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Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
Get PDFRapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to six human stool samples using Illumina HiSeq, MiSeq and Ion PGM shotgun sequencing, as well as amplicon sequencing across two variable 16S rRNA gene regions. Notably, we found that the factor responsible for the greatest variance in microbiota composition was the chosen methodology rather than the natural inter-individual variance, which is commonly one of the most significant drivers in microbiome studies. Amplicon sequencing suffered from this to a large extent, and this issue was particularly apparent when the 16S rRNA V1-V2 region amplicons were sequenced with MiSeq. Somewhat surprisingly, the choice of taxonomic binning software for shotgun sequences proved to be of crucial importance with even greater discriminatory power than sequencing technology and choice of amplicon. Optimal N50 assembly values for the HiSeq was obtained for 10 million reads per sample, whereas the applied MiSeq and PGM sequencing depths proved less sufficient for shotgun sequencing of stool samples. The latter technologies, on the other hand, provide a better basis for functional gene categorisation, possibly due to their longer read lengths. Hence, in addition to highlighting methodological biases, this study demonstrates the risks associated with comparing data generated using different strategies. We also recommend that laboratories with particular interests in certain microbes should optimise their protocols to accurately detect these taxa using different techniques
Analysis of Johne’s disease ELISA status and associated performance parameters in Irish dairy cows
Get PDFInfection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status.
Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect Screening Test. Production parameters examined included milk yield, milk fat, milk protein, somatic cell count, and calving interval. The association between MAP ELISA status and production data was investigated using multi-level mixed models. Logistic regression was used to identify risk factors for testing JD blood ELISA positive at individual cow level and to identify associations between farm management practices and herd MAP status. Results
Data were available for 3528 cows. The apparent prevalence recorded was 7.4 %. Mixed model analysis revealed no statistically significant association between testing MAP ELISA positive and dairy cow production parameters. Risk factors associated with testing positive included larger sized herds being over twice more likely to test positive than smaller herds (OR 2.4 P = \u3c0.001). Friesians were less likely to test positive relative to other breeds. A number of study farmers were engaged in management practices that have previously been identified as high risk for MAP transmission e.g., 73.1 % pooled colostrum and 84.6 % of study farmers used the calving area to house sick animals throughout the year. No significant associations however, were identified between farm management practices and herd MAP status. Conclusion
No production losses were identified; however an apparent prevalence of 7.4 % was recorded. With the abolition of EU milk quotas herd size in Ireland is expanding, as herds included in this study were larger than the national average, results may be indicative of future JD levels if no JD control programmes are implemented to minimise transmission
Six-year longitudinal study of Fasciola hepatica bulk milk antibody ELISA in the dairy dense region of the Republic Ireland
Get PDFAbstract Completion of the F. hepatica lifecycle is dependent on suitable climatic conditions for development of immature stages of the parasite, and its snail intermediate host. Few investigations have been conducted regarding temporal variations in F. hepatica status in Irish dairy herds. The current study aimed to conduct a longitudinal study examining annual and seasonal trends in bulk milk seropositivity over six years, while also investigating associations with soil temperature, rainfall and flukicide treatment. Monthly bulk milk samples (BTM) were submitted by 28 herds between March 2009 and December 2014. In all, 1337 samples were analysed using a Cathepsin L1 ELISA. Soil temperature, rainfall and management data were obtained for general estimating equation and regression analyses. A general decrease in milk seropositivity was observed over the six year study period and was associated with an increased likelihood of treating for liver fluke (OR range = 2.73–6.96). Annual and seasonal analyses of rainfall and F. hepatica BTM status yielded conflicting results. Higher annual rainfall (\u3e1150 mm) yielded a lower likelihood of being BTM positive than annual rainfall of (OR = 0.47; P = 0.036). This was most likely due to farmers being more proactive in treating for F. hepatica in wetter years, although a ‘wash effect’ by high rainfall of the free living stages and snails cannot be ruled out. Higher seasonal rainfall (\u3e120 mm), however, was associated with increased ELISA S/P% values (Coefficient = 9.63S/P%; P = 0.001). Soil temperature was not found to influence F. hepatica to the same extent as rainfall and may reflect the lack of severe temperature fluctuations in Ireland. Flukicides active against both immature and mature F. hepatica were approximately half as likely to record a positive F. hepatica herd BTM status than a flukicide active against only the mature stage of the parasite (OR ≅ 0.45; P \u3c 0.01). This study highlights the importance of examining both annual and seasonal F. hepatica data, which can vary significantly. Additionally, it highlights the progress that can be achieved in fluke control by application of a continuous BTM monitoring program
I am an Artist! What do I Know about Business?
