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2. Comparing farmers and breeders rankings in varietal selection for low-input environments: A case study of rainfed rice in eastern India

Author

Courtois, B., Bartholome, B., Chaudhary, D., McLaren, G., Misra, C.H., Mandal, N.P., Pandey, S., Paris, T., Piggin, C., Prasad, K., Roy, A.T., Sahu, R.K., Sahu, V.N., Sarkarung, S., Sharma, S.K., Singh, A., Singh, H.N., Singh, O.N., Singh, N.K., Singh, R.K., Singh, R.K., Singh, S., Sinha, P.K., Sisodia, B.V.S., and Takhur, R.

Published
2001
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4. A bioassay for prosulfocarb, pyroxasulfone and trifluralin detection and quantification in soil and crop residue

Author

Khalil, Y., Siddique, K.H.M., Ward, P., Piggin, C., Bong, S-H, Nambiar, S., Trengove, R., Flower, K., Khalil, Y., Siddique, K.H.M., Ward, P., Piggin, C., Bong, S-H, Nambiar, S., Trengove, R., and Flower, K.

Abstract

Three experiments were conducted to develop a bioassay method for assessing the bioavailability of prosulfocarb, pyroxasulfone and trifluralin in both crop residue and soil. In preliminary experiments, Italian ryegrass (Lolium multiflorum Lam.), cucumber (Cucumis sativus L.) and beetroot (Beta vulgaris L.) were tested as bioassay plant species for the three pre-emergent herbicides. Four growth parameters (shoot length, root length, fresh weight and dry weight) were measured for all plant species. Shoot-length inhibition was identified as the most responsive to the herbicide application rates. Italian ryegrass was the most sensitive species to all tested herbicides, whereas beetroot and cucumber had lower and similar sensitivity to shoot inhibition for the three herbicides. The bioassay species performed similarly in wheat and canola residues collected a few days after harvest. In bioassay calibration experiments, dose–response curves were developed for prosulfocarb, pyroxasulfone and trifluralin in a sandy loam soil typical of the grain belt of Western Australia and with wheat residue. The developed bioassay uses ryegrass shoot inhibition for relatively low suspected concentrations of herbicide, and cucumber shoot inhibition for higher rates. The bioassay was validated by spraying the three herbicides separately onto wheat residue and soil and comparing the concentrations derived from chemical analysis with those from the bioassay. All of the linear correlations between concentrations derived from chemical analyses and the bioassays were highly significant. These results indicate that the bioassay calibration curves are suitable for estimating herbicide concentrations in crop residue collected soon after harvest and a sandy-loam soil, low in organic matter.

Published
2018

5. Andy's Algorithms: new automated digital image analysis pipelines for FIJI

Author

Law, AMK, Yin, JXM, Castillo, L, Young, AIJ, Piggin, C, Rogers, S, Caldon, CE, Burgess, A, Millar, EKA, O'Toole, SA, Gallego-Ortega, D, Ormandy, CJ, and Oakes, SR

Subjects
3,3'-Diaminobenzidine, Breast Neoplasms, Immunohistochemistry, Colony-Forming Units Assay, Automation, Benchmarking, Mice, Tissue Array Analysis, Image Processing, Computer-Assisted, Animals, Humans, Female, Algorithms, Software
Abstract

Quantification of cellular antigens and their interactions via antibody-based detection methods are widely used in scientific research. Accurate high-throughput quantitation of these assays using general image analysis software can be time consuming and challenging, particularly when attempted by users with limited image processing and analysis knowledge. To overcome this, we have designed Andy's Algorithms, a series of automated image analysis pipelines for FIJI, that permits rapid, accurate and reproducible batch-processing of 3,3'-diaminobenzidine (DAB) immunohistochemistry, proximity ligation assays (PLAs) and other common assays. Andy's Algorithms incorporates a step-by-step tutorial and optimization pipeline to make batch image analysis simple for the untrained user and adaptable across laboratories. Andy's algorithms provide a simpler, faster, standardized work flow compared to existing programs, while offering equivalent performance and additional features, in a free to use open-source application of FIJI. Andy's Algorithms are available at GitHub, publicly accessed at https://github.com/andlaw1841/Andy-s-Algorithm .

