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- ItemAge-associated deficits in social behaviour are microbiota-dependent(Elsevier, 2023) Cruz-Pereira, Joana S.; Moloney, Gerard M.; Bastiaanssen, Thomaz F. S.; Boscaini, Serena; Fitzgerald, Patrick; Clarke, Gerard; Cryan, John F.; Science Foundation Ireland; Saks-Kavanaugh Foundation; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungAging is associated with remodelling of immune and central nervous system responses resulting in behavioural impairments including social deficits. Growing evidence suggests that the gut microbiome is also impacted by aging, and we propose that strategies to reshape the aged gut microbiome may ameliorate some age-related effects on host physiology. Thus, we assessed the impact of gut microbiota depletion, using an antibiotic cocktail, on aging and its impact on social behavior and the immune system. Indeed, microbiota depletion in aged mice eliminated the age-dependent deficits in social recognition. We further demonstrate that although age and gut microbiota depletion differently shape the peripheral immune response, aging induces an accumulation of T cells in the choroid plexus, that is partially blunted following microbiota depletion. Moreover, an untargeted metabolomic analysis revealed age-dependent alterations of cecal metabolites that are reshaped by gut microbiota depletion. Together, our results suggest that the aged gut microbiota can be specifically targeted to affect social deficits. These studies propel the need for future investigations of other non-antibiotic microbiota targeted interventions on age-related social deficits both in animal models and humans.
- ItemAgency and ageing in place in rural Ireland(University College Cork and Age Action, 2022-04) O'Sullivan, Siobhán; Buckley, Margaret; Desmond, Elaine; Bantry-White, Eleanor; Cassarino, Marica; Irish Research CouncilThis report explores the experiences and preferences of older adults on ageing in place in rural Ireland. This exploration is undertaken through a participatory mixed-methods approach that seeks to foreground the voices of older adults themselves. The research study involved two phases. Phase one entailed a nationwide online and postal survey co-constructed with Age Action’s Glór advocacy group and University of the Third Age (U3A) membership and distributed to Age Action members living in rural areas across Ireland. 218 people aged 55 and older who live in rural areas took part in the survey and every county was represented, with 45% of respondents from Munster, 36% from Leinster, 12% from Connaught, and 7% from Ulster. Phase two involved a series of four focus groups in which 19 people took part. The focus groups explored the survey themes in more depth. The research highlights the diversity of experience of home and community among the older adults in rural Ireland who took part. Most participants expressed a strong desire to remain in their homes and communities as they age. The sense of attachment to home and place had, for many, strengthened since the pandemic. Some participants, however, highlighted the tenuous nature of their living arrangements and their sense of alienation from place. This was particularly the case for the participants who were renting, who had recently moved locations to be closer to children, or who found the limited facilities and social opportunities in their rural environments restrictive. Whether they were settled in their homes and communities or not, all participants highlighted the uncertainty of their positions and their fears for being able to have their preference for remaining in place realised as they aged. This was related to unpredictable factors such as their future health needs and availability of home care, their ongoing ability to drive, or their capacity to afford to live independently given the ambiguity surrounding future pension provision and the escalating costs associated with utilities, healthcare, home maintenance and expenses related to rural living, such as security, water, and sewerage costs. The general decline of towns and villages was highlighted by participants, as was the poor coverage of public transport in rural areas. These aspects not only heightened the sense of isolation of participants in terms of access to services and social activities; they also served to heighten their sense of marginalisation and perceived loss of agency in terms of policy formation and political representation. Participants also noted the limited options available to them should they consider moving from their rural locations, something that would be particularly challenging for most given their emotional connection to their homes and communities. The lack of affordable and suitable housing for older adults was a particular concern. Most participants were strongly opposed to nursing homes, a view which the experience of the pandemic had often reinforced. While a small number saw their benefit in cases of critical care, most were dissatisfied with the current ‘Fair Deal’ Scheme for funding nursing home care. They argued that, instead of focussing resources on a nursing home option not favoured by older adults, the government should develop an alternative statutory home care scheme that would support older adults to remain in their homes as they age. The supports which were noted as important in relation to allowing adults to age in their homes included a