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

Follow that plant!

A report on the talks presented at the Cold Spring Harbor 2000 Meeting on Arabidopsis Genomics, New York, 7-10 December, 2000

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

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

Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)

<p>Abstract</p> <p>Background</p> <p>Castor bean (<it>Ricinus communis</it>) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of <it>R. communis </it>in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci.</p> <p>Results</p> <p>Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕ_PTvalues, <it>p </it>< 0.01).</p> <p>Conclusion</p> <p>Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.</p