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1. Assessing the impact of interfering organic matter on soil metaproteomic workflow

Author

Waibel, M., McDonnell, K., Tuohy, M., Shirran, S., Synowsky, S., Thornton, B., Paterson, E., Brennan, F., Abram, F., University of St Andrews. School of Biology, University of St Andrews. Institute of Behavioural and Neural Sciences, University of St Andrews. Biomedical Sciences Research Complex, and University of St Andrews. School of Chemistry

Subjects
MCC, Soil organic matter, QH301, Metaproteomics, Grassland soil, QH301 Biology, SB Plant culture, Chemical fractionation, DAS, SDG 2 - Zero Hunger, SB
Abstract

Funding: Matthias Waibel was funded by the University of Galway College of Science and the Irish Research Council under GOIPG/2016/1215. The James Hutton Institute receives funding support from the Rural and Environment Science and Analytical Services Division of the Scottish Government. Open access funding provided by IReL. Soil organic matter (SOM) is biologically, chemically, and physically complex. As a major store of nutrients within soil, it plays an important role in nutrient provision to plants. An enhanced understanding of SOM utilisation processes could underpin better fertiliser management for plant growth, with reduced environmental losses. Metaproteomics can allow the characterisation of protein profiles and could help gaining insights into SOM microbial decomposition mechanisms. Here, we applied three different extraction methods to two soil types to recover SOM with different characteristics. Specifically, water extractable organic matter, mineral associated organic matter and protein-bound organic matter were targeted with the aim to investigate the metaproteome enriched in those extractions. As a proof-of-concept replicated extracts from one soil were further analysed for peptide identification using liquid chromatography followed by tandem mass spectrometry. We employ a framework for mining mass spectra for both peptide assignment and fragmentation pattern characterisation. Different extracts were found to exhibit contrasting total protein and humic substance content for the two soils investigated. Overall, water extracts displayed the lowest humic substance content (in both soils) and the highest number of peptide identifications (in the soil investigated) with most frequent peptide hits associated with diverse substrate/ligand binding proteins of Proteobacteria and derived taxa. Our framework also highlighted a strong peptidic signal in unassigned and unmatched spectra, information that is currently not captured by the pipelines employed in this study. Taken together, this work points to specific areas for optimisation in chromatography and mass spectrometry to adequately characterise SOM associated metaproteomes. Publisher PDF

Published
2023

2. Outcomes of exclusive enteral nutrition in paediatric Crohn's disease

Author

Lafferty, L, Tuohy, M, Carey, A, Sugrue, S, Hurley, M, and Hussey, S

Subjects
Children -- Diseases, Tube feeding -- Patient outcomes, Crohn's disease in children -- Care and treatment -- Patient outcomes, Enteral feeding -- Patient outcomes, Crohn's disease -- Care and treatment -- Patient outcomes, Food/cooking/nutrition, Health
Abstract

Background/Objectives: Exclusive enteral nutrition (EEN) is a safe and effective treatment modality for inducing remission in paediatric Crohn's disease (CD). The primary aim of this study was to compare the outcomes of EEN to corticosteroid (CS) therapy in newly diagnosed, treatment-naïve patients with CD. A secondary aim was to describe the outcomes of EEN in a national cohort of paediatric CD patients over a 10-year period. Subjects/Methods: A retrospective chart review was conducted at the Irish national referral centre for paediatric CD. A case-matched analysis was conducted on two cohorts matched for age, gender, disease location, disease behaviour and disease activity, who received CS or EEN as their initial treatment. Subsequently, cohort analysis was conducted on all patients who undertook a course of EEN therapy between 2004 and 2013. Results: The case-matched analysis found higher remission rates after treatment with EEN (24/28, 86%) compared with those with CS (15/28, 54%; P=0.02). Dietetic contacts were found to be pivotal to the success of treatment and the attainment of remission. In total, 59 patients completed EEN at some time-point in their disease course and were included in the cohort analysis. Sixty-nine per cent of this cohort entered clinical remission (41/59). EEN was found to be most effective when used as an initial treatment (P=0.004) and less effective in patients aged under 10 years (P=0.04). Conclusions: EEN should be strongly considered as a favourable primary treatment over CS, especially in those diagnosed over the age of 10 years., Author(s): L Lafferty [sup.1] [sup.2] , M Tuohy [sup.1] [sup.2] , A Carey [sup.2] [sup.3] , S Sugrue [sup.1] , M Hurley [sup.2] , S Hussey [sup.2] [sup.3] [sup.4] [sup.5] [...]

