The oldest DNA ever found?
Genes ordered at your friendly Mr Gene’s store are as fresh as can be (a point of honour, of course!). That freshness, however, isn’t really the case with the “dirt DNA” that has been digged up by Danish biologist Eske Willerslev.
Willerslev, the head of the “Ancient DNA and Evolution” lab, is a professor at the University of Copenhagen. He likes to hang around in really barren landscapes. 1991, for example, he enjoyed collecting megafauna fossils in North Eastern Siberia, while later, he lived as a trapper among the local Yukagihr people for six-months. Since then, Willerslev again was on the roam in nice spots such as Western Greenland and Northern Canada, collecting ancient coprolites and sediment samples for DNA analyses.
Collecting coprolites and sediments at minus degrees – really nice activities, aren’t they? And, what for the world, did this professor believe to discover inside frozen faeces?
Well, the answer is quite simply ancient DNA. VERY ancient DNA. Inside Siberian permafrost the 36-year-old adventurer from Copenhagen discovered 300,000- to 400,000-year-old DNA of mammoths, bison and mosses.
In short: he discovered the most ancient DNA ever found on Earth by more than 200,000 years.
In 2007, a readable feature on Willerslev was published in Science.
Long ago, Willerslev had pioneered the “dirt DNA” field meaning “the extraction and cloning of plant and animal DNA from just a few grams of soil and ice” (read an interesting Science feature from 2003 on Willerslev’s startling discovery Ancient DNA Pulled From Soil and Willerslev’s original Science paper on the same topic).
Recently, Willerslev broke his own record for the oldest DNA ever recovered finding DNA traces that are possibly 800,000 years old (Ancient Biomolecules from Deep Ice Cores …, DOI: 10.1126/science.1141758).
Btw, scientists always assumed DNA older than 100,000 years being analysable as science fiction (remember the scornful laughter on Jurassic Park!).
Willerslev doesn’t give a damn about such doom-mongering. He is already eyeing Antarctica where ice temperatures going down to -50°C may have kept DNA preserved longer than at any other place.
Order non optimized
This tutorial shows how to order genes without optimizationPlease note: 
Adobe Flash player needed!
How to order
After you have uploaded your sequence you can order or create a quote document.
Please note: Adobe Flash player needed!
Let me know which steps you think should be made more convenient?
How to optimize
This tutorial shows how to optimize genes using mrgene.com
Please note: Adobe Flash player needed!
 Feel free to post comments on how to improve the usability!
Who’s calling? - it’s me, your houseplant!
Any hobby gardeners aboard? Recently, I came across a somehow weird website that promoted “communication between plants and people”. Plants (soundbite!) “that might otherwise be neglected are given the ability to call and text message people to request assistance”.
Plants that place phone calls for human help! No kidding!! Such well-connected networking plants will be all the rage in 2009.
Actually, on www.botanicalls.com one can even buy “Botanicalls Kits” that offer a connection to your windowsill buddy via online Twitter status updates to your mobile phone. Completely hands-off! Again quoting the Botanicalls people: “when your plant needs water, it will post to let you know, and send its thanks when you show it love.”
All you need is an ethernet connection with internet service, a 120V a/c power outlet (no idea whether they offer an alternative 220V power solution… - does anybody know?) and, of course, a neglected plant with soil at least 3″ (that is about 8 centimetres) deep.
A nice survey of such a kit with all its fiddly parts as resistors, transistors and LEDs (that have to be assembled before use!) is pictured here. Please note that you will also need several tricky tools for assembling, such as a soldering iron, needle-nosed pliers, a screwdriver and more.
Btw: the Botanicalls project was created by four New York based nerds (an artist, a neural science researcher, a computing expert and a game developer). I’m curious what they will launch next. A piddling-free puppy dog? A mobile with an included folding bicycle? A laptop computer that blogs without human assistance? I’ll keep watching.
Harvard “EXPERTS” blow away 16 billion
Ever toyed with the idea of sending your spoiled offspring to a US-based elite academy, say Harvard University?
Forget it. Harvard, the oldest institution of higher learning in the US (world-renowned for its multi-billion foundation and its 43 Nobel laureates!), is setting its sights lower.
Most laureates are still aboard, but many billions vanished recently. Blown away! Well, the convenient student life in Cambridge will soon become more expensive and uncomfortable
In-house gamblers from Harvard Management Company (HMC) have incurred startling speculation losses. They blew away the tremendous sum of US$16 billion within three months. Man, 16 billion!! That is nearly the gross domestic product (GDP) of nations like Iceland and Panama, respectively.
The statements of those who are responsible for this disaster are, well, really funny. Take Jane L. Mendillo, HMC’s president and chief executive officer, as an example. On September 12th she told the Harvard Magazine that “results for HMC for fiscal year 2008 were very solid” (har har, that was only months before Ms. Mendillo had to confess that her glorious management company pulverized 40 percent of Harvard’s US$36 billion foundation treasure).
The mission statement of James Rothenberg, HMC’s Treasurer and Chair, is almost even funnier. On the HMC website Mr Rothenberg proclaims: “It is imperative that we invest our resources with skill and care.”
“Skill, care and solid results” as synonyms for a US$16 billion loss. Nice wording.
