Traveling waves of selective sweeps

The goal of cancer genome sequencing projects is to determine the genetic alterations that cause common cancers. Many malignancies arise during the clonal expansion of a benign tumor which motivates the study of recurrent selective sweeps in an exponentially growing population. To better understand this process, Beerenwinkel et al. [PLoS Comput. Biol. 3 (2007) 2239--2246] consider a Wright--Fisher model in which cells from an exponentially growing population accumulate advantageous mutations. Simulations show a traveling wave in which the time of the first $k$-fold mutant, $T_k$, is approximately linear in $k$ and heuristics are used to obtain formulas for $ET_k$. Here, we consider the analogous problem for the Moran model and prove that as the mutation rate $\mu\to0$, $T_k\sim c_k\log(1/\mu)$, where the $c_k$ can be computed explicitly. In addition, we derive a limiting result on a log scale for the size of $X_k(t)={}$the number of cells with $k$ mutations at time $t$.Comment: Published in at http://dx.doi.org/10.1214/10-AAP721 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Evolution in predator-prey systems

We study the adaptive dynamics of predator-prey systems modeled by a dynamical system in which the traits of predators and prey are allowed to evolve by small mutations. When only the prey are allowed to evolve, and the size of the mutational change tends to 0, the system does not exhibit long term prey coexistence and the trait of the resident prey type converges to the solution of an ODE. When only the predators are allowed to evolve, coexistence of predators occurs. In this case, depending on the parameters being varied, we see (i) the number of coexisting predators remains tight and the differences in traits from a reference species converge in distribution to a limit, or (ii) the number of coexisting predators tends to infinity, and we calculate the asymptotic rate at which the traits of the least and most "fit" predators in the population increase. This last result is obtained by comparison with a branching random walk killed to the left of a linear boundary and a finite branching-selection particle system.Comment: Major revisions to the introduction and definitions of the evolutionary processes considered, minor revisions to the proofs of Propositions 1.1 and 1.

JAVA: A Research and Educational Overload

The convergence of computing and telecommunications technologies has created a need for a dynamic, distributed programming language. Sun Microsystems (Sun) hopes that Java will be that language. The goal of this tutorial is to familiarize the audience with the research and educational potential of the Java programming language. It is assumed that the individuals present will not want, and that time constraints forbid, any attempt at a syntax level description of the language

Evolutionary dynamics of tumor progression with random fitness values

Most human tumors result from the accumulation of multiple genetic and epigenetic alterations in a single cell. Mutations that confer a fitness advantage to the cell are known as driver mutations and are causally related to tumorigenesis. Other mutations, however, do not change the phenotype of the cell or even decrease cellular fitness. While much experimental effort is being devoted to the identification of the different functional effects of individual mutations, mathematical modeling of tumor progression generally considers constant fitness increments as mutations are accumulated. In this paper we study a mathematical model of tumor progression with random fitness increments. We analyze a multi-type branching process in which cells accumulate mutations whose fitness effects are chosen from a distribution. We determine the effect of the fitness distribution on the growth kinetics of the tumor. This work contributes to a quantitative understanding of the accumulation of mutations leading to cancer phenotypes.Comment: 33 pages, 2 Figure

Plant triacylglycerols as feedstocks for the production of biofuels.

Summary Triacylglycerols produced by plants are one of the most energy-rich and abundant forms of reduced carbon available from nature. Given their chemical similarities, plant oils represent a logical substitute for conventional diesel, a non-renewable energy source. However, as plant oils are too viscous for use in modern diesel engines, they are converted to fatty acid esters. The resulting fuel is commonly referred to as biodiesel, and offers many advantages over conventional diesel. Chief among these is that biodiesel is derived from renewable sources. In addition, the production and subsequent consumption of biodiesel results in less greenhouse gas emission compared to conventional diesel. However, the widespread adoption of biodiesel faces a number of challenges. The biggest of these is a limited supply of biodiesel feedstocks. Thus, plant oil production needs to be greatly increased for biodiesel to replace a major proportion of the current and future fuel needs of the world. An increased understanding of how plants synthesize fatty acids and triacylglycerols will ultimately allow the development of novel energy crops. For example, knowledge of the regulation of oil synthesis has suggested ways to produce triacylglycerols in abundant non-seed tissues. Additionally, biodiesel has poor cold-temperature performance and low oxidative stability. Improving the fuel characteristics of biodiesel can be achieved by altering the fatty acid composition. In this regard, the generation of transgenic soybean lines with high oleic acid content represents one way in which plant biotechnology has already contributed to the improvement of biodiesel