Published
2017
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14. Sustainable Farming of Bioenergy Crops

Author

Gupta, V., Tuohy, M., Kubicek, C., Saddler, J., Xu, F., Müller, Adrian, Gupta, V., Tuohy, M., Kubicek, C., Saddler, J., Xu, F., and Müller, Adrian

Abstract

Bioenergy is one option to mitigate climate change in the energy sector. Sustainable bioenergy however faces several challenges. First, there is a widely discussed land competition between food and bioenergy crops. Second, there is a widely neglected competition for biomass between using it as a fertilizer for sustainable agriculture or as feedstock for bioenergy production. Sustainability standards for bioenergy capture several environmental, social and economic aspects and often also land competition, but neglect the agronomic aspects related to the fertilizer use of biomass. Accounting for this, however, the sustainable bioenergy potential seems rather low and may only be realized in biogas production. Such can make much sense, but expectation in bioenergy to contribute significantly to global primary energy supply in a sustainable manner should not be too high.

Published
2014

17. Isolation of intact RNA from sorted S. cerevisiae cells for differential gene expression analysis

Author

Gupta, V.K., Tuohy, M., Ayyachamy, M., Turner, K.M., O’Donovan, A., Vogt, Juliane, Stahl, F., Scheper, T., Müller, Susann, Gupta, V.K., Tuohy, M., Ayyachamy, M., Turner, K.M., O’Donovan, A., Vogt, Juliane, Stahl, F., Scheper, T., and Müller, Susann

Abstract

Individuals within natural populations are highly diverse. They can vary regarding their physiological states and thus contribute differently to the performance of the whole community [1]. Hence, the characterization of microbial physiology on the single cell level is crucial for optimization and understanding of biotechnological processes. Here a protocol is presented for detecting and monitoring the functional heterogeneity in a given yeast population, on both the cellular and molecular levels, using flow cytometry and microarray analysis (first published in Nature Protocols by Achilles et al. [2]). The protocol includes staining of living S. cerevisiae cells with three different fluorescent dyes, flow cytometric analysis, sorting of live cells and stabilization of their status, the subsequent isolation of RNA from small amounts of separated cells, and finally the quantification and integrity check of this RNA. Owing to the high quality and quantity of the isolated RNA from sorted cells, gene expression analysis can be performed by using microarrays, for example.

Published
2013

30. Fungal bioconversion of agricultural by-products to vanillin

Author

UCL, Thibault, JF, Asther, M, Ceccaldi, BC, Couteau, D, Delattre, M, Duarte, JC, Faulds, C, Heldt-Hansen, HP, Kroon, P, Lesage-Meessen, L, Micard, V, Renard, CMGC, Tuohy, M, Van Hulle, S, Williamson, G, UCL, Thibault, JF, Asther, M, Ceccaldi, BC, Couteau, D, Delattre, M, Duarte, JC, Faulds, C, Heldt-Hansen, HP, Kroon, P, Lesage-Meessen, L, Micard, V, Renard, CMGC, Tuohy, M, Van Hulle, S, and Williamson, G

Abstract

The ester-linked ferulic acid of wheat bran and sugar beet pulp can be converted to vanillin using biological transformation. Free ferulic acid from sugar-beet pulp and from wheat bran was almost quantitatively obtained by extensive degradation of the cell-walls using enzyme mixtures complemented with specific ferulic acid esterases. The Basidiomycete Pycnoporus cinnabarinus then converted the released ferulic acid to vanillin. The selection of stable and highly productive strains was achieved using formal genetics. The use of cellobiose as an activator of the vanillin pathway and the sequential addition of a precursor (ferulic acid) in cultures of selected P. cinnabarinus strains, allowed 90 and 300 mg/L of vanillin to be obtained fi om ferulic acid enzymically released from wheat bran and sugar-beet pulp, respectively. This process was adapted into a two-step process involving two filamentous fungi, Aspergillus niger and P. cinnabarinus, with complementary capabilities of transformation.

Published
1998

35. Fungal Bioconversion of Agricultural By-Products to Vanillin

Author

Thibault, J, primary, Micard, V, additional, Renard, C, additional, Asther, M, additional, Delattre, M, additional, Lesage-Meessen, L, additional, Faulds, C, additional, Kroon, P, additional, Williamson, G, additional, Duarte, J, additional, Duarte, J.C, additional, Ceccaldi, B.C, additional, Tuohy, M, additional, Couteau, D, additional, Van Hulle, S, additional, and Heldt-Hansen, H.-P, additional

Published
1998
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36. Proximal sensing of the seasonal variability of pasture nutritive value using multispectral radiometry.

Author

Pullanagari, R. R., Yule, I. J., Tuohy, M. P., Hedley, M. J., Dynes, R. A., and King, W. M.