more accessible and fit-for-purpose grant system to fund modifications to the home – the most popular of these being an emergency response system, bathroom modifications, and improved heating. The need for a properly paid and resourced home help service, as well as a home and garden maintenance service, was emphasised. This was especially the case given the changing reality of ageing in Irish society and the fact that many older adults cannot rely on the availability or ability of family members to care for them in their homes. Access to broadband in rural areas was also noted as crucial, not only given the fact that more aspects of daily services are being conducted online but also given the importance of a reliable broadband connection in facilitating isolated rural older adults to connect to others. Participants highlighted their enjoyment of meeting each other and realising their difficulties were shared despite their diverse locations as benefits of the research process in the current study. They argued for the need for training in technology which could be a significant enabler to their remaining in place, as opposed to presenting a barrier to their doing so. They also argued that there was a need to tackle the covert ageism which was seen as endemic in institutions and everyday interactions, and which served to marginalise older adults further. Participants noted their preferences were they to need additional supports which could not be provided in their homes in the future. In this case, their favoured options would be co-operative or sheltered housing and retirement villages. These options were available for very few participants locally, however, meaning that they would be required to move from their communities, as well as their homes. The research, while small in scale resonates with global research on the theme,1 and highlights that the ability of older adults to age in place requires coordination among several different policy areas, not least housing, transport, technology, and healthcare. There is a need to adjust the funding focus from moving people who need help out of their homes to ensuring that the help they need is available to them in their homes for as long as possible. There is also a need to develop housing options, other than nursing homes, to address people’s preferences should staying at home be no longer a feasible option. Finally, and most importantly, there is a requirement to listen to older people in rural areas about where and how they wish to age in ways that support their sense of agency and challenge flawed assumptions about ageing. This research seeks to contribute to that aim both through its focus and its process.
- ItemBacterial toxins: Offensive, defensive, or something else altogether?(Public Library of Science, 2017-09-21) Rudkin, Justine K.; McLoughlin, Rachel M.; Preston, Andrew; Massey, Ruth C.The secretion of proteins that damage host tissue is well established as integral to the infectious processes of many bacterial pathogens. However, recent advances in our understanding of the activity of toxins suggest that the attributes we have assigned to them from early in vitro experimentation have misled us into thinking of them as merely destructive tools. Here, we will discuss the multifarious ways in which toxins contribute to the lifestyle of bacteria and, by considering their activity from an evolutionary perspective, demonstrate how this extends far beyond their ability to destroy host tissue.
- ItemBarriers and waste in the research grant application process in higher education through a lean six sigma lens(Polska Akademia Nauk, 2020-09) Dempsey, Mary; Brennan, Attracta; McAvoy, JohnHigher education institutions (HEIs) typically generate income from two main sources; student fees and research income. In contrast, the predominant waste streams in HEIs tend to include; (1) assignment/examination mark submission process, (2) photocopying process and (3) the funding application process. Unintended internal process complexities and barriers typically aggravate the challenges already inherent, in the research grant application process. Although Lean Six Sigma (LSS) has been adopted by a number of HEIs in Ireland, very few have adopted an integrated LSS approach for waste reduction in the research grant application process. To identify barriers and waste in the research grant application process within an Irish HEI in an EU environment, the authors used an online survey deployed to 240 academics and researchers. The survey response rate was 13%. The participating HEI in this pilot study generated an annual income (including student fees and research income) exceeding (sic)240 million for the academic year 2017/2018. Using an LSS lens, this paper identified the primary waste in the research grant application process from an academic and researcher perspective to be; editing and revising applications, liaising and communicating with collaborators and waiting for information. Organised thematically, the main barriers were strategic thinking, collaborator identification and co-Ordination, eligibility, process, time and support & mentoring. The results from this study can be used to inform the next stage of the research where empirical studies will be carried out in other HEIs to develop a practical roadmap for the implementation of LSS as an operational excellence improvement methodology in the research grant application process.
