Category: Misc.

The Ballad of #UCDavis from Aaron Heuckroth

The Ballad of UC Davis from the brilliant and talented Aaron Heuckroth.


Hat tip to the Davis Patch.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some articles on the uses and misuses of the "impact factor"

Collecting some articles and blog posts on impact factor uses and misuses.  Inspired by this blog post: Sick of Impact Factors | Reciprocal Space

  • Created a Mendeley Group on this topic

http://www.mendeley.com/groups/2486431/impact-factor/widget/29/10/

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

MMMMM: Microbes, Metagenomics, Minnesota, Mississippi, & Morrison

A really cool project is discussed in an issue of the University of Minnesota News: Microbes in the Mississippi : UMNews : University of Minnesota.  I found out about it through an automated web search I have running in the background via Google.  The news story discusses a project in which scientists from U. Minnesota are sampling the microbes in the Mississippi River using metagenomics.  Their data is (apparently) deposited into the IMG database and shared with the world (though I note – no link is provided).  This is exactly the kind of new project that cheap sequencing enables …  I hope to see many many more like this …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

The recursive tree of life – how a Twitter -> Blogger loop was created and broken

Earlier today I wrote a post that went something like this

Still searching for a good way to post a roundup of my twitter conversations to my blog. There don’t seem to be any good systems for doing this on Blogger. So I have, at least this week, created a Storification of my tweets and some of the associated conversations … not ideal probably but still …

I am not sure how it finished because, well, I deleted the post by accident a bit later in the day as you will see.

I do recall I posted an embedded version of this storification.

And this led to some useful responses such as

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js SO this seemed potentially interesting .. and I decided to look into IFTTT. It took a bit to figure out anything about it but at first glance it seemed not right. So I posted a response

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js So I created an IFTTT account and hacked around for a bit. I connected IFTTT to some of my social networks and then I set up two automated feeds. One that would post from Twitter to Blogger and one that would archive my Tweets to Dropbox.

 And then I ran a test. I wrote a tweet to see where it would end up and whether / how it would end up on blogger. The tweet read something like “I am testing IFTTT for autoposting my tweets to my blog” and then I went to blogger and looked to see if anything showed up there (I note – I ended up deleting this tweet later in the day – more on this in a bit). But alas it did not. At least at first. So I looked at IFTTT in more detail and something there said it usually scanned twitter every 15 minutes so it might take some time for the tweets to show up on my blog.

Meanwhile I made another test tweet that read:

Testing http://t.co/1nWox0lt again . please ignore August 12, 2012 at 09:00AM http://twitter.com/phylogenomics/status/234680659233357824 Alas I deleted this one too (again – more on this deletion frenzy in a bit).

I note – I ended up deleting this one too – but by this point I had launched the “tweet to dropbox” system at IFTTT so this tweet was archived.

And then here was the big big big mistake.  I left the house – first to go shopping and then to a wedding (of a brilliant PhD student at UC Davis).  And I shut off my phone.  After the ceremony I turned on my phone again to take some pictures.  And (of course) I checked Twitter.  And thats when I noticed something had gone horribly wrong.

This is what I saw first:

//platform.twitter.com/widgets.js “Hmm” I thought. What could that be about? First, I thought it was about all the microbe posts from yesterday. But then I saw some other posts.

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

Uh oh.  Or more like “Oh shit.”  What the $&$# was going on?  And suddenly I realized, I must still have a “blogger to twitter” autopost feature set up through blogger.  So IFTTT was posting to blogger anything I tweeted and then Blogger was posting anything there to Twitter.  A loop.  Oh no.  A loop.  Not supposed to happen to me.

So I dreadfully looked at my Twitter feed to see how many tweets had been posted in this loop.  And it was quite a few.  Oh no.  What to do?  And I panicked a bit.  I just started deleting tweets so that people would not be driven crazy by the loop (at this point I did not know how many were in the loop).  And I ended up deleting not too many but more than a few (something like ten).   I can’t embed them of course, because I deleted them.  But I do have them in my new Dropbox twitter archive.

