The theoretical basis of universal identification systems for bacteria and viruses

It is shown that the presence/absence pattern of 1000 random oligomers of length 12� in a bacterial genome is sufficiently characteristic to readily and unambiguously distinguish any known bacterial genome from any other. Even genomes of extremely closely-related organisms, such as strains of the same species, can be thus distinguished. One evident way to implement this approach in a practical assay is with hybridization arrays. It is envisioned that a single universal array can be readily designed that would allow identification of any bacterium that appears in a database of known patterns. We performed in silico experiments to test this idea. Calculations utilizing 105 publicly-available completely-sequenced microbial genomes allowed us to determine appropriate values of the test oligonucleotide length, n, and the number of probe sequences. Randomly chosen n-mers with a constant G + C content were used to form an in silico array and verify (a) how many n-mers from each genome would hybridize on this chip, and (b) how different the fingerprints of different genomes would be. With the appropriate choice of random oligomer length, the same approach can also be used to identify viral or eukaryotic genomes

Sound archaeology: terminology, Palaeolithic cave art and the soundscape

This article is focused on the ways that terminology describing the study of music and sound within archaeology has changed over time, and how this reflects developing methodologies, exploring the expectations and issues raised by the use of differing kinds of language to define and describe such work. It begins with a discussion of music archaeology, addressing the problems of using the term ‘music’ in an archaeological context. It continues with an examination of archaeoacoustics and acoustics, and an emphasis on sound rather than music. This leads on to a study of sound archaeology and soundscapes, pointing out that it is important to consider the complete acoustic ecology of an archaeological site, in order to identify its affordances, those possibilities offered by invariant acoustic properties. Using a case study from northern Spain, the paper suggests that all of these methodological approaches have merit, and that a project benefits from their integration

Electron Microscopy Of Wood Of Callixylon And Cordaites

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141638/1/ajb210693.pd

Searching for New Physics Through AMO Precision Measurements

We briefly review recent experiments in atomic, molecular, and optical physics using precision measurements to search for physics beyond the Standard Model. We consider three main categories of experiments: searches for changes in fundamental constants, measurements of the anomalous magnetic moment of the electron, and searches for an electric dipole moment of the electron.Comment: Prepared for Comments on AMO Physics at Physica Script

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

Supplementary Materials for U-Th dating of carbonate crusts reveals Neanderthal origin of Iberian cave art

Materiales suplementarios al artículo de Science 2018 sobre las dataciones de arte rupestre en la Península Ibérica mediante U-TH