Minimal Absent Words in Four Human Genome Assemblies

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species

On finding minimal absent words

<p>Abstract</p> <p>Background</p> <p>The problem of finding the shortest absent words in DNA data has been recently addressed, and algorithms for its solution have been described. It has been noted that longer absent words might also be of interest, but the existing algorithms only provide generic absent words by trivially extending the shortest ones.</p> <p>Results</p> <p>We show how absent words relate to the repetitions and structure of the data, and define a new and larger class of absent words, called minimal absent words, that still captures the essential properties of the shortest absent words introduced in recent works. The words of this new class are minimal in the sense that if their leftmost or rightmost character is removed, then the resulting word is no longer an absent word. We describe an algorithm for generating minimal absent words that, in practice, runs in approximately linear time. An implementation of this algorithm is publicly available at <url>ftp://www.ieeta.pt/~ap/maws</url>.</p> <p>Conclusion</p> <p>Because the set of minimal absent words that we propose is much larger than the set of the shortest absent words, it is potentially more useful for applications that require a richer variety of absent words. Nevertheless, the number of minimal absent words is still manageable since it grows at most linearly with the string size, unlike generic absent words that grow exponentially. Both the algorithm and the concepts upon which it depends shed additional light on the structure of absent words and complement the existing studies on the topic.</p

Minimal Absent Words in Prokaryotic and Eukaryotic Genomes

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we explore different sets of minimal absent words in the genomes of 22 organisms (one archaeota, thirteen bacteria and eight eukaryotes). We investigate if the mutational biases that may explain the deficit of the shortest absent words in vertebrates are also pervasive in other absent words, namely in minimal absent words, as well as to other organisms. We find that the compositional biases observed for the shortest absent words in vertebrates are not uniform throughout different sets of minimal absent words. We further investigate the hypothesis of the inheritance of minimal absent words through common ancestry from the similarity in dinucleotide relative abundances of different sets of minimal absent words, and find that this inheritance may be exclusive to vertebrates

A Prototype Continuous Flow Polymerase Chain Reaction LTCC Device

There is a growing need for remote biological sensing in both laboratory and harsh field environments. Sensing and detection of biological entities such as anthrax, Ebola and other micro-organisms of interest involves sampling of the environment, amplification, analysis and identification of the target DNA. A key component of such a sensor is a low cost, portable, reusable, continuous flow polymerase chain reaction (PCR) thermal cycler. Fabrication with low temperature co-fired ceramics (LTCC) can provide a reusable low cost device capable of operating in a wide range of environments. The design and manufacture of a prototype continuous flow micro-fluidic PCR device using low temperature co-fired ceramic is presented. Initial modeling of flow characteristics and heat transfer was carried out in SolidWorks™. The prototype device employs resistance heaters below the channels, buried and surface thermocouples for temperature monitoring, and air gaps for thermal isolation

Deposition of α-alumina Via Combustion Chemical Vapor Deposition

Combustion chemical vapor deposition was used to synthesize α-alumina thin films. The deposition solutions were 0.0015 M aluminum acetylacetonate dissolved in isopropanol. Fused silica and nichrome (Ni–20Cr) served as substrates. Deposition temperatures were in the range of 1050 °C to 1125 °C. Crystalline films consisting of hexagonal α-grains were produced on both substrates. Some films on nichrome displayed preferred orientations of (113) and (116) normal to substrate surfaces, while films deposited on silica showed no preferred orientation. Films deposited on nichrome seemed denser than those on silica as the grains clustered together to provide a ‘cauliflower’ appearance. The oxidation response of uncoated and alumina-coated nichrome specimens was measured by isothermal thermogravimetric analysis in pure flowing air at 900 °C, 1000 °C and 1100 °C. The coated specimens had significantly lower mass gain values and parabolic rate constants than their uncoated counterparts

Ethics, privacy and the legal framework governing medical data: opportunities or threats for biomedical and public health research?

Privacy is an important concern in any research programme that deals with personal medical data. In recent years, ethics and privacy have become key considerations when conducting any form of scientific research that involves personal data. These issues are now addressed in healthcare professional training programmes. Indeed, ethics, legal frameworks and privacy are often the subject of much confusion in discussions among healthcare professionals. They tend to group these different concepts under the same heading and delegate responsibility for "ethical" approval of their research programmes to ethics committees. Public health researchers therefore need to ask questions about how changes to legal frameworks and ethical codes governing privacy in the use of personal medical data are to be applied in practice. What types of data do these laws and codes cover? Who is involved? What restrictions and requirements apply to any research programme that involves medical data?Editorialinfo:eu-repo/semantics/publishe