Published
2017

6. A mutation in the viral sensor 2’-5’-oligoadenylate synthetase 2 causes failure of lactation

Author

Oakes, SR, Gallego-Ortega, D, Stanford, PM, Junankar, S, Au, WWY, Kikhtyak, Z, von Korff, A, Sergio, CM, Law, AMK, Castillo, LE, Allerdice, SL, Young, AIJ, Piggin, C, Whittle, B, Bertram, E, Naylor, MJ, Roden, DL, Donovan, J, Korennykh, A, Goodnow, CC, O Bryan, MK, Ormandy, CJ, Oakes, SR, Gallego-Ortega, D, Stanford, PM, Junankar, S, Au, WWY, Kikhtyak, Z, von Korff, A, Sergio, CM, Law, AMK, Castillo, LE, Allerdice, SL, Young, AIJ, Piggin, C, Whittle, B, Bertram, E, Naylor, MJ, Roden, DL, Donovan, J, Korennykh, A, Goodnow, CC, O Bryan, MK, and Ormandy, CJ

Abstract

© 2017 Oakes et al. We identified a non-synonymous mutation in Oas2 (I405N), a sensor of viral double-stranded RNA, from an ENU-mutagenesis screen designed to discover new genes involved in mammary development. The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands, characterized by greatly reduced milk protein synthesis coupled with epithelial cell death, inhibition of proliferation and a robust interferon response. Expression of mutant but not wild type Oas2 in cultured HC-11 or T47D mammary cells recapitulated the phenotypic and transcriptional effects observed in the mouse. The mutation activates the OAS2 pathway, demonstrated by a 34-fold increase in RNase L activity, and its effects were dependent on expression of RNase L and IRF7, proximal and distal pathway members. This is the first report of a viral recognition pathway regulating lactation.

Published
2017

7. A mutation in the viral sensor 2 '-5 '-oligoadenylate synthetase 2 causes failure of lactation

Author

Wells, CA, Oakes, SR, Gallego-Ortega, D, Stanford, PM, Junankar, S, Au, WWY, Kikhtyak, Z, von Korff, A, Sergio, CM, Law, AMK, Castillo, LE, Allerdice, SL, Young, AIJ, Piggin, C, Whittle, B, Bertram, E, Naylor, MJ, Roden, DL, Donovan, J, Korennykh, A, Goodnow, CC, O'Bryan, MK, Ormandy, CJ, Wells, CA, Oakes, SR, Gallego-Ortega, D, Stanford, PM, Junankar, S, Au, WWY, Kikhtyak, Z, von Korff, A, Sergio, CM, Law, AMK, Castillo, LE, Allerdice, SL, Young, AIJ, Piggin, C, Whittle, B, Bertram, E, Naylor, MJ, Roden, DL, Donovan, J, Korennykh, A, Goodnow, CC, O'Bryan, MK, and Ormandy, CJ

Abstract

We identified a non-synonymous mutation in Oas2 (I405N), a sensor of viral double-stranded RNA, from an ENU-mutagenesis screen designed to discover new genes involved in mammary development. The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands, characterized by greatly reduced milk protein synthesis coupled with epithelial cell death, inhibition of proliferation and a robust interferon response. Expression of mutant but not wild type Oas2 in cultured HC-11 or T47D mammary cells recapitulated the phenotypic and transcriptional effects observed in the mouse. The mutation activates the OAS2 pathway, demonstrated by a 34-fold increase in RNase L activity, and its effects were dependent on expression of RNase L and IRF7, proximal and distal pathway members. This is the first report of a viral recognition pathway regulating lactation.

Published
2017

8. ELF5 Drives Lung Metastasis in Luminal Breast Cancer through Recruitment of Gr1+ CD11b+ Myeloid-Derived Suppressor Cells.

