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

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

Iraqi Politics and Implications for Oil and Energy

Iraq’s ability to reach its energy potential should be of broad regional and international concern. Iraq could be poised for a dramatic transformation, one in which it finally escapes the political and technical constraints that have kept it producing less than 4 percent of the world’s oil, despite having the third-largest conventional oil reserves in the world. Should Iraq meet its ambitions to bring nearly 10 million more barrels of oil on line by 2017, it would constitute the largest ever capacity increase in the history of the oil industry. Should Iraq, more probably, bring only half this capacity to market, it would still represent a massive achievement. Translating Iraq’s energy promise into reality is in the shared interest of Iraq, the United States, Japan, and the international community more broadly. At the highest level, the health of Iraq’s energy sector—currently the source of more than 90 percent of revenues accrued by the state—is a major determinant in setting Iraq’s overall trajectory. A booming energy economy is not a guarantee of a prosperous, democratic, and stable Iraq; it could also be the hallmark of an Iraq that has returned to authoritarianism or even tyranny. But it is difficult to imagine a prosperous, democratic, and stable Iraq that does not claim a thriving energy industry among its assets

The status of intramural programs in the public high schools of Rhode Island

Thesis (Ed. M.)--Boston Universit

Constriction size distributions of granular filters: a numerical study

The retention capability of granular filters is controlled by the narrow constrictions connecting the voids within the filter. The theoretical justification for empirical filter rules used in practice includes consideration of an idealised soil fabric in which constrictions form between co-planar combinations of spherical filter particles. This idealised fabric has not been confirmed by experimental or numerical observations of real constrictions. This paper reports the results of direct, particle-scale measurement of the constriction size distribution (CSD) within virtual samples of granular filters created using the discrete-element method (DEM). A previously proposed analytical method that predicts the full CSD using inscribed circles to estimate constriction sizes is found to poorly predict the CSD for widely graded filters due to an over-idealisation of the soil fabric. The DEM data generated are used to explore quantitatively the influence of the coefficient of uniformity, particle size distribution and relative density of the filter on the CSD. For a given relative density CSDs form a narrow band of similarly shaped curves when normalised by characteristic filter diameters. This lends support to the practical use of characteristic diameters to assess filter retention capability

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

The diverse requirements of ARS2 in nuclear cap-binding complex-dependent RNA processing

ARS2 is a stable component of the nuclear cap-binding complex (CBC) and is critical for RNA Polymerase II transcript processing. Moreover, ARS2, and its orthologue SERRATE in plants, has been implicated in having a role in most established CBC-dependent functions. This review will provide insight into the functions of ARS2/SERRATE in numerous RNA Polymerase II transcript processing events, which happen co-transcriptionally from initiation to termination, and post-transcriptionally during maturation and export into the cytoplasm. Additionally, we will discuss what is known regarding ARS2/SERRATE structure in plants and in mammals

Designing a Mobile Assistive Application with and for Older Adults with AMD: A Case Study

Age-Related Macular Degeneration (AMD) is the UK’s leading cause of severe visual impairment amongst the elderly. It accounts for 16,000 blind/partial sight registrations per year and is the leading cause of blindness among people aged 55 years and older in western countries (Bressler, 2004). Our research aims to design and develop a self-monitoring, ability-reactive technology (SMART) for users with AMD to support their dietary-based AMD risk mitigation and progression retardation over time. In this paper, we reflect on our experience of adapting and applying a participatory design (PD) approach to support the effective design of our application with and for older adults with AMD. We introduce the outcome of a series of PD sessions with older adults with AMD – that is, a paper prototype of our proposed application which focuses on accessibility for our target users – and discuss implications for the eventual prototype development

Observed Faraday Effects in Damped Lyman-Alpha Absorbers and Lyman Limit Systems: The Magnetised Environment of Galactic Building Blocks at Redshift=2

Protogalactic environments are typically identified using quasar absorption lines, and these galactic building blocks can manifest as Damped Lyman-Alpha Absorbers (DLAs) and Lyman Limit Systems (LLSs). We use radio observations of Faraday effects to test whether DLAs and LLSs host a magnetised medium, by combining DLA and LLS detections throughout the literature with 1.4 GHz polarization data from the NRAO VLA Sky Survey (NVSS). We obtain a control, a DLA, and a LLS sample consisting of 114, 19, and 27 lines-of-sight respectively - all of which are polarized at $\ge8\sigma$ to ensure Rician bias is negligible. Using a Bayesian framework, we are unable to detect either coherent or random magnetic fields in DLAs: the regular coherent magnetic fields within the DLAs must be $\le2.8$ $\mu$G, and the lack of depolarization is consistent with the weakly magnetised gas in DLAs being non-turbulent and quiescent. However, we find mild suggestive evidence that LLSs have coherent magnetic fields: after controlling for the redshift-distribution of our data, we find a 71.5% probability that LLSs have a higher RM than a control sample. We also find strong evidence that LLSs host random magnetic fields, with a 95.5% probability that LLS lines-of-sight have lower polarized fractions than a control sample. The regular coherent magnetic fields within the LLSs must be $\le2.4$ $\mu$G, and the magnetised gas must be highly turbulent with a typical scale on the order of $\approx5$-20 pc, which is similar to that of the Milky Way. This is consistent with the standard dynamo pedagogy, whereby magnetic fields in protogalaxies increase in coherence and strength as a function of cosmic time. Our results are consistent with a hierarchical galaxy formation scenario, with the DLAs, LLSs, and strong magnesium II (MgII) systems exploring three different stages of magnetic field evolution in galaxies.Comment: Submitted to Ap