- ItemBifidobacterium breve UCC2003 exopolysaccharide modulates the early life Microbiota by acting as a potential dietary substrate(MDPI, 2020) Püngel, Deborah; Treveil, Agatha; Dalby, Matthew J.; Caim, Shabhonam; Colquhoun, Ian J.; Booth, Catherine; Ketskemety, Jennifer; Korcsmaros, Tamas; van Sinderen, Douwe; Lawson, Melissa A. E.; Hall, Lindsay J.; Wellcome Trust; H2020 Marie Skłodowska-Curie Actions; Science Foundation IrelandBACKGROUND: Bifidobacterium represents an important early life microbiota member. Specific bifidobacterial components, exopolysaccharides (EPS), positively modulate host responses, with purified EPS also suggested to impact microbe-microbe interactions by acting as a nutrient substrate. Thus, we determined the longitudinal effects of bifidobacterial EPS on microbial communities and metabolite profiles using an infant model colon system. METHODS: Differential gene expression and growth characteristics were determined for each strain; Bifidobacterium breve UCC2003 and corresponding isogenic EPS-deletion mutant (B. breve UCC2003del). Model colon vessels were inoculated with B. breve and microbiome dynamics monitored using 16S rRNA sequencing and metabolomics (NMR). RESULTS: Transcriptomics of EPS mutant vs. B. breve UCC2003 highlighted discrete differential gene expression (e.g., eps biosynthetic cluster), though overall growth dynamics between strains were unaffected. The EPS-positive vessel had significant shifts in microbiome and metabolite profiles until study end (405 h); with increases of Tyzzerella and Faecalibacterium, and short-chain fatty acids, with further correlations between taxa and metabolites which were not observed within the EPS-negative vessel. CONCLUSIONS: These data indicate that B. breve UCC2003 EPS is potentially metabolized by infant microbiota members, leading to differential microbial metabolism and altered metabolite by-products. Overall, these findings may allow development of EPS-specific strategies to promote infant health.
- ItemBifidobacterium breve UCC2003 induces a distinct global transcriptomic program in neonatal murine intestinal epithelial cells(Elsevier, 2020-07) Kiu, Raymond; Treveil, Agatha; Harnisch, Lukas C.; Caim, Shabhonam; Leclaire, Charlotte; van Sinderen, Douwe; Korcsmaros, Tamas; Hall, Lindsay J.; Norwich Bioscience Institutes (NBI) Computing infrastructure for Science (CiS) group; Wellcome Trust; Gut Microbes and Health; Genomics for Food security; Norwich Research Park Biosciences; Science Foundation IrelandThe underlying health-driving mechanisms of Bifidobacterium during early life are not well understood, particularly how this microbiota member may modulate the intestinal barrier via programming of intestinal epithelial cells (IECs). We investigated the impact of Bifidobacterium breve UCC2003 on the transcriptome of neonatal murine IECs. Small IECs from two-week-old neonatal mice administered B. breve UCC2003 or PBS (control) were subjected to global RNA sequencing, and differentially expressed genes, pathways, and affected cell types were determined. We observed extensive regulation of the IEC transcriptome with ∼4,000 genes significantly up-regulated, including key genes linked with epithelial barrier function. Enrichment of cell differentiation pathways was observed, along with an overrepresentation of stem cell marker genes, indicating an increase in the regenerative potential of the epithelial layer. In conclusion, B. breve UCC2003 plays a central role in driving intestinal epithelium homeostatic development during early life and suggests future avenues for next-stage clinical studies.
- ItemBroad purpose vector for site-directed insertional mutagenesis in Bifidobacterium breve(Frontiers Media S.A., 2021-03) Hoedt, Emily C.; Bottacini, Francesca; Cash, Nora; Bongers, Roger S.; van Limpt, Kees; Ben Amor, Kaouther; Knol, Jan; MacSharry, John; van Sinderen, Douwe; Nutricia Research Foundation; Science Foundation Ireland; Federation of European Microbiological SocietiesMembers of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an alpha-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.
- ItemCarbon tax ethics(John Wiley & Sons, Inc., 2023-09-06) Mintz-Woo, KianIdeal carbon tax policy is internationally coordinated, fully internalizes externalities, redistributes revenues to those harmed, and is politically acceptable, generating predictable market signals. Since nonideal circumstances rarely allow all these conditions to be met, moral issues arise. This paper surveys some of the work in moral philosophy responding to several of these issues. First, it discusses the moral drivers for estimates of the social cost of carbon. Second, it explains how national self-interest can block climate action and suggests international policies—carbon border tax adjustments and carbon clubs—that can help address these concerns. Third, it introduces some of the social science literature about the political acceptability of carbon taxes before addressing a couple common public concerns about carbon taxes. Finally, it introduces four carbon revenue usage options, arguing that redistributive and climate compensation measures are most morally justified.
