Eisen Lab Blog

Draft post cleanup #4: Gut microbes and cancer

Yet another post in my “draft blog post cleanup” series.  Here is #4:

Interesting article in the Scientist August 1, 2011:
Sharing the Bounty | The Scientist by Michelle Rooks and Wendy Garrett.

It is based on an article from the journal F1000 reports by the same authors.

The article in essence reviews other studies that suggest a possible link between microbes in one’s gut and the risk of development of certain cancers.  It is worth a look.

See abstract below:

Abstract:

Gut microbes are essential components of the human organism—helping us metabolize food into energy, produce micronutrients, and shape our immune systems. Having a particular pattern of gut microbes is also increasingly being linked to medical conditions including obesity, inflammatory bowel disease, and diabetes. Recent studies now indicate that our resident intestinal bacteria may also play a critical role in determining one’s risk of developing cancer, ranging from protection against cancer to promoting its initiation and progression. Gut bacteria are greatly influenced by diet and in this review we explore evidence that they may be the missing piece that explains how dietary intake influences cancer risk, and discuss possible prevention and treatment strategies.

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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.

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Draft post cleanup #3: The Open Knowledge Foundation

Yet another post in my “draft blog post cleanup” series.  Here is #3 from just a few weeks ago:

Interesting article in PLoS Biology:  PLoS Biology: The Open Knowledge Foundation: Open Data Means Better Science.  It discusses many issues in open science especially as they relate to open data.

Some links from this paper are worth checking out

This article reminds me that I keep meaning to push for the development of a “Datawatch” system much like the “RetractionWatch” systems of Ivan Oransky. I have discussed this with Ivan but we have not yet gotten around to doing it … 
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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.

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Note @David_Dobbs @mbeisen had nice family PM yesterday watching wrapup of 2004 ALCS @David_Dobbs @mbeisen

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Note @David_Dobbs @mbeisen had nice family PM yesterday watching wrapup of 2004 ALCS @David_Dobbs @mbeisen

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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.

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Note @David_Dobbs @mbeisen had nice family PM yesterday watching wrapup of 2004 ALCS @David_Dobbs @mbeisen

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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.

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Draft blog post cleanup #2: Metagenomics meets animals

OK – I am cleaning out my draft blog post list.  I start many posts and don’t finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is #2:

Saw an interesting story on Genome Web: ‘Denizens’ of the Deep | The Daily Scan | GenomeWeb.  I have not been able to get the original article yet, but it seems that what they have done can basically be considered metagenomics for animals.  They collected sloughed off cells and other material from a lake and surveyed it for animal DNA.  This seems like a very cool derivative of metagenomic approaches and has enormous potential.  But alas, I never got down to getting access to the paper: Monitoring endangered freshwater biodiversity using environmental DNA so this will have to stay as a mini post.  Damn non open access journals …

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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.

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Draft blog post cleanup #1: Divide and Conquer to Find Orthologs

OK – I am cleaning out my draft blog post list.  I start many posts and don’t finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is the first —

Saw an interesting paper worth checking out:
PLoS ONE: Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

It describes not only a way to speed up continual ortholog annotation in bacterial and archaeal genomes but also is linked to an ongoing open code development project.

Here is the abstract:

Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively expensive in terms of hardware requirements or computational time (requiring an estimated 18 months or more on a typical server). Here, we present xBASE-Orth, a system for ongoing ortholog annotation, which applies a “divide and conquer” approach and adopts a pragmatic scheme that trades accuracy for speed. Starting at species level, xBASE-Orth carefully constructs and uses pan-genomes as proxies for the full collections of coding sequences at each level as it progressively climbs the taxonomic tree using the previously computed data. This leads to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale. Using xBASE-Orth, we analyzed an NCBI collection of 1,288 bacterial and 94 archaeal complete genomes with more than 4 million coding sequences in 5 weeks and predicted more than 700 million ortholog pairs, clustered in 175,531 orthologous groups. We have also identified sets of highly conserved bacterial and archaeal orthologs and in so doing have highlighted anomalies in genome annotation and in the proposed composition of the minimal bacterial genome. In summary, our approach allows for scalable and efficient computation of the bacterial and archaeal ortholog annotations. In addition, due to its hierarchical nature, it is suitable for incorporating novel complete genomes and alternative genome annotations. The computed ortholog data and a continuously evolving set of applications based on it are integrated in the xBASE database, available at http://www.xbase.ac.uk/.

