Radio-Tracking a White-Tailed Deer

Author Institution: Western Illinois University, Macomb, IllinoisA female deer (Odocoileus virginianus), which had been confined all six years of her life, was immobilized with Sernylan, fitted with a collar containing a radio transmitter, and released on a study area in west-central Illinois on March 8, 1963. Her movements and daily activity were monitored, using portable radio tracking equipment, until December, 1963. Early movements and activity were thought to be related to previous confinement, while later movements and activity were considered to be more normal

Model of Cluster Growth and Phase Separation: Exact Results in One Dimension

We present exact results for a lattice model of cluster growth in 1D. The growth mechanism involves interface hopping and pairwise annihilation supplemented by spontaneous creation of the stable-phase, +1, regions by overturning the unstable-phase, -1, spins with probability p. For cluster coarsening at phase coexistence, p=0, the conventional structure-factor scaling applies. In this limit our model falls in the class of diffusion-limited reactions A+A->inert. The +1 cluster size grows diffusively, ~t**(1/2), and the two-point correlation function obeys scaling. However, for p>0, i.e., for the dynamics of formation of stable phase from unstable phase, we find that structure-factor scaling breaks down; the length scale associated with the size of the growing +1 clusters reflects only the short-distance properties of the two-point correlations.Comment: 12 page

Web-based Protocols for Bioinformatics Education

The many genome projects initiated in the last few years have brought about an explosion in the amount of DNA and protein sequence and structure data available to biologists. Computers have become essential tools for the analysis of this information, and as a result, there is a growing demand among molecular biologists for education in bioinformatics, a new field of study at the forefront of computer science and molecular genetics

GWAlpha: genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments

MOTIVATION: Sequencing pools of individuals (Pool-Seq) is a cost-effective way to gain insight into the genetics of complex traits, but as yet no parametric method has been developed to both test for genetic effects and estimate their magnitude. Here, we propose GWAlpha, a flexible method to obtain parametric estimates of genetic effects genome-wide from Pool-Seq experiments. RESULTS: We showed that GWAlpha powerfully replicates the results of Genome-Wide Association Studies (GWAS) from model organisms. We perform simulation studies that illustrate the effect on power of sample size and number of pools and test the method on different experimental data. AVAILABILITY AND IMPLEMENTATION: GWAlpha is implemented in python, designed to run on Linux operating system and tested on Mac OS. It is freely available at https://github.com/aflevel/GWAlpha CONTACT: [email protected] information: Supplementary data are available at Bioinformatics online

Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies

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Tight Clustering of Extracellular BP180 Epitopes Recognized by Bullous Pemphigoid Autoantibodies

Bullous pemphigoid is a blistering skin disease associated with autoantibodies against the BP180 antigen, a transmembrane component of the hemidesmosome. Anti-BP180 antibodies have been demonstrated to be pathogenic in a passive transfer mouse model. One extracellular site on human BP180 (MCW-1) was previously shown to be recognized by 50–60% of bullous pemphigoid sera. To facilitate the identification of additional autoantibody-reactive epitopes, recombinant forms of the BP180 ectodomain were generated using both bacterial and mammalian expression systems. One recombinant protein, sec180e, that was expressed in COS-1 cells and that contained the entire BP180 ectodomain, provided us with a tool to detect conformational epitopes. Bullous pemphigoid sera immuno-adsorbed against the major noncollagenous NC16A domain no longer reacted with sec180e, indicating that autoantibody reactivity to the BP180 ectodomain is restricted to the NC16A region. Immunoblot analysis of bullous pemphigoid sera immunoadsorbed with a series of recombinant NC16A peptides revealed the presence of three novel autoantigenic sites that, along with the MCW-1 epitope, are clustered within the N-terminal 45 amino acid stretch of NC16A. All 15 bullous pemphigoid sera tested reacted with a recombinant protein containing this BP180 segment. No disease-associated epitopes were detectable within the remaining 28 amino acids of NC16A. Thus, bullous pemphigoid patient autoantibodies react with a set of epitopes on the BP180 ectodomain that are highly clustered. This autoantibody-reactive region on human BP180 shows overlap with the corresponding murine BP180 site that is targeted by antibodies that are pathogenic in the mouse model of bullous pemphigoid. These findings suggest new directions for the development of diagnostic and therapeutic tools for this disease

The Rise and Fall of BritainsDNA: A Tale of Misleading Claims, Media Manipulation and Threats to Academic Freedom

Direct-to-consumer genetic ancestry testing is a new and growing industry that has gained widespread media coverage and public interest. Its scientific base is in the fields of population and evolutionary genetics and it has benefitted considerably from recent advances in rapid and cost-effective DNA typing technologies. There is a considerable body of scientific literature on the use of genetic data to make inferences about human population history, although publications on inferring the ancestry of specific individuals are rarer. Population geneticists have questioned the scientific validity of some population history inference approaches, particularly those of a more interpretative nature. These controversies have spilled over into commercial genetic ancestry testing, with some companies making sensational claims about their products. One such company—BritainsDNA—made a number of dubious claims both directly to its customers and in the media. Here we outline our scientific concerns, document the exchanges between us, BritainsDNA and the BBC, and discuss the issues raised about media promotion of commercial enterprises, academic freedom of expression, science and pseudoscience and the genetic ancestry testing industry. We provide a detailed account of this case as a resource for historians and sociologists of science, and to shape public understanding, media reporting and scientific scrutiny of the commercial use of population and evolutionary genetics

Group testing with Random Pools: Phase Transitions and Optimal Strategy

The problem of Group Testing is to identify defective items out of a set of objects by means of pool queries of the form "Does the pool contain at least a defective?". The aim is of course to perform detection with the fewest possible queries, a problem which has relevant practical applications in different fields including molecular biology and computer science. Here we study GT in the probabilistic setting focusing on the regime of small defective probability and large number of objects, $p \to 0$ and $N \to \infty$. We construct and analyze one-stage algorithms for which we establish the occurrence of a non-detection/detection phase transition resulting in a sharp threshold, $\bar M$, for the number of tests. By optimizing the pool design we construct algorithms whose detection threshold follows the optimal scaling $\bar M\propto Np|\log p|$. Then we consider two-stages algorithms and analyze their performance for different choices of the first stage pools. In particular, via a proper random choice of the pools, we construct algorithms which attain the optimal value (previously determined in Ref. [16]) for the mean number of tests required for complete detection. We finally discuss the optimal pool design in the case of finite $p$