The Second Conference on Lunar Bases and Space Activities of the 21st Century, volume 2

These 92 papers comprise a peer-reviewed selection of presentations by authors from NASA, the Lunar and Planetary Institute (LPI), industry, and academia at the Second Conference on Lunar Bases and Space Activities of the 21st Century. These papers go into more technical depth than did those published from the first NASA-sponsored symposium on the topic, held in 1984. Session topics included the following: (1) design and operation of transportation systems to, in orbit around, and on the Moon; (2) lunar base site selection; (3) design, architecture, construction, and operation of lunar bases and human habitats; (4) lunar-based scientific research and experimentation in astronomy, exobiology, and lunar geology; (5) recovery and use of lunar resources; (6) environmental and human factors of and life support technology for human presence on the Moon; and (7) program management of human exploration of the Moon and space

The Second Conference on Lunar Bases and Space Activities of the 21st Century, volume 1

These papers comprise a peer-review selection of presentations by authors from NASA, LPI industry, and academia at the Second Conference (April 1988) on Lunar Bases and Space Activities of the 21st Century, sponsored by the NASA Office of Exploration and the Lunar Planetary Institute. These papers go into more technical depth than did those published from the first NASA-sponsored symposium on the topic, held in 1984. Session topics covered by this volume include (1) design and operation of transportation systems to, in orbit around, and on the Moon, (2) lunar base site selection, (3) design, architecture, construction, and operation of lunar bases and human habitats, and (4) lunar-based scientific research and experimentation in astronomy, exobiology, and lunar geology

Generating Pennycress (Thlaspi arvense) Seed Triacylglycerols and Acetyl-Triacylglycerols Containing Medium-Chain Fatty Acids

Thlaspi arvense L. (pennycress) is a cold-tolerant Brassicaceae that produces large amounts of seeds rich in triacylglycerols and protein, making it an attractive target for domestication into an offseason oilseed cash cover crop. Pennycress is easily genetically transformed, enabling synthetic biology approaches to tailor oil properties for specific biofuel and industrial applications. To test the feasibility in pennycress of producing TAGs and acetyl-TAGs rich in medium-chain fatty acids (MCFAs; C6–C14) for industrial, biojet fuel and improved biodiesel applications, we generated transgenic lines with seed-specific expression of unique acyltransferase (LPAT and diacylglycerol acyltransferase) genes and thioesterase (FatB) genes isolated from Cuphea viscosissima, Cuphea avigera var. pulcherrima, Cuphea hookeriana, Coco nucifera, and Umbellularia californica. Wild-type pennycress seed TAGs accumulate no fatty acids shorter than 16C and less than 5 mol percent C16 as palmitic acid (16:0). Co-expressing UcFatB and CnLPAT produced up to 17 mol% accumulation of lauric acid (12:0) in seed TAGs, whereas CvFatB1 CvLPAT2 CpDGAT1 combinatorial expression produced up to 27 mol% medium chain FAs Medium Chain Fatty Acids mostly in the form of capric acid (10:0). CpFatB2 ChFatB2 combinatorial expression predominantly produced, in equal parts, up to 28 mol% myristic acid (14:0) and palmitic acid. Genetically crossing the combinatorial constructs into a fatty acid elongation1 (fae1) mutant that produced no 22:1 erucic acid, and with an Euonymus alatus diacylglycerol acetyltransferase (EaDAcT)-expressing line that produced 60 mol% acetyl-TAGs, had no or relatively minor effects on MCFAs accumulation, suggesting fluxes to MCFAs were largely unaltered. Seed germination assays revealed no or minor delays in seed germination for most lines, the exception being CpFatB2 ChFatB2-expressing lines, which had substantially slower seed germination rates. Taken together, these data show that pennycress can be engineered to produce seeds accumulating modest amounts of MCFAs of varying carbon-chain length in TAGs and acetyl-TAGs, with rates of seed germination being delayed in only some cases. We hypothesize that increasing MCFAs further may require functional reductions to endogenous transferases and/or other FA elongases