Money, mentoring and making friends: the impact of a multidimensional access program on student performance

There is a well established socioeconomic gradient in educational attainment in all countries: young people from a low socioeconomic status (SES) will, on average, receive less education and do less well at school. While this is true virtually everywhere, this SES gradient is noticeably higher in Ireland compared to other OECD countries despite much effort in recent decades to address this inequality. This study evaluates a university access program in Ireland that provides financial, academic and social support to low SES students both prior to and after entry to university. It uses a natural experiment involving the gradual roll-out of the program to identify the effect of the program. The program has parallels with US Affirmative Action programs, although preferential treatment in this case is based on SES rather than ethnicity. Evaluating the effectiveness of programs targeting disadvantaged students in Ireland is particularly salient given the high rate of return to education and the lack of intergenerational mobility in educational attainment. Overall, we find positive treatment effects on first year exam performance, progression to second year and final year graduation rates, with the impact often stronger for higher ability students. We find similar patterns of results for students that entered through the regular system and the 'affirmative action' group i.e. the students that entering with lower high school grades. The program affects both male and female students, albeit in different ways. The study is unable to identify which specific component of the treatment is responsible for the effects but we find no evidence that changes in the financial support have an effect on student outcomes. This study suggests that access programs can be an effective means of improving academic outcomes for socio-economically disadvantaged students.Education inequality, Access programs, Natural experiment, Economics of education

Money, Mentoring and Making Friends: The Impact of a Multidimensional Access Program on Student Performance

There is a well established socioeconomic gradient in educational attainment, despite much effort in recent decades to address this inequality. This study evaluates a university access program that provides financial, academic and social support to low socioeconomic status (SES) students using a natural experiment which exploits the time variation in the expansion of the program across schools. The program has parallels with US affirmative actions programs, although preferential treatment is based on SES rather than ethnicity. Evaluating the effectiveness of programs targeting disadvantaged students in Ireland is particularly salient given the high rate of return to education and the lack of intergenerational mobility in educational attainment. Overall, we identify positive treatment effects on first year exam performance, progression to second year and final year graduation rates, with the impact often stronger for higher ability students. We find similar patterns of results for students that entered through the regular system and the ‘affirmative action’ group i.e. the students that entered with lower high school grades. The program affects the performance of both male and female students, albeit in different ways. This study suggests that access programs can be an effective means of improving academic outcomes for socio-economically disadvantaged students.Education inequality, Access programs, Natural experiment, Economics of education

Money, Mentoring and Making Friends: The Impact of a Multidimensional Access Program on Student Performance

There is a well established socioeconomic gradient in educational attainment, despite much effort in recent decades to address this inequality. This study evaluates a university access program that provides financial, academic and social support to low socioeconomic status (SES) students using a natural experiment which exploits the time variation in the expansion of the program across schools. The program has parallels with US affirmative actions programs, although preferential treatment is based on SES rather than ethnicity. Evaluating the effectiveness of programs targeting disadvantaged students in Ireland is particularly salient given the high rate of return to education and the lack of intergenerational mobility in educational attainment. Overall, we identify positive treatment effects on first year exam performance, progression to second year and final year graduation rates, with the impact often stronger for higher ability students. We find similar patterns of results for students that entered through the regular system and the ‘affirmative action’ group i.e. the students that entered with lower high school grades. The program affects the performance of both male and female students, albeit in different ways. This study suggests that access programs can be an effective means of improving academic outcomes for socio-economically disadvantaged students.Education inequality, Access programs, Natural experiment, Economics of education

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

Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

peer-reviewedKefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.The Alimentary Pharmabiotic Centre is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan. The authors and their work were supported by SFI CSET grant APC CSET 2 grant 07/CE/B1368

Money, mentoring and making friends : the impact of a multidimensional access program on student performance

There is a well established socioeconomic gradient in educational attainment, despite much effort in recent decades to address this inequality. This study evaluates a university access program that provides financial, academic and social support to low socioeconomic status (SES) students using a natural experiment which exploits the time variation in the expansion of the program across schools. The program has parallels with US affirmative actions programs, although preferential treatment is based on SES rather than ethnicity. Evaluating the effectiveness of programs targeting disadvantaged students in Ireland is particularly salient given the high rate of return to education and the lack of intergenerational mobility in educational attainment. Overall, we identify positive treatment effects on first year exam performance, progression to second year and final year graduation rates, with the impact often stronger for higher ability students. We find similar patterns of results for students that entered through the regular system and the ‘affirmative action’ group i.e. the students that entered with lower high school grades. The program affects the performance of both male and female students, albeit in different ways. This study suggests that access programs can be an effective means of improving academic outcomes for socio-economically disadvantaged students

