Cancer has a cacophonous melody (really?)
Well, in my opinion, the following is quite bizarre: Gil Alterovitz, an electrical and biomedical engineer with proteomics skills (and MIT alumnus, as well), is developing a computer program that translates protein and gene expression into music.
I’m not kidding. Recently, the Technology Review (TR) published an article on this guy’s conversion of genetic activity into music. “Harmony represents good health and discord indicates disease”, we learn from TR writer Jennifer Chu, and, in addition, that “Alterovitz hopes that doctors will one day be able to use his music to detect health-related changes in gene expression early through the musical slip into discord”.
Wow, what an impressive approach – at least at first sight.
However – are aficionados of unorthodox and experimental music, such as jazz, industrial hip-hop or the Second Viennese School, reading this? Well then? Do you agree with Alterovitz? Is it okay that he is linking healthiness to the tunes of classical and, say, folk music, whereas connecting illnesses to more uncommon harmonies? As a former heavy metal enthusiast I shouldn’t be amused…
In either case, Alterovitz’ computer programme is a funny plaything (and excellent means for him to find further funding, as I suppose maliciously…).
gene synthesis order in less than 50 seconds
Don’t wait for quotations or emails. Start right now. Copy & paste your sequence - that’s it. You’ll be done with your gene synthesis order in less than 50 seconds.Â
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Interested? Submit your sequence >>>Â
Please note: prices are a matter of change!
High GC content gene synthesis
This success story was provided by the group of Prof. Dr. Bechthold (Pharmaceutical Biology, Albert-Ludwigs-University, Freiburg)
This synthetic gene was prepared by Mr Gene while other companies refused to synthesize the gene due to a very high GC content.
Order submitted: March 18th - gene finalized: April 17th
Length: 471 bp - GC content: 71 %
The pharmaceutical activity of many natural products, among them valuable antibiotics and anticancer therapeutics, depends on regio- and stereospecifically attached sugar moieties. The attachment of these sugars is catalyzed by glycosyltransferases (GTs). The acceptor substrate of glycosyltransferases vary widely, the donor substrate is almost always an activated sugars, with the most common activated species being NDP sugars. Landomycin A and landomycin E, both produced by different Streptomyces strains, belong to the angucycline type of natural products and possesses strong antitumor activities, in particular against prostate cancer cell lines. Detailed studies on the biosynthesis of the hexasaccharide side chain of landomycin A revealed that four glycosyltransferases are responsible for the formation of the side chain. LanGT2 is the priming glycosyltransferase connecting D-olivose to the landomycin aglycon (landomycinone) and LanGT3 is the olivosyltransferase responsible for the transfer of the fourth sugar moiety. LanGT1 is an iteratively acting olivosyltransferase catalyzing the attachment of the second and the fifth sugar and LanGT4 is an iteratively acting rhodinosyltransferase attaching the third and sixth sugar during landomycin A biosynthesis. Three glycosyltransferases are responsible for the formation of landomycin E in S. globisporus. Here LndGT2 is the priming glycosyltransferase, LndGT1 catalyzes the attachment of the second sugar and LndGT4 attaches the third sugar. We have shown that LndGT4 can not act twice during landomycin biosynthesis. The aim of studies was to detect amino acids responsible for the iterative work of LanGT4 and introduce them into LndGT4. We were able to design a gene encoding an iteratively working enzyme and Mr. Gene did the synthesis.
Thank you Mr. Gene!
Wikification of Genes – next Effort
Have you noticed, yet, that the wwweb has swollen up like people’s bellies after Christmas? As an example, take the ten thousands of wikis that congest the virtual world. Each of them is an epitome of wisdom (well, let’s face it: most wikis are as superfluous as the fifth leg of an antelope).
Recently, the wiki universe got another member and surprisingly, it could make an impact. “Gene wiki”, a project of Californian researchers around Jon W. Huss (San Diego State University) and Andrew I. Su (Genomics Institute of the Novartis Research Foundation, San Diego), is an incomplete attempt “evolved out of the existing Wikipedia framework” and “several other gene wikis that already exist [but have a poor] user base and [poor] search engine rankings”.
