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Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs
Macfadden, Andrea ; O’Donoghue, Zoe ; Silva, Patricia A.G.C. ; Chapman, Erich G. ; Olsthoorn, René C. ; Sterken, Mark G. ; Pijlman, Gorben P. ; Bredenbeek, Peter J. ; Kieft, Jeffrey S. - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Flaviviruses such as Yellow fever, Dengue, West Nile, and Zika generate disease-linked viral noncoding RNAs called subgenomic flavivirus RNAs. Subgenomic flavivirus RNAs result when the 5′–3′ progression of cellular exoribonuclease Xrn1 is blocked by RNA elements called Xrn1-resistant RNAs located within the viral genome’s 3′-untranslated region that operate without protein co-factors. Here, we show that Xrn1-resistant RNAs can halt diverse exoribonucleases, revealing a mechanism in which they act as general mechanical blocks that ‘brace’ against an enzyme’s surface, presenting an unfolding problem that confounds further enzyme progression. Further, we directly demonstrate that Xrn1-resistant RNAs exist in a diverse set of flaviviruses, including some specific to insects or with no known arthropod vector. These Xrn1-resistant RNAs comprise two secondary structural classes that mirror previously reported phylogenic analysis. Our discoveries have implications for the evolution of exoribonuclease resistance, the use of Xrn1-resistant RNAs in synthetic biology, and the development of new therapies.
Farm economic sustainability in the European Union: A pilot study
O'Donoghue, Cathal ; Devisme, Simon ; Ryan, Mary ; Conneely, Ricky ; Gillespie, Patrick ; Vrolijk, H.C.J. - \ 2016
Studies in Agricultural Economics 118 (2016)3. - ISSN 1418-2106 - p. 163 - 171.
farm Viability - FADN - farm income - opportunity costs
The measurement of farm economic sustainability has received intermittent academic interest in recent times, while the conceptual discussions are often quite limited. Moreover, this concept receives more attention at periods of diffi culty for the sector. The measurement of farm viability is an important precondition to enrich these discussions. Therefore, it is necessary to
develop more comprehensive and detailed measurement techniques to provide more clarity on viability and vulnerability levels in the sector. This paper refocuses attention on this issue, using a pilot dataset collected at farm level across a range of EU Member States which facilitates the assessment of an additional category of viability, namely that of economically sustainable
farms, i.e. farms that are economically vulnerable but which are deemed sustainable by the presence of off-farm income. Differences in viability and economic sustainability across the eight surveyed Member States are shown. The analysis is sensitive to the factors included in the measurement of viability as well as to the threshold income used to defi ne viability. Although this is a pilot study, it enhances our understanding of the factors affecting cross-country evaluation of viability and sustainability, and the policy instruments that could improve viability levels.
CAPTURED India Country Evaluation
O'Donoghue, R. ; Brouwers, J.H.A.M. - \ 2012
Wageningen : Wageningen UR Centre for Development Innovation; Environmental learning & research centre, Rhodes University - 43
This report provides the findings of the India Country Evaluation and is produced as part of the overall CAPTURED End Evaluation. After five years of support by the CAPTURED project the End Evaluation has assessed that results are commendable. I-AIM was able to design an approach in which health folk knowledge was validated by Ayurveda and Modern health Science through the PhD research program. This has been shared with communities and partners through an outreach program. Cornerstone results and outputs were the establishment of cheap technology for drinking water, researching effective village based malaria prevention practice, exploring wider holistic health concerns with health producing and curative medicines, addressing dietary deficiency producing concerns as in the case of iron and anaemia, setting priorities for conservation and verification of changing plant uses as species become more rare, probing a pressing need for authenticating plant drugs and quality, and pharmacology efficacy in biodynamic practices. These research focus areas in the PhD program have been expanded to include partnered research, materials and course development for a revival of ethnoveterinary practices and further extended to a dairy co-operative partnership program to resolve the problems of milk quality and costs related to veterinary treatment. Report number CDI-12-018
Growing grass for a green biorefinery - an option for Ireland?
O'Keeffe, S. ; Schulte, R.P.O. ; O'Kiely, P. ; O'Donoghue, C. ; Lalor, S.T.J. ; Struik, P.C. - \ 2010
T Research : research and innovation news at Teagasc 5 (2010)4. - ISSN 1649-8917 - p. 10 - 11.
biobased economy - economische haalbaarheid - graslanden - ierse republiek - bioraffinage - economic viability - grasslands - irish republic - biorefinery
Growing grass for a green biorefinery – an option for Ireland? Mind the gap: deciphering the gap between good intentions and healthy eating behaviour Halting biodiversity loss by 2020 – implications for agriculture A milk processing sector model for Ireland
Immunohistochemical studies of scrapie archival material from Irish ARQ/ARQ sheep for evidence of bovine spongiform encephalopathy-derived disease
Sharpe, A. ; McElroy, M. ; Langeveld, J.P.M. ; Bassett, H. ; O'Donoghue, A.M. ; Sweeney, T. - \ 2005
Research in Veterinary Science 79 (2005)1. - ISSN 0034-5288 - p. 29 - 35.
prion protein prp - natural scrapie - monoclonal-antibodies - lymphoid-tissues - clinical signs - bse - transmission - variants - ireland - goats
Since scrapie and bovine spongiform encephalopathy (BSE) in sheep are clinicopathologically indistinguishable, BSE in sheep may have been misdiagnosed as scrapie. Disease-specific prion protein (PrPd) patterns in archival tissues of 38 Irish ARQ/ARQ sheep diagnosed as scrapie-affected were compared to those in four Dutch BSE-challenged sheep. When medulla oblongata was immunolabelled with an antibody directed against amino acids 93-99 of ovine prion protein (ovPrP), intraneuronal PrPd was apparent in all 38 Irish sheep but was absent in BSE-challenged sheep. When lymphoid follicles were immunolabelled with antibodies directed against amino acids 93-106 of ovPrP, granule clusters of PrPd were seen in 34 of the 38 Irish sheep. Follicles of the remaining four archive sheep contained either no PrPd or single PrPd granules, similar to follicles from BSE-challenged sheep. Based on the medulla results, none of the archival cases had BSE-derived disease. The identification of some scrapie sheep with little or no intrafollicular PrPd suggests that this technique may be limited in discriminating between the two diseases.