Telescoper: de novo assembly of highly repetitive regions.

MotivationWith advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found in the genomes of most higher organisms. The telomeric regions of many genomes are particularly difficult to assemble, though much could be gained from the study of these regions, as their evolution has not been fully characterized and they have been linked to aging.ResultsIn this article, we tackle the problem of assembling highly repetitive regions by developing a novel algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. Our algorithm, Telescoper, uses short- and long-insert libraries in an integrated way throughout the assembly process. Results on real and simulated data demonstrate that our approach can effectively resolve much of the complex repeat structures found in the telomeres of yeast genomes, especially when longer long-insert libraries are used.AvailabilityTelescoper is publicly available for download at sourceforge.net/p/[email protected] informationSupplementary data are available at Bioinformatics online

Children’s Learning from Touch Screens: A Dual Representation Perspective

Parents and educators often expect that children will learn from touch screen devices, such as during joint e-book reading. Therefore an essential question is whether young children understand that the touch screen can be a symbolic medium – that entities represented on the touch screen can refer to entities in the real world. Research on symbolic development suggests that symbolic understanding requires that children develop dual representational abilities, meaning children need to appreciate that a symbol is an object in itself (i.e., picture of a dog) while also being a representation of something else (i.e., the real dog). Drawing on classic research on symbols and new research on children’s learning from touch screens, we offer the perspective that children’s ability to learn from the touch screen as a symbolic medium depends on the effect of interactivity on children’s developing dual representational abilities. Although previous research on dual representation suggests the interactive nature of the touch screen might make it difficult for young children to use as a symbolic medium, the unique interactive affordances may help alleviate this difficulty. More research needs to investigate how the interactivity of the touch screen affects children’s ability to connect the symbols on the screen to the real world. Given the interactive nature of the touch screen, researchers and educators should consider both the affordances of the touch screen as well as young children’s cognitive abilities when assessing whether young children can learn from it as a symbolic medium

Bends in the plane with variable curvature

Explicit formulae for planar variable curvature bends are constructed using Euler’s method of natural equations. The bend paths are expressed in terms of special functions. It is shown that the length of the different bend types varies linearly with increasing radius and that the curvature of variable curvature bends can be expressed as a multiple of the curvature of a circle

Marxism and science studies: a sweep through the decades

This paper outlines the distinctive contribution of marxism to science studies. It traces the trajectory of marxist ideas through the decades from the origins of marxism to the present conjuncture. It looks at certain key episodes, such as the arrival of a Soviet delegation at the International History of Science Congress in London in 1931 as well as subsequent interactions between marxists and exponents of other positions at later international congresses. It focuses on the impact of several generations of marxists who have engaged with science in different ways. It examines the influence of marxism on contemporary trends in science studies. It concludes that marxism survives in circuitous and complex ways. It argues not only for a positive interpretation of its contribution in the past but for its explanatory and ethical power in the present and future

High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

peer-reviewedBackground The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure through the ‘Cheeseboard 2015’ project. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number: 2012205

J D Bernal: philosophy, politics and the science of science

This paper is an examination of the philosophical and political legacy of John Desmond Bernal. It addresses the evidence of an emerging consensus on Bernal based on the recent biography of Bernal by Andrew Brown and the reviews it has received. It takes issue with this view of Bernal, which tends to be admiring of his scientific contribution, bemused by his sexuality, condescending to his philosophy and hostile to his politics. This article is a critical defence of his philosophical and political position

J D Bernal: philosophy, politics and the science of science

This paper is an examination of the philosophical and political legacy of John Desmond Bernal. It addresses the evidence of an emerging consensus on Bernal based on the recent biography of Bernal by Andrew Brown and the reviews it has received. It takes issue with this view of Bernal, which tends to be admiring of his scientific contribution, bemused by his sexuality, condescending to his philosophy and hostile to his politics. This article is a critical defence of his philosophical and political position

Nucleic acid-based approaches to investigate microbial-related cheese quality defects

peer-reviewedThe microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number:2012205

Thermodynamics of quantum Brownian motion with internal degrees of freedom: the role of entanglement in the strong-coupling quantum regime

We study the influence of entanglement on the relation between the statistical entropy of an open quantum system and the heat exchanged with a low temperature environment. A model of quantum Brownian motion of the Caldeira-Leggett type - for which a violation of the Clausius inequality has been stated by Th.M. Nieuwenhuizen and A.E. Allahverdyan [Phys. Rev. E 66, 036102 (2002)] - is reexamined and the results of the cited work are put into perspective. In order to address the problem from an information theoretical viewpoint a model of two coupled Brownian oscillators is formulated that can also be viewed as a continuum version of a two-qubit system. The influence of an additional internal coupling parameter on heat and entropy changes is described and the findings are compared to the case of a single Brownian particle.Comment: 10 pages, 11 figure