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Nye-Wood MG, Byrne K, Stockwell S, Juhász A, Bose U, Colgrave ML. Low Gluten Beers Contain Variable Gluten and Immunogenic Epitope Content. Foods 2023; 12:3252. [PMID: 37685187 PMCID: PMC10486350 DOI: 10.3390/foods12173252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Gluten content labels inform food choice and people practicing a gluten-free diet rely upon them to avoid illness. The regulations differ between jurisdictions, especially concerning fermented foodstuffs such as beer. Gluten abundance is typically measured using ELISAs, which have come into question when testing fermented or hydrolysed foodstuffs such as beer. Mass spectrometry can be used to directly identify gluten peptides and reveal false negatives recorded by ELISA. In this survey of gluten in control and gluten-free beers, gluten protein fragments that contain known immunogenic epitopes were detected using liquid chromatography-mass spectrometry in multiple beers that claim to be gluten-free and have sufficiently low gluten content, as measured by ELISA, to qualify as being gluten-free in some jurisdictions. In fact, several purportedly gluten-free beers showed equivalent or higher hordein content than some of the untreated, control beers. The shortcomings of ELISAs for beer gluten testing are summarised, the mismatch between ELISA and mass spectrometry results are explored, and the suitability of existing regulations as they pertain to the gluten content in fermented foods in different jurisdictions are discussed.
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Affiliation(s)
- Mitchell G. Nye-Wood
- School of Science, Edith Cowan University, Perth, WA 6027, Australia; (M.G.N.-W.); (A.J.); (U.B.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA 6027, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, St. Lucia, QLD 4067, Australia; (K.B.); (S.S.)
| | - Sally Stockwell
- CSIRO Agriculture and Food, St. Lucia, QLD 4067, Australia; (K.B.); (S.S.)
| | - Angéla Juhász
- School of Science, Edith Cowan University, Perth, WA 6027, Australia; (M.G.N.-W.); (A.J.); (U.B.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA 6027, Australia
| | - Utpal Bose
- School of Science, Edith Cowan University, Perth, WA 6027, Australia; (M.G.N.-W.); (A.J.); (U.B.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA 6027, Australia
- CSIRO Agriculture and Food, St. Lucia, QLD 4067, Australia; (K.B.); (S.S.)
| | - Michelle L. Colgrave
- School of Science, Edith Cowan University, Perth, WA 6027, Australia; (M.G.N.-W.); (A.J.); (U.B.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA 6027, Australia
- CSIRO Agriculture and Food, St. Lucia, QLD 4067, Australia; (K.B.); (S.S.)
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2
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Johnston E, Okada S, Gregg CM, Warden AC, Rolland V, Gillespie V, Byrne K, Colgrave ML, Eamens AL, Allen RS, Wood CC. The structural components of the Azotobacter vinelandii iron-only nitrogenase, AnfDKG, form a protein complex within the plant mitochondrial matrix. Plant Mol Biol 2023:10.1007/s11103-023-01363-3. [PMID: 37326800 DOI: 10.1007/s11103-023-01363-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023]
Abstract
A long-held goal of synthetic biology has been the transfer of a bacterial nitrogen-fixation pathway into plants to reduce the use of chemical fertiliser on crops such as rice, wheat and maize. There are three classes of bacterial nitrogenase, named after their metal requirements, containing either a MoFe-, VFe- or FeFe-cofactor, that converts N2 gas to ammonia. Relative to the Mo-nitrogenase the Fe-nitrogenase is not as efficient for catalysis but has less complex genetic and metallocluster requirements, features that may be preferable for engineering into crops. Here we report the successful targeting of bacterial Fe-nitrogenase proteins, AnfD, AnfK, AnfG and AnfH, to plant mitochondria. When expressed as a single protein AnfD was mostly insoluble in plant mitochondria, but coexpression of AnfD with AnfK improved its solubility. Using affinity-based purification of mitochondrially expressed AnfK or AnfG we were able to demonstrate a strong interaction of AnfD with AnfK and a weaker interaction of AnfG with AnfDK. This work establishes that the structural components of the Fe-nitrogenase can be engineered into plant mitochondria and form a complex, which will be a requirement for function. This report outlines the first use of Fe-nitrogenase proteins within a plant as a preliminary step towards engineering an alternative nitrogenase into crops.
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Affiliation(s)
- E Johnston
- CSIRO Environment, GPO Box 1700, Acton, ACT, 2601, Australia
- School of Environmental and Life Sciences, University of Newcastle, University Dr, Callaghan NSW 2308, Callaghan, Australia
| | - S Okada
- CSIRO Environment, GPO Box 1700, Acton, ACT, 2601, Australia
| | - C M Gregg
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
| | - A C Warden
- CSIRO Environment, GPO Box 1700, Acton, ACT, 2601, Australia
| | - V Rolland
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
| | - V Gillespie
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
| | - K Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - M L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - A L Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - R S Allen
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia.
| | - C C Wood
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
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3
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Byrne K, Xu W, Termaat J, Khashram M. Pre-operative sciatic nerve block vs postoperative surgeon-placed perineural stump catheter for prevention of phantom limb pain after below-knee amputation. Anaesthesia 2023. [PMID: 37204191 DOI: 10.1111/anae.16040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 05/20/2023]
Affiliation(s)
- K Byrne
- Waikato Hospital, Hamilton, New Zealand
| | - W Xu
- University of Auckland, Auckland, New Zealand
| | - J Termaat
- Waikato Hospital, Hamilton, New Zealand
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4
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Bose U, Broadbent JA, Juhász A, Karnaneedi S, Johnston EB, Stockwell S, Byrne K, Limviphuvadh V, Maurer-Stroh S, Lopata AL, Colgrave ML. Comparison of protein extraction protocols and allergen mapping from black soldier fly Hermetia illucens. J Proteomics 2022; 269:104724. [PMID: 36096435 DOI: 10.1016/j.jprot.2022.104724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/25/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022]
Abstract
Exploration of important insect proteins - including allergens - and proteomes can be limited by protein extraction buffer selection and the complexity of the proteome. Herein, LC-MS/MS-based proteomics experiments were used to assess the protein extraction efficiencies for a suite of extraction buffers and the effect of ingredient processing on proteome and allergen detection. Discovery proteomics revealed that SDS-based buffer yields the maximum number of protein groups from three types of BSF samples. Bioinformatic analysis revealed that buffer composition and ingredient processing could influence allergen detection. Upon applying multi-level filtering criteria, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. A targeted LC-MRM-MS assay was developed for the pan-allergen tropomyosin and used to assess the influence of buffer composition and ingredient processing using peptide abundance measurements. SIGNIFICANCE: We demonstrated that the selection of protein extraction buffer and the processing method could influence protein yield and cross-reactive allergen detection from processed and un-processed black soldier fly (BSF) samples. In total, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. An LC-MRM-MS assay was developed for tropomyosin, indicating the importance of buffer selection and processing conditions to reduce BSF samples' allergenicity.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Elecia B Johnston
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Sally Stockwell
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Andreas L Lopata
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia; Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; Tropical Futures Institute, James Cook University-, Singapore, Singapore
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.
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5
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Bucknell N, Hardcastle N, Woon B, Bressel M, Byrne K, Selbie L, Callahan J, Hanna G, Hofman M, Ball D, Kron T, Siva S. EP05.01-023 Feasibility of Functional Lung Avoidance using Ga-68 4D Ventilation Perfusion PET/CT: The HI-FIVE Trial. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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6
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Siva S, Bressel M, Sogono P, Shaw M, Chander S, Chu J, Plumridge N, Byrne K, Kothari G, Bucknell N, Hardcastle N, Kron T, Wheeler G, MacManus M, Hanna G, Ball D, David S. MO-0711 Impact of operability and total metastatic ablation on outcomes after SABR for oligometastases. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)02409-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Zhang Q, Pritchard J, Mieog J, Byrne K, Colgrave ML, Wang JR, Ral JPF. Over-Expression of a Wheat Late Maturity Alpha-Amylase Type 1 Impact on Starch Properties During Grain Development and Germination. Front Plant Sci 2022; 13:811728. [PMID: 35422830 PMCID: PMC9002352 DOI: 10.3389/fpls.2022.811728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/04/2022] [Indexed: 05/14/2023]
Abstract
The hydrolysis of starch is a complex process that requires synergistic action of multiple hydrolytic enzymes, including α-amylases. Wheat over-expression of TaAmy1, driven by seed specific promoter, resulted in a 20- to 230-fold total α-amylase activity in mature grains. Ectopic expression of TaAmy1 showed a significant elevated α-amylase activity in stem and leaf without consequences on transitory starch. In mature grain, overexpressed TaAMY1 was mainly located in the endosperm with high expression of TaAmy1. This is due to early developing grains having effect on starch granules from 18 days post-anthesis (DPA) and on soluble sugar accumulation from 30 DPA. While accumulation of TaAMY1 led to a high degree of damaged starch in grain, the dramatic alterations of starch visco-properties caused by the elevated levels of α-amylase essentially occurred during processing, thus suggesting a very small impact of related starch damage on grain properties. Abnormal accumulation of soluble sugar (α-gluco-oligosaccharide and sucrose) by TaAMY1 over-expression reduced the grain dormancy and enhanced abscisic acid (ABA) resistance. Germination study in the presence of α-amylase inhibitor suggested a very limited role of TaAMY1 in the early germination process and starch conversion into soluble sugars.