Author

Gallego-Ortega, D, Ledger, A, Roden, DL, Law, AMK, Magenau, A, Kikhtyak, Z, Cho, C, Allerdice, SL, Lee, HJ, Valdes-Mora, F, Herrmann, D, Salomon, R, Young, AIJ, Lee, BY, Sergio, CM, Kaplan, W, Piggin, C, Conway, JRW, Rabinovich, B, Millar, EKA, Oakes, SR, Chtanova, T, Swarbrick, A, Naylor, MJ, O'Toole, S, Green, AR, Timpson, P, Gee, JMW, Ellis, IO, Clark, SJ, Ormandy, CJ, Gallego-Ortega, D, Ledger, A, Roden, DL, Law, AMK, Magenau, A, Kikhtyak, Z, Cho, C, Allerdice, SL, Lee, HJ, Valdes-Mora, F, Herrmann, D, Salomon, R, Young, AIJ, Lee, BY, Sergio, CM, Kaplan, W, Piggin, C, Conway, JRW, Rabinovich, B, Millar, EKA, Oakes, SR, Chtanova, T, Swarbrick, A, Naylor, MJ, O'Toole, S, Green, AR, Timpson, P, Gee, JMW, Ellis, IO, Clark, SJ, and Ormandy, CJ

Abstract

During pregnancy, the ETS transcription factor ELF5 establishes the milk-secreting alveolar cell lineage by driving a cell fate decision of the mammary luminal progenitor cell. In breast cancer, ELF5 is a key transcriptional determinant of tumor subtype and has been implicated in the development of insensitivity to anti-estrogen therapy. In the mouse mammary tumor virus-Polyoma Middle T (MMTV-PyMT) model of luminal breast cancer, induction of ELF5 levels increased leukocyte infiltration, angiogenesis, and blood vessel permeability in primary tumors and greatly increased the size and number of lung metastasis. Myeloid-derived suppressor cells, a group of immature neutrophils recently identified as mediators of vasculogenesis and metastasis, were recruited to the tumor in response to ELF5. Depletion of these cells using specific Ly6G antibodies prevented ELF5 from driving vasculogenesis and metastasis. Expression signatures in luminal A breast cancers indicated that increased myeloid cell invasion and inflammation were correlated with ELF5 expression, and increased ELF5 immunohistochemical staining predicted much shorter metastasis-free and overall survival of luminal A patients, defining a group who experienced unexpectedly early disease progression. Thus, in the MMTV-PyMT mouse mammary model, increased ELF5 levels drive metastasis by co-opting the innate immune system. As ELF5 has been previously implicated in the development of antiestrogen resistance, this finding implicates ELF5 as a defining factor in the acquisition of the key aspects of the lethal phenotype in luminal A breast cancer.

Published
2015

9. Farmer participatory breeding and participatory varietal selection in Eastern India: Lessons learned

Author

Paris, T.R., Singh, Rakesh Kumar, Atlin, G., Sarkarung, S., McLaren, Graham, Courtois, Brigitte, Mc Allister, K., Piggin, C., Pandey, S., Singh, A., Singh, H.N., Singh, O.N., Singh, S., Mandal, N.P., Prasad, K., Sahu, R.K., Sahu, V.N., Sharma, M.L., Singh, R.K.P., Thakur, R., Singh, N.K., Chaudhary, D., and Ram, S.

Subjects
Agriculteur, Oryza, Amélioration des plantes, F30 - Génétique et amélioration des plantes, méthode, approches participatives, Riz pluvial, Critère de sélection
Abstract

This paper describes the objectives and methods used in a participatory breeding (PPB) project in several rice ecosystems in eastern India. Farmers were interested in a large range and combinations of traits. The selection criteria of farmers were determined by hydrological conditions (water depth) and land types (toposequence) followed by the adaptation of the variety to different user needs (food, livestock fodder, thatching, cash). Other factors determining preference were: the compatibility of the variety in the cropping systems, socioeconomic status, gender and culture. Several lessons learned from the three years' experience led to the refinements in the participatory methods in the next phase of the project.

Published
2002

10. Comparing farmers and breeders rankings in varietal selection for low-input environments : A case study of rainfed rice in eastern India

Author

Courtois, Brigitte, Bartholomé, B., Chaudhary, D., McLaren, Graham, Misra, C.H., Mandal, N.P., Pandey, S., Paris, T., Piggin, C., Prasad, K., Roy, A.T., Sahu, R.K., Sahu, V.N., Sarkarung, S., Sharma, S.K., Singh, A., Singh, H.N., Singh, O.N., Singh, N.K., Singh, Rakesh Kumar, Singh, S., Sinha, P.K., Sisodia, B.V.S., and Takhur, R.