Get PDFWhat has business to do with art? Should artists understand business? This research is concerned with the world of the artist who must operate in a business world. In the words of the late singer, Luciano Pavarotti (2003), artists must „be heard and be seen‟ to be successful. Commercial entities expose their products and services to clients to survive, and for the artist, this is no different. The paper examines if there is a need to ensure that our artistic graduates are „market ready‟, and specifically examines this concept in the context of an Irish Institute of Technology (IT). Artists generally do not view the world in terms of business and commerce, only as a creative space, so investigation is warranted if there is a need for a special purpose award that would allow already qualified or working artists who have missed out on business education to take business modules at any stage in their careers. A post-positivistic qualitative method was applied to gather the empirical data. This consisted of eleven face to face interviews using a semi-structured interview guide, and one additional focus group. The findings of this study reveal that a disconnection exists between the artistic world and the business one. Artists do indeed require business education for their future careers, and it will be necessary to ensure inclusion of business modules at undergraduate level in the future. The findings of this study recommend that new entrant undergraduate performing and visual art students should be able to take business modules throughout their studies, starting initially by facilitating these subjects as electives, and after an initial review of one year, including businesses modules as compulsory subjects. For presently working musicians, this study advocates the development of a Special Purpose Award with business subjects for all artists who are working in this field. These can include artists who have no previous Higher Education qualifications, but this specific cohort would need to take an initial bridging course to ease their return to education. Finally, working and surviving as an artist can be difficult, therefore enabling a route to education through any means for the artist could be a vital bridge to eliminate the disconnect between art and business. This will in the future ensure that artists can be better informed, and be able to differentiate and market themselves in a competitive commercial world
Genome Sequence of Jumbo Phage vB_AbaM_ME3 of Acinetobacter baumanni
Get PDFBacteriophage (phage) vB_AbaM_ME3 was previously isolated from wastewater effluent using the propagating host Acinetobacter baumannii DSM 30007. The full genome was sequenced, revealing it to be the largest Acinetobacter bacteriophage sequenced to date with a size of 234,900 bp and containing 326 open reading frames (ORFs)
Comparative Genomic Analysis of Two Serotype 1/2b Listeria monocytogenes Isolates from Analogous Environmental Niches Demonstrates the Influence of Hypervariable Hotspots in Defining Pathogenesis
Get PDFThe vast majority of clinical human listeriosis cases are caused by serotype 1/2a, 1/2b, 1/2c, and 4b isolates of Listeria monocytogenes. The ability of L. monocytogenes to establish a systemic listeriosis infection within a host organism relies on a combination of genes that are involved in cell recognition, internalization, evasion of host defenses, and in vitro survival and growth. Recently, whole genome sequencing and comparative genomic analysis have proven to be powerful tools for the identification of these virulence-associated genes in L. monocytogenes. In this study, two serotype 1/2b strains of L. monocytogenes with analogous isolation sources, but differing infection abilities, were subjected to comparative genomic analysis. The results from this comparison highlight the importance of accessory genes (genes that are not part of the conserved core genome) in L. monocytogenes pathogenesis. In addition, a number of factors, which may account for the perceived inability of one of the strains to establish a systemic infection within its host, have been identified. These factors include the notable absence of the Listeria pathogenicity island 3 and the stress survival islet, of which the latter has been demonstrated to enhance the survival ability of L. monocytogenes during its passage through the host intestinal tract, leading to a higher infection rate. The findings from this research demonstrate the influence of hypervariable hotspots in defining the physiological characteristics of a L. monocytogenes strain and indicate that the emergence of a non-pathogenic isolate of L. monocytogenes may result from a cumulative loss of functionality rather than by a single isolated genetic event
