Sunday, September 14, 2008

The DNA Network

The DNA Network

It's Miller Time - Lake Arrowhead Microbial Genomes Conference -- about to begin [The Tree of Life]

Posted: 14 Sep 2008 08:13 PM CDT

Well, I am back.  Every two years I come back to this small meeting about small genomes.  The meeting is officially the "16th Annual International Meeting on Microbial Genomics at Lake Arrowhead, CA" but in reality, every two years it is at Lake Arrowhead and every other two years it is elsewhere.  And I rarely go to the other one -- but I keep coming back to Lake Arrowhead.

Why?  Well, you might guess it is because it is at UCLA's conference center up in the mountains.  But you would be wrong.  You might guess it is because I generally hate big meetings and this one is nice and small/medium.  But you would be wrong again.  For there are lots of meetings in pretty places.  And there are lots of medium sized meetings an omnivore like me could go to.  I go back every two years because of Jeffrey H. Miller, the organizer.  He invites me.  I can never say no.  

Why? Well, many reasons.  Sure one is that I like him.  Another is that he does meetings in the right way (not too many talks in one day --- some time to relax and talk with other people and to interact, etc).  But the truth is, I say yes because he is one of the few people I know who is interested in both DNA repair processes and microbial genomes.  And his meetings reflect this interest.  So I guess even though I do not spend enough time working on DNA repair any more, I did do my PhD on it, and I did basically try and copy some classic Jeffrey Miller mutator experiments.  So I just have to go to this meeting.  And here I am (see my 2006 meeting notes here) - despite having been very sick this summer and getting ready to teach a new class in the fall with 400+ students.

Anyway - More on the meeting coming.Here are the talks for those interested

James C. Liao
University of California, Los Angeles, CA
"Non-fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels"

Jonathan Eisen
University of California, Davis, CA
"A Genomic Encyclopedia of Bacteria and Archaea"

Bernhard Palsson
University of California, San Diego, CA
"The Genetic Basis for Adaptive Evolution in E. coli"

George Weinstock
Baylor College of Medicine, Cambridge, MA
"The Human Microbiome: Progress and Challenges"

Gary Siuzdak
The Scripps Research Institute, La Jolla, CA
"Metabolomics Reveals Large Effect of Gut Microflora on Biochemistry and Activation of a Host Response"

Jim Bristow
DOE Joint Genomme Institute, Walnut Creek, CA
"Microbial Sequencing for Biofuels Applications"

 Eric Wommack
University of Delaware, Newark, DE
"Making sense of the chaff: What will metagenomic approaches tell us about viral ecology?

Valérie de Crécy-Lagard
University of Florida, Gainesville, FL
"Making Sense of Genomes: Linking Gene and Function by Comparative Genomics"

Trent Northen
The Scripps Research Institute, La Jolla, CA
"High Throughput Mass Spectrometry Based Metabolomic and Enzymatic Assays for Functional Genomics"

Matteo Pellegrini
University of California, Los Angeles, CA
"New Methods for Processing High-throughput Sequencing Data: Improving the Solexa/Illumina Data Analysis Pipeline"

Sabeeha S. Merchant
University of California, Los Angeles, CA
"Transcriptomics of Nutritional Copper Homeostasis in Chlamydomonas"

Lynn L. Silver
LL Silver Consulting, LLC, Springfield, NJ
"The State of Antibacterial Discovery in 15 minutes"

Julian Parkhill
Welcome Trust Sanger Institute, Cambridge, UK
"Discovering Variation in Genetically Monomorphic Bacteria: SNPs and the Evolution of Salmonella Typhi"

Tiffany Williams
Baylor College of Medicine, Houston, TX
"Global Health and Next Generation Sequencing Technologies: Streptococcus pneumoniae sertoype 1 in Africa"

Kim Lewis
Northeastern University, Boston, MA
"Persister Cells and Biofilm Resistance"

Jeffery F. Miller
University of California, Los Angeles, CA
"Diversity-Generating Retroelements"

Steven A. Benner
Foundation for Applied Molecular Evolution, Gainesville, FL
"Molecular Paleoscience"

Joe Zhou
University of Oklahoma, Norman, OK
"Metagenomics Insights of the Feedback Responses of a Grassland Ecosystem to Elevated Atmospheric CO2"
Heather Allen
University of Wisconsin-Madison, WI
"Using Functional Metagenomics to Discover Antibiotic Resistance Genes in Natural Environments"

David A. Relman
Stanford University School of Medicine, Stanford, CA
"Response of the Human Distal Gut Mircobiota to Disturbance: The Effect of Antibiotics"

Ashlee Earl
Harvard Medical School, Boston, MA
"Bacillus subtilis Biofilm Diversity"