Check the relevant PLoS paper by Huss et al.
Do we really need this “Gene wiki” thing? Don’t we have enough gene and model organism portals, yet, such as Entrez Gene, Ensembl and Flybase?
In my opinion this “Gene wiki” effort could emerge as a huge success. Flybase and Co. are complex stuff intended for very few experienced scientists, whereas the new born “Gene wiki” baby could attract a more manifold mixture of interested people.
We should never forget: many an interested greenhorn is tomorrow’s researcher.
Be a record holder (and a Nobel Price winner, too)!
How’s work going? For my share, experiments have been going awry for weeks (and still are) while my demanding lab taskmaster is becoming more and more bad-tempered (and so am I!).
Tons of failed experiments in mind, my research grant running out at lightning-speed and the next sensational blockbuster paper out of reach, I brainstormed about career alternatives – and had a sudden inspiration.
If you are one of these countless successful scientists, please jump ship immediately. The following is addressed to washed-up lab nerds.
++ Want to publish something in an illustrious medium (and gain fame at that)? ++
++ Want to hit the big time (and the Noble Price, if possible)? ++
++ Don’t want to manage millions of lab experiments for that goal? ++
Here’s the perfect answer: become part of the Guinness Book of World Records!
What to do?
A piece of cake: be the first to read the three billion pairs of bases of a human genome out loud and without stopping. That task will take about 9.5 years at reasonable reading rate (10 bases per second), according to calculations made by the Human Genome Organisation. After this, you should have earned an entry in the Guinness Book of World Records (and lifelong hoarseness, too).
Marc Abrahams, the mastermind of Improbable Research (“Research that makes people LAUGH and then THINK”), will also be enormously interested to hear from you. Maybe there’s another Ig Nobel Prize on the way?
BTW: Mr Gene would of course also be pleased to receive any information on your ground-breaking record experiment.
E.coli codon usage optimization
How to optimize a gene for E.coli codon usage using mrgene.com’s online software tool.
The movie below explains how to optimize a gene for E.coli codon usage.
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Mr. Gene’s online tool automatically tries to eliminate DNA motifs known to hamper expression in E.coli (and other prokarya). Ribosomal entry sites, TATA-Boxes or -35 Boxes present within the open reading frame worsen protein expression in almost any case.
Toward the end the movie shows how the codon optimized synthetic gene can be ordered online.
Please note: prices are a matter of change!
Play the protein game!
You have spent ages protecting Earth against alien invaders and other evil fellows. Now it’s high time to leave your imaginary “Universe At War” for a while and contribute your game power to curing deadly diseases in reality. Researchers from Washington University around HHMI scientist David Baker recently provided the perfect opportunity for helpers: they launched an online protein folding computer game.
Its name is Foldit (http://fold.it/portal/adobe_main).
Foldit is a product of collaboration between computer science and biochemistry researchers from the HHMI at University of Washington. It’s a free game in which players compete to design proteins. The game teaches the competitors the basics of protein folding before letting them loose on real proteins from nature. Afterwards, HHMI scientists will test the freshly designed proteins to see if they make viable candidate compounds for new drugs.
At the moment, Foldit only uses proteins whose 3D structures have been solved. But soon puzzles will be introduced for which the solution is unknown.
The understanding of protein folding is the Holy Grail of biochemistry. Dozens of computer algorithms were created in the past to predict how a linear string of amino acids will fold into a given 3D structure (however, none of them acts properly). With Rosetta@Home, launched in 2005, Baker’s group once has created another legendary computer project to use computational methods for the prediction of protein structures. But this distributed computing project which currently pools the resources of 420,000 active PCs to a cumulative processing power of 62 TeraFLOPS (making trillions of calculations possible) has a drawback.
Computers do silly things occasionally.
The multiplayer online game Foldit could be a better way to go, Baker thinks. What do you think?
Calling Neanderthal
Aaargh!
Ough!
Huh-huh-grumpf… ouch!?
Well, speaking isn’t always that easy.