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Affiliation(s)
- Qin Zhang
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jenifer Pritchard
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Jos Mieog
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Keren Byrne
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), St Lucia, QLD, Australia
| | - Michelle L. Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), St Lucia, QLD, Australia
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jean-Philippe F. Ral
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
- *Correspondence: Jean-Philippe F. Ral,
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8
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Zhang Q, Pritchard J, Mieog J, Byrne K, Colgrave ML, Wang J, Ral JF. Overexpression of a wheat α-amylase type 2 impact on starch metabolism and abscisic acid sensitivity during grain germination. Plant J 2021; 108:378-393. [PMID: 34312931 PMCID: PMC9290991 DOI: 10.1111/tpj.15444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 05/27/2023]
Abstract
Despite being of vital importance for seed establishment and grain quality, starch degradation remains poorly understood in organs such as cereal or legume seeds. In cereals, starch degradation requires the synergetic action of different isoforms of α-amylases. Ubiquitous overexpression of TaAmy2 resulted in a 2.0-437.6-fold increase of total α-amylase activity in developing leaf and harvested grains. These increases led to dramatic alterations of starch visco-properties and augmentation of soluble carbohydrate levels (mainly sucrose and α-gluco-oligosaccharide) in grain. Interestingly, the overexpression of TaAMY2 led to an absence of dormancy in ripened grain due to abscisic acid (ABA) insensitivity. Using an allosteric α-amylase inhibitor (acarbose), we demonstrated that ABA insensitivity was due to the increased soluble carbohydrate generated by the α-amylase excess. Independent from the TaAMY2 overexpression, inhibition of α-amylase during germination led to the accumulation of soluble α-gluco-oligosaccharides without affecting the first stage of germination. These findings support the hypotheses that (i) endosperm sugar may overcome ABA signalling and promote sprouting, and (ii) α-amylase may not be required for the initial stage of grain germination, an observation that questions the function of the amylolytic enzyme in the starch degradation process during germination.
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Affiliation(s)
- Qin Zhang
- Agriculture and foodCSIRO Agriculture and FoodCanberraACT2601Australia
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuan611130China
| | - Jenifer Pritchard
- Agriculture and foodCSIRO Agriculture and FoodCanberraACT2601Australia
| | - Jos Mieog
- Agriculture and foodCSIRO Agriculture and FoodCanberraACT2601Australia
- Present address:
Plant ScienceSouthern Cross UniversityLismoreACTAustralia
| | - Keren Byrne
- Agriculture and foodCSIRO Agriculture and FoodCanberraACT2601Australia
- CSIRO Agriculture and FoodSt. LuciaQLD4067Australia
| | - Michelle L. Colgrave
- Agriculture and foodCSIRO Agriculture and FoodCanberraACT2601Australia
- CSIRO Agriculture and FoodSt. LuciaQLD4067Australia
| | - Ji‐Rui Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuan611130China
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9
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Bose U, Juhász A, Yu R, Bahmani M, Byrne K, Blundell M, Broadbent JA, Howitt CA, Colgrave ML. Proteome and Nutritional Shifts Observed in Hordein Double-Mutant Barley Lines. Front Plant Sci 2021; 12:718504. [PMID: 34567030 PMCID: PMC8458801 DOI: 10.3389/fpls.2021.718504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Lysine is the most limiting essential amino acid in cereals, and efforts have been made over the decades to improve the nutritional quality of these grains by limiting storage protein accumulation and increasing lysine content, while maintaining desired agronomic traits. The single lys3 mutation in barley has been shown to significantly increase lysine content but also reduces grain size. Herein, the regulatory effect of the lys3 mutation that controls storage protein accumulation as well as a plethora of critically important processes in cereal seeds was investigated in double mutant barley lines. This was enabled through the generation of three hordein double-mutants by inter-crossing three single hordein mutants, that had all been backcrossed three times to the malting barley cultivar Sloop. Proteome abundance measurements were integrated with their phenotype measurements; proteins were mapped to chromosomal locations and to their corresponding functional classes. These models enabled the prediction of previously unknown points of crosstalk that connect the impact of lys3 mutations to other signalling pathways. In combination, these results provide an improved understanding of how the mutation at the lys3 locus remodels cellular functions and impact phenotype that can be used in selective breeding to generate favourable agronomic traits.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Ronald Yu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Mahya Bahmani
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | | | | | | | - Michelle L. Colgrave
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
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10
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Bose U, Broadbent JA, Juhász A, Karnaneedi S, Johnston EB, Stockwell S, Byrne K, Limviphuvadh V, Maurer-Stroh S, Lopata AL, Colgrave ML. Protein extraction protocols for optimal proteome measurement and arginine kinase quantitation from cricket Acheta domesticus for food safety assessment. Food Chem 2021; 348:129110. [PMID: 33508605 DOI: 10.1016/j.foodchem.2021.129110] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Insects have been consumed by people for millennia and have recently been proposed as a complementary, sustainable source of protein to feed the world's growing population. Insects and crustaceans both belong to the arthropod family. Crustacean (shellfish) allergies are common and potentially severe; hence, the cross-reactivity of the immune system with insect proteins is a potential health concern. Herein, LC-MS/MS was used to explore the proteome of whole, roasted whole and roasted powdered cricket products. Eight protein extraction protocols were compared using the total number of protein and distinct peptide identifications. Within these data, 20 putative allergens were identified, of which three were arginine kinase (AK) proteoforms. Subsequently, a multiple reaction monitoring MS assay was developed for the AK proteoforms and applied to a subset of extracts. This targeted assay demonstrated that allergen abundance/detectability varies according to the extraction method as well as the food processing method.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Elecia B Johnston
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Sally Stockwell
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Andreas L Lopata
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.