Will Harvard University axe the big-mouthed HMC gamblers and consult wiser people? They could do as they actually have a lot of expertise in-house. Take men like Thomas Schelling and Robert Merton. They are Harvard faculty members and they have been awarded Nobel Prizes in economics (as half a dozen of their Harvard colleagues have, too). Thus, why should Harvard furthermore pin its hopes on HMC?
Genetic Code
E. crassus - a marine protozoan - uses UAG to code for cysteine AND seleno selenocysteine. I don’t think that I will need to implement this ambiguity into the algorithms used for codon optimization but I will stay tuned.
Read more at:
http://sciencenow.sciencemag.org/cgi/content/full/2009/108/3
http://www.the-scientist.com/blog/display/55327/Â (registration needed)
Crichton’s “crazy” concepts
A visionary but also controversial genius recently has left us. Michael Crichton, the famous writer, filmmaker and, less familiar to most people, skilled anthropologist and medical doctor, died of cancer at the age of 66.
Crichton by no means was a blatherer. Far from it! He was a Harvard graduate, a lecturer in anthropology at Cambridge University, UK, in the 1960s and afterwards became a post-doctoral fellow at the Salk Institute for Biological Sciences, La Jolla. Soon, however, Crichton backslided the natural sciences and became a science writer (although his first bestseller, The Andromeda Strain, was published while he was still a medical student in 1969).
Why did he backslide at that time? Just ask him, on www.crichton-official.com, he answers as follows: “It’s what I always wanted to do.”
Even though natural scientists by the majority disliked him, Crichton has done a lot for us. His fast-paced technological thrillers, sold in the tens of millions, dealt with medical technology, computer science, chaos theory and genetic engineering. This “gee-whiz science” was an assist that was easily adapted by Hollywood. “Jurassic Park,” based on his book and on which he shared screenwriting credit, is the No. 10 top grossing film of all times (in 2002, a newly discovered ankylosaur was named after him: Crichtonsaurus bohlini – see photo above).
In other words: with his novels and films and his special kind of science propaganda, Crichton produced interest in science in many millions of people.
By the way, many of his visions in fact became true! In the Discovery magazine blog, you can find “The Top 5 “Crazy” Michael Crichton Ideas That Actually Came True”, such as …
- linguistic abilities of apes (as in “Congo”, 1980)
- self-replicating nanorobots (as is “Prey”, 2002)
- brain implants (as in “The Terminal Man”, 1972)
But I admire him most for Jurassic Park. Crichton made dinosaurs (and also palaeontologists!) socially fully acceptable.
Thank you, Michael!!
Spitting and popping genes
Did you ever toy with the idea of having your own DNA analysed? You didn’t? Well, 25-year-old reporter girl Boonsri Dickinson from the NYC-based Discover magazine did.
Dickinson spat and popped, then she sent, ugh!, saliva and cheek cells by mail and subsequently was disclosed frightening things.
DNA testing isn’t no more bloody expensive. There are a handful of companies that offer DNA analyses, such as Navigenics from California (“Understand what your genes have to say about the future”), Icelandic deCode Genetics (“Revealing what lies within your DNA”) and 23andMe (“See your genes in a new light”), the latter founded by the wife of Google’s Sergey Brin, Anne Wojcicki.
The price range for a SNP analysis, what the companies actually really do, is from $2500 for a Navigenics test to a $399 special offer provided by 23andMe. But what do customers get for their money?
Well, reporter girl Dickinson got a lot.
Navigenics equipped her with macular degeneration, osteoarthritis, obesity, psoriasis, diarrhoea and Crohn’s disease.
23andMe donated dry earwax and a stinky sense of smell. Additionally, the company knew from her SNP profile that Dickinson had the enzyme to digest milk (even though she had suffered from lactose intolerance for years, as Dickinson noted).
At DeCode Genetics’ subsidiary DeCodeMe, finally, CEO Kári Stefánsson himself interpreted Dickinson’s results comprising a risk of developing type 2 diabetes, colorectal cancer, rheumatoid arthritis and atrial fibrillation.
Apparently, testing DNA for health purposes is making people sicker than ever.
Quicker change - conventional vs. convenient mutant generation
This success story was provided by Dr. B. Pohn & Dr. S. Feichtenhofer (Institute of Molecular Biotechnology, Graz University of Technology, Austria)
11 mutations and a deletion at one sweep
evolving mutant generation from conventional to convenient
To answer the question concerning the correlation between a structural feature of a wild-type enzyme and the activity towards a certain substrate we needed to excise seventeen amino acids of the sequence and introduce eleven mutations in the regions around the excision.
Obviously with a standard mutation strategy this task would have been reached only by a multi-step process. At first we would have done the excision using an overlap PCR strategy. For the introduction of the site directed mutations in the second step either a rather long primer ensuring the binding in homologous regions of the gene in the neighborhood of the mutated region or several shorter primers would have been needed. To generate the mutated gene by ourselves the estimated costs only for the needed oligonucleotides would have been about € 190. Additionaly we would have needed polymerase, sequence analysis and labor time. The price Mr. Gene offerted us for the synthesised mutated gene in a plasmid provided with the cutting sites for cloning in our vector system was € 200.
The decision for the ordering of a synthetic gene at these costs was very easy to argue in our company. Two weeks after placing the order the synthesised gene and the sequencing data were delivered. We were very pleased with the service and the agreed price of Mr. Gene for that task. When we would have done the needed mutational changes by ourselves, neither we would have obtained the ready construct within two weeks, nor for that low costs.