The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system for posting tweets to… http://t.co/xtuELMBb
August 12, 2012 at 09:06AM
http://twitter.com/phylogenomics/status/234682399693352962
– – – – –
The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting tweet to blogger system from IFTTT http://t.co/THhFkG7S
August 12, 2012 at 09:06AM
http://twitter.com/phylogenomics/status/234682401337524224
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system for posting… http://t.co/LKd976jR
August 12, 2012 at 09:22AM
http://twitter.com/phylogenomics/status/234686366678654976
– – – – –
The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting tweet to blogger… http://t.co/bOVmkEB0
August 12, 2012 at 09:22AM
http://twitter.com/phylogenomics/status/234686368612245505
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting… http://t.co/EGWmjifq
August 12, 2012 at 09:37AM
http://twitter.com/phylogenomics/status/234690113525915648
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system… http://t.co/h8iOJFey
August 12, 2012 at 09:37AM
http://twitter.com/phylogenomics/status/234690132605804545
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please… http://t.co/RYKpNwdE
August 12, 2012 at 09:51AM
http://twitter.com/phylogenomics/status/234693721545920512
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/iXtneMx2… http://t.co/Ueg9mK2F
August 12, 2012 at 10:07AM
http://twitter.com/phylogenomics/status/234697523661512705
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing… http://t.co/lwELrRso
August 12, 2012 at 10:21AM
http://twitter.com/phylogenomics/status/234701228347633664
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/Vz9GDrUI
August 12, 2012 at 10:36AM
http://twitter.com/phylogenomics/status/234704905246494721
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/PcTqp1mg
August 12, 2012 at 10:51AM
http://twitter.com/phylogenomics/status/234708632443441152
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/YecKMslQ
August 12, 2012 at 11:05AM
http://twitter.com/phylogenomics/status/234712346797428736
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/T2rE2shW
August 12, 2012 at 11:21AM
http://twitter.com/phylogenomics/status/234716246023745536
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/lYFK57gx
August 12, 2012 at 11:35AM
http://twitter.com/phylogenomics/status/234719738536796160
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/7X0Bypuj
August 12, 2012 at 11:50AM
http://twitter.com/phylogenomics/status/234723474831204352
– – – – – 

Oooh – that was bad.  But how to control it?  I first tried to unlink the IFTTT app from Twitter from inside Twitter.  That is, I tried to remove the permissions the IFTTT app had to post/read my twitter feed.  But Twitter seems to not provide access to applications control from a mobile device.  Crap.
So then I tried to log on to Google Blogger and unlink it from IFTTT.  Also no success.  Seems that many systems default to mobile options and do not provide access to full features no matter what.  
So then I called up my brother and thankfully he was there and after telling him my Twitter password (risky I know .. given my families tendency for pranks) – he deactivated the IFTTT access to Twitter.  Phew.  That hopefully would break the loop.  But to be safe I decided to check Blogger.  And Oh man- there were a lot of posts there too.  That was going to drive people crazy I am sure just as all the tweets did.  So I kind of panicked again and deleted all the IFTTT posts.  And I even accidentally deleted the post that launched all of this (see above).  Uggh.  I don’t like it when people delete posts but I needed to get control of this loop.  I figured, even if the IFTT Twitter -> Blogger system kept going – because it apparently only checked Twitter every 15 minutes I could keep the loop under control by monitoring Twitter and Blogger and deleting any posts before they got reposted somewhere else. 
So – while sitting at the wedding reception I did exactly this.  And it seemed under control.  So I posted to Twitter to apologize and tell people things seemed better.

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js So – seemed under control – sort of. And then I made the mistake of looking at Facebook. Oh no. Autofeeds there up the wazoo too. I am going to delete those later. What a nightmare. And it could have ben much worse if I did not catch it at the wedding. Because now I have to head to Berkeley for a birthday party for my brother’s kids. Hopefully – the loop is broken. And I have only one think left to say. The tree of life. The tree of life. The tree of life. The tree of life ….

UPDATE: My brother did indeed make use of my Twitter password, the bastard

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Interested in MiSeq Illumina sequencing of low diversity libs – read this

Everyone -if you are interested in using the Illumina MiSeq to sequencing low diversity libraries – read this … Sequencing low diversity libraries on Illumina MiSeq from THE Nick Loman.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Courtesy employee notice regarding annual systemwide payroll disclosure

Just received this … seemed to be something that should be shared publicly.

Silly microbiologist, genomes are for mutualists

New paper in PLoS Genetics of possible interest: PLoS Genetics: Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medica.

The abstract does an OK job with the technical details:

Abstract:
The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5–2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome – with mean diversity (θπ) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization.

I think the author summary is a bit more, well, friendly:

Facultative mutualisms are relationships between two species that can live independently, but derive benefits when living together with their mutualistic partners. The facultative mutualism between rhizobial bacteria and legume plants contributes approximately half of all biologically fixed nitrogen, an essential plant nutrient, and is an important source of nitrogen to both natural and agricultural ecosystems. We resequenced the genomes of 44 strains of two closely related species of the genus Sinorhizobium that form facultative mutualisms with the model legme Medicago truncatula. These data provide one of the most complete examinations of genomic diversity segregating within microbial species that are not causative agents of human illness. Our analyses reveal that horizontal gene transfer, a common source of new genes in microbial species, disproportionately affects genes with direct roles in the rhizobia-plant symbiosis. Analyses of nucleotide diversity segregating within each species suggests that strong selection, along with genetic hitchhiking has sharply reduced diversity along an entire chromosome half in S. meliloti. Despite the two species’ ecological similarity, we did not find evidence for selection acting on the same genetic targets. In addition to providing insight into the evolutionary history of rhizobial, this study shows the feasibility and potential power of applying population genomic analyses to microbial species.