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11
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Bose U, Broadbent JA, Byrne K, Blundell MJ, Howitt CA, Colgrave ML. Proteome Analysis of Hordein-Null Barley Lines Reveals Storage Protein Synthesis and Compensation Mechanisms. J Agric Food Chem 2020; 68:5763-5775. [PMID: 32374605 DOI: 10.1021/acs.jafc.0c01410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hordeins are the major barley seed storage proteins and are elicitors of celiac disease. Attempts to reduce the hordein level in barley have been made; however, the resultant pleiotropic effects are less understood. Here, data-independent acquisition mass spectrometry was used to measure proteome-wide abundance differences between wild-type and single hordein-null barley lines. Using comparative quantitative proteomics, we detected proteome-wide changes (∼59%) as a result of the specific reduction in hordein proteins. The comparative analysis and functional annotation revealed an increase in non-gluten storage proteins, such as globulins and lipid transfer proteins, and proteins rich in essential amino acids in the null lines. This study yields an informative molecular portrait of the hordein-null lines and the underlying mechanisms of storage protein biosynthesis. This study indicates the extent to which protein content can be manipulated without biological consequence, and we envision its wide-scale application for studying modified crops.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Malcolm J Blundell
- CSIRO Agriculture and Food, General Post Office Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - Crispin A Howitt
- CSIRO Agriculture and Food, General Post Office Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, Queensland 4067, Australia
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12
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Bose U, Juhász A, Broadbent JA, Byrne K, Howitt CA, Colgrave ML. Identification and Quantitation of Amylase Trypsin Inhibitors Across Cultivars Representing the Diversity of Bread Wheat. J Proteome Res 2020; 19:2136-2148. [PMID: 32267703 DOI: 10.1021/acs.jproteome.0c00059] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
α-Amylase/trypsin inhibitors (ATIs) may have a role in nonceliac wheat sensitivity (NCWS) and celiac disease (CD), but the ATI content and diversity across a range of wheat cultivars are not well characterized. Discovery proteomics was used to detect ATIs across two wheat cultivars: Chara and Magenta. Comprehensive mapping of detected ATIs with the ATIs from the recently published wheat genome RefSeq v1.0 shows the presence of three major subclasses: monomeric (9%), dimeric (61%), and chloroform-methanol (CM) type (30%). Subsequently, the level of 18 ATI isoforms (63 peptides) grouped into four subtypes was monitored across 15 commercial wheat cultivars and the eight parental lines from a multiparent advanced-generation intercross (MAGIC) population using liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS). The ATI content of wheat cultivars Janz, Sunvale, Diamond Bird, and Longreach Scout was significantly lower than that of other wheat cultivars. The MAGIC parental cultivars Baxter and Xiaoyan 54 contain higher levels (∼115% relative to the average wheat ATI content), whereas cultivar Pastor contained the lowest levels (∼87%). Comprehensive sequence analysis, annotation, chromosomal locations, and epitope mapping enabled us to build an LC-MRM-MS method to monitor and quantify the immunostimulatory ATI proteins potentially related to NCWS, autoimmune diseases, and metabolic disorders. This provides an opportunity to select wheat cultivars with significantly lower levels of ATIs.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- School of Science, Edith Cowan University, Joondalup, WA6027, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Crispin A Howitt
- CSIRO Agriculture and Food, G.P.O. Box 1700, Canberra, ACT 2601, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia.,School of Science, Edith Cowan University, Joondalup, WA6027, Australia
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Okada S, Gregg CM, Allen RS, Menon A, Hussain D, Gillespie V, Johnston E, Byrne K, Colgrave ML, Wood CC. A Synthetic Biology Workflow Reveals Variation in Processing and Solubility of Nitrogenase Proteins Targeted to Plant Mitochondria, and Differing Tolerance of Targeting Sequences in a Bacterial Nitrogenase Assay. Front Plant Sci 2020; 11:552160. [PMID: 33013970 PMCID: PMC7511584 DOI: 10.3389/fpls.2020.552160] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/21/2020] [Indexed: 05/13/2023]
Abstract
While industrial nitrogen fertilizer is intrinsic to modern agriculture, it is expensive and environmentally harmful. One approach to reduce fertilizer usage is to engineer the bacterial nitrogenase enzyme complex within plant mitochondria, a location that may support enzyme function. Our current strategy involves fusing a mitochondrial targeting peptide (MTP) to nitrogenase (Nif) proteins, enabling their import to the mitochondrial matrix. However, the process of import modifies the N-terminus of each Nif protein and may impact nitrogenase assembly and function. Here we present our workflow assessing the mitochondrial processing, solubility and relative abundance of 16 Klebsiella oxytoca Nif proteins targeted to the mitochondrial matrix in Nicotiana benthamiana leaf. We found that processing and abundance of MTP::Nif proteins varied considerably, despite using the same constitutive promoter and MTP across all Nif proteins tested. Assessment of the solubility for all MTP::Nif proteins when targeted to plant mitochondria found NifF, M, N, S, U, W, X, Y, and Z were soluble, while NifB, E, H, J, K, Q, and V were mostly insoluble. The functional consequence of the N-terminal modifications required for mitochondrial targeting of Nif proteins was tested using a bacterial nitrogenase assay. With the exception of NifM, the Nif proteins generally tolerated the N-terminal extension. Proteomic analysis of Nif proteins expressed in bacteria found that the relative abundance of NifM with an N-terminal extension was increased ~50-fold, while that of the other Nif proteins was not influenced by the N-terminal extension. Based on the solubility, processing and functional assessments, our workflow identified that K. oxytoca NifF, N, S, U, W, Y, and Z successfully met these criteria. For the remaining Nif proteins, their limitations will need to be addressed before proceeding towards assembly of a complete set of plant-ready Nif proteins for reconstituting nitrogenase in plant mitochondria.
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Affiliation(s)
- Shoko Okada
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Christina M. Gregg
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Robert Silas Allen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Amratha Menon
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Dawar Hussain
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Vanessa Gillespie
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Ema Johnston
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Keren Byrne
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
| | - Michelle Lisa Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Queensland Biosciences Precinct, St. Lucia, QLD, Australia
| | - Craig C. Wood
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
- *Correspondence: Craig C. Wood,
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14
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Colgrave ML, Byrne K, Caine J, Kowalczyk L, Vibhakaran Pillai S, Dong B, Lovrecz G, MacIntosh S, Scoble JA, Petrie JR, Singh S, Zhou XR. Proteomics reveals the in vitro protein digestibility of seven transmembrane enzymes from the docosahexaenoic acid biosynthesis pathway. Food Chem Toxicol 2019; 130:89-98. [PMID: 31085220 DOI: 10.1016/j.fct.2019.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022]
Abstract
The measurement of protein digestibility is one of the key steps in determining the safety of a genetically modified crop that has been traditionally accomplished using antibodies. Membrane proteins are often extremely difficult to express with replicated authentic tertiary structure in heterologous systems. As a result raising antibodies for use in safety assessment may not be feasible. In this study, LC-MS based proteomics was used to characterise seven transmembrane enzymes from the docosahexaenoic acid biosynthetic pathway that had been introduced into canola. The application of a two-stage digestion strategy involving simulated gastric fluid followed by trypsin enabled the measurement of protein digestibility in vitro. Tryptic peptide markers that spanned the length of each desaturase protein were monitored and showed that these proteins were readily degraded (>95% within 5 min) and highlighted regions of the elongase enzymes that showed limited resistance to simulated gastric digestion. Traditional gel-based and Western blotting analysis of ω3-desaturase and Δ6-elongase revealed rapid hydrolysis of the intact proteins within seconds and no fragments (>3 kDa) remained after 60 min, complementing the novel approach described herein. The LC-MS approach was sensitive, selective and did not require the use of purified proteins.
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Affiliation(s)
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - Joanne Caine
- CSIRO Manufacturing, 343 Royal Parade, Parkville, VIC, 3052, Australia
| | - Lukasz Kowalczyk
- CSIRO Manufacturing, 343 Royal Parade, Parkville, VIC, 3052, Australia
| | | | - Bei Dong
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - George Lovrecz
- CSIRO Manufacturing, 343 Royal Parade, Parkville, VIC, 3052, Australia
| | - Susan MacIntosh
- Nuseed Americas, 11901 S. Austin Avenue, Alsip, IL, 60803, USA
| | - Judith A Scoble
- CSIRO Manufacturing, 343 Royal Parade, Parkville, VIC, 3052, Australia
| | - James R Petrie
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Surinder Singh
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Xue-Rong Zhou
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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15
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Bose U, Byrne K, Howitt CA, Colgrave ML. Targeted proteomics to monitor the extraction efficiency and levels of barley α-amylase trypsin inhibitors that are implicated in non-coeliac gluten sensitivity. J Chromatogr A 2019; 1600:55-64. [PMID: 31036362 DOI: 10.1016/j.chroma.2019.04.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 12/19/2022]
Abstract
Plant defense protein α-amylase trypsin inhibitors (ATIs) have been proposed as one of the triggers of non-coeliac gluten sensitivity, however there have been no focused studies on their optimal extraction and quantitation from cereal grains. The efficiency of extraction is of utmost interest for the downstream detection and characterisation. In the present study, three extraction buffers and two modified protocols were investigated using LC-MRM-MS in order to examine their ability to efficiently and repeatably extract ATIs from selected barley cultivars. Initially, three extraction buffers IPA/DTT, urea and Tris-HCl were used to extract ATIs from two selected barley cultivars, Commander and Hindmarsh. The results obtained from the preliminary study showed that IPA/DTT and urea-based buffer extraction could yield ∼70% and ∼45% more ATIs, respectively than a buffer based on Tris-HCl extraction, with all methods showing high repeatability (CV < 15%). A multi-step protocol, employing IPA/DTT and urea improved the extraction efficiency in comparison to the single buffer extraction protocols (p<0.0001). When solutions from parallel extractions using IPA/DTT and urea were combined, the results were comparable (p = 0.99) with a sequential multi-step IPA/DTT-urea protocol. However, the repeatability of the combined process was compromised, as discerned by greater variation (CV>30%). The optimised sequential two-step extraction protocol was successfully used to extract and quantify ATIs from 12 barley cultivars. LC-MS analysis revealed that cv Yagan and cv Scope contain the higher levels (∼143% relative to the average barley ATI content), whereas cultivars Fleet (61%), Baudin (77%) and Commander (79%) contained the lowest levels. The libraries of ATIs identified and the quantitative methods described here provide a foundation for the future application of MS-based quantitative methodologies to detect and quantify ATIs in barley varieties and in food products.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD, 4067, Australia.
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD, 4067, Australia.
| | - Crispin A Howitt
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia.
