Genome sequencing in microfabricated high-density picolitre reactors

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.     

SEPRAN:A Versatile Finite-Element Package for a Wide Variety of Problems in Geosciences

Numerical modelling of geological processes, such as mantle convection, flow in porous media, and geothermal heat transfer, has become quite common with the increase in computing and the availability o...     

Intragenic recombination leads to pilus antigenic variation in Neisseria gonorrhoeae

The pilus of the bacterium Neisseria gonorrhoeae is a fimbriate surface structure which promotes attachment of the bacterium to host epithelial cells. Gonococcal pilus phase variation is characterized by a rapid on/off switch in which piliated (P+) cells throw off non-piliated (P-) variants and vice versa. Two regions of the gonococcal chromosome (pilE1 and pilE2) act as pilin expression loci, reminiscent of the MAT locus in the yeast Saccharomyces cerevisiae, while several other chromosomal regions contain silent (non-expressing) pilin sequences. Biochemical and antigenic diversity is seen in pili from a wide variety of clinical isolates. Pilins (pilus subunits) are composed of conserved N-terminal and variable C-terminal regions; the conserved region of gonococcal pilin is also found in pilins produced by widely disparate bacteria. We show here that the gonococcal pilin undergoes antigenic variation in vitro and in vivo. The protein consists of constant, semi-variable and hypervariable regions. This antigenic variation probably involves gene conversion of mini-cassettes of pilin information.     

Three unpublished letters to Charles Darwin: the solution to a ‘geometrico-geological’ problem

While Charles Darwin wrote his Observations on South America, he often sought the advice and help of other scientists in solving specific problems. Three letters that the Cambridge geologist and mathematician William Hopkins wrote to Darwin exemplify such aid. In these letters Hopkins was able to show Darwin how he could calculate the position of the sedimentary beds on the Chonos Archipelago, which Darwin had visited. In his first letter Hopkins sent a solution, part of which eluded Darwin. Darwin's letters to Hopkins have not yet been found, but two additional letters gave Darwin the solution he was looking for.     

Rab protein evolution and the history of the eukaryotic endomembrane system

Spectacular increases in the quantity of sequence data genome have facilitated major advances in eukaryotic comparative genomics. By exploiting homology with classical model organisms, this makes possible predictions of pathways and cellular functions currently impossible to address in intractable organisms. Echoing realization that core metabolic processes were established very early following evolution of life on earth, it is now emerging that many eukaryotic cellular features, including the endomembrane system, are ancient and organized around near-universal principles. Rab proteins are key mediators of vesicle transport and specificity, and via the presence of multiple paralogues, alterations in interaction specificity and modification of pathways, contribute greatly to the evolution of complexity of membrane transport. Understanding system-level contributions of Rab proteins to evolutionary history provides insight into the multiple processes sculpting cellular transport pathways and the exciting challenges that we face in delving further into the origins of membrane trafficking specificity.     

The National Science Foundation and philosophy of science's withdrawal from social concerns

At some point during the 1950s, mainstream American philosophy of science began increasingly to avoid questions about the role of non-cognitive values in science and, accordingly, increasingly to avoid active engagement with social, political and moral concerns. Such questions and engagement eventually ceased to be part of the mainstream. Here we show that the eventual dominance of ‘value-free’ philosophy of science can be attributed, at least in part, to the policies of the U.S. National Science Foundation's “History and Philosophy of Science” sub-program. In turn, the sub-program's policies were set by logical empiricists who espoused value-free philosophy of science; these philosophers' actions, we also point out, fit a broad pattern, one in which analytic philosophers used institutional control to marginalize rival approaches to philosophy. We go on to draw on existing knowledge of this pattern to suggest two further, similar, contributors to the withdrawal from value-laden philosophy of science, namely decisions by the editors of Philosophy of Science and by the editors of The Journal of Philosophy. Political climate was, we argue, at most an indirect contributor to the withdrawal and was neither a factor that decided whether it occurred nor one that was sufficient to bring it about. Moreover, we argue that the actions at the National Science Foundation went beyond what was required by its senior administrators and are better viewed as part of what drove, rather than as what was being driven by, the adoption of logical empiricism by the philosophy of science community.