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Book ; Conference proceedings: Special issue: Soil change matters

MacEwan, Richard

[the International Workshop 'Soil Change Matters', in Bendigo, Victoria 24 - 27 March 2014 ... ten of the presentations]

(Soil research ; 53,6)

2015

Title variant	Soil change matters
Event/congress	International Workshop Soil Change Matters (2014, Bendigo)
Author's details	guest ed.: Richard MacEwan
Series title	Soil research ; 53,6
Collection
Language	English
Size	I, S. [577] - 715 : Ill., graph. Darst., Kt.
Publisher	CSIRO
Publishing place	Collingwood, Victoria
Publishing country	Australia
Document type	Book ; Conference proceedings
HBZ-ID	HT018809628
Database	Catalogue ZB MED Nutrition, Environment, Agriculture

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Shelf mark	Loan status	Location
Z 1994 (53,6)	available for loan (reading room)	Freihandmagazin (U1)

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Article ; Online: Interobserver variation in clinical target volume (CTV) delineation for stereotactic radiotherapy to non-spinal bone metastases in prostate cancer: CT, MRI and PET/CT fusion.

Chapman, Ewan Richard / Nicholls, Luke / Suh, Yae-Eun / Khoo, Vincent / Levine, Daniel / Ap Dafydd, Derfel / Van As, Nicholas

Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology

2023 Volume 180, Page(s) 109461

Abstract: Background and purpose: The use of SBRT for the treatment of oligometastatic prostate cancer is increasing rapidly. While consensus guidelines are available for non-spinal bone metastases practice continues to vary widely. The aim of this study is to ... ...

Abstract	Background and purpose: The use of SBRT for the treatment of oligometastatic prostate cancer is increasing rapidly. While consensus guidelines are available for non-spinal bone metastases practice continues to vary widely. The aim of this study is to look at inter-observer variability in the contouring of prostate cancer non-spinal bone metastases with different imaging modalities. Materials and methods: 15 metastases from 13 patients treated at our centre were selected. 4 observers independently contoured clinical target volumes (CTV) on planning CT alone, planning CT with MRI fusion, planning CT with PET-CT fusion and planning CT with both MRI and PET-CT fusion combined. The mean inter-observer agreement on each modality was compared by measuring the delineated volume, generalized conformity index (CIgen), and the distance of the centre of mass (dCOM), calculated per metastasis and imaging modality. Results: Mean CTV volume delineated on planning CT with MRI and PET-CT fusion combined was significantly larger compared to other imaging modalities (p = 0.0001). CIgen showed marked variation between modalities with the highest agreement between planning CT + PET-CT (mean CIgen 0.55, range 0.32-0.73) and planning CT + MRI + PET-CT (mean CIgen 0.59, range 0.34-0.73). dCOM showed small variations between imaging modalities but a significantly shorter distance found on planning CT + PET-CT when compared with planning CT + PET-CT + MRI combined (p = 0.03). Conclusions: Highest consistency in CTV delineation between observers was seen with planning CT + PET-CT and planning CT + PET-CT + MRI combined.
MeSH term(s)	Bone Neoplasms/diagnostic imaging ; Bone Neoplasms/radiotherapy ; Magnetic Resonance Imaging ; Neoplasm Metastasis/diagnostic imaging ; Neoplasm Metastasis/radiotherapy ; Observer Variation ; Positron Emission Tomography Computed Tomography ; Prostatic Neoplasms/pathology ; Prostatic Neoplasms/surgery ; Radiosurgery ; Radiotherapy Planning, Computer-Assisted ; Tomography, X-Ray Computed ; Humans ; Male
Language	English
Publishing date	2023-01-09
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605646-5
ISSN	1879-0887 ; 0167-8140
ISSN (online)	1879-0887
ISSN	0167-8140
DOI	10.1016/j.radonc.2022.109461
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Article ; Online: The ubiquitin-proteasome system: central modifier of plant signalling.

