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

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

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

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

Temporal and spatial differences in microbial composition during the manufacture of a Continental-type cheese

peer-reviewedWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine salted Continental-type cheese in cheeses produced early and late in the production day. Differences in microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that late production day cheeses had a more diverse microbial population than their early day equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were found to initially have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas and Bifidobacterium, not routinely associated with a Continental-type cheese produced from pasteurised milk were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.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: 201220

Influence of protein concentration and coagulation temperature on rennet-induced gelation characteristics and curd microstructure

peer-reviewedThis study characterized the coagulation properties and defined the cutting window (CW; time between storage modulus values of 35 and 70 Pa) using rheometry for milk standardized to 4, 5, or 6% protein and set at 28, 32, or 36°C. Milks were standardized to a protein-to-fat ratio of approximately 1 by blending ultrafiltration retentate, skim milk, and whole milk. The internal curd microstructure for selected curd samples was analyzed with transmission electron microscopy and scanning electron microscopy. Lowering the coagulation temperature caused longer rennet coagulation time and time to reach storage modulus of 35 Pa, translating into a wider CW. It also led to a lower maximum curd-firming rate (MCFR) with lower firmness at 40 min at a given protein level. Increasing protein levels resulted in the opposite effect, although without an effect on rennet coagulation time at a given temperature. On coagulation at 28°C, milk with 5% protein resulted in a similar MCFR (∼4 Pa/min) and CW (∼8.25 min) compared with milk with 4% protein at 32°C, which reflects more standard conditions, whereas increasing milk to 6% protein resulted in more than doubling of the curd-firming rate (MCFR = 9.20 Pa/min) and a shorter CW (4.60 min). Gels set at 28°C had lower levels of rearrangement of protein network after 40 min compared with those set at 36°C. Protein levels, on the other hand, had no influence on the levels of protein network rearrangement, as indicated by loss tangent values. The internal structure of curd particles, as investigated by both scanning electron microscopy and transmission electron microscopy, appeared to have less cross-linking and smaller casein aggregates when coagulated at 28°C compared with 36°C, whereas varying protein levels did not show a marked effect on aggregate formation. Overall, this study showed a marked interactive effect between coagulation temperature and protein standardization of milk on coagulation properties, which subsequently requires adjustment of the CW during cheesemaking. Lowering of the coagulation temperature greatly altered the curd microstructure, with a tendency for less syneresis during cutting. Further research is required to quantify the changes in syneresis and in fat and protein losses to whey due to changes in the microstructure of curd particles arising from the different coagulation conditions applied to the protein-fortified milk

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