LIVIVO - Search results -

Search results

Result 1 - 10 of total 131

Search options

Article ; Online: Antiviral roles of plant ARGONAUTES.

Carbonell, Alberto / Carrington, James C

2015 Volume 27, Page(s) 111–117

Abstract: ARGONAUTES (AGOs) are the effector proteins functioning in eukaryotic RNA silencing pathways. AGOs associate with small RNAs and are programmed to target complementary RNA or DNA. Plant viruses induce a potent and specific antiviral RNA silencing host ... ...

Abstract	ARGONAUTES (AGOs) are the effector proteins functioning in eukaryotic RNA silencing pathways. AGOs associate with small RNAs and are programmed to target complementary RNA or DNA. Plant viruses induce a potent and specific antiviral RNA silencing host response in which AGOs play a central role. Antiviral AGOs associate with virus-derived small RNAs to repress complementary viral RNAs or DNAs, or with endogenous small RNAs to regulate host gene expression and promote antiviral defense. Here, we review recent progress towards understanding the roles of plant AGOs in antiviral defense. We also discuss the strategies that viruses have evolved to modulate, attenuate or suppress AGO antiviral functions.
MeSH term(s)	Antiviral Agents/metabolism ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Gene Expression Regulation, Plant ; Plant Diseases/genetics ; Plant Diseases/immunology ; Plant Diseases/virology ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Viruses/genetics ; Plant Viruses/physiology ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; RNA, Viral/genetics ; RNA, Viral/metabolism
Chemical Substances	Antiviral Agents ; Argonaute Proteins ; Plant Proteins ; RNA, Small Interfering ; RNA, Viral
Language	English
Publishing date	2015-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1418472-2
ISSN	1879-0356 ; 1369-5266
ISSN (online)	1879-0356
ISSN	1369-5266
DOI	10.1016/j.pbi.2015.06.013
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 2005/717: Show issues

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes.

Gilbert, Kerrigan B / Holcomb, Emily E / Allscheid, Robyn L / Carrington, James C

PloS one

2019 Volume 14, Issue 7, Page(s) e0219207

Abstract: The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to ...

Abstract	The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
MeSH term(s)	Base Sequence ; DNA-Directed RNA Polymerases/metabolism ; Fungi/virology ; Genome, Viral ; Open Reading Frames/genetics ; Phylogeny ; RNA, Double-Stranded/genetics ; RNA, Viral/genetics ; Transcriptome/genetics
Chemical Substances	RNA, Double-Stranded ; RNA, Viral ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2019-07-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0219207
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum.

Campo, Sonia / Gilbert, Kerrigan B / Carrington, James C

PLoS pathogens

2016 Volume 12, Issue 6, Page(s) e1005640

Abstract: Even though the fungal kingdom contains more than 3 million species, little is known about the biological roles of RNA silencing in fungi. The Colletotrichum genus comprises fungal species that are pathogenic for a wide range of crop species worldwide. ... ...

Abstract	Even though the fungal kingdom contains more than 3 million species, little is known about the biological roles of RNA silencing in fungi. The Colletotrichum genus comprises fungal species that are pathogenic for a wide range of crop species worldwide. To investigate the role of RNA silencing in the ascomycete fungus Colletotrichum higginsianum, knock-out mutants affecting genes for three RNA-dependent RNA polymerase (RDR), two Dicer-like (DCL), and two Argonaute (AGO) proteins were generated by targeted gene replacement. No effects were observed on vegetative growth for any mutant strain when grown on complex or minimal media. However, Δdcl1, Δdcl1Δdcl2 double mutant, and Δago1 strains showed severe defects in conidiation and conidia morphology. Total RNA transcripts and small RNA populations were analyzed in parental and mutant strains. The greatest effects on both RNA populations was observed in the Δdcl1, Δdcl1Δdcl2, and Δago1 strains, in which a previously uncharacterized dsRNA mycovirus [termed Colletotrichum higginsianum non-segmented dsRNA virus 1 (ChNRV1)] was derepressed. Phylogenetic analyses clearly showed a close relationship between ChNRV1 and members of the segmented Partitiviridae family, despite the non-segmented nature of the genome. Immunoprecipitation of small RNAs associated with AGO1 showed abundant loading of 5'U-containing viral siRNA. C. higginsianum parental and Δdcl1 mutant strains cured of ChNRV1 revealed that the conidiation and spore morphology defects were primarily caused by ChNRV1. Based on these results, RNA silencing involving ChDCL1 and ChAGO1 in C. higginsianum is proposed to function as an antiviral mechanism.
MeSH term(s)	Amino Acid Sequence ; Chromatography, Liquid ; Colletotrichum/genetics ; Colletotrichum/immunology ; Colletotrichum/virology ; Gene Knockout Techniques ; Immunoblotting ; Immunoprecipitation ; Microscopy, Electron, Transmission ; Phylogeny ; Polymerase Chain Reaction ; RNA Interference/physiology ; RNA Viruses/physiology ; Tandem Mass Spectrometry
Language	English
Publishing date	2016-06-02
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1005640
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Fast-forward generation of effective artificial small RNAs for enhanced antiviral defense in plants.