Sadanandom, Ari / Bailey, Mark / Ewan, Richard / Lee, Jack / Nelis, Stuart

The New phytologist

2012 Volume 196, Issue 1, Page(s) 13–28

Abstract: Ubiquitin is well established as a major modifier of signalling in eukaryotes. However, the extent to which plants rely on ubiquitin for regulating their lifecycle is only recently becoming apparent. This is underlined by the over-representation of genes ...

Abstract	Ubiquitin is well established as a major modifier of signalling in eukaryotes. However, the extent to which plants rely on ubiquitin for regulating their lifecycle is only recently becoming apparent. This is underlined by the over-representation of genes encoding ubiquitin-metabolizing enzymes in Arabidopsis when compared with other model eukaryotes. The main characteristic of ubiquitination is the conjugation of ubiquitin onto lysine residues of acceptor proteins. In most cases the targeted protein is rapidly degraded by the 26S proteasome, the major proteolysis machinery in eukaryotic cells. The ubiquitin-proteasome system is responsible for removing most abnormal peptides and short-lived cellular regulators, which, in turn, control many processes. This allows cells to respond rapidly to intracellular signals and changing environmental conditions. This review maps out the roles of the components of the ubiquitin-proteasome system with emphasis on areas where future research is urgently needed. We provide a flavour of the diverse aspects of plant lifecycle where the ubiquitin-proteasome system is implicated. We aim to highlight common themes using key examples that reiterate the importance of the ubiquitin-proteasome system to plants. The future challenge in plant biology is to define the targets for ubiquitination, their interactors and their molecular function within the regulatory context.
MeSH term(s)	Plant Development ; Plants/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; Signal Transduction ; Ubiquitin/metabolism
Chemical Substances	Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2012-08-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/j.1469-8137.2012.04266.x
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Article ; Online: Ecosystem services in agricultural landscapes: a spatially explicit approach to support sustainable soil management.

Forouzangohar, Mohsen / Crossman, Neville D / MacEwan, Richard J / Wallace, D Dugal / Bennett, Lauren T

TheScientificWorldJournal

2014 Volume 2014, Page(s) 483298

Abstract: Soil degradation has been associated with a lack of adequate consideration of soil ecosystem services. We demonstrate a broadly applicable method for mapping changes in the supply of two priority soil ecosystem services to support decisions about ... ...

Abstract	Soil degradation has been associated with a lack of adequate consideration of soil ecosystem services. We demonstrate a broadly applicable method for mapping changes in the supply of two priority soil ecosystem services to support decisions about sustainable land-use configurations. We used a landscape-scale study area of 302 km(2) in northern Victoria, south-eastern Australia, which has been cleared for intensive agriculture. Indicators representing priority soil services (soil carbon sequestration and soil water storage) were quantified and mapped under both a current and a future 25-year land-use scenario (the latter including a greater diversity of land uses and increased perennial crops and irrigation). We combined diverse methods, including soil analysis using mid-infrared spectroscopy, soil biophysical modelling, and geostatistical interpolation. Our analysis suggests that the future land-use scenario would increase the landscape-level supply of both services over 25 years. Soil organic carbon content and water storage to 30 cm depth were predicted to increase by about 11% and 22%, respectively. Our service maps revealed the locations of hotspots, as well as potential trade-offs in service supply under new land-use configurations. The study highlights the need to consider diverse land uses in sustainable management of soil services in changing agricultural landscapes.
MeSH term(s)	Conservation of Natural Resources ; Ecosystem ; Soil
Chemical Substances	Soil
Language	English
Publishing date	2014-01-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075968-X
ISSN	1537-744X ; 1537-744X
ISSN (online)	1537-744X
ISSN	1537-744X
DOI	10.1155/2014/483298
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Article ; Online: Ubiquitination of the Dishevelled DIX domain blocks its head-to-tail polymerization.

Madrzak, Julia / Fiedler, Marc / Johnson, Christopher M / Ewan, Richard / Knebel, Axel / Bienz, Mariann / Chin, Jason W

Nature communications

2015 Volume 6, Page(s) 6718

Abstract: Dishevelled relays Wnt signals from the plasma membrane to different cytoplasmic effectors. Its signalling activity depends on its DIX domain, which undergoes head-to-tail polymerization to assemble signalosomes. The DIX domain is ubiquitinated in vivo ... ...

