All the beers I drink and more

All the beers a plant pathologist drinks

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Terminal apps and nano modifications

Are you tired of your mac's Terminal app? 

I recently discovered iTerm2 which probably is not big news for old mac users but when you are transitioning from other systems to OSX this app might be handy. Also it is free!

I also found another terminal app for windows, MobaXterm. Has some great features which will help you a lot if you don't have access to a Linux/OSX machine at home or work. I think it is not entirely free but for basic usage it should be fine. 

Another helpful and simple trick that I wasn't aware of: 

The nano editor has a number of "profiles" that can be found in /usr/share/nano

So if you want to modify nano to highlight the syntax of your scripts you can simply do this (for example if you want highlighting on shell scripts):

echo include '/usr/share/nano/sh.nanorc' > /yourhome/.nanorc

Saved me from a couple of headaches! :)

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Free time: Richard Galliano

I think he's one of the accordion elite. You should check him out! Itunes has lots of his albums.

I highly recommend the "New York Tango"

Check the wikipedia page here.

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Plant parasite haustoria, a Cladosporium retrospect and Rusts

1. The Haustorium, a Specialized Invasive Organ in Parasitic Plants

A review on the feeding structure of parasitic plants like Orobanche

http://www.annualreviews.org/doi/full/10.1146/annurev-arplant-043015-111702

2. Annual review of Phytopathology Biography article

Cladosporium fulvum Effectors: Weapons in the Arms Race with Tomato

http://www.annualreviews.org/doi/abs/10.1146/annurev-phyto-011516-040249

3. The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression

Very paper with nice comparisons of RNAseq quantification methods.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2684-4

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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

This paper is very rich in information and needs several reads. Also worth looking into the methods. 

Interesting point in the "Footprints of Selection in the Genome" paragraph:

[...] Three associations are characterized by a much higher derived allele frequency in the Iberian relicts than in the general population, possibly indicative of local adaptation from new mutations. One affects the ERF1 drought response regulator (Cheng et al., 2013). ERF1 is also involved in resistance to several fungal pathogens (Berrocal-Lobo and Molina, 2004), as is MLO11 (Acevedo-Garcia et al., 2014), which is located near two of the other variants. The connection to drought response and fungal defense suggests that selection could be due to tradeoffs between abiotic and biotic stress. [...]

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EMBL-EBI exercises and course material on different topics

I found some very nice exercises and teaching material from the EMBL workshop on Plant and Pathogen Genomics! 

I got the link from here:

https://twitter.com/widdowquinn/status/734495123397038080

Make sure also to have a look on the "train on-line part" of the website:

https://www.ebi.ac.uk/training/online/course-list

It has very interesting courses. Some of them have also video from the actual course.

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How to keep shell history in dated files

Usually bash has an upper limit of commands that keeps in history and the history file is not very useful if you want to use it a digital lab book. You can work around it, by increasing the number of commands that it will keep track but I was looking for something more useful.

The point would be to have a command history file for everyday, like:

YYYYMMDD.hist

...with all the commands typed from the day. This way it will be easier to record what is being done.

I did some reading and I came across two very nice tutorials:

https://www.digitalocean.com/community/tutorials/how-to-use-bash-history-commands-and-expansions-on-a-linux-vps (has details on history)

http://bradchoate.com/weblog/2006/05/19/daily-history-files-for-bash (describing the how-to)

And this is what I end up adding in my .bash_profile

export HISTFILE=~/.history/`date +%Y%m%d`.hist #makes a file per day in a history folder HISTSIZE=5000 #this sets the amount of commands loged in current session HISTFILESIZE=10000 #this sets the total amount of commands logged

shopt -s histappend # append instead of overwrite history export PROMPT_COMMAND="history -a; history -c; history -r; $PROMPT_COMMAND" #this is to append, clear and read history file

Hope it works great!

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Free time: The desert blues

I highly recommend listening to Ali Farka Touré's music. Especially the album with Ry Cooder "Talking Timbuktu". You can easily find it on Spotify or Youtube.