I have highlighted the section dissing pathogen studies …

As with every good paper, it starts with a tree

Figure 1. Neighbor-joining trees showing relationships among 32 S. meliloti (blue squares) and 12 S. medicae (red circles). 
A) chromosomes, B) pSymA and pSMED02, and C) pSymB and pSMED01. Trees were constructed using sequences from coding regions only. The length of the branch separating S. medicae from S. meliloti strains is shown at a scale that is 5% of the true scale. The 24-strain S. meliloti group is marked by asterisks. All branches had 100% bootstrap support unless otherwise indicated. Branches with <80% bootstrap support were collapsed into polytomies. An identical tree with strain identifications is provided as Figure S2.

The tree lays out the phylogeny of the strains sequenced in this study.  And it provides the main framework for much of the rest of the paper.  
Some comments:
  • The genomes were sequenced to ~ 100x coverage with on an Illumina GAIIx.
  • Reads were then aligned to reference genomes of close relatives of the sequenced strains.
  • These alignments were then used for various comparative and population genetic analyses
  • As far as I can tell no de novo assemblies were done
  • I am quite confused about their methods for detecting putative regions that have undergone horizontal gene transfer:
    • In the methods: “We identified genes likely to have experienced recent horizontal gene transfer by comparing the ratio of polymorphisms that were shared between species to fixed differences between species. Based on the whole-genome distribution of this ratio (Figure S3) we identified putatively transferred genes as those with a ratio of shared polymorphisms to fixed differences >0.2.”
    • Not sure how/why this should work.  Not saying it is a bad idea – I just don’t really understand it.
  • They also examine various population genetic parameters including possible selection, SNPs, Tajima’s D, and more. 
It is worth a read.  They summarize their various findings with:

Population genetic analyses of nucleotide diversity segregating within Sinorhizobium medicae and S. meliloti have provided unprecedented insight into the evolutionary history of these ecologically important facultative symbionts. While previous analyses have detected evidence for horizontal gene transfer between these species, our data reveal that gene transfer is restricted almost exclusively to plasmid genes and that the plasmid regions that show evidence of transfer have less interspecific divergence than other genomic regions. Interestingly, nucleotide variation segregating within a 24-strain subpopulation of S. meliloti is highly structured along the chromosome, with one half of the chromosome harboring approximately one-fifth as much diversity as the other. The causes of the difference between the two chromosome halves may be a selective sweep coupled with extensive hitchhiking, if this is correct it would suggest that bouts of strong selection may be important in driving the divergence of bacterial species. Finally, we’ve identified genes that bear a signature of having evolved in response to recent positive selection. Functional characterization of these genes will provide insight into the selective forces that drive rhizobial adaptation.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Curiosity on Mars

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Scifoo Notes via Storify

http://storify.com/phylogenomics/scifoo-2012.js?template=slideshow[View the story “scifoo 2012” on Storify]

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

#PLoSOne paper on the "horse #microbiome" and colitis; wonder if they will study ‘poo tea’

There is a new paper on the horse microbiome: PLoS ONE: Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene

They discuss the microbial community in the feces of healthy horses and those with colitis.  In the conclusions, they also discuss the possibility of “fecal transplants” to treat problems in the gut microbiome.

“Bacterial species richness and diversity are thought to be important components of a ‘healthy’ intestinal microbiome. Decreases in richness and diversity have been associated with conditions such as chronic diarrhea and recurrent C. difficile infection (CDI) in humans [24], [40]. Restoration of bacterial diversity and richness is the principle behind fecal microbiota transplantation, an approach that has received much attention recently for successful treatment of recurrent CDI [41], [42]. Surprisingly, equine colitis was not associated with loss of diversity and richness, but further studies using more uniform groups of horses with specific etiologies are required. Microbiota transplantation might potentially be an effective treatment to restore this complex environment towards is considered more ‘normal’.”

 I find it very surprising that they do not discussion “transfaunation” which is basically fecal transplantation in animals.  For more on transfaunation see:

And I think they should have / could have mentioned “poo tea” which some old school horse caretakers make for horses with colitis.  For more on that I suppose you can watch my Tedmed/Ted talk where I talk about this issue briefly

http://video.ted.com/assets/player/swf/EmbedPlayer.swf

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–