Chromosomal G + C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres

The G + C content at synonymous codon positions (GC3s) in genes varies along chromosomes in most eukaryotes. In Saccharomyces cerevisiae, regions of high GC3s are correlated with recombination hot spots, probably due to biased gene conversion. Here we examined how GC3s differs among groups of related yeast species in the Saccharomyces and Candida clades. The chromosomal locations of GC3s peaks and troughs are conserved among four Saccharomyces species, but we find that there have been highly consistent small shifts in their GC3s values. For instance, 84% of all S. cerevisiae genes have a lower GC3s value than their S. bayanus orthologs. There are extensive interspecies differences in the Candida clade both in the median value of GC3s (ranging from 22% to 49%) and in the variance of GC3s among genes. In three species—Candida lusitaniae, Pichia stipitis, and Yarrowia lipolytica—there is one region on each chromosome in which GC3s is markedly reduced. We propose that these GC-poor troughs indicate the positions of centromeres because in Y. lipolytica they coincide with the five experimentally identified centromeres. In P. stipitis, the troughs contain clusters of the retrotransposon Tps5. Likewise, in Debaryomyces hansenii, there is one cluster of the retrotransposon Tdh5 per chromosome, and all these clusters are located in GC-poor troughs. Locally reduced G + C content around centromeres is consistent with a model in which G + C content correlates with recombination rate, and recombination is suppressed around centromeres, although the troughs are unexpectedly wide (100–300 kb)

Trialling HyFlex at TU Dublin – stakeholders’ voices and experiences

HyFlex is a multi-modal instructional approach that offers students the opportunity to engage with modules face-to-face and online in a mode that best suits their learning style and situation. Covid-19 forced many universities and lecturers to offer HyFlex opportunities. This emergency flip and required agility to deliver HyFlex provides the opportunity to learn from the experiences of using this mode of teaching and learning. This research presents the results of a survey of 44 lecturers who were part of the HyFlex Community of Practice (COP) or who were employing HyFlex in their practice, and 490 students who engaged with HyFlex at Technological University Dublin (TU Dublin), Ireland. Mini vignettes are used to provide deeper insight. Key findings are that HyFlex was viewed positively by both students and lecturers, and 92% of students would recommend this form of attendance in the future. From a lecturer\u27s perspective, key challenges related to the technology, student engagement and high cognitive load. The research showed that some students who avail of university learning supports preferred the HyFlex approach as it felt that it gave them equal opportunity and allowed them to learn in a way that suited them best. While the majority of students believe that the HyFlex approach resulted in the same level of academic rigour and quality as face-to-face delivery, several lecturers had some concerns. This research is valuable as it positions HyFlex as a feasible form of delivery at a time when a new University Educational Model (UEM) is being developed for TU Dublin. However, it is particularly valuable as it identifies key issues and gives voice to various stakeholders, which is important in terms of contributing to international and institutional debates and policies going forward regarding the changing pedagogical landscape post-Covid

Revealing the Nature of Algol Disks through Optical and UV Spectroscopy, Synthetic Spectra, and Tomography of TT Hydrae

We have developed a systematic procedure to study the disks in Algol-type binaries using spectroscopic analysis, synthetic spectra, and tomography. We analyzed 119 H-alpha spectra of TT Hya, an Algol-type eclipsing interacting binary, collected from 1985-2001. The new radial velocities enabled us to derive reliable orbital elements, including a small non-zero eccentricity, and to improve the accuracy of the absolute dimensions of the system. High resolution IUE spectra were also analyzed to study the formation of the ultraviolet lines and continuum. Synthetic spectra of the iron curtain using our new shellspec program enabled us to derive a characteristic disk temperature of 7000K. We have demonstrated that the UV emission lines seen during total primary eclipse cannot originate from the accretion disk, but most likely arise from a hotter disk-stream interaction region. The synthetic spectra of the stars, disk, and stream allowed us to derive a lower limit to the mass transfer rate of 2e-10 solar masses per year. Doppler tomography of the observed H-alpha profiles revealed a distinct accretion disk. The difference spectra produced by subtracting the synthetic spectra of the stars resulted in an image of the disk, which virtually disappeared once the composite synthetic spectra of the stars and disk were used to calculate the difference spectra. An intensity enhancement of the resulting tomogram revealed images of the gas stream and an emission arc. We successfully modeled the gas stream using shellspec and associated the emission arc with an asymmetry in the accretion disk.Comment: 46 pages, 15 figures, 6 tables, accepted by Ap

Learning from and Engaging with Assessment and Feedback (LEAF): Growing Practice

The LEAF (Learning from and Engaging with Assessment and Feedback) project addressed a key issue in third-level teaching and learning: assessment and feedback. The LEAF team comprised 18 academics from across the TU Dublin City Campus and representatives from all Colleges, along with the Director of Student Affairs and the Students’ Union Education Officer. This paper presents the findings of the LEAF project. Assessment strategies have been shown to have a large impact on shaping student learning process strategies which feedforward into key employability skills. Learning from best practice, surveys from staff and students and analysis of the quality documents, the project developed a set of recommendations to enhance practices in assessment and feedback. Many challenges were identified over the course of this project in relation to the timeliness, amount and quality of feedback, assessment load, burden on staff and students, student expectations, monologue versus dialogue approach to feedback, inconsistency across programmes and poor integration of assessment and feedback into the academic quality framework. Key drivers identified throughout the project that are necessary to enhance assessment and feedback strategies include adequate resourcing, alignment of assessment with graduate attributes, inclusion of the student voice and more widespread use of technology