Sit back, relax, grab a book and some coffee and enjoy the blues of the sub-Saharan desert. 

To know more about Ali Farka Touré, check this wikipedia page. 

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Natural history of model  organisms on eLIFE

eLIFE has recently published a series of very interesting articles on the natural history of different lab pets!

I just read the one on Arabidopsis by Ute Krämer. I am really intrigued in reading many of the references included in the article. There are many aspects of Arabidopsis that I hadn't thought about before, as for example that 

"In the past few 100 years, A. thaliana has further expanded its geographic and climatic range in synanthropy (see Glossary), migrating to and across North America, as well as southward in Africa, and more recently to East Asia (see Figure 3). The present climatic and geographic range of A. thaliana is larger than that of any of its close relatives, which have either not expanded into warmer climates or are local endemics (Koch and Matschinger, 2007; Hohmann et al., 2014)."

Plus: The figure with the different parts of Arabidopsis  (above) is really great!

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Gene gain and loss linked to transposable elements in M. oryzae

Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements on BMC genomics

Very interesting read

Some quick notes:

Genes with redundant functional domains are more likely to be lost

Genes in the proximity of transposons have higher incidence of polymorphisms

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Free time: Abandonware games made easy with Boxer

I just discovered the great world of abandonware games!

Do you remember those games you were playing on your Amstrad 1512 or your custom made 386 PC? Which after a couple of years became a Pentium with a VGA graphic and a Sound Blaster card?

Those were the times!

If you're interested in playing the first DOOM, Wolfenstein or Lemmings again then you should check out http://www.myabandonware.com .

As far as I understand, abandonware games are games that belong in a grey area of copyright that nobody is interested in (https://en.wikipedia.org/wiki/Abandonware). I am not really sure how true this is, so I guess caution is advised.

Or you might still have some games on floppy disks as I do :)

Anyway, if you want to run old DOS software on your mac, I found this great emulator. It is like DOSbox, but it seems very very very simple and easy to use. I was really impressed. It's called Boxer (http://boxerapp.com) and you can also find it on GitHub (https://github.com/alunbestor/Boxer)

Have fun!

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This Primer assesses recent evidence that the microbiome of plants contains microbial networks and keystone species that influence plant health and ecosystem functioning. Read the accompanying Research Article.

Nice primer on the plant microbiome on PLOS Biology.

Also this figure in the paper is really interesting, showing that the plant microbiome is different in organic and conventional farming. I think it's based on this paper:

http://www.nature.com/ismej/journal/v9/n5/full/ismej2014210a.html

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Author Summary: The innate immune system is an important driver of quantitative resistance among all eukaryotes and is the primary immune system for many multicellular organisms, including plants, fungi, and insects. While some components of the innate immune system are known, many components are still undiscovered. Here we use genome wide association (GWA) mapping in a natural population of the Arabidopsis thaliana host against four phenotypically and genetically distinct isolates of the fungal pathogen Botrytis cinerea to describe and validate components of the plant innate immune system. Using both the induced production of a known defense compound, camalexin, and lesion area as quantified outputs of the plant innate immune system, we found approximately 2,982 and 3,354 genes associated with quantitative resistance respectively. Genes associated with variation in the plant immune system were largely dependent on the pathogen genotype, indicating the presence of specificity in pathogen detection and response by the host. Associated genes, which were filtered into co-expression networks followed by GO enrichment analysis, showed both known and novel biological processes associated with pathogen response. Validation of associated genes using single gene knockouts in a common genetic background indicates an ability to validate causal genes with a 60% validation rate.

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Secretome prediction tools perform differently in fungal and oomycete genomes

This is actually a very interesting paper! They compare the different versions of SignalP and other tools which are usually used to predict effectors and they comment on the different output they get. 

The result is not unexpected, I mean different algorithms/software/... different results right? But the message for me is that don't take the output of SignalP as the absolute truth and also that it seems that the earlier version (3.0) seems to perform better on oomycete. Nice! :)

The link to the article is http://journal.frontiersin.org/article/10.3389/fpls.2015.01168/full

Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors