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Article ; Online: A growth quantification assay for Hyaloperonospora arabidopsidis isolates in Arabidopsis thaliana.

Tomé, Daniel F A / Steinbrenner, Jens / Beynon, Jim L

Methods in molecular biology (Clifton, N.J.)

2014 Volume 1127, Page(s) 145–158

Abstract: There is a considerable interest in determining the role of individual oomycete effectors in promoting disease. Widely used strategies are based on manipulating effector-expression levels in the pathogen and by over-expressing particular effectors in the ...

Abstract	There is a considerable interest in determining the role of individual oomycete effectors in promoting disease. Widely used strategies are based on manipulating effector-expression levels in the pathogen and by over-expressing particular effectors in the host by genetic transformation. In the case of the oomycete, Hyaloperonospora arabidopsidis (Hpa) genetic manipulation is not yet possible, so over-expression of predicted effectors in stably transformed Arabidopsis lines is used to investigate their capability for promoting virulence. Here, we describe a technique for quantifying pathogen growth based on the counting of asexual reproductive structures called sporangiophores in the compatible interaction between the Hpa isolate Noks1 and the Col-0 Arabidopsis accession.
MeSH term(s)	Arabidopsis/microbiology ; Biological Assay/methods ; Cells, Cultured ; Oomycetes/isolation & purification ; Plants, Genetically Modified ; Spores/physiology
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-986-4_12
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Article: Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting.

Coker, Timothy L R / Cevik, Volkan / Beynon, Jim L / Gifford, Miriam L

Frontiers in plant science

2015 Volume 6, Page(s) 527

Abstract: Changes in gene expression form a crucial part of the plant response to infection. In the last decade, whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model ... ...

Abstract	Changes in gene expression form a crucial part of the plant response to infection. In the last decade, whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model plant Arabidopsis thaliana and a diverse range of pathogens. However, with some pathogens such as downy mildew caused by the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis (Hpa), whole-leaf profiling may fail to capture the complete Arabidopsis response encompassing responses of non-infected as well as infected cells within the leaf. Highly localized expression changes that occur in infected cells may be diluted by the comparative abundance of non-infected cells. Furthermore, local and systemic Hpa responses of a differing nature may become conflated. To address this we applied the technique of Fluorescence Activated Cell Sorting (FACS), typically used for analyzing plant abiotic responses, to the study of plant-pathogen interactions. We isolated haustoriated (Hpa-proximal) and non-haustoriated (Hpa-distal) cells from infected seedling samples using FACS, and measured global gene expression. When compared with an uninfected control, 278 transcripts were identified as significantly differentially expressed, the vast majority of which were differentially expressed specifically in Hpa-proximal cells. By comparing our data to previous, whole organ studies, we discovered many highly locally regulated genes that can be implicated as novel in the Hpa response, and that were uncovered for the first time using our sensitive FACS technique.
Language	English
Publishing date	2015-07-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2015.00527
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Article ; Online: Hyaloperonospora Arabidopsidis as a pathogen model.

Coates, Mary E / Beynon, Jim L

Annual review of phytopathology

2009 Volume 48, Page(s) 329–345

Abstract: Hyaloperonospora arabidopsidis, a downy mildew pathogen of the model plant Arabidopsis, has been very useful in the understanding of the relationship between oomycetes and their host plants. This naturally coevolving pathosystem contains an amazing level ...

Abstract	Hyaloperonospora arabidopsidis, a downy mildew pathogen of the model plant Arabidopsis, has been very useful in the understanding of the relationship between oomycetes and their host plants. This naturally coevolving pathosystem contains an amazing level of genetic diversity in host resistance and pathogen avirulence proteins. Oomycete effectors identified to date contain a targeting motif, RXLR, enabling effector entry into the host cell. The availability of the H. arabidopsidis genome sequence has enabled bioinformatic analyses to identify at least 130 RXLR effectors, potentially used to quell the host's defense mechanism and manipulate other host cellular processes. Currently, these effectors are being used to reveal their targets in the host cell. Eventually this will result in an understanding of the mechanisms used by a pathogen to sustain a biotrophic relationship with a plant.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/immunology ; Arabidopsis/parasitology ; Host-Pathogen Interactions/physiology ; Oomycetes/genetics ; Oomycetes/immunology ; Oomycetes/pathogenicity ; Plant Diseases/genetics ; Plant Diseases/immunology ; Plant Diseases/parasitology
Language	English
Publishing date	2009-04-28
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	207934-3
ISSN	1545-2107 ; 0066-4286
ISSN (online)	1545-2107
ISSN	0066-4286
DOI	10.1146/annurev-phyto-080508-094422
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Article: Improving crop disease resistance: lessons from research on Arabidopsis and tomato.

Piquerez, Sophie J M / Harvey, Sarah E / Beynon, Jim L / Ntoukakis, Vardis

Frontiers in plant science

2014 Volume 5, Page(s) 671

Abstract: One of the great challenges for food security in the 21st century is to improve yield stability through the development of disease-resistant crops. Crop research is often hindered by the lack of molecular tools, growth logistics, generation time and ... ...

Abstract	One of the great challenges for food security in the 21st century is to improve yield stability through the development of disease-resistant crops. Crop research is often hindered by the lack of molecular tools, growth logistics, generation time and detailed genetic annotations, hence the power of model plant species. Our knowledge of plant immunity today has been largely shaped by the use of models, specifically through the use of mutants. We examine the importance of Arabidopsis and tomato as models in the study of plant immunity and how they help us in revealing a detailed and deep understanding of the various layers contributing to the immune system. Here we describe examples of how knowledge from models can be transferred to economically important crops resulting in new tools to enable and accelerate classical plant breeding. We will also discuss how models, and specifically transcriptomics and effectoromics approaches, have contributed to the identification of core components of the defense response which will be key to future engineering of durable and sustainable disease resistance in plants.
Language	English
Publishing date	2014-12-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2014.00671
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Article ; Online: A simple and fast protocol for the protein complex immunoprecipitation (Co-IP) of effector: host protein complexes.

Steinbrenner, Jens / Eldridge, Matthew / Tomé, Daniel F A / Beynon, Jim L

Methods in molecular biology (Clifton, N.J.)

2014 Volume 1127, Page(s) 195–211

Abstract: Plant pathogens are responsible for enormous damage in natural and cultured ecosystems. One strategy most pathogenic organisms follow is the secretion of effector proteins that manipulate the host immune system to suppress defense responses. There is ... ...

Abstract	Plant pathogens are responsible for enormous damage in natural and cultured ecosystems. One strategy most pathogenic organisms follow is the secretion of effector proteins that manipulate the host immune system to suppress defense responses. There is considerable interest in finding host targets of pathogen effectors as this helps to shape our understanding of how those proteins work in planta. The presented protocol describes a protein complex immunoprecipitation method aimed at verifying protein-protein interactions derived from protein complementation assays like Yeast-two-Hybrid.
MeSH term(s)	Agrobacterium/cytology ; Agrobacterium/metabolism ; DNA Primers/metabolism ; Gene Expression ; Green Fluorescent Proteins/metabolism ; Host-Pathogen Interactions ; Immunoprecipitation/methods ; Plant Proteins/metabolism ; Time Factors ; Nicotiana/cytology ; Nicotiana/metabolism ; Transformation, Genetic
Chemical Substances	DNA Primers ; Plant Proteins ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2014-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-986-4_16
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Article: Hyaloperonospora arabidopsidis as a Pathogen Model

Coates, Mary E / Beynon, Jim L

Annual review of phytopathology. 2010, v. 48

2010

Keywords	Arabidopsis thaliana ; Peronosporales ; plant pathogenic fungi ; downy mildew ; host plants ; host-pathogen relationships ; virulence ; fungal proteins ; plant proteins ; resistance mechanisms ; defense mechanisms ; gene-for-gene relationship ; cell invasion ; chemical structure ; genome ; nucleotide sequences ; bioinformatics ; coevolution
Language	English
Size	p. 329–345.
Document type	Article
ZDB-ID	207934-3
ISSN	1545-2107 ; 0066-4286
ISSN (online)	1545-2107
ISSN	0066-4286
DOI	10.1146/annurev-phyto-080508-094422
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The Transcription Factor ATHB5 Affects GA-Mediated Plasticity in Hypocotyl Cell Growth during Seed Germination.

Stamm, Petra / Topham, Alexander T / Mukhtar, Nur Karimah / Jackson, Matthew D B / Tomé, Daniel F A / Beynon, Jim L / Bassel, George W

Plant physiology

2016 Volume 173, Issue 1, Page(s) 907–917

Abstract: Gibberellic acid (GA)-mediated cell expansion initiates the seed-to-seedling transition in plants and is repressed by DELLA proteins. Using digital single-cell analysis, we identified a cellular subdomain within the midhypocotyl, whose expansion drives ... ...

