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

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

A department of methodology can coordinate transdisciplinary sport science support

In the current sporting landscape, it is not uncommon for professional sport teams and organizations to employ multidisciplinary sport science support teams. In these teams and organizations, a “head of performance” may manage a number of sub-discipline specialists with the aim of enhancing athlete performance. Despite the best intentions of multidisciplinary sport science support teams, difficulties associated with integrating sub-disciplines to enhance performance preparation have become apparent. It has been suggested that the problem of integration is embedded in the traditional reductionist method of applied sport science, leading to the eagerness of individual specialists to quantify progress in isolated components. This can lead to “silo” working and decontextualized learning environments that can hinder athlete preparation. To address this challenge, we suggest that ecological dynamics is one theoretical framework that can inform common principles and language to guide the integration of sport science sub-disciplines in a Department of Methodology. The aim of a Department of Methodology would be for group members to work within a unified conceptual framework to (1) coordinate activity through shared principles and language, (2) communicate coherent ideas, and (3) collaboratively design practice landscapes rich in information (i.e., visual, acoustic, proprioceptive and haptic) and guide emergence of multi-dimensional behaviors in athlete performance

Signatures of quantum chaos in rare-earth elements: I. Characterization of the Hamiltonian matrices and coupling matrices of Ce I and Pr I using the statistical predictions of Random Matrix Theory.

Using the relativistic configuration interaction Hartree–Fock method the Hamiltonian matrices of Ce I, J = 4±, and Pr I, J = 11/2±, are studied. These matrices can be characterized as sparse, banded matrices, with a leading diagonal. Diagonalization of the Hamiltonian results in a set of energy eigenvalues and corresponding eigenvectors and the purpose of this investigation will be to characterize the Hamiltonian matrices and coupling matrices of Ce I and Pr I, for both ls and jj coupling representations, using various statistical predictions of Random Matrix Theory

The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects

Doctoral thesisHigh throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencingbased approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbeassociated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.Teagasc Walsh Fellowship Programm

Multifractal analysis of selected rare-earth elements.

The multifractal formalism is applied to the energy eigenvalues of Ce I, CeII, Nd II, SmI, SmII, and Tb I. The R´enyi dimensionsDq , mass exponents τ(q) and f (α) spectra are calculated and used to characterize the eigenvalue spectra. It is found that these elements show multi-scaling behaviour that can be accurately modelled by simple multifractal recursive Cantor sets. The effect of unfolding the spectra is also investigated

Beginning primary teachers' perspectives on becoming a teacher in the workplace: Contextual, emotional, and temporo-spatial dimensions of identity shaping

The issue, with international and national overtones, of direct relevance to the present study, relates to the shaping of beginning teachers’ identities in the workplace. As the shift from an initial teacher education programme into initial practice in schools is a period of identity change worthy of investigation, this study focuses on the transformative search by nine beginning primary teachers for their teaching identities, throughout the course of their initial year of occupational experience, post-graduation. The nine beginning teacher participants work in a variety of primary school settings, thus strengthening the representativeness of the research cohort. Privileging ‘insider’ perspectives, the research goal is to understand the complexities of lived experience from the viewpoints of the participating informants. The shaping of identity is conceived of in dimensional terms. Accordingly, a framework composed of three dimensions of beginning teacher experience is devised, namely: contextual; emotional; temporo-spatial. Data collection and analysis is informed by principles derived from sociocultural theories; activity theory; figured worlds theory; and, dialogical self theory. Individual, face-to-face semi-structured interviews, and the maintenance of solicited digital diaries, are the principal methods of data collection employed. The use of a dimensional model fragments the integrated learning experiences of beginning teachers into constituent parts for the purpose of analysis. While acknowledging that the actual journey articulated by each participant is a more complex whole than the sum of its parts, key empirically-based claims are presented as per the dimensional framework employed: contextuality; emotionality; temporo-spatiality. As a result of applying the foci of an international literature to an under-researched aspect of Irish education, this study is offered as a context-specific contribution to the knowledge base on beginning teaching. As the developmental needs of beginning teachers constitute an emerging area of intense policy focus in Ireland, this research undertaking is both relevant and timely

What enhances the formation of social bonds & facilitates better engagement & retention in an addiction service?