Results from Ireland north and south\u27s 2016 report card on physical activity for children and youth
Get PDFBackground: Physical activity (PA) is a key performance indicator for policy documents in both the Republic of Ireland and Northern Ireland. Building on baseline grades set in 2014, Ireland\u27s second Report Card on Physical Activity for Children and Youth allows for continued surveillance of indicators related to PA in children and youth. Methods: Data and information were extracted and collated for 10 indicators and graded using an international standardized grading system. Results: Overall, 7 grades stayed the same, 2 increased, and 1 decreased. Grades were assigned as follows: Overall PA, D (an increase); Sedentary Behavior (TV), C-; Physical Education, D-; Active Play, Incomplete/Inconclusive (INC); Active Transportation, D; School, D (a decrease); Home (Family), INC; Community and the Built Environment, B+ (an increase); and Government, INC. Unlike 2014\u27s report card, different grades for the Republic (C-) and Northern Ireland (C+) were assigned for Organized Sport Participation. Conclusions: Although the grade for Overall PA levels increased to a D, this may reflect the increased quality and quantity of data available. The double burden of low PA and high sedentary levels are concerning and underscore the need for advocacy toward, and surveillance of, progress in achieving targets set by the new National Physical Activity Plan in the Republic and obesity and sport plans in the North
Tev Gamma-Ray Observations Of The Galactic Center Ridge By Veritas
Get PDFThe Galactic Center ridge has been observed extensively in the past by both GeV and TeV gamma-ray instruments revealing a wealth of structure, including a diffuse component and the point sources G0.9+0.1 (a composite supernova remnant) and Sgr A* (believed to be associated with the supermassive black hole located at the center of our Galaxy). Previous very high energy (VHE) gamma-ray observations with the H.E.S.S. experiment have also detected an extended TeV gamma-ray component along the Galactic plane in the \u3e300 GeV gamma-ray regime. Here we report on observations of the Galactic Center ridge from 2010 to 2014 by the VERITAS telescope array in the \u3e2 TeV energy range. From these observations we (1) provide improved measurements of the differential energy spectrum for Sgr A* in the \u3e2 TeV gamma-ray regime, (2) provide a detection in the \u3e2 TeV gamma-ray emission from the composite SNR G0.9+0.1 and an improved determination of its multi-TeV gamma-ray energy spectrum, and (3) report on the detection of VER J1746-289, a localized enhancement of \u3e2 TeV gamma-ray emission along the Galactic plane
A century of trends in adult human height
Get PDFBeing taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3–19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8–144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries
Very high energy observations of the binaries v 404 cyg and 4u 0115+634 during giant x-ray outbursts
Get PDFTransient X-ray binaries produce major outbursts in which the X-ray flux can increase over the quiescent level by factors as large as 107. The low-mass X-ray binary V 404 Cyg and the high-mass system 4U 0115+634 underwent such major outbursts in 2015 June and October, respectively. We present here observations at energies above hundreds of GeV with the VERITAS observatory taken during some of the brightest X-ray activity ever observed from these systems. No gamma-ray emission has been detected by VERITAS in 2.5 hr of observations of the microquasar V 404 Cyg from 2015, June 20–21. The upper flux limits derived from these observations on the gamma-ray flux above 200 GeV of F cm−2 s−1 correspond to a tiny fraction (about 10−6) of the Eddington luminosity of the system, in stark contrast to that seen in the X-ray band. No gamma-rays have been detected during observations of 4U 0115+634 in the period of major X-ray activity in 2015 October. The flux upper limit derived from our observations is F cm−2 s−1 for gamma-rays above 300 GeV, setting an upper limit on the ratio of gamma-ray to X-ray luminosity of less than 4%