Definitely worth checking out.

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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.

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UC Davis Chancellor putting increased emphasis on communications

Just got this email announcement and I thought I would share.  As many know, in the aftermath of the pepper spray incident, whether you support the UC Davis Chancellor or not, it was pretty clear that communications regarding the incident were, well, poor at best.  Hopefully this will improve things.  Of course, action is more important than communication — but I am glad to see the Chancellor responding to communication issues —

Dear Colleagues, 
  
I write to inform you about additional actions that I am taking immediately to strengthen Strategic Communications. These steps will help us address needs and challenges facing UC Davis today while preparing us to take advantage of opportunities that lie ahead. 

You may recall that in September 2011 I eliminated the office of Vice Chancellor of University Relations and shifted Communications, Government Relations, and Special Events to the Office of the Chancellor, reporting directly to me. Shortly thereafter, Cynthia Barbera was brought on to serve as the acting Executive Director of Strategic Communications pending the appointment of a permanent director. 
  
In meetings with various colleges and departments over the past three weeks as well as in other contexts, I heard many comments and clearly expressed concerns about the ability of Strategic Communications to meet our present needs. I share many of these concerns. 
  
Accordingly, I have asked Barry Shiller to serve as interim Executive Director of Strategic Communications. He will assume day-to-day management of the campus’s central communications activities, effective January 5, 2012. 
  
Barry brings to us an extensive background in strategic communications, diverse career experiences from the UC system and elsewhere, and – as a proud Aggie parent (Class of 2007) – particular appreciation for UC Davis’ distinctions and excellence. 
  
Most recently, Barry served for more than three years as the Associate Vice Chancellor for Communications & Marketing at the University of California, Santa Cruz (UCSC). There, he guided UCSC’s marketing and institutional communication efforts including media relations, branding and marketing, and campus communications. He closely collaborated with students, faculty, staff, foundation and alumni representatives, campus leadership and others on a comprehensive effort to highlight UCSC’s many distinctions in teaching, research and service. Under his leadership, UCSC achieved greater regional and national prominence. 
  
Barry previously served in a similar capacity for nearly five years at Saint Mary’s College of California. Prior to that, he held communications and public affairs leadership positions at a San Francisco public relations agency; an e-commerce start-up firm and the northern California affiliate of the American Automobile Association (AAA). Barry earned his bachelor’s degree from the University of San Francisco and completed advanced studies in insurance and risk management. 
  
I am confident that Barry will serve us extremely well as the interim leader of our central communications activities. I hope you will join me in warmly welcoming him to the UC Davis family. 
  
It is also essential that we launch and complete a comprehensive national search for the permanent director of our central communications unit. Many faculty and others have expressed an interest in helping to shape and inform the long-term direction of our campus communications activities. Community input will be critical to this search as well as the ongoing evolution of our strategic communications efforts. 
  
I have asked Jessie Ann Owens, Dean of Humanities, Arts and Cultural Studies, to chair the Recruitment and Selection Committee for this important position, and Dean Owens has graciously agreed. You may expect details early in the New Year about the search process and in particular how faculty, students, staff and other members of the campus community can contribute to this endeavor. 
  
I’ll continue to share updates as we work to improve our communications efforts. Your assistance is critical to our success. 
  
I wish each of you much peace as we enter the New Year. 
  
