Genomics in Latin America: Reaching the Frontiers

When an undergraduate student in science from Latin America is asked about career goals, the answer will probably invoke dreams of using cutting-edge technologies to investigate the frontiers of science. For these students, the realities of life in their countries almost always reduce their options for achieving this goal to only one: Emigrate to a developed country. Although many of these countries produce numerous international scientific papers relative to their small research budget (Macilwain 1999a), their access to the latest-generation technology is fairly limited. This is particularly true in the field of genomics, in which the need for automated, high-throughput equipment raises the cost even more. However, when done wisely, genomics research and development has proven to be an affordable reality for developing countries

Are obese plant genomes on a diet?

Richard Dawkins' (1976) selfish DNA hypothesis (that the only purpose of DNA is to perpetuate itself) is clearly reflected in the case of repetitive DNA, especially retrotransposons. These ubiquitous, self-replicating DNA elements do not seem to do anything but invade the host's genome (Orgel and Crick 1980; Doolittle and Sapienza 1980). Mutations caused by the activity of retrotransposons may eventually be evolutionarily advantageous, but are more likely to be deleterious for the host organism and thus eliminated from the population (Charlesworth et al. 1994). However, insertions of those elements that do not alter any functional region of the genome may be perpetuated in the population

Genomics: More than the sum of the parts

It has been known for some time that DNA composition varies across a given genome as well as between genomes (Filipski et al. 1973;Wagner and Capesius 1981). Genomic sequencing projects allow this observation to be confirmed at the sequence level (The Arabidopsis Genome Initiative 2000; Ashikawa 2001). However, the cause and function of these compositional differences are still obscure. Among the theories that may explain these phenomena (Eyre-Walker and Hurst 2001), mutation bias from C to T due to deamination of methylated C has been commonly used to account for them (Coulondre et al. 1978). As methylation is probably involved in a mechanism to silence transposable elements (Martienssen 1998), it makes sense that inactive methylated transposons can easily undergo C to T transition because they are under no selective pressure. However, this theory cannot explain other related compositional biases such as the CpG suppression observed in animal mitochondria (Cardon et al. 1994), where there is no DNA methylation

Breakdown of disordered media by surface loads

We model an interface layer connecting two parts of a solid body by N parallel elastic springs connecting two rigid blocks. We load the system by a shear force acting on the top side. The springs have equal stiffness but are ruptured randomly when the load reaches a critical value. For the considered system, we calculate the shear modulus, G, as a function of the order parameter, \phi, describing the state of damage, and also the ``spalled'' material (burst) size distribution. In particular, we evaluate the relation between the damage parameter and the applied force and explore the behaviour in the vicinity of material breakdown. Using this simple model for material breakdown, we show that damage, caused by applied shear forces, is analogous to a first-order phase transition. The scaling behaviour of G with \phi is explored analytically and numerically, close to \phi=0 and \phi=1 and in the vicinity of \phi_c, when the shear load is close but below the threshold force that causes material breakdown. Our model calculation represents a first approximation of a system subject to wear induced loads.Comment: 15 pages, 7 figure

Sequencing the maize genome

Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis

Body-assisted van der Waals interaction between two atoms

Using fourth-order perturbation theory, a general formula for the van der Waals potential of two neutral, unpolarized, ground-state atoms in the presence of an arbitrary arrangement of dispersing and absorbing magnetodielectric bodies is derived. The theory is applied to two atoms in bulk material and in front of a planar multilayer system, with special emphasis on the cases of a perfectly reflecting plate and a semi-infinite half space. It is demonstrated that the enhancement and reduction of the two-atom interaction due to the presence of a perfectly reflecting plate can be understood, at least in the nonretarded limit, by using the method of image charges. For the semi-infinite half space, both analytical and numerical results are presented.Comment: 17 pages, 9 figure

Rolling friction of a viscous sphere on a hard plane

A first-principle continuum-mechanics expression for the rolling friction coefficient is obtained for the rolling motion of a viscoelastic sphere on a hard plane. It relates the friction coefficient to the viscous and elastic constants of the sphere material. The relation obtained refers to the case when the deformation of the sphere $\xi$ is small, the velocity of the sphere $V$ is much less than the speed of sound in the material and when the characteristic time $\xi/V$ is much larger than the dissipative relaxation times of the viscoelastic material. To our knowledge this is the first ``first-principle'' expression of the rolling friction coefficient which does not contain empirical parameters.Comment: 6 pages, 2 figure

Time-Resolved Studies of Stick-Slip Friction in Sheared Granular Layers

Sensitive and fast force measurements are performed on sheared granular layers undergoing stick-slip motion, along with simultaneous imaging. A full study has been done for spherical particles with a +-20% size distribution. Stick-slip motion due to repetitive fluidization of the layer occurs for low driving velocities. Between major slip events, slight creep occurs that is variable from one event to the next. The effects of changing the stiffness k and velocity V of the driving system are studied in detail. The stick-slip motion is almost periodic for spherical particles over a wide range of parameters, but becomes irregular when k is large and V is relatively small. At larger V, the motion becomes smoother and is affected by the inertia of the upper plate bounding the layer. Measurements of the period T and amplitude A of the relative motion are presented as a function of V. At a critical value Vc, a transition to continuous sliding motion occurs that is discontinuous for k not too large. The time dependence of the instantaneous velocity of the upper plate and the frictional force produced by the granular layer are determined within individual slipping events. The force is a multi-valued function of the instantaneous velocity, with pronounced hysteresis and a sudden drop prior to resticking. Measurements of vertical displacement reveal a small dilation of the material (about one tenth of the mean particle size in a layer 20 particles deep) associated with each slip event. Finally, optical imaging reveals that localized microscopic rearrangements precede (and follow) each slip event. The behavior of smooth particles is contrasted with that of rough particles.Comment: 20, pages, 17 figures, to appear in Phys. Rev.

Where would we be without counterfactuals?

Huw Price gives his inaugural lecture as Bertrand Russell Professor of Philosophy. Bertrand Russell’s celebrated essay “On the Notion of Cause” was first delivered to the Aristotelian Society on 4 November 1912, as Russell’s Presidential Address. The piece is best known for a passage in which its author deftly positions himself between the traditional metaphysics of causation and the British crown, firing broadsides in both directions: “The law of causality”, Russell declares, “Like much that passes muster in philosophy, is a relic of a bygone age, surviving, like the monarchy, only because it is erroneously supposed to do no harm.” To mark the lecture’s centenary, we offer a contemporary view of the issues Russell here puts on the table, and of the health or otherwise, at the end of the essay’s first century, of his notorious conclusion

Simulations of the Static Friction Due to Adsorbed Molecules

The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent with macroscopic friction laws. Crystalline alignment, sliding direction, and the number of adsorbed molecules are not controlled in most experiments and are shown to have little effect on the friction. Temperature, molecular geometry and interaction potentials can have larger effects on friction. The observed trends in friction can be understood in terms of a simple hard sphere model.Comment: 13 pages, 13 figure