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16
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Byrne K, Hallworth P, Monfared AAT, Moshyk A, Shaw JW. Real-world systemic therapy treatment patterns for squamous cell carcinoma of the head and neck in Canada. ACTA ACUST UNITED AC 2019; 26:e167-e174. [PMID: 31043823 DOI: 10.3747/co.26.3946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background In the present study, we examined real-world treatment patterns for squamous cell carcinoma of the head and neck (scchn) in Canada, which are largely unknown. Methods Oncologists across Canada provided data for disease history, characteristics, and treatment patterns during May-July 2016 for 6-8 consecutive patients receiving first-line or second-line drug treatment for scchn (including locally advanced and recurrent or metastatic disease). Results Information from 16 physicians for 109 patients receiving drug treatment for scchn was provided; 1 patient was excluded from the treatment-pattern analysis. Median age in the cohort was 63 years [interquartile range (iqr): 57-68 years], and 24% were current smokers, with a mean exposure of 26.2 ± 12.7 pack-years. The most common tumour site was the oropharynx (48%). Most patients (84%) received platinum-based regimens as first-line treatment (44% received cisplatin monotherapy). Use of cetuximab-based regimens as first-line treatment was limited (17%). Of 53 patients receiving second-line treatment, 87% received a first-line platinum-based regimen. Median time between first-line treatment with a platinum-based regimen and initiation of second-line treatment was 55 days (iqr: 20-146 days). The most common second-line regimen was cetuximab monotherapy (43%); platinum-based regimens were markedly infrequent (13%). Conclusions Our analysis provides real-world insight into scchn clinical practice patterns in Canada, which could inform reimbursement decision-making. High use of platinum-based regimens in first-line drug treatment was generally reflective of treatment guidelines; cetuximab use in the second-line was higher than anticipated. Additional real-world studies are needed to understand the effect of novel therapies such as immuno-oncology agents on clinical practice and outcomes, particularly for recurrent or metastatic scchn.
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Affiliation(s)
- K Byrne
- Adelphi Real World, Bollington, Cheshire, U.K
| | - P Hallworth
- Adelphi Real World, Bollington, Cheshire, U.K
| | - A Abbas Tahami Monfared
- Market Access and Public Affairs, Bristol-Myers Squibb, Montreal, QC.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC
| | - A Moshyk
- Market Access and Public Affairs, Bristol-Myers Squibb, Montreal, QC
| | - J W Shaw
- Worldwide Health Economics and Outcomes Research, Bristol-Myers Squibb, Princeton, NJ, U.S.A
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17
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Colgrave ML, Byrne K, Pillai SV, Dong B, Leonforte A, Caine J, Kowalczyk L, Scoble JA, Petrie JR, Singh S, Zhou XR. Quantitation of seven transmembrane proteins from the DHA biosynthesis pathway in genetically engineered canola by targeted mass spectrometry. Food Chem Toxicol 2019; 126:313-321. [PMID: 30831153 DOI: 10.1016/j.fct.2019.02.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/04/2019] [Accepted: 02/25/2019] [Indexed: 12/31/2022]
Abstract
Examining tissue-specific expression and the measurement of protein abundance are important steps when assessing the performance of genetically engineered crops. Liquid chromatography-mass spectrometry offers many advantages over traditional methods for protein quantitation, especially when dealing with transmembrane proteins that are often difficult to express or generate antibodies against. In this study, discovery proteomics was used to detect the seven transgenic membrane-bound enzymes from the docosahexaenoic acid (DHA) biosynthetic pathway that had been engineered into canola. Subsequently, a targeted LC-MS/MS method for absolute quantitation was developed and applied to the simultaneous measurement of the seven DHA biosynthetic pathway enzymes in genetically modified canola grown across three sites. The results of this study demonstrated that the enzymatic proteins that drive the production of DHA using seed-specific promoters were detected only in mature and developing seed of DHA canola. None of the DHA biosynthesis pathway proteins were detected in wild-type canola planted in the same site or in the non-seed tissues of the transgenic canola, irrespective of the sampling time or the tissues tested. This study describes a streamlined approach to simultaneously measure multiple membrane-bound proteins in planta.
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Affiliation(s)
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | | | - Bei Dong
- CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT 2601, Australia
| | | | - Joanne Caine
- CSIRO Manufacturing, 343 Royal Parade, Parkville, VIC, 3052, Australia
| | - Lukasz Kowalczyk
- CSIRO Manufacturing, 343 Royal Parade, Parkville, VIC, 3052, Australia
| | - Judith A Scoble
- CSIRO Manufacturing, 343 Royal Parade, Parkville, VIC, 3052, Australia
| | - James R Petrie
- CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Surinder Singh
- CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Xue-Rong Zhou
- CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT 2601, Australia
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18
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Myles PS, Smith JA, Kasza J, Silbert B, Jayarajah M, Painter T, Cooper DJ, Marasco S, McNeil J, Bussières JS, McGuinness S, Byrne K, Chan MT, Landoni G, Wallace S, Forbes A, Myles P, Smith J, Cooper DJ, Silbert B, McNeil J, Marasco S, Esmore D, Krum H, Tonkin A, Buxton B, Heritier S, Merry A, Liew D, McNeil J, Forbes A, Cooper D, Wallace S, Meehan A, Myles P, Wallace S, Galagher W, Farrington C, Ditoro A, Wutzlhofer L, Story D, Peyton P, Baulch S, Sidiropoulos S, Potgieter D, Baker R, Pesudovs B, O'Loughlin J Wells E, Coutts P, Bolsin S, Osborne C, Ives K, Smith J, Hulley A, Christie-Taylor G, Painter T, Lang S, Mackay H, Cokis C, March S, Bannon P, Wong C, Turner L, Scott D, Silbert B, Said S, Corcoran P, Painter T, de Prinse L, Bussières J, Gagné N, Lamy A, Semelhago L, Chan M, Underwood M, Choi G, Fung B, Landoni G, Lembo R, Monaco F, Simeone F, Marianello D, Alvaro G, De Vuono G, van Dijk D, Dieleman J, Numan S, McGuinness S, Parke R, Raudkivi P, Gilder E, Byrne K, Dunning J, Termaat J, Mans G, Jayarajah M, Alderton J, Waugh D, Platt M, Pai A, Sevillano A, Lal A, Sinclair C, Kunst G, Knighton A, Cubas G, Saravanan P, Millner R, Vasudevan V, Patteril M, Lopez E, Basu R, Lu J. Tranexamic acid in coronary artery surgery: One-year results of the Aspirin and Tranexamic Acid for Coronary Artery Surgery (ATACAS) trial. J Thorac Cardiovasc Surg 2019; 157:644-652.e9. [DOI: 10.1016/j.jtcvs.2018.09.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/13/2018] [Accepted: 09/27/2018] [Indexed: 11/30/2022]
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19
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Rowan CR, Keegan D, Byrne K, Cullen G, Mulcahy HE, Sheridan J, Ryan EJ, de Vries A, D'Haens G, Doherty GA. Subcutaneous rather than intravenous ustekinumab induction is associated with comparable circulating drug levels and early clinical response: a pilot study. Aliment Pharmacol Ther 2018; 48:333-339. [PMID: 29920697 DOI: 10.1111/apt.14834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/18/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Ustekinumab (USK) is licenced for intravenous induction and subcutaneous (S/C) maintenance in Crohn's disease. AIM To evaluate ustekinumab trough concentrations and clinical response with exclusive subcutaneous ustekinumab induction. METHODS Patients with Crohn's disease who initiated treatment with subcutaneous ustekinumab at a single academic centre were included in this pilot study. A dosage of 360 mg ustekinumab was given subcutaneously in divided doses; 180 mg at Week 0, 90 mg at Week 1 and 90 mg at Week 2, with corresponding ustekinumab trough concentrations assessed to Week 8. The primary outcome measures were trough serum ustekinumab levels and clinical remission at Week 8. Secondary outcome measures were trough serum ustekinumab levels at Week 1 & 2 and changes in C-reactive protein, albumin and faecal calprotectin at Week 8. RESULTS Nineteen patients were included. Median Week 8 ustekinumab trough concentrations were 6.1 μg/mL (Inter-quartile range 4-9.8 μg/mL). There was a significant improvement in Harvey Bradshaw index from Week 0 (median HBI 5; interquartile range 2-8) to Week 8 (median HBI 1; interquartile range 0-3) (P = 0.002). C-reactive protein levels did not change significantly but faecal calprotectin improved significantly; median faecal calprotectin at Week 0 was 533 μg/g; at Week 8, it was 278 μg/g (P = 0.038). CONCLUSIONS Ustekinumab trough concentrations are comparable whether ustekinumab induction treatment was administered subcutaneously or intravenously. A significant improvement in symptoms and faecal calprotectin was noted. These results support the use of subcutaneous induction as an alternative if there are barriers to intravenous induction.