Abstract	Dishevelled relays Wnt signals from the plasma membrane to different cytoplasmic effectors. Its signalling activity depends on its DIX domain, which undergoes head-to-tail polymerization to assemble signalosomes. The DIX domain is ubiquitinated in vivo at multiple lysines, which can be antagonized by various deubiquitinases (DUBs) including the CYLD tumour suppressor that attenuates Wnt signalling. Here, we generate milligram quantities of pure human Dvl2 DIX domain mono-ubiquitinated at two lysines (K54 and K58) by genetically encoded orthogonal protection with activated ligation (GOPAL), to investigate their effect on DIX polymerization. We show that the ubiquitination of DIX at K54 blocks its polymerization in solution, whereas DIX58-Ub remains oligomerization-competent. DUB profiling identified 28 DUBs that cleave DIX-ubiquitin conjugates, half of which prefer, or are specific for, DIX54-Ub, including Cezanne and CYLD. These DUBs thus have the potential to promote Dvl polymerization and signalosome formation, rather than antagonize it as previously thought for CYLD.
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; Amino Acid Motifs ; Chromatography, Liquid ; Dishevelled Proteins ; Escherichia coli ; Humans ; Lysine/metabolism ; Mass Spectrometry ; Organisms, Genetically Modified ; Phosphoproteins/metabolism ; Polymerization ; Spectrometry, Mass, Electrospray Ionization ; Tandem Mass Spectrometry ; Tumor Suppressor Proteins ; Ubiquitination ; Wnt Signaling Pathway
Chemical Substances	Adaptor Proteins, Signal Transducing ; DVL2 protein, human ; Dishevelled Proteins ; Phosphoproteins ; Tumor Suppressor Proteins ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2015-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/ncomms7718
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Article ; Online: E3 ubiquitin ligases and plant innate immunity.

Craig, Adam / Ewan, Richard / Mesmar, Joelle / Gudipati, Venugopal / Sadanandom, Ari

Journal of experimental botany

2009 Volume 60, Issue 4, Page(s) 1123–1132

Abstract: In yeast and in animals the ubiquitin-proteasome system (UPS) is responsible for removing or modifying most abnormal peptides and also short-lived cellular regulators. The UPS therefore influences many processes such as the cell cycle, signal ... ...

Abstract	In yeast and in animals the ubiquitin-proteasome system (UPS) is responsible for removing or modifying most abnormal peptides and also short-lived cellular regulators. The UPS therefore influences many processes such as the cell cycle, signal transduction, transcription, and stress responses including defence. In recent years, similar regulatory roles have been identified in plants. In Arabidopsis, mutations in the ubiquitin-proteasome pathway block development, circadian rhythms, photomorphogenesis, floral homeosis, hormone responses, senescence, and pathogen invasion. Plants have evolved an armoury of defence mechanisms that allow them to counter infection. These encompass both basal responses, triggered by recognition of conserved pathogen-associated molecular patterns, and pathogen-specific responses, mediated via pathogen- and plant-specific gene-for-gene recognition events. The role of E3 ubiquitin ligases in mediating plant defence signalling is reviewed and examples where pathogens impinge on the host's ubiquitination machinery acting as molecular mimics to undermine defence are also highlighted.
MeSH term(s)	Immunity, Innate ; Plants/enzymology ; Plants/immunology ; Receptors, Pattern Recognition/metabolism ; Signal Transduction ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
Chemical Substances	Receptors, Pattern Recognition ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2009-03-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erp059
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Article: E3 ubiquitin ligases and plant innate immunity

Craig, Adam / Ewan, Richard / Mesmar, Joelle / Gudipati, Venugopal / Sadanandom, Ari

