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.

Thank you Mr. Gene!

#1
iPod® touch:
Martin Jennings, PhD, University of Manchester, UK

#2
iPod® nano:
Irina Borodina, PhD, Technical University of Denmark, Denmark

#3 … 10
iPod® shuffle:
Nicholas Wall, Graduate Student, Salk Institute for Biological Studies, USA
Craig Ellermeier, Assistant Professor, University of Iowa, USA
Filipe Pinto, PhD Student, Instituto de Biologia Molecular e Celular, Portugal
Ramireddy Bommireddy, Assistant Professor, University of Arizona, USA
Chris Upton, Professor, University of Victoria, Canada
Boris Ermolinsky, Assistant Professor, University of Texas at Brownsville, USA
Roby Jose, PhD Student, James Cook University, Australia
Gemma Sutherland, Technical Officer, Charles Sturt University, Australia

Looking forward to see you at the next synthetic biology conference - synbio5.0!

Does anyone know where it will take place?

It’s the author’s ranking on the resulting publication. This ranking always gives pain, being the reason for hassle and hatred between former colleagues and close collaboration partners.

Of course, the most important position on a scientific paper is the first one. The first author is the person who achieves fame and honour and later a lucrative job. In addition, most people think that the first author is the person that has optimised and executed most of the experiments.

The last author position is sought-after, too. Usually we suppose that it’s the venerable person behind the team (normally the full professor or at least a skilled post doc). For most people, the senior author is the ingenious mastermind behind the scenes and the experiments.

Nice belief – but completely wrong.

If you are interested in seeing how the cat jumps, just look at this web page. There you will learn to give credit where credit is due.

Really comical stuff, this PhD comics site.

This Wikipedia list is an interesting read on this topic. Please note: it’s a long, long list of doping cases (and it’s solely about cycling!!). You will have to scroll a while to reach the last cases from 2008.

From time to time, one of these guys kicks the bucket. These “sudden deaths” of healthy(?) young athletes more and more raised questions on the riskiness of sports in general (an appropriate entry is the out-dated Springer textbook “Performance enhancing drugs and sudden death – a case report and review of the literature”).

Well, is sport really life-threatening? Should even leisure athletes better avoid working up a sweat?

A recent study performed by Vienna-based nutritional scientists gives a surprising answer. Karl-Heinz Wagner and his colleagues investigated the effect of an Ironman triathlon on DNA stability. They measured the number of micronuclei, nucleoplasmic bridges and nuclear buds as biomarkers of genomic instability in lymphocytes of 20 male triathletes (before, within and after the race).

Wagner’s results were appeasing. Sport, even ultra-endurance exercises, does not cause long-lasting DNA damage in well-trained athletes. The paper’s abstract can be found here.

As their next project the scientists should investigate the correlation of illegal doping practices with the state of mind of doping swindlers. I suppose such a study would produce interesting results, too.

When I recently had a routine check at my GP, he noticed that my immunisation protection against Tetanus bacteria (given by a combined Td-Polio vaccine) had expired. He smiled maliciously – and made way for his nurse who came along with SUCH A HUGE AND HORRIBLE INJECTION GUN…

Phew! I barely survived it. Now I’m safe from infections as well as injections for the coming five years. However, what then? Avoiding doctors and needles but running the risk of falling ill by tetanus?

Why has Big Pharma so far failed to develop Td Polio vaccine alternatives such as oral and nasal vaccination?

Recent research offers at least two additional possibilities.

Firstly, how about a “vaccine plaster”? A study recently published by Greg Glenn and Sarah Frech (Iomai Corp., acquired in May 08 by Austria’s Intercell) reports promising results for patches that vaccinate travellers against diarrhoea (“Use of a patch containing heat-labile toxin from Escherichia coli against travellers’ diarrhoea: a phase II, randomised, double-blind, placebo-controlled field trial”, Lancet 2008, 371(9629):2019). Other groups are testing this vaccination way on Alzheimer’s disease for a while.

Wow, glittering – just stick a small plaster to people’s skins!

Another way to escape nasty nurses with huge needles would be nasal vaccination – studied or yet developed against RSV, HIV, Alzheimer’s, Haemophilus influenzae, Flu, etc etc etc.

Why, for the world, haven’t they developed a smooth and gentle Td Polio vaccine, yet? Or have they already? Who knows?

I refer to the world’s first “mad science contest” (themed “Build a Life Form and We’ll Send You to Hong Kong”). Searching for “biology to be brazen”, the contest ought to identify “mad scientists with homebrew closet labs, grassroots geneticists, and garage genome hackers”. These mad scientists were “the people most likely to change the world”, the organisers believe.