- ItemA compliant-mechanism-based lockable prismatic joint for high-load morphing structures(Elsevier Ltd., 2022-09-12) Zhao, Yinjun; Hao, Guangbo; Chai, Luguang; Tian, Yingzhong; Xi, Fengfeng; China Scholarship CouncilLockable joints are widely used in robotic systems and adaptive structures for energy management and/or topology reconfiguration. However, it is still challenging to design a joint with desired properties, including high locking load, infinite locking positions, short switching time, energy-efficient control, and a compact and lightweight structure. This paper aims at this open problem by presenting a novel piezoelectric (PZT) actuated lockable prismatic joint. This joint is a compliant mechanism (CM) consisting of a compound bridge-type compliant mechanism (CBCM) and a pair of compound multibeam parallelogram mechanisms (CMPMs). It can produce the required input/output stiffness to transmit large forces for high-load locking. It can also provide a desired input/output motion range for PZT actuation-based unlocking and for facilitating preloading adjustment. An analytical model is presented based on a compliance matrix method and the nonlinear model of the CMPM to predict the joint's static characteristics under various input/output conditions. A two-step optimization framework is proposed for locking applications. The theoretical study and nonlinear FEA/experimental verification confirm the feasibility of the design and the accuracy of the proposed model.
- ItemConstans II, Cherson or Bosporus, and the reform of the copper coinage under Constantine IV(Royal Numismatic Society, 2019-12) Woods, DavidIt is argued that an unusually heavy copper type of Constans II which has traditionally been dated to about 658/9 and attributed to either Cherson or Bosporus was probably a halffollis struck in Constantinople just before the accession of Constantine IV in 668 and his reform of the copper coinage.
- ItemDelineation of a lactococcal conjugation system reveals a restriction-modification evasion system(John Wiley & Sons, Inc., 2023-06) Ortiz Charneco, Guillermo; Kelleher, Philip; Buivydas, Andrius; Dashko, Sofia,; de Waal, Paul P.; van Peij, Noël N. M. E.; Roberts, Richard John; Mahony, Jennifer; van Sinderen, Douwe; Science Foundation IrelandPlasmid pUC11B is a 49.3-kb plasmid harboured by the fermented meat isolate Lactococcus lactis subsp. lactis UC11. Among other features, pUC11B encodes a pMRC01-like conjugation system and tetracycline-resistance. In this study, we demonstrate that this plasmid can be conjugated at high frequencies to recipient strains. Mutational analysis of the 22 genes encompassing the presumed pUC11B conjugation cluster revealed the presence of several genes with essential conjugation functions, as well as a gene, trsR, encoding a putative transcriptional repressor of this conjugation cluster. Furthermore, plasmid pUC11B encodes an anti-restriction protein, TrsAR, which facilitates higher conjugation frequencies when pUC11B is transferred into recipient strains containing Type II or Type III RM systems. These findings demonstrate how RM mechanisms can be circumvented when they act as a biological barrier for conjugation events.
- ItemDietary fat intakes in Irish children: changes between 2005 and 2019(Cambridge University Press on behalf of The Nutrition Society, 2020-10-26) O'Connor, Aileen; Buffini, Maria; Nugent, Anne; Kehoe, Laura; Flynn, Albert; Walton, Janette; Kearney, John; McNulty, Breige; Department of Agriculture, Food and the Marine, IrelandObjective: To examine current dietary fat intakes and compliance in Irish children and to examine changes in intakes from 2005 to 2019. Design: Analyses were based on data from the Irish National Children’s Food Survey (NCFS) and the NSFS II, two cross-sectional studies that collected detailed food and beverage intake data through 7-day and 4-day weighed food diaries, respectively. Setting: NCFS and NCFS II, Republic of Ireland. Participants: A nationally representative sample of 594 (NCFS) and 600 (NCFS II) children aged 5–12 years. Current intakes from the NCFS II were compared with those previously reported in the NCFS (www.iuna.net). Results: Current intakes of total fat, SFA, MUFA, PUFA and trans fat as a percentage of total energy are 33·3, 14·0, 13·6, 5·6 and 0·5 %, respectively. Total fat, SFA and trans fat intakes since 2005 remained largely stable over time with all displaying minor decreases of <1 %. Adherence to SFA recommendations remains inadequate, with only 7 % of the population complying. Insufficient compliance with PUFA (71 %) and EPA and DHA (DHA; 16 %) recommendations was also noted. Conclusion: Children in Ireland continue to meet the total fat and trans fat target goals. Adherence to MUFA and PUFA recommendations has also significantly improved. However, deviations for some fats remain, in particular SFA. These findings are useful for the development of dietary strategies to improve compliance with current recommendations.