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Affiliation(s)
- C R Rowan
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - D Keegan
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - K Byrne
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - G Cullen
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - H E Mulcahy
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - J Sheridan
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - E J Ryan
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - A de Vries
- Sanquin Diagnostic Services, Amsterdam, The Netherlands
| | - G D'Haens
- Department of Gastroenterology, Amsterdam Medical Centre, Amsterdam, The Netherlands
| | - G A Doherty
- Center for Colorectal Disease, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
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20
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Li H, Byrne K, Galiamov R, Mendoza-Porras O, Bose U, Howitt CA, Colgrave ML. Using LC-MS to examine the fermented food products vinegar and soy sauce for the presence of gluten. Food Chem 2018; 254:302-308. [DOI: 10.1016/j.foodchem.2018.02.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/29/2018] [Accepted: 02/05/2018] [Indexed: 10/18/2022]
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21
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Ferris HA, Ryan FM, Byrne K, Fleming E, O’ Sullivan H, Hamilton D. Scombrotoxic Fish Poisoning Secondary to Tuna Ingestion. Ir Med J 2018; 111:773. [PMID: 30520278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Scombrotoxic poisoning results from the improper handling and refrigeration of fish containing naturally occurring histidine. Scombroid fish species such as tuna, mackerel and swordfish contain histidine, which is converted to histamine when inadequately chilled. European legislation states that scombroid fish species should be tested for the presence of histamine and mean values should be <100mg/kg1. The authors report an outbreak of scombrotoxic fish poisoning in 12 individuals following ingestion of tuna. Symptoms occurred rapidly and included flushing, headache, palpitations and diarrhoea. Fortunately, symptoms were short lived and self-limiting except in one individual, who required anti-histamine medication. Adequate refrigeration practices are crucial in preventing scombrotoxic food poisoning.
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Affiliation(s)
- H A Ferris
- Department of Public Health Medicine, HSE-South, Cork, Ireland
| | - F M Ryan
- Department of Public Health Medicine, HSE-South, Cork, Ireland
| | - K Byrne
- South Lee Environmental Health Services, HSE- South, Cork, Ireland
| | - E Fleming
- South Lee Environmental Health Services, HSE- South, Cork, Ireland
| | - H O’ Sullivan
- South Lee Environmental Health Services, HSE- South, Cork, Ireland
| | - D Hamilton
- South Lee Environmental Health Services, HSE- South, Cork, Ireland
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22
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Byrne K, Ambrose L, Bromley R, Cruikshank S, Guo L, Morgia M, Lamoury G. PO4 Toxicity outcomes from conformal prone breast radiotherapy and a dosimetric comparison with hybrid IMRT prone radiotherapy. Breast 2018. [DOI: 10.1016/j.breast.2018.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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23
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Dawson C, Mendoza-Porras O, Byrne K, Hooper T, Howitt C, Colgrave M. Oat of this world: Defining peptide markers for detection of oats in processed food. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Charlotte Dawson
- CSIRO Agriculture and Food; 306 Carmody Road; St Lucia QLD 4067 Australia
| | | | - Keren Byrne
- CSIRO Agriculture and Food; 306 Carmody Road; St Lucia QLD 4067 Australia
| | - Thomas Hooper
- CSIRO Agriculture and Food; 306 Carmody Road; St Lucia QLD 4067 Australia
| | - Crispin Howitt
- CSIRO Agriculture and Food; GPO Box 1700; Canberra ACT 2601 Australia
| | - Michelle Colgrave
- CSIRO Agriculture and Food; 306 Carmody Road; St Lucia QLD 4067 Australia
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24
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Colgrave ML, Byrne K, Howitt CA. Liquid Chromatography-Mass Spectrometry Analysis Reveals Hydrolyzed Gluten in Beers Crafted To Remove Gluten. J Agric Food Chem 2017; 65:9715-9725. [PMID: 29047268 DOI: 10.1021/acs.jafc.7b03742] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
During brewing, gluten proteins may be solubilized, modified, complexed, hydrolyzed, and/or precipitate. Gluten fragments that persist in conventional beers render them unsuitable for people with celiac disease (CD) or gluten intolerance. Barley-based beers crafted to remove gluten using proprietary precipitation and/or application of enzymes, e.g. prolyl endopeptidases (PEP) that degrade the proline-rich gluten molecules, are available commercially. Gluten measurement in fermented products remains controversial. The industry standard, a competitive ELISA, may indicate gluten values <20 mg/kg, which is deemed safe for people with CD. However, in this study, liquid chromatography-mass spectrometry analyses revealed gluten peptides derived from hydrolyzed fragments, many >30 kDa in size. Barley gluten (hordeins) were detected in all beers analyzed with peptides representing all hordein classes detected in conventional beers but also, alarmingly, in many gluten-reduced beers. It is evident that PEP digestion was incomplete in several commercial beers, and peptides comprising missed cleavages were identified, warranting further optimization of PEP application in an industrial setting.
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Affiliation(s)
- Michelle L Colgrave
- CSIRO Agriculture and Food , 306 Carmody Road, St. Lucia, QLD 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food , 306 Carmody Road, St. Lucia, QLD 4067, Australia
| | - Crispin A Howitt
- CSIRO Agriculture and Food , GPO Box 1700, Canberra, ACT 2601, Australia
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25
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Rider A, Simpson S, Bennett B, Byrne K, Hallworth P, Desai T, Cocks K. Generating patient reported outcome norms for an EU cancer population using real world data (FACT-G). Ann Oncol 2017. [DOI: 10.1093/annonc/mdx385.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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26
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McNeil H, McMurray J, Byrne K, Grindrod K, McKinnon A, Stolee P. ENGAGING OLDER ADULTS AND THEIR CAREGIVERS IN INNOVATION ECOSYSTEMS FOR HEALTH AND AGING. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- H. McNeil
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Ontario, Canada,
| | - J. McMurray
- Wilfrid Laurier University, Waterloo, Ontario, Canada,
| | - K. Byrne
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Ontario, Canada,
| | - K. Grindrod
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Ontario, Canada,
| | - A. McKinnon
- Arthritis Research Canada, Richmond, British Columbia, Canada
| | - P.T. Stolee
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Ontario, Canada,
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Colgrave ML, Byrne K, Howitt CA. Food for thought: Selecting the right enzyme for the digestion of gluten. Food Chem 2017; 234:389-397. [PMID: 28551252 DOI: 10.1016/j.foodchem.2017.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/29/2017] [Accepted: 05/01/2017] [Indexed: 12/24/2022]
Abstract
Gluten describes a complex mixture of proteins found in wheat, rye, barley and oats that pose a health risk to people affected by conditions such as coeliac disease and non-coeliac gluten sensitivity. Complete digestion of gluten proteins is of critical importance during quantitative analysis. To this end, chymotrypsin was investigated for its ability to efficiently and reproducibly digest specific classes of gluten in barley. Using proteomics a chymotryptic peptide marker panel was elucidated and subjected to relative quantification using LC-MRM-MS. Thorough investigation of peptide markers revealed robust and reproducible quantification with CVs <15% was possible, however a greater proportion of non-specific cleavage variants were observed relative to trypsin. The selected peptide markers were assessed to ensure their efficient liberation from their parent proteins. While trypsin remains the preferred enzyme for quantification of the avenin-like A proteins, the B-, D- and γ-hordeins, chymotrypsin was the enzyme of choice for the C-hordeins.
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Affiliation(s)
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Crispin A Howitt
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
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Abstract
The efficiency of gluten extraction is of critical importance to the results derived from any analytical method for gluten detection and quantitation, whether it employs reagent-based technology (antibodies) or analytical instrumentation (mass spectrometry). If the target proteins are not efficiently extracted, the end result will be an under-estimation in the gluten content posing a health risk to people affected by conditions such as celiac disease (CD) and nonceliac gluten sensitivity (NCGS). Five different extraction protocols were investigated using LC-MRM-MS for their ability to efficiently and reproducibly extract gluten. The rapid and simple "IPA/DTT" protocol and related "two-step" protocol were enriched for gluten proteins, 55/86% (trypsin/chymotrypsin) and 41/68% of all protein identifications, respectively, with both methods showing high reproducibility (CV < 15%). When using multistep protocols, it was critical to examine all fractions, as coextraction of proteins occurred across fractions, with significant levels of proteins existing in unexpected fractions and not all proteins within a particular gluten class behaving the same.