The study explored whether there are key skills that staff use to relate to service users which help with the formation of social bonds, which in turn leads to increased levels of service user engagement and retention. Data for the study was collected through a literature review, ethnographic observation, interviews and focus groups with staff and service users. The findings showed that staff are successful at engaging and retaining service users and it is their ability to form strong social bonds which is the key to its success. This is achieved through the philosophy of the project which is made up of three central tenets: a non-punitive approach, person-centred care and trauma informed care. The person-centred care approach facilitates the formation of a partnership between staff and service users in which they work together to achieve personalised recovery goals unique to each individual service user. The non-punitive approach stipulates that service users are not punished or judged for having a relapse, which results in the reduction of shame and the promotion of honesty. This non-punitive stance is experienced by service users as facilitative to their recovery, with some participants reporting that this approach was less evident in other models of addiction treatment. Trauma Informed Care allows service users to seek appropriate treatment for any possible underlying issues they may have, allowing them to fully engage in the service. The three interrelated strands of the philosophy produce an approach to the treatment of substance misuse that is considered to be unique and different to many mainstream addiction models and provides a platform for the formation of social bonds. There are some trade-offs as a result of adopting such a philosophy. It was discovered that staff place a large emphasis on trauma informed care; it is commendable that staff have committed to an approach which endeavours to identify people who have been exposed to trauma and are impacted by symptoms of Post-Traumatic Stress Disorder, as well as their recognition of the value of referral to appropriate treatment services. Given that there are a number of other confounding factors which may also be decisive, it is recommended that staff consider a balanced approach which remains open to other factors besides trauma such as the community reinforcement approach, motivational interviewing and the person centred approach. Secondly, the desire to unconditionally support service users while supportive and empowering has the possible drawback of fostering dependency and impeding autonomy. It is recommended that the balance between high levels of support and promoting independence continues to be a central element of the service approach to active discharge planning. Finally, the research identified a need to upskill in areas such as mental health and couple counselling to further support service users who may have dual diagnosis or who are experiencing relationship problems due to substance misuse

Radium-223 in asymptomatic patients with castration-resistant prostate cancer and bone metastases treated in an international early access program

Radium-223; mCRPC, asymptomatic; Bone metastasesRadio-223; mCRPC, asintomático; Metástasis de huesoRadi-223; mCRPC, asimptomàtic; Metàstasis d'osBACKGROUND: Radium-223, a targeted alpha therapy, is used to treat symptomatic patients with castration-resistant prostate cancer (CRPC) and bone metastases. Data for radium-223 in asymptomatic CRPC patients with bone metastases are lacking. METHODS: This was a prospective, single-arm phase 3b study. Patients with metastatic CRPC (malignant lymphadenopathy not exceeding 6 cm was allowed, visceral disease was excluded) received radium-223, 55 kBq/kg intravenously, every 4 weeks for up to 6 cycles. Co-primary endpoints were safety and overall survival. Post hoc analyses were performed according to baseline asymptomatic or symptomatic disease status. Asymptomatic status was defined as no pain and no opioid use at baseline. RESULTS: Seven hundred eight patients received ≥1 radium-223 injection: 548 (77%) were symptomatic to various degrees, and 135 (19%) were asymptomatic. Asymptomatic patients had more favorable baseline disease characteristics than symptomatic. A lower proportion of asymptomatic versus symptomatic patients had received prior abiraterone (25% vs 35%) and prior docetaxel (52% vs 62%). A higher proportion of asymptomatic (71%) versus symptomatic (55%) patients completed radium-223 treatment. Overall survival (hazard ratio [HR] 0.486), time to disease progression (HR 0.722) and time to first symptomatic skeletal event (HR 0.328) were better in asymptomatic than symptomatic patients. Alkaline phosphatase (ALP) response rates were similar (46% vs 47%), and ALP normalization (44% vs 25%) and prostate-specific antigen response rates (21% vs 13%) were higher in asymptomatic than symptomatic patients. A lower proportion of asymptomatic patients reported treatment-emergent adverse events (TEAEs, 61% vs 79%), grade 3-4 TEAEs (29% vs 40%) and drug-related TEAEs (28% vs 44%). There were two treatment-related deaths, both in patients with baseline symptomatic disease. CONCLUSIONS: Using radium-223 earlier in the disease course, when patients are asymptomatic or minimally symptomatic, may enable patients to complete treatment and optimize treatment outcome compared to symptomatic patients, and therefore may allow sequencing with other life-prolonging therapie