DNA Mapping Algorithms: The DNA Simulator

This report documents the intent and use of a suite of programs for simulating the production of DNA restriction fragment data, as might come from the biological laboratory doing work in DNA mapping. This suite includes programs for (a) creating a random strand of DNA, (b) creating random clones given a strand of DNA, (c) taking a clone and applying a restriction enzyme to create restriction fragments, and (d) creating a nucleotide map of how the clones relate to one another within the original DNA strand. Besides this fundamental software, there are a number of a programs for introducing different forms of random error (nre, nce) intro the restriction fragments produced, and aggregating and filtering the clones in different ways to select those with appropriate properties

DNA Mapping Algorithms: Fragment Splitting and Combining

When using random clone overlap based methods to make DNA maps, fragment matching mistakes, the incorrect matching of similar length restriction fragments, are a common problem that produces incorrect maps. This technical report discusses techniques for fragment splitting and fragment combining, which attempts to correct maps containing a fragment matching mistake, given that the location of the mistake is known. These techniques are based on operations that decompose and merge virtual fragments (a collection of matched real fragments), add virtual fragments to existing groups in the map and insert virtual fragments between existing groups in the map. Examples of applying these techniques to both contrived and actual DNA maps are presented

Superhard Phases of Simple Substances and Binary Compounds of the B-C-N-O System: from Diamond to the Latest Results (a Review)

The basic known and hypothetic one- and two-element phases of the B-C-N-O system (both superhard phases having diamond and boron structures and precursors to synthesize them) are described. The attention has been given to the structure, basic mechanical properties, and methods to identify and characterize the materials. For some phases that have been recently described in the literature the synthesis conditions at high pressures and temperatures are indicated.Comment: Review on superhard B-C-N-O phase

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Selection on plant height through the interplay of landscape and large herbivores

Many herbaceous and graminoid plants from open communities are characterized by their relatively small size and by seeds that appear to lack any clear traits for dispersal. Such syndrome is likely the result of several selective pressures and their tradeoffs acting together. Drawing on the putative relationship of these plants with large mammals that graze on them, with respect to defoliation and the dispersal of seeds (endozoochory), we included plant stature as a trait in a simulation model to elaborate on these animals’ relative contribution in plant evolution. Different configurations of the landscape were used as a template, as these are known to affect the response of plants through additional costs levied in dispersal. As such, two herbivore parameters (the intensity of grazing and the efficacy of endozoochorous dispersal) were tested along with two parameters of the landscape (the proportion and connectivity of suitable habitat). Plants were allowed to evolve freely under these conditions, assuming that taller plants 1) produce more seeds and 2) have a more distant seed rain in wind dispersal, but 3) are also more likely to suffer failed reproduction because of herbivory. Our model confirmed the effects of landscape on the resulting dispersal capacity of plants, although these effects were readily overruled by the actions of grazers. We found the evolution of plant size to primarily result from the effects of defoliation, but also (though to a lesser degree) from endozoochory. This provides support for the adaptive value of unassisted dispersal syndromes in plants. Endozoochory also succeeded in maintaining increased population densities. However, these effects only hold when grazers sustain a considerable transfer of seeds towards suitable plant habitat