Subjects
Intéraction génotype environnement, Sélection, Enquête sur exploitations agricoles, Oryza, F30 - Génétique et amélioration des plantes, Riz pluvial, Critère de sélection
Abstract

A number of breeding institutions developed a project to assess importance of participatory plant breeding approaches for rainfed rice improvement in eastern India. The results of the first two years of participatory varietal selection are reported here. The objective was to evaluate the respective effects of participation of farmers in varietal evaluation and decentralization of varietal testing from breeding stations to farmers' fields on varietal ranking. Fields representing various hydrological situations were chosen in two to three villages at four rainfed lowland sites and one upland site. Sets of 15 to 25 varieties were tested both in farmers' fields and on-station in 1997 and 1998 and ranked by both farmers and breeders. The effect of participation was judged by comparing the rankings attributed by farmers and breeders to a given set of material in a given trial. The effect of decentralization was determined through comparisons between individual breeders' rankings across trials. Farmers' rankings were not randomly allocated, but agreement within the farmers' group was not always very strong. Except at one site, concordance among breeders' ranking was high, but, because of the limited number of breeders involved, it was seldom significant. In about two-thirds of the trials, there was a good agreement between farmers' and breeders' mean rankings. The consensus was particularly strong when severe constraints induced contrasting behavior in the genotypes. The decentralization effect appeared to be moderate, but variations due to a breeder effect were recorded. The part of genotype by environment interactions for grain yield due to location within one site and year was evaluated through various methods, showing more effect of G x E interactions at some sites than at others. Crossover interactions inducing changes in ranks represented a limited part of the yearly G x E interactions at all sites. Both farmer participation and decentralization of varietal testing in farmers' field would help in best matching the varieties to the needs, although their combined contribution would be more useful in some sites than in others.

Published
2001

12. IRRI upland rice ecosystem program: directions and achievements : directions and achievements

Author

Piggin, C., Courtois, Brigitte, George, Thomas, Pandey, Sushil, Lafitte, T., Kirk, G., Kondo, Motohiko, Leung, Hei, Nelson, R., Olofsdotter, Maria, Prot, J.C., Reversat, Georges, Roder, Walter, Schmit, Véronique, Singh, V.P., Trébuil, Guy, Zeigler, R., Fahrney, K., and Castella, Jean-Christophe

Subjects
Coopération internationale, Amélioration des plantes, Projet de recherche, A50 - Recherche agronomique, Germplasm, Conservation du matériel génétique, Riz pluvial, Système de culture
Abstract

About 17 million hectares of upland rice are grown annually worldwide, with 10.5 million ha in Asia, 3.7 million ha in Latin America, and 2.8 million ha in Africa (IRRI 1993). Total upland production is about 20 million tons. Rice is a major staple crop for upland farmers in many parts of Asia, Africa, and Latin America. The total area supporting upland rice-based cropping is considerably larger because of rotation with fallow and other crops. The crop is grown alone or in diverse mixtures in shifting or permanent fields under a wide range of conditions of climate, slope, and soil type, often as a subsistence crop receiving few purchased inputs, although it is commonly a commercial crop receiving inputs in favourable areas such as Brazil, Indonesia, and the southern Philippines. Reported upland rice areas have remained stable or have increased in some countries, including the major Asian producers Bangladesh, India, and Indonesia, but have declined for others such as Thailand, the Philippines, and Myanmar (Table 1). Care needs to be taken, however, in interpreting upland rice area estimates, which can be unreliable. For example, the 1991 upland rice area in the Philippines was reported as 68,000 ha in the 1993 IRRI Rice Almanac (IRRI 1993), as 17 1,000 ha in the 1997 IRRI Rice Almanac (IRRI 1997), and as 126,000 ha by the Philippine Bureau of Agricultural Statistics (Pandey, unpublished 1997)

Published
1998

13. Breeding better rainfed rice varieties through farmer participation: some early lessons from Eastern India

Author

Courtois, Brigitte, Singh, Rakesh Kumar, Pandey, Sushil, Piggin, C., Paris, T., Sarkarung, S., Singh, V.P., McLaren, Graham, Baghel, S.S., Sahu, R.K., Sahu, V.N., Sharma, S.K., Singh, S., Singh, H.N., Singh, A., Singh, O.N., Sisodia, B.V.S., Misra, C.H., Roy, J.K., Chaudhary, D., Prasad, K., Sinha, P.K., and Mandal, N.P.

