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01 Jul 12:12

Major events in the life of a cyanobacterium: elucidating the "to-do list" for wet-up, normal activity, and dry-down

by matt, Geodermatophilia

Fig 1. Subtract out these grasses, and you might have a good analog for the first ecological communities to colonize the land (Beraldi et al. 2013, image: Bowker et al. 2002).

Ever since about 3.5 (+?) billion years ago Earth has been the planet of the cyanobacteria (also correctly called blue-green bacteria and incorrectly called blue-green algae). We may have invented all kinds of interesting names for different parts of Earth's history (age of the fishes, age of the reptiles, etc.) in our animal-centric way, but in the background of all that there were the cyanobacteria quietly conducting the yin of global ecosystem function, primary production (decomposition being the yang). They "invented" oxygenic photosynthesis. They became engulfed by other organisms and were modified into the chloroplasts of plants and one could argue that cyanobacteria and modified cyanobacteria still conduct most of Earth's photosynthesis. These organisms drove mass extinctions, rusted the planet, and allowed a radiation of oxygen consuming organisms like humans by creating an oxygen rich atmosphere. They may have induced some glacial periods by locking up carbon dioxide. They were early colonizers of land, perhaps among the first (Beraldi-Campesi 2013; Fig.1).  They engage in mutualistic relationships with plants and a variety of fungi. They are dominant phytoplankton in the oceans, and they are found in all terrestrial ecosystems from the hottest to the coldest, wettest to the driest. In short the Earth would be a fundamentally different planet without them.

In addition to being a pillar of the biosphere, they must have some very intriguing capabilities to exist essentially anywhere with light and at least occasional water. A case in point are the desert biocrusts, whose chief architect in the cooler deserts is the cyanobacterium Microcoleus vaginatus. They need light to photosynthesize, so they have to be near the soil surface....but think about what that implies: they must be able to tolerate their environment drying out, and they must be able to handle that sun, especially UV, exposure. This leads to two interesting abilities: desiccation tolerance and the ability to move in response to stimuli. Cyanobacteria inhabit the world's deserts because some of them are masters of desiccation tolerance: drying without dying. They pay a cost in terms of cellular damage when they dry down, but unlike you, me, your houseplants, or your dog, losing almost all of their water does not kill them. When dry, they power down completely, and simply sit there until they are moistened by liquid water and can restart their metabolism.

Fig 2. Multiple filaments of Microcoleus vaginatus (appears green) in a shared polysaccharide tube (appears white). Source:
It gets even more interesting. Microcoleus forms threads of cells called filaments. Many filaments bundle together inside a tube of polysaccharides (what a normal person might call slime) that they goop out into the environment (Fig. 2). The tubes often run from a few mm below the soil surface to the very surface. They can slide up and down these slime tubes! Why might they move up? If water is adequate, but light could be better (for example during a rainstorm), the very surface is the place to be. Because of their susceptibility to UV, they can also retreat down a bit if light intensity increases. They also retract back into the soil as it dries, because they don't "want" to desiccate on the surface only to site there for days, weeks or months degrading in the sun (Garcia-Pichel & Pringault 2000).

Because rain events and solar influx are not exactly scheduled events, one might hypothesize that all of these things ought to be regulated by gene expression triggered and set into motion by the wet-up and dry-down events themselves. Recently a team of researchers at the Lawrence Berkeley National Laboratory made the news when they tracked a wetup and dry down period in a biocrust, continually monitoring what genes turned on and off and therefore which processes where engaged. This gives us a glimpse for the first time of a desert cyanobacterium's prioritized to-do list when activated. 

First, check out this video by the Berkeley team of a wet-up event below. You see bubbles of gas forming. This is probably mostly carbon dioxide at first giving way to mostly oxygen later, because respiration is engaged immediately to repair the damage sustained in the last dry-down and photosythesis takes a bit longer to ramp up. You'll see a visible greening as the filaments migrate up their slime tubes to the surface.

Next, check out their other video of a dry-down event. This video begins with a green surface because the filaments are lying there, then you can see the surface become less green because the filaments are retracting into their sheaths. The retracted filaments can now dry-down in peace below the surface without too much risk of major damage by the sun. 

Rajeev L, Nunes da Rocha U, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfield CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A. (2013) Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. The ISME Journal. DOI: 10.1038/ismej.2013.83  

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust

28 May 11:45

A quick guide to making your software installable

by biomickwatson

This post is a blatant excuse to give myself the opportunity to vent some steam :) Some bioinformatics software packages/pipelines are notoriously difficult to install; others have just given no thought whatsoever to environments other than their own.  Here is quick check list of “DOs and DON’Ts” – well, in fact it’s mostly DON’Ts.

When considering the people who will install your software:

  1. Do not assume, under any circumstance, that we have root access.  We may very well have to obey the orders of a paranoid sys/admin who does not allow us root access.  We have to try and work round that.
  2. Do not assume that our system is in any way standard.  It won’t be.  It isn’t.  It never has been.
  3. Do not assume we have the latest anything.  We might do, but it won’t be where you think it is (see (1)).
  4. Do not assume that our Perl, Python etc libraries are in standard places.  See (1) above – we probably had to install them somewhere we could write to.  Yes, we know about $PERL5LIB and $PYTHONPATH – does your install script?
  5. Do not assume the system (/usr/bin/) Perl, Python etc is the one we use.  See (1) above – we probably had to put newer versions of Perl, Python etc somewhere we could write to.
  6. Do not assume, just because it’s not in our PATH, that we don’t have it.  There are all sorts of reasons why we might have something, but not put it in our PATH.
  7. Don’t force us to install, or link, software into a sub-directory of your software.
  8. Don’t force us to download, or link, large databases into a sub-directory of your software.
  9. Don’t assume the user, or the server, has internet access.
  10. Just because you are a developer, doesn’t mean we have all the *-dev packages installed.  Don’t assume we do.
  11. Don’t write an install script that installs something else which installs something else which installs something else etc etc.  If you have multiple dependencies, give us a separate script for each one and let us decide how, when and where it is installed.
  12. We will absolutely, 100% shut down and remove anything that tries to gather statistics and “call home”.  If this feature was a person, we would punch it, it makes us that angry.   Just. Don’t. Do. It.
  13. Do not think, for one second, that providing a VM circumvents any of these problems – it doesn’t.  VMs are occasionally useful, but ultimately, we will need the software on a local server – and the day our sys/admin lets us put your VM onto our network is the day hell freezes over.  And no, AWS is not the solution.  Not at those prices.
  14. DO – write a good step-by-step tutorial on how to install all of the dependencies and your software.  It’ll take time, and you will really not want to do it.  But good devleopers write good documentation.  So go write some.

And breath…..

DISCLAIMER: if you think I am talking about your software and feel offended, then I promise I am not talking about your software.

13 May 12:32

Visualizing the Connectome

by Neuroskeptic, Neuroskeptic_Discover

wow...there are a lot of omes...

Last year, I blogged about a new and very pretty way of displaying the data about the human ‘connectome’ – the wiring between different parts of the brain. But there are many beautiful ways of visualizing the brain’s connections, as neuroscientists Daniel Margulies and colleagues of Leipzig discuss in a colourful paper showcasing these techniques. Here, [...]...

Margulies DS, Böttger J, Watanabe A, & Gorgolewski KJ. (2013) Visualizing the Human Connectome. NeuroImage. PMID: 23660027  

Visualizing the Human Connectome.