In Jean-Jacques Annaud’s film “Quest for Fire” a group of Palaeolithic humans travels its primeval world in search of a flame to relight their extinct fire. The film’s most startling feature is the invented language spoken by the prehistoric humans. It was created by British novelist and composer Anthony Burgess, and is rich in words like “Aaaargh!”, “Grumpf!” and so on.
When Annaud directed the shooting in 1981 there was nothing known about the genetic principles of language.
That has changed. 17 years after the premiere of “Quest for Fire” British geneticist, Anthony Monaco, discovered the “language gene” FOXP2 (coding for a transcription factor) that is implicated in the development of language skills.
Recently, however, another amazing result of anthropological research was published. Robert McCarthy, an Assistant Professor at Florida Atlantic University, has reconstructed Neanderthal vocal tracts to simulate prehistoric man’s voice. Listen to the breathy sound of a Neanderthal saying “E”.
And now compare this 50,000-year-old rattle to another “E” pronounced by one of today’s humans. Lovely sound, right?
Fortunately, McCarthy’s linguistic team won’t stop at the “E”. They’re planning to simulate an entire Neanderthal sentence soon. Stay tuned!
Dachshund, Werewolf, and other crazy genes
Have you ever wondered about the origin of strange and notable gene names, such as hedgehog or swiss cheese? Most of the current genetic nomenclature has meaningful origins, while other genes were named on a mere whim.
Take the above mentioned hedgehog gene discovered in the 1970s by Nobel Prize laureates Edward Lewis, Christiane Nüsslein-Volhard and Eric Wieschaus, when studying genetic mutations in Drosophila embryogenesis. Hegdehog encodes an intercellular signalling molecule, the Hedgehog (Hh) protein that regulates a pivotal pathway in the development of body segmentation, from flies to humans. Mutant Hedgehog Drosophila larvae sometimes appear stubby and hairy – an observation that led researchers to this quirky name.
The origin of the gene name swiss cheese is similar: The brains of fruit flies with mutated versions of this gene have holes, resembling the tasty dairy treat from Switzerland.
Another comical name is dickkopf (which translates loosely to “bullhead”) first described in 1998. When overexpressed, the dickkopf gene causes polliwogs to grow with elongated heads. Even worse, one can create headless polliwogs if the dickkopf protein is deactivated by antibodies, or create multi-headed animals in individuals expressing an abnormal number of dickkopf genes (see picture).
It’s no surprise that humans have four different dickkopf genes.
If you know a clever or comical gene name like dachshund and huckebein (Drosophila), werewolf (Arabidopsis) and the mad/max twins (Homo sapiens) please let us know!
Blue Pill Anniversary
This year marks the tenth anniversary of the event that revolutionized consumer pharmaceuticals. Sadly, we are not referring to the Schweinsohr (Swine’s ear a.k.a. Gomphus clavatus), the 1998 German “Fungus of the Year” winner.
You would be getting fairly close if you’ve guessed the 1998 Nobel Prize in Physiology or Medicine awarded to Ferid Murad, Robert Furchgott, and Louis Ignarro who discovered the pivotal role of nitric oxide (NO) as an important physiological signaling molecule.
This past March, scientists and couples worldwide celebrated 10 years of benefits of 1-[4-ethoxy-3-(6,7-dihydro-1-methyl-7-oxo-3-propyl-1H-pyrazolo[4,3-d]pyrimidin-5-yl) phenylsulfonyl]-4-methylpiperazine citrate,
also known as sildenafil citrate,
but best known as…[disable your spam filters!]… Viagra.
On March 27, 1998, those little blue pills entered the market, becoming one of the most successful pharmaceutical rollouts in recent years. Pfizer, Inc. had revenues of $788 million in 1998 and still earns nearly $2 billion per year, while its competitors Eli Lilly (makers of “Cialis”) and Bayer (“Levitra”) earn 1.6 billion annually with their little yellow pills.
Over 35 million men have consumed Viagra since 1998, according to Pfizer – millions more were taken in by placebos with no active agent.
Perhaps Nobel laureates Murad, Furchgott and Ignarro can be credited with Viagra’s success. Its mechanism of action is the enhancement of the NO by inhibiting the enzyme that normally breaks down cGMP.
The result is, well, quite a strong rise.
