story. Zero City (1988) is better known to western movie lovers. Surrealistic story was a harsh satire on dim reality of late Soviet Union. This kind of movies you don't want to change anything in them and they don't need a "refreshing" modern remake. They good as they are.
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Third group is light weight Sci-Fi made in 1970s. Here goes Moscow-Kassiopeia & Teens in the Universe and Per Aspera ad Astra (1981). They are not really interesting to watch today. The cultural reference and communist propaganda is too far to understand and appreciate even for modern generation of Russians. But, both have really interesting ideas and were technically very well done for it's time. Especially, Moscow-Kassiopeia can be turned into good young-adult movie or tv show.

Forth group movies I didn't see and most likely won't. In my case here are most of the Tarkovsky movies. I know people on the west value his work as a film director, but hear me out. When it comes to Solaris (1972) and Stalker (1979) I cannot accept his interpretation. Both stories are written by S. Lem and author himself wasn't happy how Tarkovsky interpreted his work. He almost completely destroyed original message turning it into cinematically pleasing Hollywood-style drama. I value Lem more than Tarkovsky.


Tuesday, June 26, 2018

Caddisflies

These are adult forms of Zebra caddisflies (Macrostemum zebratum). They barely eat and live only couple of weeks. Only thing they do is fuck, as much and as fast as they can. Life is short, you must try everything.
Before becoming adults they spend most of their lives as larvae crawling on the river bottom eating garbage and building houses out of junk. Once again we can see how creative mother nature is. How much we can learn from it. Even if you hit rock bottom it's not a reason to stop being creative.

Google images "caddisfly larvae case" you'll be amazed how extremely beautiful they are.


Thursday, April 26, 2018

Fail of democracy?

This guy definitely has a point. Democracies are not very effective way of governance. One the main issues Moyo points he calls short-termism. Politicians tend to concentrate on short term solutions, because time in office is short. They need to bring results within 4-5 years to win another elections, as a result politicians leave out long term goals, like infrastructure development.

But, where he misses the point is to develop any stable, effective culture of government takes time. And continuation of culture is most important virtue of effective society.
So, Moyo argument is valid only for countries which experienced interruptions in their cultural continuity. Basically developing countries. The brightest examples here are Asian "developmental dictatorships" (China, Singapore, etc).

In developing countries everything is broken and dilemma is simple: you get a dictator everything is done withing say 25 years or you can establish democracy and wait for 50 years. So, paradoxically enough "developmental dictatorships" appear as a result of the same short-termism Moyo blames makes democracies ineffective.
If we to get rid of short-termism the only known so far viable way to sustain society long term is to develop some form of democratic government. It especially seems to be true if we look at those "developmental dictatorships" today.

Also, bringing US in discussion uncovers weakness of Moyo argument. Because the whole philosophy of American democracy is ineffective, weak federal government. Tern things other way, according to Americans, is going to be dictatorship. As a result US deals with long term issues mostly in state to state level. So, my point is that US is too much of an outlier in that kind of analysis.

Friday, March 23, 2018

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.

Tuesday, March 6, 2018

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.