Abstract	Gibberellic acid (GA)-mediated cell expansion initiates the seed-to-seedling transition in plants and is repressed by DELLA proteins. Using digital single-cell analysis, we identified a cellular subdomain within the midhypocotyl, whose expansion drives the final step of this developmental transition under optimal conditions. Using network inference, the transcription factor ATHB5 was identified as a genetic factor whose localized expression promotes GA-mediated expansion specifically within these cells. Both this protein and its putative growth-promoting target EXPANSIN3 are repressed by DELLA, and coregulated at single-cell resolution during seed germination. The cellular domains of hormone sensitivity were explored within the Arabidopsis (Arabidopsis thaliana) embryo by putting seeds under GA-limiting conditions and quantifying cellular growth responses. The middle and upper hypocotyl have a greater requirement for GA to promote cell expansion than the lower embryo axis. Under these conditions, germination was still completed following enhanced growth within the radicle and lower axis. Under GA-limiting conditions, the athb5 mutant did not show a phenotype at the level of seed germination, but it did at a cellular level with reduced cell expansion in the hypocotyl relative to the wild type. These data reveal that the spatiotemporal cell expansion events driving this transition are not determinate, and the conditional use of GA-ATHB5-mediated hypocotyl growth under optimal conditions may be used to optionally support rapid seedling growth. This study demonstrates that multiple genetic and spatiotemporal cell expansion mechanisms underlie the seed to seedling transition in Arabidopsis.
MeSH term(s)	Anisotropy ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Gene Expression Regulation, Plant ; Germination/genetics ; Gibberellins/metabolism ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Hypocotyl/cytology ; Hypocotyl/growth & development ; Plants, Genetically Modified ; Seedlings/growth & development ; Seeds/cytology ; Seeds/physiology ; Single-Cell Analysis/methods ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	ATHB5 protein, Arabidopsis ; Arabidopsis Proteins ; EXPANSIN A7 protein, Arabidopsis ; Gibberellins ; Homeodomain Proteins ; Transcription Factors ; gibberellic acid (BU0A7MWB6L)
Language	English
Publishing date	2016-11-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1104/pp.16.01099
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Article: Trafficking arms: oomycete effectors enter host plant cells.

Birch, Paul R J / Rehmany, Anne P / Pritchard, Leighton / Kamoun, Sophien / Beynon, Jim L

Trends in microbiology

2006 Volume 14, Issue 1, Page(s) 8–11

Abstract: Oomycetes cause devastating plant diseases of global importance, yet little is known about the molecular basis of their pathogenicity. Recently, the first oomycete effector genes with cultivar-specific avirulence (AVR) functions were identified. Evidence ...

Abstract	Oomycetes cause devastating plant diseases of global importance, yet little is known about the molecular basis of their pathogenicity. Recently, the first oomycete effector genes with cultivar-specific avirulence (AVR) functions were identified. Evidence of diversifying selection in these genes and their cognate plant host resistance genes suggests a molecular "arms race" as plants and oomycetes attempt to achieve and evade detection, respectively. AVR proteins from Hyaloperonospora parasitica and Phytophthora infestans are detected in the plant host cytoplasm, consistent with the hypothesis that oomycetes, as is the case with bacteria and fungi, actively deliver effectors inside host cells. The RXLR amino acid motif, which is present in these AVR proteins and other secreted oomycete proteins, is similar to a host-cell-targeting signal in virulence proteins of malaria parasites (Plasmodium species), suggesting a conserved role in pathogenicity.
MeSH term(s)	Algal Proteins/genetics ; Algal Proteins/metabolism ; Amino Acid Motifs ; Arabidopsis ; Oomycetes/genetics ; Oomycetes/metabolism ; Oomycetes/pathogenicity ; Plant Diseases/microbiology ; Plant Proteins/metabolism ; Solanum tuberosum
Chemical Substances	Algal Proteins ; Plant Proteins
Language	English
Publishing date	2006-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2005.11.007
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Article ; Online: An RxLR effector from Phytophthora infestans prevents re-localisation of two plant NAC transcription factors from the endoplasmic reticulum to the nucleus.

McLellan, Hazel / Boevink, Petra C / Armstrong, Miles R / Pritchard, Leighton / Gomez, Sonia / Morales, Juan / Whisson, Stephen C / Beynon, Jim L / Birch, Paul R J

PLoS pathogens

2013 Volume 9, Issue 10, Page(s) e1003670

Abstract: The potato late blight pathogen Phytophthora infestans secretes an array of effector proteins thought to act in its hosts by disarming defences and promoting pathogen colonisation. However, little is known about the host targets of these effectors and ... ...