Subjects
food and beverages
Abstract

Almost 45% of the world's rice land is rainfed (IRRI 1997). These areas depend solely on rainfall and runoff for water supply. Rice yields are low and fluctuate widely because of highly variable rainfall patterns. The rural poor of Asia are concentrated in rainfed areas. Rice is their staple food and rice production is their major economic activity. Reducing poverty for these populations will require a major increase in agricultural productivity, which entails, among other factors, a higher and more stable rice yield. A challenge facing the agricultural research sector is to develop rice varieties for these complex rainfed environments and make them available to farmers. Classical breeding approaches for developing improved rice varieties have been highly effective in the relatively homogenous irrigated ecosystem. In contrast, the success of such an approach has been limited in rainfed environments because of high levels of agroecological diversity. Farmers' social and economic environments are diverse and interact with biophysical factors resulting in a multitude of rice-based systems, each demanding specific management strategies. Despite continued effort to develop suitable varieties for these environments, the adoption rate has remained low and farmers rely predominantly on traditional rice varieties. The limited impact of breeding programs is relatively well quantified in some areas and less documented in others

Published
1998

14. The IRRI Rainfed Lowland Rice Research Program

Author

Piggin, C., Bhuiyan, S., Ito, O., Kam, S., Kirk, G., Ladha, J.K., McLaren, G., Moody, K., Mortimer, M., Nelson, R., Pandey, S., Paris, T., Reichardt, W., Sarkarung, S., Setter, T., Singh, R.K., Singh, U., Singh, V.P., Trebuil, G., Tuong, T., Wade, L., and Zeigler, R.

Subjects
Teaching/Communication/Extension/Profession
Published
1998
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15. Trip report to Brazil 9 14 March 1997

Author

Courtois, Brigitte, Lafitte, Renée Honor, and Piggin, C.

Subjects
Ressource génétique, Riz pluvial, Oryza, Variété, F30 - Génétique et amélioration des plantes
Published
1997

16. Trip report to South China 23-27 september 1996

Author

Courtois, Brigitte and Piggin, C.

Subjects
Projet de développement, Coopération internationale, Riz pluvial, Variété, F30 - Génétique et amélioration des plantes
Published
1996

17. Upland rice research in partnership : proceedings of the Upland Rice Consortium Workshop, 4-13 January 1996, Padang, Indonesia

Author

Piggin, C. (ed.), Courtois, Brigitte (ed.), and Schmit, Véronique (ed.)

Subjects
Oryza, Amélioration des plantes, F30 - Génétique et amélioration des plantes, Protection des plantes, Substance nutritive, Résistance à la sécheresse, F01 - Culture des plantes, Fertilité du sol, situation économique, Riz pluvial, Variété, production
Abstract

L'URRC (Upland Rice Research Consortium) travaille en réseau sur les principales contraintes de productivité et de durabilité des sytèmes de production à base de riz pluvial. Une analyse de la situation mondiale de la culture du riz pluvial est faite. L'accent est mis sur les problèmes de sécheresse, d'acidité des sols, de disponibilité des substances nutritives, d'érosion, de protection des plantes et de tolérance au froid. Ainsi sont abordés successivement la sécheresse en Inde, la fertilité des sols en Indonésie, la gestion des sols en Thaïlande, la gestion des mauvaises herbes aux Philippines et les maladies du riz à l'IRRI. Les scientifiques privilégient une approche intégrée des contraintes

Published
1996

20. Weeds:a looming problem in modern rice production

Author

Dowling, N. G., Greenfield, S. M., Fischer, K. S., Olofsdotter, M., Watson, A., Piggin, C., Dowling, N. G., Greenfield, S. M., Fischer, K. S., Olofsdotter, M., Watson, A., and Piggin, C.

Published
1998

21. Control of Echium plantagineum L. with 2,4-D and grazing management.

Author

Piggin, C. M.