- ItemDiscursive strategies of legitimization: The case of abortion in Ireland in 2018(Irish Association for Applied Linguistics, 2021-06-11) O'Donovan, Jennifer; Siller, BarbaraThe following article is based on a study on abortion discourse carried out in Ireland in 2018 prior to and after the Referendum to Repeal the Eighth Amendment to the Constitution allowing for legislation to be introduced regulating termination of pregnancy. Its main focus was to identify the strategies of legitimization employed by both online users and campaign bodies in the period directly before and after the historic referendum to create the possibility to legislate for abortion in Ireland. The study also aimed at examining how the discursive strategies engaged in creating identities on both a national level and also of the collective voter groups. The corpus included unregulated textual and regulated visual data collected between May and June 2018. The textual data derived from the Facebook pages of four prominent campaigning bodies from both sides of the referendum one month before and after the referendum while the visual data originated from photos taken of the campaign posters displayed in Ireland. Critical Discourse Analysis formed the conceptual framework of the study: the study employed Reyes’ (2011) model of strategies of legitimization in political discourse as well as the two visual analysis frameworks as proposed by Van Leeuwen (2008) and Ledin and Machin (2018). A mixed-method approach in the format of a triangulation design (Creswell & Plano Clark, 2007) was used, whereby qualitative textual and visual discourses were transformed into quantitative data for the purpose of analysis. The findings indicated that the strategy of emotion was the most utilized; this became apparent through the quantitatively high use of terms such as ‘rape’, ‘incest’ or ‘murder’, in order to provoke an emotional reaction in the message perceiver. The results also pointed to high instances of ‘othering’ strategies of the different groups participating in the discourse.
- ItemDynamic conceptual framework to investigate adoption of healthy diet through agent-based modelling(Emerald Publishing Ltd., 2021-02-17) Rahmani, Jamal; MirzayRazaz, Jalaledin; Kalantari, Naser; Garcia, Leandro M. T.; Shariatpanahi, Seyed Peyman; Bawadi, Hiba; Thompson, Jacqueline Y.; Ryan, Paul M.; Santos, Heitor O.; Haghighian Roudsari, ArezooPurpose: The purpose of this research is to develop a dynamic conceptual framework depicting factors related to the adoption of a healthy diet, which will underpin the development of an agent-based model (ABM) to uncover the dynamic interplay between these factors. Design/methodology/approach: The conceptual framework was developed in three steps using available empirical data from a semi-structured in-depth interview qualitative study, comprehensive systematic literature searches, existing theories and models and expert opinions from across the world. Findings: The conceptual framework explicitly presents intention as the key determinant of the tendency to adopt a healthy diet. Intention is determined by demographic, psychological and behavioural factors and individual dietary mindset factors and dynamically affected by social environment and the person's past behaviour. The relationship between intention and behaviour is dynamically moderated by perceived control factors (price and accessibility of healthy food and time). Originality/value: The conceptual framework developed in this study is well supported by evidence and experts' opinions. This conceptual framework will be used to design the ABM of this study, and it can be used in future investigations on the tendency to adopt healthy diet and food choices.
- ItemEnvisioning emerging frontiers on human gut microbiota and its applications(Wiley, 2020-09) Ventura, Marco; Milani, Christian; Turroni, Francesca; van Sinderen, Douwe; European Commission; Fondazione Cariparma; Science Foundation Ireland; GenProbioThe human gut microbiota is involved in multiple health-influencing host interactions during the host's entire life span. Microbes colonize the infant gut instantaneously after birth and subsequently the founding and interactive progress of this early gut microbiota is considered to be driven and modulated by different host- and microbe-associated forces. A rising number of studies propose that the composition of the human gut microbiota in the early stages of life impact on the human health conditions at later stages of life. This notion has powered research aimed at detailed investigations of the infant gut microbiota composition. Nevertheless, the molecular mechanisms supporting the gut microbiome functionality and the interaction of the early gut microbes with the human host remain largely unknown.
- ItemExploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium(Nature Research, 2022-10) Alessandri, Giulia; Fontana, Federico; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Tarracchini, Chiara; Argentini, Chiara; Longhi, Giulia; Viappiani, Alice; Milani, Christian; Turroni, Francesca; van Sinderen, Douwe; Ventura, Marco; GenProbio srl; Università degli Studi di Parma; Science Foundation Ireland; Fondazione Cariparma; Ministero della SaluteIn vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the "infant-like" gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.
- ItemExploring structural diversity among adhesion devices encoded by lactococcal P335 phages with AlphaFold2(MDPI, 2022-11) Goulet, Adeline; Mahony, Jennifer; Cambillau, Christian; van Sinderen, Douwe; Science Foundation IrelandBacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and adhesion to, a suitable host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limit their structural analyses by experimental approaches. The protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of adhesion devices from siphophages belonging to the P335 group infecting Lactococcus spp., one of the most extensively applied lactic acid bacteria in dairy fermentations. The predictions of representative adhesion devices from types I-IV P335 phages illustrate their very diverse topology. Adhesion devices from types III and IV phages share a common topology with that of Skunavirus p2, with a receptor binding protein anchored to the virion by a distal tail protein loop. This suggests that they exhibit an activation mechanism similar to that of phage p2 prior to host binding.