Abstract	The potato late blight pathogen Phytophthora infestans secretes an array of effector proteins thought to act in its hosts by disarming defences and promoting pathogen colonisation. However, little is known about the host targets of these effectors and how they are manipulated by the pathogen. This work describes the identification of two putative membrane-associated NAC transcription factors (TF) as the host targets of the RxLR effector PITG_03192 (Pi03192). The effector interacts with NAC Targeted by Phytophthora (NTP) 1 and NTP2 at the endoplasmic reticulum (ER) membrane, where these proteins are localised. Transcripts of NTP1 and NTP2 rapidly accumulate following treatment with culture filtrate (CF) from in vitro grown P. infestans, which acts as a mixture of Phytophthora PAMPs and elicitors, but significantly decrease during P. infestans infection, indicating that pathogen activity may prevent their up-regulation. Silencing of NTP1 or NTP2 in the model host plant Nicotiana benthamiana increases susceptibility to P. infestans, whereas silencing of Pi03192 in P. infestans reduces pathogenicity. Transient expression of Pi03192 in planta restores pathogenicity of the Pi03192-silenced line. Moreover, colonisation by the Pi03192-silenced line is significantly enhanced on N. benthamiana plants in which either NTP1 or NTP2 have been silenced. StNTP1 and StNTP2 proteins are released from the ER membrane following treatment with P. infestans CF and accumulate in the nucleus, after which they are rapidly turned over by the 26S proteasome. In contrast, treatment with the defined PAMP flg22 fails to up-regulate NTP1 and NTP2, or promote re-localisation of their protein products to the nucleus, indicating that these events follow perception of a component of CF that appears to be independent of the FLS2/flg22 pathway. Importantly, Pi03192 prevents CF-triggered re-localisation of StNTP1 and StNTP2 from the ER into the nucleus, revealing a novel effector mode-of-action to promote disease progression.
MeSH term(s)	Active Transport, Cell Nucleus/genetics ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Endoplasmic Reticulum/genetics ; Endoplasmic Reticulum/metabolism ; Gene Silencing ; Phytophthora infestans/genetics ; Phytophthora infestans/metabolism ; Plant Diseases ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Nicotiana/genetics ; Nicotiana/metabolism ; Nicotiana/microbiology ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Plant Proteins ; Transcription Factors
Language	English
Publishing date	2013-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1003670
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Article: The arabidopsis TIR-NB-LRR gene RAC1 confers resistance to Albugo candida (white rust) and is dependent on EDS1 but not PAD4.

Borhan, Mohammad H / Holub, Eric B / Beynon, Jim L / Rozwadowski, Kevin / Rimmer, S Roger

Molecular plant-microbe interactions : MPMI

2004 Volume 17, Issue 7, Page(s) 711–719

Abstract: Resistance to Albugo candida isolate Acem1 is conferred by a dominant gene, RAC1, in accession Ksk-1 of Arabidopsis thaliana. This gene was isolated by positional cloning and is a member of the Drosophila toll and mammalian interleukin-1 receptor (TIR) ... ...

Abstract	Resistance to Albugo candida isolate Acem1 is conferred by a dominant gene, RAC1, in accession Ksk-1 of Arabidopsis thaliana. This gene was isolated by positional cloning and is a member of the Drosophila toll and mammalian interleukin-1 receptor (TIR) nucleotide-binding site leucine-rich repeat (NB-LRR) class of plant resistance genes. Strong identity of the TIR and NB domains was observed between the predicted proteins encoded by the Ksk-1 allele and the allele from an Acem1-susceptible accession Columbia (Col) (99 and 98%, respectively). However, major differences between the two predicted proteins occur within the LRR domain and mainly are confined to the beta-strand/beta-turn structure of the LRR. Both proteins contain 14 imperfect repeats. RAC1-mediated resistance was analyzed further using mutations in defense regulation, including: pad4-1, eds1-1, and NahG, in the presence of the RAC1 allele from Ksk-1. White rust resistance was completely abolished by eds1-1 but was not affected by either pad4-1 or NahG.
MeSH term(s)	Amino Acid Sequence ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis/microbiology ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Base Sequence ; Carboxylic Ester Hydrolases/genetics ; Carboxylic Ester Hydrolases/metabolism ; Chromosomes, Artificial, Yeast ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Immunity, Innate/genetics ; Molecular Sequence Data ; Oomycetes/growth & development ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Sequence Homology, Amino Acid ; Signal Transduction/genetics ; Signal Transduction/physiology
Chemical Substances	Arabidopsis Proteins ; DNA-Binding Proteins ; EDS1 protein, Arabidopsis ; RAC1 protein, Arabidopsis ; Carboxylic Ester Hydrolases (EC 3.1.1.-) ; PAD4 protein, Arabidopsis (EC 3.1.1.-)
Language	English
Publishing date	2004-07-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI.2004.17.7.711
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