Subjects
COMPOSITION of forage plants, PASTURES, PLANT nutrition, GRAZING, RADIATION measurements, SPECTRAL reflectance, REGRESSION analysis
Abstract

The nutritive value of pasture is an important determinant of the performance of grazing livestock. Proximal sensing of in situ pasture is a potential technique for rapid prediction of nutritive value. In this study, multispectral radiometry was used to obtain pasture spectral reflectance during different seasons (autumn, spring and summer) in 2009-2010 from commercial farms throughout New Zealand. The analytical data set ( n = 420) was analysed to develop season-specific and combined models for predicting pasture nutritive-value parameters. The predicted parameters included crude protein ( CP), acid detergent fibre ( ADF), neutral detergent fibre ( NDF), ash, lignin, lipid, metabolizable energy ( ME) and organic matter digestibility ( OMD) using a partial least squares regression analysis. The calibration models were tested by internal and external validation. The results suggested that the global models can predict the pasture nutritive value parameters ( CP, ADF, NDF, lignin, ME and OMD) with moderate accuracy (0·64 ≤ r2 ≤ 0·70) while ash and lipid are poorly predicted (0·33 ≤ r2 ≤ 0·40). However, the season-specific models improved the prediction accuracy, in autumn (0·73 ≤ r2 ≤ 0·83) for CP, ADF, NDF and lignin; in spring (0·61 ≤ r2 ≤ 0·78) for CP and ash; in summer (0·77 ≤ r2 ≤ 0·80) for CP and ash, indicating a seasonal impact on spectral response. [ABSTRACT FROM AUTHOR]

Published
2013
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43. Use of a High-Resolution Melt Assay To Characterize Codon 54 of the cyp51AGene of Aspergillus fumigatuson a Rotor-Gene 6000 Instrument

Author

Tuohy, M. J., Reja, V., Park, S., Perlin, D. S., Wnek, M., Procop, G. W., and Yen-Lieberman, B.

Abstract

ABSTRACTA high-resolution melt (HRM) assay using a Rotor-Gene 6000 instrument was developed to characterize the codon for glycine 54 in the cyp51Agenes from 13 reference isolates and 12 clinical isolates of Aspergillus fumigatus. Mutations in this codon confer reduced susceptibility to itraconazole and posaconazole. The assay is simple to perform, and a result of “wild type” or “mutant” is available after approximately 1 h following DNA extraction using commercially available reagents and conventional primers.

Published
2010
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44. The use of diffuse reflectance spectroscopy for in situcarbon and nitrogen analysis of pastoral soils

Author

Kusumo, Bambang H., Hedley, C. B., Hedley, M. J., Hueni, A., Tuohy, M. P., and Arnold, G. C.

Abstract

A field method has been developed for rapid in situassessment of soil carbon (C) and nitrogen (N) content using a portable spectroradiometer (ASD FieldSpecPro). The technique was evaluated at 7 field sites in permanent pasture, and in 1-year, 3-year, and 5-year pine-to-pasture conversions on Pumice, Allophanic, and Tephric Recent Soils in the Taupo and Rotorua region of New Zealand. A total of 210 samples were collected from 2 depths: 37.5 and 112.5 mm. Field measurement of diffuse spectral reflectance was recorded from a flat sectioned horizontal soil surface of a soil core using a purpose-built contact probe attached by fibre optic cable to the spectroradiometer. A 15-mm soil slice was collected from each cut surface for analysis of total C and N using a LECO Analyser. Soils had a wide range of total C and N (0.26–11.21% C, 0.02–1.01% N). Partial least-squares regression analysis was used to develop calibration models between smoothed-first derivative 5-nm-spaced spectral data and LECO-measured total C and N. The models successfully predicted total C and N in the validation sets with the best prediction for C (RPD 2.01, r20.75, RMSEP 1.21%) and N (RPD 2.66, r20.86, RMSEP 0.07%). Prediction accuracy using different selection methods of calibration and validation set is reported. This study indicates that in situassessment of soil C and N by field spectroscopy has considerable potential for spatially rapid measurement of soil C and N in the landscape.

Published
2008
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49. Relapsing polychondritis: reversible airway obstruction or asthma

Author

Mohammad, A., Ambrose, N., Tuohy, M., Richard Conway, Costello, R., and Kearns, G.

Subjects
Airway Obstruction, Humans, Prednisone, Female, Isoxazoles, Polychondritis, Relapsing, Middle Aged, Asthma, Immunosuppressive Agents, Leflunomide
Abstract

We describe a patient who presented with poorly controlled asthma. Bronchoscopy showed collapsing airways, characteristic of RP (relapsing polychondritis).

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