Mary E. Lidstrom
University of Washington, Seattle, WA
"Coupling Function to Phylogeny via Single-Cell Phenotyping"

John Dueber
University of California, Berkeley, CA
"Use of Synthetic Protein Scaffolds to Balance Pathway Flux of Engineered Metabolic Pathways"

Maria L. Ghirardi
National Renewable Energy Laboratory, Golden, CO
"Hydrogen Fuel Production by Microalgae: Issues and Future Directions"

Caroline S. Harwood
University of Washington, Seattle, WA
"Redirection of Metabolism of Hydrogen Production"

Byung-Kwan Cho
University of California, San Diego, CA
"The Reconstruction of the Transcriptional Regulatory Network in E. coli "

E. Virginia Armbrust
University of Washington, Seattle, WA
"Molecular Insights into Silicon Bioprocesses in Marine Diatoms"

Athanasios Typas
University of California, San Francisco
"High-throughput Quantitative Analysis of Genetic and Chemical-Genetic Interactions in E. coli"

Devaki Bhaya
Carnegie Institution for Science, Stanford, CA
"Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes."

Erin Sanders-Lorenz
University of California, Los Angeles, CA
"Integrating Discovery-based Undergraduate Research Experiences into UCLA Courses Using a Collaborative Curriculum Model"

Cheryl Kerfeld
DOE Joint Genome Institute, Walnut Creek, CA
"The JGI Microbial Genome Annotation Program"

Fredrick Blattner
University of Wisconsin, Madison, Wisconsin
"Insights from the Genomes of Commonly Used Lab Strains"

Colin J. Ingham
Wageningen University, Wageningen, The Netherlands
"Reinventing the Petri Dish: Miniaturized Tools for High Throughput Microbial Culture"

Maureen Hillenmeyer
Stanford University, Stanford, CA
"The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes"

Simon Prochnik
DOE – Joint Genome Institute, Walnut Creek, CA
"The Genome Sequence of the Deep-Branching Amoeboflagellate Naegleria gruberi Reveals Ancestral Eukarotic Functions"

Elizabeth Fozo
National Institute of Allergy and Infectious Diseases, Bethesda,MD
"Regulating Bacterial Expression of Short Hydrophobic Toxic Proteins with Small RNAs"

Mariusz Nowacki
Princeton University, Princeton, NJ
"RNA-mediated Epigenetic Programming of a Genome-Rearrangement Pathway"

Barry L. Wanner
Purdue University, West Lafayette, IN
"Development of the Information Resource"

Hirotada Mori
Nara Institute of Science and Technology, Nara, Japan
"Systematic Analysis of Genetic Interaction of Esccherichia coli"

Hoy-ploy wear drool as the new black [biomarker-driven mental health 2.0]

Posted: 14 Sep 2008 07:30 PM CDT

Brazillian top model Gisele Bündchen, on Fashi...Image via Wikipedia Just thought it was strange to see the beautiful people drooling into 23andMe spit cups in today's "Style" section of the NY Times. Strange in a good way.

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Spit Party for those who want to break their own code and The Law [The Gene Sherpa: Personalized Medicine and You]

Posted: 14 Sep 2008 12:55 PM CDT

The New York Times article was lovely..... So was the New York State Department of Health.... the State Department of Health sent letters informing the companies that it is illegal to offer medical...

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DNA for Terrorism [Eye on DNA]

Posted: 14 Sep 2008 12:13 PM CDT

 image for id L0029724New Scientist reports that the Industry Association of Synthetic Biology (IASB) will begin issuing a seal of approval for members to post on their websites which will show that the companies screen their orders for potentially dangerous DNA sequences. The US National Science Advisory Board had been concerned about the potential for terrorists to purchase synthetic DNA to create deadly viruses.

In order to reduce the the chances of bioterrorism using commercially available genetic engineering, IASB committed to:

  1. An anonymized survey of industrially produced and delivered genes
  2. A sequence database accessible for all companies involved in gene synthesis that will help to identify orders requiring closer scrutiny

In related news, New York City Mayor Michael Bloomberg said last week the city ranks only 21st out of 54 eligible states and cities in the amount of funding for bioterrorism prevention despite the city being the number one target for terrorists. The mayor said funding is allocated irrespective of the risk for terrorist attack.

Because of the anthrax episodes in 2001, New York is one of only a handful of places in the nation that’s ever experienced a bio-terror attack. Yet in Fiscal Year 2008, we received $2.72 per capita, putting us an incredible 21st out of 54 eligible states and cities.

For more about bioterrorism, see previous Eye on DNA posts - Beware of Genetic Bioviolence and Could Altering DNA in Bacteria Post a Terrorist Threat?