Subjects
ECHIUM, PASTURES, GRAZING, HERBICIDES, PESTICIDES
Abstract

Copyright of Weed Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1979
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22. Dispersal of Echium plantagineum L. by sheep.

Author

Piggin, C. M.

Subjects
ECHIUM plantagineum, WEED control, SHEEP, GRAZING, MASTICATION
Abstract

Copyright of Weed Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1978
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23. Flowering and seed production of Echium plantagineum L.

Author

Piggin, C. M.

Subjects
GREENHOUSE plants, SEED industry, ECHIUM plantagineum, SEEDS
Abstract

Copyright of Weed Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1978
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24. Competitive growth of Echium plantagineum L. and Trifolium subterraneum L.

Author

Piggin, C. M.

Subjects
ECHIUM plantagineum, SUBTERRANEAN clover, SOILS, NITROGEN, PHOSPHORUS, FERTILIZERS, PASTURES
Abstract

Copyright of Weed Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1978
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25. The nutritive value of Echium plantagineum L. and Trifolium subterraneum L.

Author

Piggin, C. M.

Subjects
ECHIUM plantagineum, PASTURES, PLANT species, FORAGE plants, LIVESTOCK, ANIMAL nutrition
Abstract

Copyright of Weed Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1977
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26. Factors affecting seed germination of Echium plantagineum L. and Trifolium subterraneum L.

Author

Piggin, C. M.

Subjects
GERMINATION, ECHIUM plantagineum, ECHIUM, SUBTERRANEAN clover
Abstract

Copyright of Weed Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1976
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27. Factors affecting seedling establishment and survival of Echium plantagineum L., Trifolium subterraneum L. and Lolium rigidum Gaud.

Author

Piggin, C. M.

Subjects
ECHIUM plantagineum, ECHIUM, SUBTERRANEAN clover, RYEGRASSES, SEEDLINGS, SEED size, PLANTING
Abstract

Copyright of Weed Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1976
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30. Analysis of the acute E74 like ETS transcription factor 5 (ELF5)-dependent transcriptome in the mouse mammary tumor virus-Polyoma Middle T (PyMT/ELF5) model of luminal breast cancer

Author

Gallego-Ortega, D, primary, Ledger, A, additional, Roden, DL, additional, Law, AM, additional, Magenau, A, additional, Kikhtyak, Z, additional, Cho, C, additional, Allerdice, SL, additional, Lee, HJ, additional, Valdes-Mora, F, additional, Herrmann, D, additional, Salomon, R, additional, Young, AI, additional, Lee, BY, additional, Sergio, CM, additional, Kaplan, W, additional, Piggin, C, additional, Conway, JR, additional, Rabinovich, B, additional, Millar, EK, additional, Oakes, SR, additional, Chtanova, T, additional, Swarbrick, A, additional, Naylor, MJ, additional, O'Toole, S, additional, Green, AR, additional, Timpson, P, additional, Gee, JM, additional, Ellis, IO, additional, Clark, SJ, additional, and Ormandy, CJ, additional

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32. Andy's Algorithms: new automated digital image analysis pipelines for FIJI.

Author

Law AMK, Yin JXM, Castillo L, Young AIJ, Piggin C, Rogers S, Caldon CE, Burgess A, Millar EKA, O'Toole SA, Gallego-Ortega D, Ormandy CJ, and Oakes SR

Subjects
3,3'-Diaminobenzidine metabolism, Animals, Automation, Benchmarking, Breast Neoplasms pathology, Colony-Forming Units Assay, Female, Humans, Immunohistochemistry, Mice, Tissue Array Analysis, Algorithms, Image Processing, Computer-Assisted, Software
Abstract

Quantification of cellular antigens and their interactions via antibody-based detection methods are widely used in scientific research. Accurate high-throughput quantitation of these assays using general image analysis software can be time consuming and challenging, particularly when attempted by users with limited image processing and analysis knowledge. To overcome this, we have designed Andy's Algorithms, a series of automated image analysis pipelines for FIJI, that permits rapid, accurate and reproducible batch-processing of 3,3'-diaminobenzidine (DAB) immunohistochemistry, proximity ligation assays (PLAs) and other common assays. Andy's Algorithms incorporates a step-by-step tutorial and optimization pipeline to make batch image analysis simple for the untrained user and adaptable across laboratories. Andy's algorithms provide a simpler, faster, standardized work flow compared to existing programs, while offering equivalent performance and additional features, in a free to use open-source application of FIJI. Andy's Algorithms are available at GitHub, publicly accessed at https://github.com/andlaw1841/Andy-s-Algorithm .