Surveillance Data Highlights Feed Form, Biosecurity, and Disease Control as Significant Factors Associated with Salmonella Infection on Farrow-to-Finish Pig Farms

Copyright © 2018 Argüello, Manzanilla, Lynch, Walia, Leonard, Egan, Duffy, Gardiner and Lawlor. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.[EN] Among the zoonotic pathogens affecting pigs, Salmonella stands out due to the high number of human cases linked to pork consumption. In the last two decades many countries have put considerable effort into the control of the infection by surveillance and control strategies on farm. Despite this effort, many herds still have a high Salmonella prevalence and they require guidance to address this problem. The present study, using the serological surveillance data of finishing pigs from the Irish National pig Salmonella Control Programme, aimed to highlight factors associated with increased risk or that might mitigate Salmonella occurrence on farm. A questionnaire with 33 questions regarding herd characteristics, management, feeding, biosecurity, and health was completed for 61 individual herds. After the multivariate analysis by linear regression, nine variables were retained in the final model and linked to herd seroprevalence. Home produced-feed linked to the use of meal showed an eight points reduction in Salmonella prevalence compared to purchased feed (p = 0.042). Different biosecurity measures were associated to lower seroprevalence. Changing of footwear from outside to inside the farm decreased seroprevalence nearly 20 units (p = 0.014) and policies not permitting access to the farmyard to feed trucks (p = 0.048) or avoiding the presence of cats on the farm (p = 0.05) were estimated in 10 units less of seroprevalence. In contrast, the lack of perimeter fence increased the chance to have higher seroprevalence in five units (p = 0.05). Finally, intestinal diseases such as swine dysentery (p = 0.044) and E. coli diarrhea (p = 0.1) were estimated to increase Salmonella prevalence in ~20 and 10 units, respectively, demonstrating the importance of controlling other enteric pathogens in an on-farm Salmonella control programme. These results show the usefulness of surveillance data to improve on-farm control and confirm that Salmonella infection in pigs is multi-factorial and the approach to its control should be multifaceted.SIThis study was funded by the Food Institutional Research Measure (FIRM) administered by the Department of Agriculture Food and the Marine (DAFM) (FIRM/RSF/CoFoRD 2011 Project 11/SF/329).The authors gratefully acknowledge the staff at Longtown Research Farm and the Central Veterinary Research Laboratory (CVRL) Backweston for their expert help in the serological analyses of the study

Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs

[EN] Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animalsSIThis study was funded by the Food Institutional Research Measure (FIRM) administered by the Department of Agriculture Food and the Marine (DAFM). H.A. is a postdoctoral researcher supported by the Juan de la Cierva Postdoctoral Trainee Program of the Spanish Ministry of Economy and Competitiveness (IJCI-2016-30795). H.A. was funded by the PiGutNet COST action (FA1401) for a Short-Term Scientific Mission at INRA’s GABI laboratory (Jouy-en-Josas, France). We gratefully acknowledge the Central Veterinary Research Laboratory (CVRL) Backweston for their expert help with the serological analyses. H.A. participated in the study design, sample collection and processing, data analysis, and manuscript writing. F.C.L. participated in study design and manuscript correction. J.E. participated in data analysis and manuscript revision. P.D.C. and F.C. participated in microbiome sequencing and manuscript revision. O.O. performed part of the data analysis and manuscript revision. H.L. and K.W. participated in sample collection and processing. G.D. and P.G.L. participated in the study design and manuscript correction. G.E.G. participated in the study design, data analysis, and manuscript writin

Edible crabs “Go West”: migrations and incubation cycle of Cancer pagurus revealed by electronic tags

Crustaceans are key components of marine ecosystems which, like other exploited marine taxa, show seasonable patterns of distribution and activity, with consequences for their availability to capture by targeted fisheries. Despite concerns over the sustainability of crab fisheries worldwide, difficulties in observing crabs’ behaviour over their annual cycles, and the timings and durations of reproduction, remain poorly understood. From the release of 128 mature female edible crabs tagged with electronic data storage tags (DSTs), we demonstrate predominantly westward migration in the English Channel. Eastern Channel crabs migrated further than western Channel crabs, while crabs released outside the Channel showed little or no migration. Individual migrations were punctuated by a 7-month hiatus, when crabs remained stationary, coincident with the main period of crab spawning and egg incubation. Incubation commenced earlier in the west, from late October onwards, and brooding locations, determined using tidal geolocation, occurred throughout the species range. With an overall return rate of 34%, our results demonstrate that previous reluctance to tag crabs with relatively high-cost DSTs for fear of loss following moulting is unfounded, and that DSTs can generate precise information with regards life-history metrics that would be unachievable using other conventional means

Research Priorities for Children's Nursing in Ireland: A Delphi Study

This paper is a report of a study which identified research priorities for children's nursing in an acute care setting in Ireland. A limited number of studies have examined research priorities for children's nursing. This study was undertaken against the backdrop of significant proposed changes to the delivery of of children's healthcare. A three round Delphi survey design was used to identify and rate the importance of research priorities for children's nursing. In round 1 participants were asked to identify five of the most important research priorities for children's nursing. Participants in round 2 were asked to rate the importance of each of each research priority on a seven point Likert scale. In round 3 participants were presented with the mean scoreof each research priority from the second questionaire, and again asked to consider the importance of each topic on a 7 point Likert scale. The aim was to reach a consensus on the priorities. The top three priorities identified were recognition and care of the deteriorating child, safe transfer of the critically ill child between acute health care facilities, and the child and families perceptions of care at end-of life. The wide variation of priorities reflects the scope of care delivery of children's nurses and mirrors many global care concerns in caring for children