An integrated semiconductor device enabling non-optical genome sequencing

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.     

Early experience of tactile stimulation influences organization of somatic sensory cortex

Visual experience is essential for the establishment of the cerebral cortical circuitry that allows normal binocular vision. For example, the pattern of right-eye, left-eye dominance columns is permanently altered by simply closing an eye of a young primate. A critical issue is whether environmental factors also influence the development of other cortical sensory areas. In the present experiments we manipulated the tactile experience of young rats by depriving them of the sensory information that is normally provided by their large facial whiskers. Electrophysiological analyses showed that simply trimming the whiskers from the day of birth results in pronounced abnormalities in the response properties of single neurons in the adult somatic sensory cortex. Thus functional plasticity in response to early experience appears to be a fundamental aspect of cortical development.     

A functional barrier to movement of lipids in polarized neurons.

In polarized neurons, axons and dendrites perform different functions, which are reflected in their different molecular organization. Studies on the sorting of viral and endogenous glycoproteins in epithelial cells and hippocampal neurons suggest that there may be similarities in the mechanism of sorting in these two cell types. The mechanisms that maintain the distinct composition of the two plasma membrane domains in these two cell types must, however, be different. We have proposed the existence of a functional barrier at the axonal hillock/initial segment which prevents the intermixing of membrane constituents. Here we test this hypothesis by fusing liposomes containing fluorescent phospholipids into the plasma membrane of polarized hippocampal cells in culture. Fusion was induced by lowering the pH and mediated by influenza virus haemagglutinin expressed on the axonal surface of neurons infected with fowl plague virus. Labelling was found exclusively on axons after fusion. Although the fused lipids were mobile on the axonal membrane, no labelling was detected on the cell body and dendritic surfaces. These results suggest that there is a diffusion barrier at the axonal hillock/initial segment which maintains the compositional differences between the axonal and somatodendritic domains.     

The many encounters of Thomas Kuhn and French epistemology

The work of Thomas Kuhn has been very influential in Anglo-American philosophy of science and it is claimed that it has initiated the historical turn. Although this might be the case for English speaking countries, in France an historical approach has always been the rule. This article aims to investigate the similarities and differences between Kuhn and French philosophy of science or ‘French epistemology’. The first part will argue that he is influenced by French epistemologists, but by lesser known authors than often thought. The second part focuses on the reactions of French epistemologists on Kuhn’s work, which were often very critical. It is argued that behind some superficial similarities there are deep disagreements between Kuhn and French epistemology. This is finally shown by a brief comparison with the reaction of more recent French philosophers of science, who distance themselves from French epistemology and are more positive about Kuhn. Based on these diverse appreciations of Kuhn, a typology of the different positions within the philosophy of science is suggested.     

Primary structure of bovine thyroglobulin deduced from the sequence of its 8,431-base complementary DNA

In mammals, an adequate supply of thyroid hormones is essential for normal growth and neurological development. The biosynthesis of thyroid hormones involves an iodinated precursor protein, thyroglobulin, which may be considered an extreme example of a pro-hormone. Thyroglobulin is a dimeric glycoprotein of relative molecular mass (Mr) 660,000 (660K), which is secreted by the thyrocyte and stored in the lumen of the thyroid follicle. The hormonogenic reaction is extracellular, and involves iodination of tyrosyl residues of thyroglobulin and the intramolecular coupling of a subset of these into thyroxine (T4) and triiodothyronine (T3), which remain part of the polypeptide chain. Secretion of hormones results from the endocytosis of thyroglobulin followed by its complete hydrolysis in lysosomes. Considering that the maximum yield of hormones is approximately 6-8 per 660K protein, the whole process is apparently wasteful. However, the efficiency of thyroglobulin as a thyroid hormone precursor is extremely high when the supply of iodine is short; in such conditions, almost all the iodine incorporated is found in iodothyronine. Hence it is suggested that the thyroglobulin structure has evolved to allow for the preferential and efficient iodination and coupling of the hormonogenic tyrosines. Here we report the complete primary structure of bovine thyroglobulin, derived from the sequence of its 8,431-base-pair complementary DNA. The 2,769-amino-acid sequence is characterized by a pattern of imperfect repeats derived from three cysteine-rich motifs. Four hormonogenic tyrosines have been precisely localized near the amino and carboxyl ends of the protein.     

Antisense c-myb oligonucleotides inhibit intimal arterial smooth muscle cell accumulation in vivo.

Synthetic antisense oligonucleotides have been used to dissect gene function in vitro. Technical difficulties prevented the use of this approach for investigating the effect of gene products in vivo. Here we report the use of local delivery of antisense c-myb oligonucleotide to suppress intimal accumulation of rat carotid arterial smooth muscle cells. Our results suggest that antisense oligonucleotides can be used to define the in vivo biological role of specific macromolecules in the blood vessel wall and could potentially serve as a new class of therapeutic agents for cardiovascular disorders.     

The tight junction does not allow lipid molecules to diffuse from one epithelial cell to the next

The tight junction (zonula occludens) links epithelial cells into a monolayer by forming a continuous belt of sealing contacts around the apex of each cell. They appear in thin sections as if they were 'fusions' between the apposed plasma membranes and in freeze-fracture replicas as patterns of complementary strands and furrows. These images have led to the proposal that the core of the tight junction is formed by a hexagonal cylinder of lipids. In this model, the cytoplasmic leaflet of the apical and basolateral plasma membrane domains would be continuous, whereas the exoplasmic leaflets of the two plasma membrane domains of the same cell would be separated at the tight junction and are instead predicted to be continuous between the plasma membranes of neighbouring cells. We demonstrate here that this prediction does not hold true. An endogenous glycolipid (Forssman antigen), present in the exoplasmic leaflet of the apical membrane of MDCK strain II cells, is unable to pass to MDCK strain I cells (which lack this glycolipid) under conditions where these cells are connected by tight junctions. In addition, fluorescent lipids which have been fused into the plasma membrane of one MDCK cell do not diffuse to neighbouring cells while the tight junctions between the cells are intact.     

Long-range correlations in nucleotide sequences.

DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations. We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term a 'DNA walk'. We then use the mapping to provide a quantitative measure of the correlation between nucleotides over long distances along the DNA chain. Thus we uncover in the nucleotide sequence a remarkably long-range power law correlation that implies a new scale-invariant property of DNA. We find such long-range correlations in intron-containing genes and in nontranscribed regulatory DNA sequences, but not in complementary DNA sequences or intron-less genes.     

Analysis of one million base pairs of Neanderthal DNA

Neanderthals are the extinct hominid group most closely related to contemporary humans, so their genome offers a unique opportunity to identify genetic changes specific to anatomically fully modern humans. We have identified a 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA. Direct high-throughput sequencing of a DNA extract from this fossil has thus far yielded over one million base pairs of hominoid nuclear DNA sequences. Comparison with the human and chimpanzee genomes reveals that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago. Existing technology and fossil resources are now sufficient to initiate a Neanderthal genome-sequencing effort.