M-Coffee: combining multiple sequence alignment methods with T-Coffee

We introduce M-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee is an extension of T-Coffee and uses consistency to estimate a consensus alignment. We show that the procedure is robust to variations in the choice of constituent methods and reasonably tolerant to duplicate MSAs. We also show that performances can be improved by carefully selecting the constituent methods. M-Coffee outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase. We also show that on a case-by-case basis, M-Coffee is twice as likely to deliver the best alignment than any individual method. Given a collection of pre-computed MSAs, M-Coffee has similar CPU requirements to the original T-Coffee. M-Coffee is a freeware open-source package available from

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

peer-reviewedBackground High-throughput sequencing has enabled detailed insights into complex microbial environments, including the human gut microbiota. The accuracy of the sequencing data however, is reliant upon appropriate storage of the samples prior to DNA extraction. The aim of this study was to conduct the first MiSeq sequencing investigation into the effects of faecal storage on the microbiota, compared to fresh samples. Culture-based analysis was also completed. Methods Seven faecal samples were collected from healthy adults. Samples were separated into fresh (DNA extracted immediately), snap frozen on dry ice and frozen for 7 days at -80°C prior to DNA extraction or samples frozen at -80°C for 7 days before DNA extraction. Sequencing was completed on the Illumina MiSeq platform. Culturing of total aerobes, anaerobes and bifidobacteria was also completed. Results No significant differences at phylum or family levels between the treatment groups occurred. At genus level only Faecalibacterium and Leuconostoc were significantly different in the fresh samples compared to the snap frozen group (p = 0.0298; p = 0.0330 respectively). Diversity analysis indicated that samples clustered based on the individual donor, rather than by storage group. No significant differences occurred in the culture-based analysis between the fresh, snap or -80°C frozen samples. Conclusions Using the MiSeq platform coupled with culture-based analysis, this study highlighted that limited significant changes in microbiota occur following rapid freezing of faecal samples prior to DNA extraction. Thus, rapid freezing of samples prior to DNA extraction and culturing, preserves the integrity of the microbiota.Jennifer Deane is in receipt of a Teagasc Walsh Fellowship. The authors and their work were supported by the Science Foundation Ireland and funded by the Centre for Science, Engineering and Technology (SFI-CSET) grant 02/CE/B124 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerbations: Results Stratified, Grant Agreement no. 603038). The Alimentary Pharmabiotic Centre is a research centre funded by Science Foundation Ireland (SFI). This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273

Exercise and the microbiota

The authors are supported in part by research grants from Science Foundation Ireland including a centre grant (Alimentary Pharmabiotic Centre; Grant Numbers SFI/12/RC/2273 and 12/RC/2273). Dr. Orla O’Sullivan is funded by a Starting Investigator Research Grant from Science Foundation Ireland (Grant number 13/SIRG/2160). Dr. Paul Cotter is funded by a Principal Investigator Award from Science Foundation Ireland P.D.C are supported by a SFI PI award (Grant number 11/PI/1137).peer-reviewedSedentary lifestyle is linked with poor health, most commonly obesity and associated disorders, the corollary being that exercise offers a preventive strategy. However, the scope of exercise biology extends well beyond energy expenditure and has emerged as a great ‘polypill’, which is safe, reliable and cost-effective not only in disease prevention but also treatment. Biological mechanisms by which exercise influences homeostasis are becoming clearer and involve multi-organ systemic adaptations. Most of the elements of a modern lifestyle influence the indigenous microbiota but few studies have explored the effect of increased physical activity. While dietary responses to exercise obscure the influence of exercise alone on gut microbiota, professional athletes operating at the extremes of performance provide informative data. We assessed the relationship between extreme levels of exercise, associated dietary habits and gut microbiota composition, and discuss potential mechanisms by which exercise may exert a direct or indirect influence on gut microbiota.The authors are supported in part by research grants from Science Foundation Ireland including a centre grant (Alimentary Pharmabiotic Centre; Grant Numbers SFI/12/RC/2273 and 12/RC/2273). Dr. Orla O’Sullivan is funded by a Starting Investigator Research Grant from Science Foundation Ireland (Grant number 13/SIRG/2160). Dr. Paul Cotter is funded by a Principal Investigator Award from Science Foundation Ireland P.D.C are supported by a SFI PI award (Grant number 11/PI/1137)