As seawater freezes into sea ice, all of the dissolved constituents of the water become concentrated within the solid ice matrix that forms. Because it is more dense than seawater due to the high salt content, a lot of this ‘brine’ will drain from the ice by gravity. However, some brine remains in the ice [...]

One way to assess the microbial community structure in an environment is to use a ‘fingerprinting’ technique, like T-RFLP or ARISA, to interrogate the ’species’ living there as determined from their 16S rRNA genes or some functional gene like amoA. Here’s an example of a T-RFLP electropherogram from sea ice:

You can see that most of [...]

I wrote my last paper in LaTeX and the submitted file was named ‘paper_v26′. Various other files with similar names are floating around and it is a chore to keep up with which is the latest version when they are split between two computers and three operating systems. For my thesis I decided to [...]

I added the following lines to my ‘/etc/apt/sources.list’
deb http://techno.mikro.biologie.tu-muenchen.de/debian intrepid non-free
deb http://techno.mikro.biologie.tu-muenchen.de/debian hardy non-free
and installed the packages arb (base installation), transfig (something to do with LaTeX), xfig (for exporting trees), and libmotif3 (for library libXm.so.3)
sudo apt-get install arb transfig, xfig, libmotif3
More info here: http://techno.mikro.biologie.tu-muenchen.de/

This is my general phylogeny workflow, starting with raw FASTA sequences and ending in a maximum parsimony or maximum likelihood phylogenetic tree with distances. Programs used: ARB 07.12.06org, Seaview, PAUP* 4.0 beta 10 (MacOSX), PHYLIP 3.68, ModelTest Server 1.0, PRAP2, Inkscape, XFIG.

get sequences into ARB, via e.g. greengenes or SILVA or RDP. If importing [...]