Photo credit: Wellcome Library, 1927 Anthrax poster

deCODE and Radboud University Discover Common Variants in the Human Genome Conferring Risk of Bladder Cancer [deCODE You]

Posted: 14 Sep 2008 12:00 PM CDT

Urinary bladder cancer is something many people have never heard of. But it is the sixth most common form of cancer in the United States, and its environmental risk factors include exposure to toxic chemicals, including some used in industrial processing as well as cigarette smoke. Genetic factors also play a role and may help to [...]

Gene Genie #37: Human Genomes Are a Dime a Dozen [The Genetic Genealogist]

Posted: 14 Sep 2008 11:37 AM CDT

image Welcome to the September 14, 2008 edition of Gene Genie!  Bloggers have begun to pick up posting with the end of summer, and it seems like everyday there’s a bunch of new interesting posts about the human genome.

96well at Reportergene presents “Trends in development of reporter genes.”  Reportergene is also looking for bloggers/reporters to join the blog’s community and help create the “main repository of news and tools for reportergenomists.”  See here for more information.

fightingfatigue presents » Have Japanese Researchers Found Diagnostic Tool for ME/CFS? posted at Fighting Fatigue.  According to a study discussed in the article, there might now be a test able to diagnose Chronic Fatigue Syndrome.

Genomes by the Handful

Human genomes are being sequenced by the handful these days.  Knome has recently delivered their first sequenced genomes to customers on 8gb USB drives placed in engraved boxes.  Additionally, news came last week that the first Arab genome had been sequenced.  As Mailund on the Internet asks, is this news anymore?

What good are all these genomes if the non-scientist citizen doesn’t understand anything about genetics?  Andrew at Think Gene discusses a lesson created by Dana Waring and colleagues at the Personal Genetics Education Project in “Personal Genetics Education Project: Lesson 1

Lower Prices

DNA Scanning On September 8th, 23andMe announced a reduction in the price of their DNA analysis from $999 to $399.  The news was discussed on Dienekes’ Anthropology Blog, Eye on DNA, bbgm, ScienceRoll, and at Geneforum.  It even led Attila to buy a kit.  The price drop also prompted a great discussion among some of the members of the DNA Network.  First, see “Cheap personal genomics: the death-knell for the industry?” at Genetic Future.  Andrew at Think Gene writes “23andMe Is DTC Genomics and Nobody Should Be Surprised” and “Why the "Database Sale Story" is Silly.”  This in turn is mentioned by Steve the Gene Sherpa at “A lot to chew and then spit!“  See also my “Follow-Up to 23andMe's Price Drop.”

The Marriage Gene?

Mary Meets Dolly discusses “The marriage gene“, in which an article in the Baltimore Sun writes that “men who lack a particular variant of a gene that influences brain activity are more likely to be devoted, loving husbands and more likely to be involved with women who praise them as emotionally close and available.”  Rebecca Taylor mentions that genes are rarely the sole influencing factor in anyone’s behavior.

As a bit of housekeeping, if you aren’t already subscribed to the DNA Network, be sure to note that Daniel’s Genetic Future has moved to Scienceblogs.  Update your RSS feed!

Dinosaur Beer

Last but not least, news about ancient yeast.  Although this isn’t related to human genetics, I did my graduate research on yeast and thought I would indulge a little here.  Aminopop mentions that a new brewing company, Fossil Fuels, is making beer with revived 25-million year-old yeast.  Apparently, “the ancient yeast provides the wheat beer with a distinctively ‘clove-y’ taste and a ‘weird spiciness at the finish.’”

So ends the 37th edition of Gene Genie.  Edition 38 will be hosted in a few weeks.  You can submit your blog article for the next edition at the carnival submission form. Past posts and future hosts can be found on the blog carnival index page, or at the official Gene Genie blog!

First “insert name” genome [Mailund on the Internet]

Posted: 14 Sep 2008 03:40 AM CDT

Roald from CLC Bio complained to me that I haven’t mentioned this news … sorry, I’ve had a cold all week and couldn’t be bothered to blog :-(  … anyway, here goes:

First of 100 Arab Human Genomes Sequenced by Saudi Biosciences, Beijing Genomics Institute Shenzhen, and CLC bio

So, at CLC Bio they are participating in a project to sequence 100 arab human genomes using next generation sequencing technologies.

First of all, I find it pretty cool that you can actually completely sequence a hundred human genomes in a couple of years, and I look forward to the population genetics we can do in the very near future as a consequence of this.

The mind boggles at what we can learn from hundreds of full sequences once we start getting them from populations all over the world.