Journal of experimental botany. 2009 Mar., v. 60, no. 4

2009

Abstract	In yeast and in animals the ubiquitin-proteasome system (UPS) is responsible for removing or modifying most abnormal peptides and also short-lived cellular regulators. The UPS therefore influences many processes such as the cell cycle, signal transduction, transcription, and stress responses including defence. In recent years, similar regulatory roles have been identified in plants. In Arabidopsis, mutations in the ubiquitin-proteasome pathway block development, circadian rhythms, photomorphogenesis, floral homeosis, hormone responses, senescence, and pathogen invasion. Plants have evolved an armoury of defence mechanisms that allow them to counter infection. These encompass both basal responses, triggered by recognition of conserved pathogen-associated molecular patterns, and pathogen-specific responses, mediated via pathogen- and plant-specific gene-for-gene recognition events. The role of E3 ubiquitin ligases in mediating plant defence signalling is reviewed and examples where pathogens impinge on the host's ubiquitination machinery acting as molecular mimics to undermine defence are also highlighted.
Keywords	Arabidopsis ; animals ; cell cycle ; circadian rhythm ; defense mechanisms ; hormones ; hosts ; ligases ; mutation ; pathogens ; peptides ; plants ; senescence ; signal transduction ; stress response ; ubiquitin ; yeasts
Language	English
Dates of publication	2009-03
Size	p. 1123-1132.
Document type	Article
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
Database	NAL-Catalogue (AGRICOLA)

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Article: Deubiquitinating enzymes AtUBP12 and AtUBP13 and their tobacco homologue NtUBP12 are negative regulators of plant immunity

Ewan, Richard / Pangestuti, Ratih / Thornber, Sarah / Craig, Adam / Carr, Craig / O'Donnell, Liz / Zhang, Cunjn / Sadanandom, Ari

New phytologist. 2011 July, v. 191, no. 1

2011

Abstract: Signalling by ubiquitination is implicated in diverse aspects of the plant lifecycle, and enzymes of ubiquitin metabolism are overrepresented in the Arabidopsis genome compared with other model eukaryotes. Despite the importance of ubiquitination in ... ...

Abstract	• Signalling by ubiquitination is implicated in diverse aspects of the plant lifecycle, and enzymes of ubiquitin metabolism are overrepresented in the Arabidopsis genome compared with other model eukaryotes. Despite the importance of ubiquitination in the regulation of signalling, little is known about deubiquitinating enzymes, which reverse the process of ubiquitination. • Transgenic RNA interference-based cosuppression and the isolation of Atubp12/13 double mutants collectively provides the first report that AtUBP12 and AtUBP13 are functionally redundant and are required for immunity against virulent Pseudomonas syringae pv tomato in Arabidopsis. The Solanaceous AtUBP12 orthologue NtUBP12 was identified. Viral-induced gene silencing and transient gain-of-function assays were employed to establish that the NtUBP12 protein functions as a negative regulator of the Cf-9-triggered hypersensitive response. • Here, we demonstrate that NtUBP12 and AtUBP12 are bona fide deubiquitinating enzymes capable of cleaving lysine-48-linked ubiquitin chains. AtUBP12 and NtUBP12 are functionally interchangeable and their deubiquitinating activity is required to suppress plant cell death. • Overall, our data implicate AtUBP12- and NtUBP12-dependent deubiquitination in the stabilization of common substrates across Solanaceae and Brassicaceae which regulate disease resistance.
Keywords	Arabidopsis ; Pseudomonas syringae pv. tomato ; RNA ; Solanaceae ; cell death ; disease resistance ; enzymes ; eukaryotic cells ; gene silencing ; genome ; hypersensitive response ; immunity ; metabolism ; mutants ; tobacco
Language	English
Dates of publication	2011-07
Size	p. 92-106.
Publishing place	Blackwell Publishing Ltd
Document type	Article
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/j.1469-8137.2011.03672.x
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Article ; Online: Modelling aquatic exposure and effects of insecticides--application to south-eastern Australia.

Burgert, Sinje / Schäfer, Ralf B / Foit, Kaarina / Kattwinkel, Mira / Metzeling, Leon / MacEwan, Richard / Kefford, Ben J / Liess, Matthias

The Science of the total environment

2011 Volume 409, Issue 14, Page(s) 2807–2814

Abstract: Agricultural pesticides are widely used and can affect freshwater organisms. We applied a spatially explicit exposure model, validated for central Europe, to estimate exposure to insecticides through runoff for streams in south-eastern Australia. The ... ...