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Affiliation(s)
- Azadeh Fallahbaghery
- CSIRO Agriculture and Food , 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Wei Zou
- CSIRO Agriculture and Food , 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food , 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Crispin A Howitt
- CSIRO Agriculture and Food , GPO Box 1700, Canberra, ACT 2601, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food , 306 Carmody Road, St. Lucia, Queensland 4067, Australia
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Byrne K, Waller J, Piercy J, Shaw J, Dastani H. P18.10 Impact of glioblastoma multiforme (GBM) on patients’ quality of life (QoL). Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Clowry J, Sheridan J, Healy R, Deady S, Keegan D, Byrne K, Cullen G, Mulcahy H, Comber H, Parnell A, Doherty G, Lally A. Increased non-melanoma skin cancer risk in young patients with inflammatory bowel disease on immunomodulatory therapy: a retrospective single-centre cohort study. J Eur Acad Dermatol Venereol 2017; 31:978-985. [DOI: 10.1111/jdv.14105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/14/2016] [Indexed: 02/06/2023]
Affiliation(s)
- J. Clowry
- Department of Dermatology; St Vincent's University Hospital; Dublin 4 Ireland
| | - J. Sheridan
- Department of Gastroenterology; St Vincent's University Hospital; Dublin 4 Ireland
| | - R. Healy
- School of Mathematics and Statistics; University College Dublin; Dublin 4 Ireland
| | - S. Deady
- National Cancer Registry of Ireland; Cork Ireland
| | - D. Keegan
- Department of Gastroenterology; St Vincent's University Hospital; Dublin 4 Ireland
| | - K. Byrne
- Department of Gastroenterology; St Vincent's University Hospital; Dublin 4 Ireland
| | - G. Cullen
- Department of Gastroenterology; St Vincent's University Hospital; Dublin 4 Ireland
| | - H. Mulcahy
- Department of Gastroenterology; St Vincent's University Hospital; Dublin 4 Ireland
| | - H. Comber
- National Cancer Registry of Ireland; Cork Ireland
| | - A.C. Parnell
- School of Mathematics and Statistics; University College Dublin; Dublin 4 Ireland
| | - G. Doherty
- Department of Gastroenterology; St Vincent's University Hospital; Dublin 4 Ireland
| | - A. Lally
- Department of Dermatology; St Vincent's University Hospital; Dublin 4 Ireland
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Abstract
Dabigatran is a direct thrombin inhibitor, which is increasingly likely to be encountered in patients presenting for surgery. This study examines whether there is a consistent effect of dabigatran on the thromboelastogram (TEG) and whether this correlates with the effects of dabigatran on traditional coagulation parameters. Twenty patients taking dabigatran had blood sampled for kaolin-activated whole blood TEG analysis and routine coagulation testing. There was a statistically significant correlation between thrombin clotting time (TCT) and R-time (R=0.77, P=0.0001) and between activated partial thromboplastin time (APTT) and R-time (R=0.68, P=0.0013), but not between TCT and alpha-angle (R= -0.4232, P=0.071). Despite the moderate to high correlation between the TEG R-time and the TCT and APTT, there appeared to be no consistent effect of dabigatran on the TEG. These findings suggest that use of kaolin-activated whole blood TEG does not add additional benefit to traditional coagulation tests when monitoring the effect of dabigatran.
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Affiliation(s)
- A 'Aho
- Anaesthesia Registrar, Department of Anaesthesia, Waikato Hospital, Hamilton, New Zealand
| | - K Byrne
- Specialist Anaesthetist, Department of Anaesthesia, Waikato Hospital, Hamilton, New Zealand
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Colgrave ML, Byrne K, Blundell M, Heidelberger S, Lane CS, Tanner GJ, Howitt CA. Comparing Multiple Reaction Monitoring and Sequential Window Acquisition of All Theoretical Mass Spectra for the Relative Quantification of Barley Gluten in Selectively Bred Barley Lines. Anal Chem 2016; 88:9127-35. [PMID: 27533879 DOI: 10.1021/acs.analchem.6b02108] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Celiac disease (CD) is a disease of the small intestine that occurs in genetically susceptible subjects triggered by the ingestion of cereal gluten proteins for which the only treatment is strict adherence to a life-long gluten-free diet. Barley contains four gluten protein families, and the existence of barley genotypes that do not accumulate the B-, C-, and D-hordeins paved the way for the development of an ultralow gluten phenotype. Using conventional breeding strategies, three null mutations behaving as recessive alleles were combined to create a hordein triple-null barley variety. Proteomics has become an invaluable tool for characterization and quantification of the protein complement of cereal grains. In this study multiple reaction monitoring (MRM) mass spectrometry, viewed as the gold standard for peptide quantification, was compared to the data-independent acquisition strategy known as SWATH-MS (sequential window acquisition of all theoretical mass spectra). SWATH-MS was comparable (p < 0.001) to MRM-MS for 32/33 peptides assessed across the four families of hordeins (gluten) in eight barley lines. The results of SWATH-MS analysis further confirmed the absence of the B-, C-, and D-hordeins in the triple-null barley line and showed significantly reduced levels ranging from <1% to 16% relative to wild-type (WT) cv Sloop for the minor γ-hordein class. SWATH-MS represents a valuable tool for quantitative proteomics based on its ability to generate reproducible data comparable with MRM-MS, but has the added benefits of allowing reinterrogation of data to improve analytical performance, ask new questions, and in this case perform quantification of trypsin-resistant proteins (C-hordeins) through analysis of their semi- or nontryptic fragments.
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Affiliation(s)
| | - Keren Byrne
- CSIRO Agriculture, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Malcolm Blundell
- CSIRO Agriculture, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | | | - Catherine S Lane
- SCIEX, Phoenix House, Lakeside Drive, Centre Park, Warrington, WA1 1RX, U.K
| | - Gregory J Tanner
- CSIRO Agriculture, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Crispin A Howitt
- CSIRO Agriculture, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
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Colgrave ML, Byrne K, Blundell M, Howitt CA. Identification of barley-specific peptide markers that persist in processed foods and are capable of detecting barley contamination by LC-MS/MS. J Proteomics 2016; 147:169-176. [PMID: 27068799 DOI: 10.1016/j.jprot.2016.03.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 02/26/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
Abstract
UNLABELLED Consumers, especially those with allergies and/or intolerances, should have confidence in two critical areas of food safety: foods should be correctly labelled and free from contamination. To this end, global proteomic analysis employing LC-MS/MS of gluten-enriched extracts derived from 12 barley cultivars was undertaken, providing a foundation for the development of MS-based quantitative methodologies that would enable the detection of barley contamination in foods. Subsequently, a number of candidate barley-specific peptide markers were evaluated by multiple-reaction monitoring MS. From an initial panel of 26, 9 peptide markers were unique to barley, yet present in a wide range of barley varieties. The analytical method was then used to examine a range of breakfast cereals and was able to detect barley in a barley-based breakfast cereal and a muesli, but additionally allowed detection of contamination of cereals that were comprised of ancient grains and in commercially-sourced flours, including amaranth, chia, buckwheat, millet, rice, corn, oats, rye, spelt and green wheat (0.01-0.08%). LC-MS/MS provides an alternative to ELISA approaches to monitor food safety and the identification of robust and sensitive cereal-specific peptide markers is the first step toward the adoption of this technology. SIGNIFICANCE Coeliac disease is a serious health issue affecting up to 70million people globally for which there is no cure. The only treatment is a life-long gluten-free diet. Contamination of foods can occur at many stages of food production from farm to fork. As such, accurate quantification and identification of the source (i.e. cereal) and type (e.g. gluten) of contamination is critical to the health and well-being of a subset of the population, including those affected by coeliac disease and non-coeliac gluten sensitivity.
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Affiliation(s)
| | - Keren Byrne
- CSIRO Agriculture, 306 Carmody Rd., St. Lucia, QLD 4067, Australia
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Colgrave ML, Goswami H, Byrne K, Blundell M, Howitt CA, Tanner GJ. Proteomic Profiling of 16 Cereal Grains and the Application of Targeted Proteomics To Detect Wheat Contamination. J Proteome Res 2015; 14:2659-68. [DOI: 10.1021/acs.jproteome.5b00187] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michelle L. Colgrave
- CSIRO Agriculture Flagship, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Hareshwar Goswami
- CSIRO Agriculture Flagship, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture Flagship, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Malcolm Blundell
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Crispin A. Howitt
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Gregory J. Tanner
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
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Fernandes C, Shik A, Byrne K, Lynall D, Blumin M, Saveliev I, Ruda HE. Axial p-n-junctions in nanowires. Nanotechnology 2015; 26:085204. [PMID: 25656461 DOI: 10.1088/0957-4484/26/8/085204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The charge distribution and potential profile of p-n-junctions in thin semiconductor nanowires (NWs) were analyzed. The characteristics of screening in one-dimensional systems result in a specific profile with large electric field at the boundary between the n- and p- regions, and long tails with a logarithmic drop in the potential and charge density. As a result of these tails, the junction properties depend sensitively on the geometry of external contacts and its capacity has an anomalously large value and frequency dispersion. In the presence of an external voltage, electrons and holes in the NWs can not be described by constant quasi-Fermi levels, due to small values of the average electric field, mobility, and lifetime of carriers. Thus, instead of the classical Sah-Noice-Shockley theory, the junction current-voltage characteristic was described by an alternative theory suitable for fast generation-recombination and slow diffusion-drift processes. For the non-uniform electric field in the junction, this theory predicts the forward branch of the characteristic to have a non-ideality factor η several times larger than the values 1 < η < 2 from classical theory. Such values of η have been experimentally observed by a number of researchers, as well as in the present work.