Still, this quote from the press release looked a little hyped to me:

An international consortium consisting of Saudi Biosciences, Beijing Genomics Institute Shenzhen, and CLC bio have in a joint effort performed an initial sequencing and analysis of the first Arab human genome

Ok, so you have sequenced “yet another human genome”. To make this into a news story, you have to mention that it is an arab genome, ’cause we haven’t sequenced any of those yet.

It was also a news story when we had the first Chinese genome and when we had the first — snigger — female genome.

Is it going to be a news story when we get the first Danish genome?  Outside of Denmark, that is.  When we get the first Aarhusian genome? Will we have a press release when we get the first genome from Paludan-Müllersvej?

Sequencing genomes is cool, and what we can learn from the genomes is even cooler, but do we really need to make up reasons why a new sequence is newsworthy?

Top Trumps for Science Competition [Sciencebase Science Blog]

Posted: 12 Sep 2008 07:00 AM CDT

top-trumps-scienceSomething a little different today. A tale of family playtime, a poll, and a competition to win prizes from the RSC and the

Card Competition

Okay, here’s the competition bit. What you have to do to be in with a chance of winning is to subscribe to the Sciencebase email newsletter and then send me a good reason (in not more than 15 words) for your choice - chemical trumps or cell trumps - you could win a pack of Cell Trumps and some other goodies or Elemental Trumps.

Here’s how:

First, signup for the Sciencebase email newsfeed using the Feedblitz system.

Then, use the same subscribed email address to send me your reason why - is the address to use. If you already subscribe to the Sciencebase email newsletter then please subscribe to sibling site instead (via Feedburner) and then send me your choice and reason. If you’re already subscribed to both Sciencebase and Sciencetext by email, then I’ll be able to see from the subscriber lists, so either way, your subscribed email must be valid to qualify.

Finally, I’ll pick the best ideas from the comments and emails and announce the winner in the next couple of weeks. Judge’s decision will be final and if no entries come up to scratch then I reserve the right to throw my rattle out of the pram.

And, now on with the story…

This term, both my kids are learning about the elements at school. My daughter, who is still in primary school is learning about the ancient elements - earth, air, fire, water. While my son, who is half way through high school returned home with tales of electron shells and the elements of the periodic table.

It was, therefore quite timely that Royal Society of Chemistry press officer and Satrianialike, Jon Edwards, should send me a pack of Visual Elements Trumps. The cards follow in the classic tradition of the Top Trumps game, my friends and I collected and played when we were at school - trains, planes, automobiles and a few more sciencey ones, including dinosaurs were around at that time. There have been others since, including a spinoff from the defunct BBC TV show and magazine Tomorrow’s World, Star Wars, and Harry Potter have also fallen under the trumping spell. And, of course, Pokemon and Digimon cards, which swept through playground a few years ago, are also based on the trump theme, albeit with a few more bizarre properties than top speed and height.

Anyway, the kids and I had a quick round of Elemental trumps. My daughter won, having quickly latched on to the notions of automatic atomic radius and ionistation ionisation energy. She was also rather intrigued by the idea of hydrogen gas having a boiling point. We all enjoyed the game, but obviously it’s the educational and promotional value it may have for kids studying science and chemistry that underpin its production by the RSC. I have to admit the writing in the element description bubble is too small for me to see in dim light. With a magnifying glass, however, I can see that they have packed the main elemental essentials on to each card together with the RSC’s well-known artistic images associated with each.

A related product on the science educational stuff market is Elementeo, which is a hybrid of sword & sorcery game and science, with a Sodium Dragon and Oxygen the Lifegiver. They’re very tongue in cheek but there’s not as much chemical information. So unless you’re a science fantasy addict, I’d opt for the RSC game. Another variation on the theme is available from the WebElements shop and was developed by the University of Brighton. This version has more facts and also comes with approval (for what that’s worth) from the Top Trumps people .

We then moved on to a game of Cell Trumps, produced by the Centre of the Cell at Queen Mary University of London, which arrived at roughly the same time as the RSC cards. However, a quick fan of the deck reveals them to be slightly simpler, swapping number in body for 1st ionisation energy, and number of their scientists working on the particular type of cell for atomic radius. But the kids coped, although my daughter favoured the slightly more esoteric Element Trumps over the cell. She was quite taken by the adipocytes having spotted the connection with the name of the fatty, alien Adipose characters from a recent Doctor Who episode.

Scientific Trumps seemed just right for introducing some scientific concepts in a fun way to kids at the higher end of primary school or even heading towards high school exams. They might even be inspirational to money-free undergraduates lacking beer towards the end of term, who knows? And, if you arrived here looking for science education materials check out the learn with Sciencebase page, which has links to various science project resources.

Top Trumps for Science Competition

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