Abstract	Agricultural pesticides are widely used and can affect freshwater organisms. We applied a spatially explicit exposure model, validated for central Europe, to estimate exposure to insecticides through runoff for streams in south-eastern Australia. The model allows the identification of streams potentially affected by insecticide runoff located in 10×10 km grid cells. The computation of runoff relies on key environmental factors such as land use, soil texture, slope and precipitation. Additionally, the model predicted the ecological effect of insecticides on the macroinvertebrate community. We predicted insecticide surface runoff that results in a moderate to poor ecological quality for streams in half of the grid cells containing agricultural land. These results are in good accordance with the results obtained by estimating pesticide stress with a biotic index (SPEAR(pesticides)) based on macroinvertebrate monitoring data. We conclude that the exposure and effect model can act as an effective and cost-saving tool to identify high risk areas of insecticide exposure and to support stream management.
MeSH term(s)	Animals ; Aquatic Organisms ; Australia ; Environmental Exposure/analysis ; Environmental Exposure/statistics & numerical data ; Geographic Information Systems ; Insecticides/analysis ; Models, Biological ; Models, Chemical ; Risk Assessment ; Rivers/chemistry ; Water Pollutants, Chemical/analysis ; Water Pollution, Chemical/statistics & numerical data
Chemical Substances	Insecticides ; Water Pollutants, Chemical
Language	English
Publishing date	2011-06-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2011.02.042
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Article ; Online: OEP61 is a chaperone receptor at the plastid outer envelope.

von Loeffelholz, Ottilie / Kriechbaumer, Verena / Ewan, Richard A / Jonczyk, Rafal / Lehmann, Susann / Young, Jason C / Abell, Ben M

The Biochemical journal

2011 Volume 438, Issue 1, Page(s) 143–153

Abstract: Chloroplast precursor proteins encoded in the nucleus depend on their targeting sequences for delivery to chloroplasts. There exist different routes to the chloroplast outer envelope, but a common theme is the involvement of molecular chaperones. Hsp90 ( ... ...

Abstract	Chloroplast precursor proteins encoded in the nucleus depend on their targeting sequences for delivery to chloroplasts. There exist different routes to the chloroplast outer envelope, but a common theme is the involvement of molecular chaperones. Hsp90 (heat-shock protein 90) delivers precursors via its receptor Toc64, which transfers precursors to the core translocase in the outer envelope. In the present paper, we identify an uncharacterized protein in Arabidopsis thaliana OEP61 which shares common features with Toc64, and potentially provides an alternative route to the chloroplasts. Sequence analysis indicates that OEP61 possesses a clamp-type TPR (tetratricopeptide repeat) domain capable of binding molecular chaperones, and a C-terminal TMD (transmembrane domain). Phylogenetic comparisons show sequence similarities between the TPR domain of OEP61 and those of the Toc64 family. Expression of mRNA and protein was detected in all plant tissues, and localization at the chloroplast outer envelope was demonstrated by a combination of microscopy and in vitro import assays. Binding assays show that OEP61 interacts specifically with Hsp70 (heat-shock protein 70) via its TPR clamp domain. Furthermore, OEP61 selectively recognizes chloroplast precursors via their targeting sequences, and a soluble form of OEP61 inhibits chloroplast targeting. We therefore propose that OEP61 is a novel chaperone receptor at the chloroplast outer envelope, mediating Hsp70-dependent protein targeting to chloroplasts.
MeSH term(s)	Amino Acid Sequence ; Arabidopsis/genetics ; Arabidopsis/growth & development ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Blotting, Western ; Chloroplasts/metabolism ; DNA, Plant/genetics ; HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/metabolism ; Protein Binding ; Protein Biosynthesis ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Transcription, Genetic
Chemical Substances	Arabidopsis Proteins ; DNA, Plant ; HSP70 Heat-Shock Proteins ; Molecular Chaperones ; OEP61 protein, Arabidopsis ; RNA, Messenger ; RNA, Plant
Language	English
Publishing date	2011-05-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BJ20110448
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