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Affiliation(s)
- C Fernandes
- Centre for Advanced Nanotechnology, University of Toronto, Toronto M5S 3E4, Canada
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Whan A, Dielen AS, Mieog J, Bowerman AF, Robinson HM, Byrne K, Colgrave M, Larkin PJ, Howitt CA, Morell MK, Ral JP. Engineering α-amylase levels in wheat grain suggests a highly sophisticated level of carbohydrate regulation during development. J Exp Bot 2014; 65:5443-57. [PMID: 25053646 PMCID: PMC4157717 DOI: 10.1093/jxb/eru299] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 05/20/2023]
Abstract
Wheat starch degradation requires the synergistic action of different amylolytic enzymes. Our spatio-temporal study of wheat α-amylases throughout grain development shows that AMY3 is the most abundant isoform compared with the other known α-amylases. Endosperm-specific over-expression of AMY3 resulted in an increase of total α-amylase activity in harvested grains. Unexpectedly, increased activity did not have a significant impact on starch content or composition but led to an increase of soluble carbohydrate (mainly sucrose) in dry grain. In AMY3 overexpression lines (A3OE), germination was slightly delayed and triacylglycerol (TAG) content was increased in the endosperm of mature grain. Despite increased AMY3 transcript and protein content throughout grain development, alterations of α-amylase activity and starch granule degradation were not detected until grain maturation, suggesting a post-translational inhibition of α-amylase activity in the endosperm during the starch filling period. These findings show unexpected effects of a high level of α-amylase on grain development and composition, notably in carbon partitioning and TAG accumulation, and suggest the presence of a hitherto unknown regulatory pathway during grain filling.
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Affiliation(s)
- Alex Whan
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Anne-Sophie Dielen
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jos Mieog
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Andrew F Bowerman
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Hannah M Robinson
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Keren Byrne
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. CSIRO Animal, Food and Health Sciences, St Lucia, Queensland, Australia
| | - Michelle Colgrave
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. CSIRO Animal, Food and Health Sciences, St Lucia, Queensland, Australia
| | - Philip J Larkin
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia. CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601 Australia
| | - Crispin A Howitt
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Matthew K Morell
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia
| | - Jean-Philippe Ral
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601 Australia.
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Li J, Greenwood PL, Cockett NE, Hadfield TS, Vuocolo T, Byrne K, White JD, Tellam RL, Schirra HJ. Impacts of the Callipyge mutation on ovine plasma metabolites and muscle fibre type. PLoS One 2014; 9:e99726. [PMID: 24937646 PMCID: PMC4061035 DOI: 10.1371/journal.pone.0099726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/17/2014] [Indexed: 12/02/2022] Open
Abstract
The ovine Callipyge mutation causes postnatal muscle hypertrophy localized to the pelvic limbs and torso, as well as body leanness. The mechanism underpinning enhanced muscle mass is unclear, as is the systemic impact of the mutation. Using muscle fibre typing immunohistochemistry, we confirmed muscle specific effects and demonstrated that affected muscles had greater prevalence and hypertrophy of type 2X fast twitch glycolytic fibres and decreased representation of types 1, 2C, 2A and/or 2AX fibres. To investigate potential systemic effects of the mutation, proton NMR spectra of plasma taken from lambs at 8 and 12 weeks of age were measured. Multivariate statistical analysis of plasma metabolite profiles demonstrated effects of development and genotype but not gender. Plasma from Callipyge lambs at 12 weeks of age, but not 8 weeks, was characterized by a metabolic profile consistent with contributions from the affected hypertrophic fast twitch glycolytic muscle fibres. Microarray analysis of the perirenal adipose tissue depot did not reveal a transcriptional effect of the mutation in this tissue. We conclude that there is an indirect systemic effect of the Callipyge mutation in skeletal muscle in the form of changes of blood metabolites, which may contribute to secondary phenotypes such as body leanness.
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Affiliation(s)
- Juan Li
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
| | - Paul L. Greenwood
- CSIRO Animal, Food and Health Sciences, FD McMaster Laboratory, Armidale, Australia
- New South Wales Department of Primary Industries, Beef Industry Centre of Excellence, University of New England, Armidale, Australia
| | - Noelle E. Cockett
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Tracy S. Hadfield
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Tony Vuocolo
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
| | - Keren Byrne
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
| | - Jason D. White
- The University of Melbourne, School of Veterinary Science, Parkville, Australia
| | - Ross L. Tellam
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
- * E-mail: (RLT); (HJS)
| | - Horst Joachim Schirra
- The University of Queensland, Centre for Advanced Imaging, Brisbane, Australia
- * E-mail: (RLT); (HJS)
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Byrne K, McWilliam S, Vuocolo T, Gondro C, Cockett NE, Tellam RL. Genomic architecture of histone 3 lysine 27 trimethylation during late ovine skeletal muscle development. Anim Genet 2014; 45:427-38. [PMID: 24673416 PMCID: PMC4286725 DOI: 10.1111/age.12145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2014] [Indexed: 12/21/2022]
Abstract
The ruminant developmental transition from late foetus to lamb is associated with marked changes in skeletal muscle structure and function that reflect programming for new physiological demands following birth. To determine whether epigenetic changes are involved in this transition, we investigated the genomic architecture of the chromatin modification, histone 3 lysine 27 trimethylation (H3K27me3), which typically regulates early life developmental processes; however, its role in later life processes is unclear. Chromatin immunoprecipitation coupled with next‐generation sequencing was used to map H3K27me3 nucleosomes in ovine longissimus lumborum skeletal muscle at 100 days of gestation and 12 weeks post‐partum. In both states, H3K27me3 modification was associated with genes, transcription start sites and CpG islands and with transcriptional silencing. The H3K27me3 peaks consisted of two major categories, promoter specific and regional, with the latter the dominant feature. Genes encoding homeobox transcription factors regulating early life development and genes involved in neural functions, particularly gated ion channels, were strongly modified by H3K27me3. Gene promoters differentially modified by H3K27me3 in the foetus and lamb were enriched for gated ion channels, which may reflect changes in neuromuscular function. However, most modified genes showed no changes, indicating that H3K27me3 does not have a large role in late muscle maturation. Notably, promyogenic transcription factors were strongly modified with H3K27me3 but showed no differences between the late gestation foetus and lamb, likely reflecting their lack of involvement in the myofibre fusion process occurring in this transition. H3K27me3 is a major architectural feature of the epigenetic landscape of ruminant skeletal muscle, and it comments on gene transcription and gene function in the context of late skeletal muscle development.
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Affiliation(s)
- K Byrne
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
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Byrne K, Leahy T, McCulloch R, Colgrave ML, Holland MK. Comprehensive mapping of the bull sperm surface proteome. Proteomics 2012; 12:3559-79. [DOI: 10.1002/pmic.201200133] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 07/23/2012] [Accepted: 09/10/2012] [Indexed: 12/27/2022]
Affiliation(s)
| | | | - Russell McCulloch
- CSIRO Food Futures National Research Flagship; Division of Livestock Industries; Queensland Biosciences Precinct; St. Lucia; Queensland; Australia
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Sun W, Hudson NJ, Reverter A, Waardenberg AJ, Tellam RL, Vuocolo T, Byrne K, Dalrymple BP. An Always Correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an "equivalent" bovine landscape. BMC Res Notes 2012; 5:632. [PMID: 23148653 PMCID: PMC3543716 DOI: 10.1186/1756-0500-5-632] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/07/2012] [Indexed: 11/21/2022] Open
Abstract
Background We have recently described a method for the construction of an informative gene expression correlation landscape for a single tissue, longissimus muscle (LM) of cattle, using a small number (less than a hundred) of diverse samples. Does this approach facilitate interspecies comparison of networks? Findings Using gene expression datasets from LM samples from a single postnatal time point for high and low muscling sheep, and from a developmental time course (prenatal to postnatal) for normal sheep and sheep exhibiting the Callipyge muscling phenotype gene expression correlations were calculated across subsets of the data comparable to the bovine analysis. An “Always Correlated” gene expression landscape was constructed by integrating the correlations from the subsets of data and was compared to the equivalent landscape for bovine LM muscle. Whilst at the high level apparently equivalent modules were identified in the two species, at the detailed level overlap between genes in the equivalent modules was limited and generally not significant. Indeed, only 395 genes and 18 edges were in common between the two landscapes. Conclusions Since it is unlikely that the equivalent muscles of two closely related species are as different as this analysis suggests, within tissue gene expression correlations appear to be very sensitive to the samples chosen for their construction, compounded by the different platforms used. Thus users need to be very cautious in interpretation of the differences. In future experiments, attention will be required to ensure equivalent experimental designs and use cross-species gene expression platform to enable the identification of true differences between different species.