Sincerely, 
Linda P.B. Katehi 
Chancellor

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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.

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Top 10 Humorous Science Videos of the Year

I was starting to compile a Top 10 list of best humorous Science-related videos of the year.  And I got stuck on #1 because it is so so so good.  But I was able to find some others I liked (and listed them in no particular order)… so here goes.  If you know of other good ones please post/tweet …

1. Bad Project video from the Zheng lab.  This is simply awesome.

2. Top 10 quirky science tricks for parties.  I found out about this from Twitter … and it is very good.

3. Cracked.Com has some funny spoofs, though usually not about science.  Here is one I found about science, sort of.

4. The Onion has some great science spoofs of course.  I found this one but there are many more.

http://www.theonion.com/video_embed/?id=26842
Brooke Alvarez Has All The Answers, Even About Particle Physics 

5. Colbert has some brilliant Science spoofs.  This one however takes the cake in a way: Colbert nuclear explosion

6. Robotic Operation (which I found through http://www.sciencehumor.org/category/videos/)

7. OK – so it’s very very long.  But there are some funny parts – the 2011 Ig Nobel Award Ceremony

8. Abby Harrison is very funny. … I first saw here microorganism stand up stuff but I think this one is better.

9. OK so this is not the funniest video with Brian Malow but it give some background on “The Science Comedian”

10. And perhaps my favorite – from the Daily Show — Science – What’s it up to?

Please suggest others …

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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.

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If you subscribe to the NY Times – you might want to cancel to get their secret discount

Just got this email

Dear New York Times Reader, 


You may have received an e-mail today from The New York Times with the subject line “Important information regarding your subscription.” 


This e-mail was sent by us in error. Please disregard the message. We apologize for any confusion this may have caused. 


Sincerely,


The New York Times

Which then caused me to go back to my trash and read the previous one:
Dear Home Delivery Subscriber, 

Our records indicate that you recently requested to cancel your home delivery subscription. Please keep in mind when your delivery service ends, you will no longer have unlimited access to NYTimes.com and our NYTimes apps. 

We do hope you’ll reconsider. 

As a valued Times reader we invite you to continue your current subscription at an exclusive rate of 50% off for 16 weeks. This is a limited-time offer and will no longer be valid once your current subscription ends.* 

Continue your subscription and you’ll keep your free, unlimited digital access, a benefit available only for our home delivery subscribers. You’ll receive unlimited access to NYTimes.com on any device, full access to our smartphone and iPad® apps, plus you can now share your unlimited access with a family member.† 

To continue your subscription call 1-877-698-0025 and mention code 38H9H (Monday–Friday, 8:30 a.m. to 8:30 p.m.; Saturday, 9 a.m. to 3 p.m. E.D.T.). 

This is a service message. You are receiving this e-mail to confirm your New York Times home delivery cancellation. 

*This 50% promotional offer is available for the first 16 weeks. At the end of this promotional period, delivery will continue at the regular rate unless you notify us otherwise. You will be billed or your credit card automatically charged in advance of each 4-week billing period. This offer is valid only in areas served by The New York Times Delivery Service. Prices are subject to change. Offer is subject to additional restrictions or limitations. State and local taxes will be added where applicable. Product availability and price may vary by region. This is a limited-time offer and will no longer be valid once your current subscription ends. Offer is not transferable and is only available to the recipient of this e-mail.

†Mobile apps are not supported on all devices. Does not include e-reader editions, Premium Crosswords or The New York Times Crosswords apps. Book Review and Large Print Weekly subscriptions do not include All Digital Access. Other restrictions apply. 

So apparently if I had cancelled my subscription I would be able to get a temporary discount to restart my subscription.  Well, that is interesting.  Gonna be canceling my subscription soon I think …
I note – despite the generally excellent writing at the NY Times I am a bit perplexed by the signature suggesting this email was actually coming from the newspaper and not a person in the circulation department …
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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.

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