Published
2017
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33. A mutation in the viral sensor 2'-5'-oligoadenylate synthetase 2 causes failure of lactation.

Author

Oakes SR, Gallego-Ortega D, Stanford PM, Junankar S, Au WWY, Kikhtyak Z, von Korff A, Sergio CM, Law AMK, Castillo LE, Allerdice SL, Young AIJ, Piggin C, Whittle B, Bertram E, Naylor MJ, Roden DL, Donovan J, Korennykh A, Goodnow CC, O'Bryan MK, and Ormandy CJ

Subjects
2',5'-Oligoadenylate Synthetase metabolism, Adenine Nucleotides metabolism, Animals, Cell Culture Techniques, Endoribonucleases metabolism, Female, Humans, Mammary Glands, Animal metabolism, Mice, Milk, Mutation genetics, Oligoribonucleotides metabolism, RNA, Double-Stranded metabolism, Signal Transduction genetics, 2',5'-Oligoadenylate Synthetase genetics, Lactation genetics
Abstract

We identified a non-synonymous mutation in Oas2 (I405N), a sensor of viral double-stranded RNA, from an ENU-mutagenesis screen designed to discover new genes involved in mammary development. The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands, characterized by greatly reduced milk protein synthesis coupled with epithelial cell death, inhibition of proliferation and a robust interferon response. Expression of mutant but not wild type Oas2 in cultured HC-11 or T47D mammary cells recapitulated the phenotypic and transcriptional effects observed in the mouse. The mutation activates the OAS2 pathway, demonstrated by a 34-fold increase in RNase L activity, and its effects were dependent on expression of RNase L and IRF7, proximal and distal pathway members. This is the first report of a viral recognition pathway regulating lactation.

Published
2017
Full Text
View/download PDF

34. ELF5 Drives Lung Metastasis in Luminal Breast Cancer through Recruitment of Gr1+ CD11b+ Myeloid-Derived Suppressor Cells.

Author

Gallego-Ortega D, Ledger A, Roden DL, Law AM, Magenau A, Kikhtyak Z, Cho C, Allerdice SL, Lee HJ, Valdes-Mora F, Herrmann D, Salomon R, Young AI, Lee BY, Sergio CM, Kaplan W, Piggin C, Conway JR, Rabinovich B, Millar EK, Oakes SR, Chtanova T, Swarbrick A, Naylor MJ, O'Toole S, Green AR, Timpson P, Gee JM, Ellis IO, Clark SJ, and Ormandy CJ

Subjects
Animals, Breast Neoplasms immunology, Breast Neoplasms physiopathology, Breast Neoplasms virology, Capillary Permeability, Cell Proliferation, DNA-Binding Proteins, Female, Green Fluorescent Proteins genetics, Green Fluorescent Proteins metabolism, Hemorrhage etiology, Hemorrhage prevention & control, Humans, Leukocytes immunology, Leukocytes pathology, Lung blood supply, Lung immunology, Lung pathology, Lung Neoplasms blood supply, Lung Neoplasms pathology, Lung Neoplasms prevention & control, Lymphocyte Depletion, Mice, Transgenic, Myeloid Cells immunology, Myeloid Cells pathology, Neoplasm Proteins genetics, Neovascularization, Pathologic etiology, Neovascularization, Pathologic prevention & control, Neutrophil Infiltration, Polyomavirus pathogenicity, Proto-Oncogene Proteins c-ets genetics, Recombinant Fusion Proteins metabolism, Survival Analysis, Transcription Factors, Tumor Burden, Breast Neoplasms metabolism, Lung metabolism, Lung Neoplasms secondary, Neoplasm Proteins metabolism, Proto-Oncogene Proteins c-ets metabolism
Abstract

