Genome Biology was sad to learn of Frederick Sanger’s death on Tuesday, November 19th. Although Sanger retired from scientific research 30 years ago, long before the journal Genome Biology ever started, it is safe to say that without his work we wouldn’t even be here.
The journal was launched in 2001, the same year that the completion of sequencing of the human genome was reported. The sequencing was done entirely using the method Sanger had devised for determining genetic sequences. Although his was not the first technique for reading DNA sequence, it was the first really practical one and, like many methods that revolutionize fields, it was an elegant and conceptually simple idea. Sanger had, in …
Two rarities seldom seen by Bostonians are the American Society of Human Genetics Annual Meeting (aka ASHG) and the baseball World Series. The former was last in Boston 60 years ago, in 1953 – the year of the double helix. The latter, a contest between grown men – as evidenced by a dazzling roster of beards – playing some sort of rounders derivative, has not been won on home turf by the city's Red Sox since 1918. But both events converged this year, with the geneticists of ASHG more than equal to the task of keeping all four bases covered. That is, the DNA bases A, C, G and T.
Mo' data, mo' solutions?
The most …
It seems that scientific research in the last two hundred years or so has made a full conceptual circle. In the good old days of the nineteenth century, any Englishman with a vaguely middle-class background, a source of modest income and an insatiable curiosity could treat research as an eccentric pastime. Whether that meant sea voyages and bird watching or hiking trips and rock collecting, what mattered first of all was the pursuit of the understanding of how the world works.
But times changed, and the world changed, and research moved from gentleman’s clubs to academic institutions. And although it gained more structure, and although, as hobbyists turned into professionals, scientific dillydallying turned into a rigorous process, we …
The writers of popular forensics drama franchise CSI would be well advised to read Genome Biology today, as we publish an article that employs a widely used epigenetics assay to show that age can be predicted with reasonable accuracy from pretty much any human DNA sample, so long as it is sourced from healthy tissue.
In other words, a swab of the perp's DNA, even if not matched to an individual on a database, could yield seriously good clues about the age of a suspect, alongside what the wiliest of TV detectives have already shown we can determine about gender and obscure genetic diseases.
Incredibly, the 'epigenetic clock' characterized by UCLA biostatistican Steve Horvath, from which he …
Nobel prizes can sometimes set me a-wondering what the point in journals is. One of the most well-known Nobel-winning papers, that of Watson & Crick, was published in Nature – sixty years ago – without peer review (readers of Science's recent so-called 'sting' on Open Access and peer review might want to take note of the fact that Nature is not, nor has it ever been, an Open Access journal).
Reverse to the trigger-happy antics at Nature, which generally did not bother with peer review in the 1950s (and when it did, viewed a bit of a chinwag in a Pall Mall gentleman's club to be up to the task), was the Journal …
It is estimated that in a single mammalian cell the median copy number of an mRNA is 17 molecules, with the dynamic range spread over four orders of magnitude. At the same time, an average microRNA can recognize as many as 400 target sites, and has to be able to do so equally effectively for both those mRNA species that have only a few copies and those that have a few thousand copies in the cell. Our understanding of this highly dynamic regulation network therefore depends to a high degree on our ability to accurately quantify microRNA.
Of the three major approaches to RNA quantification, microarrays and RT-PCR suffer from the same ailment: they are …
With great fanfare comes great cynicism, and so it should: science is built on the tug-of-war between novel claims and kneejerk skeptism, and the probity that follows. When a sound bite leaked out of last year's ENCODE publications, of which Genome Biology was a participatory journal, that '80% of the human genome has a function', evolutionary biologists were cynical all right, and they took to the journals to say so.
While some of the disagreement hinged on the semantics of the word 'function', a key sticking point was the scientific validity of declaring a stretch of the genome functional when there is no evidence for evolutionary constraint on its constituent DNA sequence. In other words, how …
On April 25, Genome Biology published an interview with Raymond Gosling, who took the famous Photo 51 upon which Watson & Crick's model of DNA's double helix was based. Gosling had worked closely with Rosalind Franklin, whose contribution to the discovery is now rightly celebrated. However, he had initially been recruited to the project by John Randall, head of the MRC Biophysics Unit at King's College London, where the research took place.
Gosling expressed his disappointment at the lack of recognition Randall has received for his role in the discovery, and emphasized that this omission was the most important message he wanted to convey to Genome Biology's readership.
After publishing the interview, Genome Biology was contacted by …
You may recall that July's issue of Genome Biology was dedicated to the field of plant genomics (more info on the issue can be found in this blog post).
When putting together the issue, we recorded a podcast with some of the featured researchers in which we discussed their contributions.
We also spoke to co-Guest Editor Mario Caccamo (read his and Erich Grotewold's Editorial here) and, as a bonus, we solicited the thoughts of Dale Sanders on GM crops – a perennially hot button topic.
For the aurally challenged, Biome has posted a full text of the Q&A from which Sanders' podcast clips are excerpted.
Nematodes have been propelled into fame in the scientific community by the widespread use of Caenorhabditis elegans as a model organism. Investigation of this nematode has provided insights into key areas of biology, including development and apoptosis. While C. elegans is one of the most widely studied organisms in biology, other nematodes have also become interesting targets of investigation. Since the publication of the genome of C. elegans in 1998 the genomes of numerous other nematodes have been sequenced and analyzed; details of other nematode genome project can be found at WormBase. This work is now further expanded by the publication of the genome the strongylid nematode Hemonchus contortus which has been sequenced and analyzed by two independent …