- ItemFactors associated with staffing provision and medical equipment acquisition in Irish general practice(Irish Medical Organisation, 2012-11) Bourke, Jane; Bradley, C. P.GPs form an integral part of Irish primary care provision. However, current information concerning general practice structure, staffing and development in Ireland is quite limited. This report provides a profile of General Practice in Ireland in 2010 drawing on a national survey of practices using a standardised questionnaire. On average, there are 2.7 GPs per practice, although one in four practices remains single-handed. The majority of practices employ nursing 485(80.7%) and clerical 549(91.3%) support. A high proportion of practices have the following items of equipment: ECG machine 496(82.5%), 24 hour blood pressure monitor 481(80.1%), spirometer 383(63.8%), cryotherapy equipment 505(84%), minor surgery equipment 453(74.3%) and foetal monitor 484(80.5%). Using chi square analysis, we find statistically significant positive relationships between nursing support and possession of each of the six items of medical equipment (X2 = 81.57, p<0.01; X2 = 105.4, p<0.01; X2 = 38.5, p<0.01; X2 = 16.6, p<0.01; X2 = 39.5, p<0.01; X2 = 19.5, p<0.01)and between practice size and possession of each item of medical equipment (X2 = 26.3, p<0.01; X2 = 45, p<0.01; X2 = 16.5, p<0.01; X2 = 44.4, p<0.01; X2 = 13.8, p<0.01; X2 = 14.7, p<0.01).
- ItemFrom lab bench to formulated ingredient: characterization, production, and commercialization of human milk oligosaccharides(Elsevier, 2020-09) Walsh, Clodagh; Lane, Jonathan A.; van Sinderen, Douwe; Hickey, Rita M.; H & H Group; Science Foundation IrelandHuman milk oligosaccharides (HMOs) are known to positively influence infant health. Extensive variation exists in the levels, diversity, and complexity of oligosaccharides in the milk of a lactating mother. Until recently, limited availability of HMOs hampered their use in clinical applications. Most HMOs are unique to human milk, and have proven difficult and expensive to isolate and synthesize. Added to that, analysis of these complex glycans in milk samples requires state-of-the-art analytical instruments and associated technologies. The current review provides a critical overview of methods used in HMO analysis, and highlights the importance of understanding the factors which influence their composition and structural diversity. We also discuss recently employed strategies to overcome the availability of HMOs at industrial scale including microbial metabolic engineering and chemoenzymatic techniques. Finally, we examine how these recent advancements have opened up new avenues for future research and nutraceutical applications.
- ItemHuman milk oligosaccharide-sharing by a consortium of infant derived Bifidobacterium species(Nature Research, 2022-03) Walsh, Clodagh; Lane, Jonathan A.; van Sinderen, Douwe; Hickey, Rita M.; H and H Group; Science Foundation IrelandBifidobacteria are associated with a host of health benefits and are typically dominant in the gut microbiota of healthy, breast-fed infants. A key adaptation, facilitating the establishment of these species, is their ability to consume particular sugars, known as human milk oligosaccharides (HMO), which are abundantly found in breastmilk. In the current study, we aimed to characterise the co-operative metabolism of four commercial infant-derived bifidobacteria (Bifidobacterium bifidum R0071, Bifidobacterium breve M-16V, Bifidobacterium infantis R0033, and Bifidobacterium infantis M-63) when grown on HMO. Three different HMO substrates (2 '-fucosyllactose alone and oligosaccharides isolated from human milk representing non-secretor and secretor status) were employed. The four-strain combination resulted in increased bifidobacterial numbers (> 21%) in comparison to single strain cultivation. The relative abundance of B. breve increased by > 30% during co-cultivation with the other strains despite demonstrating limited ability to assimilate HMO in mono-culture. HPLC analysis revealed strain-level variations in HMO consumption. Metabolomics confirmed the production of formate, acetate, 1,2-propanediol, and lactate with an overall increase in such metabolites during co-cultivation. These results support the concept of positive co-operation between multiple bifidobacterial strains during HMO utilisation which may result in higher cell numbers and a potentially healthier balance of metabolites.