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.     

Indexed Dendrograms on random Dissimilarities

This paper studies the random indexed dendograms produced by agglomerative hierarchical algorithms under the non-classifiability hypothesis of independent identically distributed (i.i.d.) dissimilarities. New tests for classifiability are deduced. The corresponding test statistics are random variables attached to the indexed dendrograms, such as the indices, the survival time of singletons, the value of the ultrametric between two given points, or the size of classes in the different levels of the dendogram. For an indexed dendogram produced by the Single Link method on i.i.d. dissimilarities, the distribution of these random variables is computed, thus leading to explicit tests. For the case of the Average and Complete Link methods, some asymptotic results are presented. The proofs rely essentially on the theory of random graphs.     

The molecular nature of the zebrafish tail organizer

Based on grafting experiments, Mangold and Spemann showed the dorsal blastopore lip of an amphibian gastrula to be able to induce a secondary body axis. The equivalent of this organizer region has been identified in different vertebrates including teleosts. However, whereas the graft can induce ectopic head and trunk, endogenous and ectopic axes fuse in the posterior part of the body, raising the question of whether a distinct organizer region is necessary for tail development. Here we reveal, by isochronic and heterochronic transplantation, the existence of a tail organizer deriving from the ventral margin of the zebrafish embryo, which is independent of the dorsal Spemann organizer. Loss-of-function experiments reveal that bone morphogenetic protein (BMP), Nodal and Wnt8 signalling pathways are required for tail development. Moreover, stimulation of naive cells by a combination of BMP, Nodal and Wnt8 mimics the tail-organizing activity of the ventral margin and induces surrounding tissues to become tail. In contrast to induction of the vertebrate head, known to result from the triple inhibition of BMP, Nodal and Wnt, here we show that induction of the tail results from the triple stimulation of BMP, Nodal and Wnt8 signalling pathways.     

Scale invariance and universality of force networks in static granular matter

Force networks form the skeleton of static granular matter. They are the key factor that determines mechanical properties such as stability, elasticity and sound transmission, which are important for civil engineering and industrial processing. Previous studies have focused on investigations of the global structure of external forces (the boundary condition) and on the probability distribution of individual contact forces. So far, however, precise knowledge of the disordered spatial structure of the force network has remained elusive. Here we report that molecular dynamics simulations of realistic granular packings reveal scale invariance of clusters of particles interacting by means of relatively strong forces. Despite visual variation, force networks for various values of the confining pressure and other parameters have identical scaling exponents and scaling function, thereby determining a universality class. Unexpectedly, the flat ensemble of force configurations (a simple generalization of equilibrium statistical mechanics) belongs to this universality class, whereas some widely studied simplified models do not. This implies that the elasticity of the grains and their geometrical disorder do not affect the universal mechanical properties.     

Characterization of 64-, 123- and 182-base-pair exons in the mouse alpha 2(IV) collagen gene

Genes encoding types I, II and III collagens (fibrillar collagens) contain many discrete-size exons, most of them 54 base pairs (bp) long, in addition to the 45-, 99-, 108- and 162-bp exons. It has been suggested that these collagen genes evolved from an ancestral coding unit of 54 bp. Type IV collagen is a specific component of basement membranes and contains two genetically distinct polypeptides, the alpha 1(IV) and alpha 2(IV) chains. It differs from the types I-III collagens in that it contains interruptions in the Gly-X-Y repeat sequence and does not form ordered fibrillar structures. We have isolated complementary DNA and genomic clones for the mouse alpha 2(IV) collagen chain and here characterize 64-, 123- and 182-bp exons in the Gly-X-Y coding domain of the gene. The data suggest that the alpha 2(IV) collagen gene may have evolved differently from those encoding the fibrillar collagens.     

Detection of prokaryotic mRNA signifies microbial viability and promotes immunity

Live vaccines have long been known to trigger far more vigorous immune responses than their killed counterparts. This has been attributed to the ability of live microorganisms to replicate and express specialized virulence factors that facilitate invasion and infection of their hosts. However, protective immunization can often be achieved with a single injection of live, but not dead, attenuated microorganisms stripped of their virulence factors. Pathogen-associated molecular patterns (PAMPs), which are detected by the immune system, are present in both live and killed vaccines, indicating that certain poorly characterized aspects of live microorganisms, not incorporated in dead vaccines, are particularly effective at inducing protective immunity. Here we show that the mammalian innate immune system can directly sense microbial viability through detection of a special class of viability-associated PAMPs (vita-PAMPs). We identify prokaryotic messenger RNA as a vita-PAMP present only in viable bacteria, the recognition of which elicits a unique innate response and a robust adaptive antibody response. Notably, the innate response evoked by viability and prokaryotic mRNA was thus far considered to be reserved for pathogenic bacteria, but we show that even non-pathogenic bacteria in sterile tissues can trigger similar responses, provided that they are alive. Thus, the immune system actively gauges the infectious risk by searching PAMPs for signatures of microbial life and thus infectivity. Detection of vita-PAMPs triggers a state of alert not warranted for dead bacteria. Vaccine formulations that incorporate vita-PAMPs could thus combine the superior protection of live vaccines with the safety of dead vaccines.     

Independent evolution of striated muscles in cnidarians and bilaterians

Striated muscles are present in bilaterian animals (for example, vertebrates, insects and annelids) and some non-bilaterian eumetazoans (that is, cnidarians and ctenophores). The considerable ultrastructural similarity of striated muscles between these animal groups is thought to reflect a common evolutionary origin. Here we show that a muscle protein core set, including a type II myosin heavy chain (MyHC) motor protein characteristic of striated muscles in vertebrates, was already present in unicellular organisms before the origin of multicellular animals. Furthermore, 'striated muscle' and 'non-muscle' myhc orthologues are expressed differentially in two sponges, compatible with a functional diversification before the origin of true muscles and the subsequent use of striated muscle MyHC in fast-contracting smooth and striated muscle. Cnidarians and ctenophores possess striated muscle myhc orthologues but lack crucial components of bilaterian striated muscles, such as genes that code for titin and the troponin complex, suggesting the convergent evolution of striated muscles. Consistently, jellyfish orthologues of a shared set of bilaterian Z-disc proteins are not associated with striated muscles, but are instead expressed elsewhere or ubiquitously. The independent evolution of eumetazoan striated muscles through the addition of new proteins to a pre-existing, ancestral contractile apparatus may serve as a model for the evolution of complex animal cell types.     

迷向周期和方法在β-簪结构折褶模拟中的应用

采用新近提出的迷向周期和方法（IPS），结合自导Lang evin动态模拟，模拟研究9-余肽折褶成β-箨结构的情况，表明了该结构与NMR观察到的基本一致，而Ewald模拟由于是强烈的镜像相互作用会产生构型偏差，获得致密构型的几率增大，表明IPS方法更适合于周期边界条件的模拟。