What was the challenge about? Well, the contestants were asked on June 7th this year to build a real life form using “scientifically plausible” materials (whatever this might be).

After almost three months, the winners had been found: champion in the “biobricks life form category” is Vijaykumar Meli with his novel class of rhizobial bacteria that do symbiosis with rice roots what makes nitrogen synthesis more efficiently. Meli is a biotechnology Ph.D. student from New Delhi, India. Take a look at his “mad” idea (actually quite conventional, isn’t it?).

Other synthetic life forms suggested by the competitors are worlds more bizarre – such as Elliott Gresswell’s carnivorous, water-going tree and Naor Livne’s Spliterphage.

The question of whether top-ranking politicians are life forms, too, remains to be answered.

1st place: iPod touch
2nd place: iPod nano
3rd to 10th place: iPod shuffle

Apple and iPod are registered trademarks of Apple, Inc. Apple is not a participant or sponsor of this promotion.

Anyway – enjoy the comical incident when Erik Fransén, a Swedish researcher, went away on a Neuroscience conference in the USA for two weeks and noticed on his return that his computer keyboard had come to life.

You can read about the whole affair on the website of Fransén’s colleague Johannes Hjorth:
http://www.nada.kth.se/~hjorth/krasse/english.html

Really a bad joke, isn’t it? If I had been in the place of unfortunate Fransén, I’d have been scared witless and immediately would have tested my hard drive for further green infestations.

The Swede’s joke has spawned imitators. Here is one eternized on Youtube. Here is another.  

By the way, gardening already appears to be a topic for jokers. When investigating for the “growing cress on a keyboard” story, I stumbled upon this nice gardening clip:
http://www.youtube.com/watch?v=n5F04ItE3Oo&feature=user

Well, one has to have a sense of humour at Canadian colleges when Paul Telner is around!

(“That Smell” by US rock band Lynyrd Skynyrd, released in 1977 – a song about Skynyrd guitarist Gary Rossington who bought a new car, got drunk and crashed it into a tree and then into a house.)

You remember this ole song? It crossed my mind when I heard of the following: US chemist Michelle Gallagher and colleagues recently presented the first odour profile for skin cancer (Gallagher is employed by Monell Chemical Senses Center, a non-profit institute dedicated to basic research on the senses of taste, smell and chemosensory irritation). The scientist was inspired by previous research reports that dogs could be trained to detect the scent of cancer.

ScienCentral (where you can view this interview with Gallagher) commented: “That [the first odour profile for skin cancer] could lead to a new cancer sniffing technology”.

Ha-ha! – A new sniffing technology. Nice wording!

Well, this story’s background actually isn’t that funny. Skin cancer (basal cell carcinoma, BCC) is the most common type of cancer in industrialised countries, killing 17,000 every year in Europe and nearly 9,000 in the USA. A prominent skin cancer patient is US president nominee John McCain.

Such a “synthetic nose” could be a much easier and less painful way to get patient’s diagnosis. At present, doctors diagnose skin cancer by visual examination, followed by an invasive biopsy.

Gallagher’s experimental methods (when developing an assay to distinguish between normal and cancerous skin) were unorthodox, too: she used a tool that looked like an upside down martini glass to sample the air above skin from volunteers (Gallagher detected 92 chemicals using gas chromatography and mass spectrometry).

An upside down martini glass. Amazing. Lynyrd Skynyrd’s musicians would have been amused.

Unfortunately, it’s beyond their power. Half the rock band was killed in a tragic plane crash a few days after their 1977 tour had started.

However, I have to muddy the good mood a little. Quit the OSM (= Olympic Smile Mode) for a while, please, and arm yourself for a bad word:

Gene - yuck! - doping. Gene doping.

For years, naysayers gloomily have predicted that gene doping will soon emerge to a great challenge, forecasting souped-up muscle monsters prizing up heavy-weight barbells in a flash and finishing the 100 meters in less than 9 seconds afterwards. But let’s stay cool – actually, the topic “gene doping” is rather science fiction (at least, if you allude to successful gene therapy in humans).

Still, the USADA (the US Antidoping agency) and the WADA (the World Anti-Doping Agency) want to be prepared. They have commissioned Canadian researcher Jim Rupert to develop new testing methods which will track down those misusing gene-based medical treatments in the future. Mr Rupert got a $325,000 grant last year to come up with a prototype assay to detect siRNA mediated gene doping (to tell the difference between real hormones and those created by gene therapy).

Rupert admitted this could be difficult. To look after something that still doesn’t exist is a tricky job.