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Affiliation(s)
- Wei Sun
- Animal Science and Technology College, Yangzhou University, Yangzhou 225009, China
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Siva S, Byrne K, Seel M, Bressel M, Jacobs D, Callahan J, Laing J, MacManus M, Hicks R. FDG-PET Scanning has a High Impact on the Management of Patients With Merkel Cell Carcinoma. Int J Radiat Oncol Biol Phys 2012. [DOI: 10.1016/j.ijrobp.2012.07.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ringer RV, Hansen BC, Byrne K, Larson AM, Zuercher J, Loschky LC. Amplitude Spectrum Slope is More Important than Orientation in Rapid Scene Categorization. J Vis 2012. [DOI: 10.1167/12.9.844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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44
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Craven C, Byrne K, Sims-Gould J, Martin-Matthews A. Types and patterns of safety concerns in home care: staff perspectives. Int J Qual Health Care 2012; 24:525-31. [DOI: 10.1093/intqhc/mzs047] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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45
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Ball SL, Panter SG, Redley M, Proctor CA, Byrne K, Clare ICH, Holland AJ. The extent and nature of need for mealtime support among adults with intellectual disabilities. J Intellect Disabil Res 2012; 56:382-401. [PMID: 21988217 DOI: 10.1111/j.1365-2788.2011.01488.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND For many adults with an intellectual disability (ID), mealtimes carry significant health risks. While research and allied clinical guidance has focused mainly on dysphagia, adults with a range of physical and behavioural difficulties require mealtime support to ensure safety and adequate nutrition. The extent of need for and nature of such support within the wider ID population has yet to be reported. METHODS In this study, we have estimated the prevalence of need for mealtime support among people with ID in the UK, using a population of 2230 adults known to specialist ID services (in Cambridgeshire, UK, total population 586,900). In a sample (n = 69, aged 19 to 79 years, with mild to profound ID), we characterised the support provided, using a structured proforma to consult support workers and carers providing mealtime support, and health and social care records. RESULTS Mealtime support was found to be required by a significant minority of people with ID for complex and varied reasons. Prevalence of need for such support was estimated at 15% of adults known to specialist ID services or 56 per 100,000 total population. Within a sample, support required was found to vary widely in nature (from texture modification or environmental adaptation to enteral feeding) and in overall level (from minimal to full support, dependent on functional skills). Needs had increased over time in almost half (n = 34, 49.3%). Reasons for support included difficulties getting food into the body (n = 56, 82.2%), risky eating and drinking behaviours (n = 31, 44.9%) and slow eating or food refusal (n = 30, 43.5%). These proportions translate into crude estimates of the prevalence of these difficulties within the known ID population of 11.9%, 6.6% and 6.4% respectively. Within the sample of those requiring mealtime support, need for support was reported to be contributed to by the presence of additional disability or illness (e.g. visual impairment, poor dentition and dementia; n = 45, 65.2%) and by psychological or behavioural issues (e.g. challenging behaviour, emotional disturbance; n = 36, 52.2%). CONCLUSIONS These findings not only highlight the need for a multidisciplinary approach to mealtime interventions (paying particular attention to psychological and environmental as well as physical issues), but also signal the daily difficulties faced by carers and paid support workers providing such support and illustrate their potentially crucial role in managing the serious health risks associated with eating and drinking difficulties in this population.
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Affiliation(s)
- S L Ball
- Cambridge Intellectual & Developmental Disabilities Research Group, Department of Psychiatry, University of Cambridge, Cambridge, UK.
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Kogelman LJA, Byrne K, Vuocolo T, Watson-Haigh NS, Kadarmideen HN, Kijas JW, Oddy HV, Gardner GE, Gondro C, Tellam RL. Genetic architecture of gene expression in ovine skeletal muscle. BMC Genomics 2011; 12:607. [PMID: 22171619 PMCID: PMC3265547 DOI: 10.1186/1471-2164-12-607] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 12/15/2011] [Indexed: 01/15/2023] Open
Abstract
Background In livestock populations the genetic contribution to muscling is intensively monitored in the progeny of industry sires and used as a tool in selective breeding programs. The genes and pathways conferring this genetic merit are largely undefined. Genetic variation within a population has potential, amongst other mechanisms, to alter gene expression via cis- or trans-acting mechanisms in a manner that impacts the functional activities of specific pathways that contribute to muscling traits. By integrating sire-based genetic merit information for a muscling trait with progeny-based gene expression data we directly tested the hypothesis that there is genetic structure in the gene expression program in ovine skeletal muscle. Results The genetic performance of six sires for a well defined muscling trait, longissimus lumborum muscle depth, was measured using extensive progeny testing and expressed as an Estimated Breeding Value by comparison with contemporary sires. Microarray gene expression data were obtained for longissimus lumborum samples taken from forty progeny of the six sires (4-8 progeny/sire). Initial unsupervised hierarchical clustering analysis revealed strong genetic architecture to the gene expression data, which also discriminated the sire-based Estimated Breeding Value for the trait. An integrated systems biology approach was then used to identify the major functional pathways contributing to the genetics of enhanced muscling by using both Estimated Breeding Value weighted gene co-expression network analysis and a differential gene co-expression network analysis. The modules of genes revealed by these analyses were enriched for a number of functional terms summarised as muscle sarcomere organisation and development, protein catabolism (proteosome), RNA processing, mitochondrial function and transcriptional regulation. Conclusions This study has revealed strong genetic structure in the gene expression program within ovine longissimus lumborum muscle. The balance between muscle protein synthesis, at the levels of both transcription and translation control, and protein catabolism mediated by regulated proteolysis is likely to be the primary determinant of the genetic merit for the muscling trait in this sheep population. There is also evidence that high genetic merit for muscling is associated with a fibre type shift toward fast glycolytic fibres. This study provides insight into mechanisms, presumably subject to strong artificial selection, that underpin enhanced muscling in sheep populations.
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Affiliation(s)
- Lisette J A Kogelman
- CSIRO Livestock Industries, ATSIP, PMB CSIRO Aitkenvale, Townsville, QLD 4814, Australia
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Byrne K, Vuocolo T, Gondro C, White JD, Cockett NE, Hadfield T, Bidwell CA, Waddell JN, Tellam RL. A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development. BMC Genomics 2010; 11:378. [PMID: 20546621 PMCID: PMC2894804 DOI: 10.1186/1471-2164-11-378] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 06/15/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The developmental transition between the late fetus and a newborn animal is associated with profound changes in skeletal muscle function as it adapts to the new physiological demands of locomotion and postural support against gravity. The mechanisms underpinning this adaption process are unclear but are likely to be initiated by changes in hormone levels. We tested the hypothesis that this developmental transition is associated with large coordinated changes in the transcription of skeletal muscle genes. RESULTS Using an ovine model, transcriptional profiling was performed on Longissimus dorsi skeletal muscle taken at three fetal developmental time points (80, 100 and 120 d of fetal development) and two postnatal time points, one approximately 3 days postpartum and a second at 3 months of age. The developmental time course was dominated by large changes in expression of 2,471 genes during the interval between late fetal development (120 d fetal development) and 1-3 days postpartum. Analysis of the functions of genes that were uniquely up-regulated in this interval showed strong enrichment for oxidative metabolism and the tricarboxylic acid cycle indicating enhanced mitochondrial activity. Histological examination of tissues from these developmental time points directly confirmed a marked increase in mitochondrial activity between the late fetal and early postnatal samples. The promoters of genes that were up-regulated during this fetal to neonatal transition were enriched for estrogen receptor 1 and estrogen related receptor alpha cis-regulatory motifs. The genes down-regulated during this interval highlighted de-emphasis of an array of functions including Wnt signaling, cell adhesion and differentiation. There were also changes in gene expression prior to this late fetal--postnatal transition and between the two postnatal time points. The former genes were enriched for functions involving the extracellular matrix and immune response while the latter principally involved functions associated with transcriptional regulation of metabolic processes. CONCLUSIONS It is concluded that during late skeletal muscle development there are substantial and coordinated changes in the transcription of a large number of genes many of which are probably triggered by increased estrogen levels. These changes probably underpin the adaption of muscle to new physiological demands in the postnatal environment.
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Affiliation(s)
- Keren Byrne
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, 4067 Queensland, Australia
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Borradaile K, Ford R, O'Neal JM, Byrne K. Analysis of the cause of discordance between two radiologists on the assessment of radiographic response and progression for subjects enrolled in breast cancer clinical trials employing blinded independent central review. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.6044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL. The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PLoS One 2010; 5:e8638. [PMID: 20072617 PMCID: PMC2799525 DOI: 10.1371/journal.pone.0008638] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 12/15/2009] [Indexed: 01/22/2023] Open
Abstract
Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1) is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3), PEG11 (RTL1), PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as) contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural or functional domains of the protein suggesting co-evolution of the sense and antisense genes.
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Affiliation(s)
- Keren Byrne
- CSIRO Livestock Industries, St Lucia, Queensland, Australia
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