During pregnancy, the ETS transcription factor ELF5 establishes the milk-secreting alveolar cell lineage by driving a cell fate decision of the mammary luminal progenitor cell. In breast cancer, ELF5 is a key transcriptional determinant of tumor subtype and has been implicated in the development of insensitivity to anti-estrogen therapy. In the mouse mammary tumor virus-Polyoma Middle T (MMTV-PyMT) model of luminal breast cancer, induction of ELF5 levels increased leukocyte infiltration, angiogenesis, and blood vessel permeability in primary tumors and greatly increased the size and number of lung metastasis. Myeloid-derived suppressor cells, a group of immature neutrophils recently identified as mediators of vasculogenesis and metastasis, were recruited to the tumor in response to ELF5. Depletion of these cells using specific Ly6G antibodies prevented ELF5 from driving vasculogenesis and metastasis. Expression signatures in luminal A breast cancers indicated that increased myeloid cell invasion and inflammation were correlated with ELF5 expression, and increased ELF5 immunohistochemical staining predicted much shorter metastasis-free and overall survival of luminal A patients, defining a group who experienced unexpectedly early disease progression. Thus, in the MMTV-PyMT mouse mammary model, increased ELF5 levels drive metastasis by co-opting the innate immune system. As ELF5 has been previously implicated in the development of antiestrogen resistance, this finding implicates ELF5 as a defining factor in the acquisition of the key aspects of the lethal phenotype in luminal A breast cancer.

Published
2015
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35. Opioid prescribing in palliative care.

Author

Stevens AM and Piggin C

Subjects
Humans, Palliative Care standards, Practice Guidelines as Topic, Specialties, Nursing standards, United Kingdom, Analgesics, Opioid administration & dosage, Analgesics, Opioid adverse effects, Palliative Care methods
Published
2012

36. Malignant fungating wounds: an analysis of the lived experience.

Author

Piggin C and Jones V

Subjects
Adult, Female, Humans, Interpersonal Relations, Neoplasms nursing, Neoplasms psychology, Odorants, Self Concept, Skin Ulcer etiology, Skin Ulcer nursing, Social Identification, Neoplasms complications, Quality of Life, Skin Ulcer psychology
Abstract

Aim: This paper reports upon a study that aimed to illuminate the meaning and experience of living with a malignant fungating wound., Background: The current understanding of living with a malignant fungating wound is derived from professionals' rather than the patient's perspective. An appreciation of the lived experience may assist in the development of more empathetic support approaches., Method: A Heideggerian hermeneutic phenomenological approach was used as the philosophical framework. Unstructured interviews were conducted with a purposive sample of five participants. Content hermeneutic analysis was adopted to analyse the data., Findings: Four themes were identified: representing the worst part of the patient's cancer; living within a body that cannot be trusted; a changing relationship with the patient's family and friends; and a loss of identity while continuously striving to be normal, yet feeling different., Conclusion: Health care professionals must possess a heightened awareness of: the importance of the impact of the wound upon day-to-day living, identity and purpose; the value of adopting the phrase used by the patient to describe their wound; and to focus more upon the subjective meaning of a visibly changing wound rather than objective measurement.

Published
2007
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37. Malodorous fungating wounds: uncertain concepts underlying the management of social isolation.

Author

Piggin C

Subjects
Adaptation, Psychological, Body Image, Fear, Grief, Humans, Models, Psychological, Necrosis, Needs Assessment, Neoplasms complications, Nursing Research, Practice Guidelines as Topic, Skin Care nursing, Social Support, Wounds and Injuries etiology, Wounds and Injuries pathology, Odorants, Palliative Care methods, Skin Care methods, Social Isolation, Wounds and Injuries nursing, Wounds and Injuries psychology
Abstract

Malodorous fungating wounds can exacerbate the social isolation of patients with palliative care needs through changes in patients' body image. There is a lack of consensus regarding the most effective management approaches for patients with malodorous fungating wounds. This appears to relate to the existence of different theoretical frameworks for understanding altered body image. This article explores the theories used to create frameworks that have been used for interventions with patients experiencing social isolation arising from altered body image. It argues that there is a need for health care professionals to appreciate the lack of consensus within the literature and to understand this in the context of the relationship between theory and research. The author offers research and clinical recommendations.

Published
2003
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