Carbonell, Alberto / Carrington, James C / Daròs, José-Antonio

RNA & disease (Houston, Tex.)

2016 Volume 3, Issue 1

Abstract: Artificial small RNAs (sRNAs) are short ≈21-nt non-coding RNAs engineered to inactivate sequence complementary RNAs. In plants, they have been extensively used to silence cellular transcripts in gene function analyses and to target invading RNA viruses ... ...

Abstract	Artificial small RNAs (sRNAs) are short ≈21-nt non-coding RNAs engineered to inactivate sequence complementary RNAs. In plants, they have been extensively used to silence cellular transcripts in gene function analyses and to target invading RNA viruses to induce resistance. Current artificial sRNA-based antiviral resistance in plants is mainly limited to a single virus, and is jeopardized by the emergence of mutations in the artificial sRNA target site or by the presence of co-infecting viruses. Hence, there is a need to further develop the artificial sRNA approach to generate more broad and durable antiviral resistance in plants. A recently developed toolbox allows for the time and cost-effective large-scale production of artificial sRNA constructs in plants. The toolbox includes the P-SAMS web tool for the automated design of artificial sRNAs, and a new generation of artificial microRNA and synthetic
Language	English
Publishing date	2016-01-12
Publishing country	United States
Document type	Journal Article
ISSN	2375-2467
ISSN	2375-2467
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Antiviral ARGONAUTEs Against

Zheng, Xingguo / Fahlgren, Noah / Abbasi, Arash / Berry, Jeffrey C / Carrington, James C

Plant physiology

2019 Volume 180, Issue 3, Page(s) 1418–1435

Abstract: RNA-based silencing functions as an important antiviral immunity mechanism in plants. Plant viruses evolved to encode viral suppressors of RNA silencing (VSRs) that interfere with the function of key components in the silencing pathway. As effectors in ... ...

Abstract	RNA-based silencing functions as an important antiviral immunity mechanism in plants. Plant viruses evolved to encode viral suppressors of RNA silencing (VSRs) that interfere with the function of key components in the silencing pathway. As effectors in the RNA silencing pathway, ARGONAUTE (AGO) proteins are targeted by some VSRs, such as that encoded by
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/immunology ; Arabidopsis/virology ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/immunology ; Arabidopsis Proteins/metabolism ; Argonaute Proteins/genetics ; Argonaute Proteins/immunology ; Argonaute Proteins/metabolism ; Capsid Proteins/genetics ; Capsid Proteins/immunology ; Capsid Proteins/metabolism ; Carmovirus/genetics ; Carmovirus/immunology ; Carmovirus/physiology ; Disease Resistance/genetics ; Disease Resistance/immunology ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/immunology ; Image Processing, Computer-Assisted/methods ; Mutation ; Plant Diseases/genetics ; Plant Diseases/immunology ; Plant Diseases/virology ; Plant Leaves/genetics ; Plant Leaves/immunology ; Plant Leaves/virology ; Protein Binding ; RNA Interference/immunology
Chemical Substances	AGO3 protein, Arabidopsis ; Arabidopsis Proteins ; Argonaute Proteins ; Capsid Proteins ; ZIPPY protein, Arabidopsis ; argonaute 2 protein, Arabidopsis
Language	English
Publishing date	2019-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1104/pp.19.00121
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Bonn / Germany

Z 1193: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Improving cassava bacterial blight resistance by editing the epigenome.

Veley, Kira M / Elliott, Kiona / Jensen, Greg / Zhong, Zhenhui / Feng, Suhua / Yoder, Marisa / Gilbert, Kerrigan B / Berry, Jeffrey C / Lin, Zuh-Jyh Daniel / Ghoshal, Basudev / Gallego-Bartolomé, Javier / Norton, Joanna / Motomura-Wages, Sharon / Carrington, James C / Jacobsen, Steven E / Bart, Rebecca S

Nature communications

2023 Volume 14, Issue 1, Page(s) 85

Abstract: Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease ... ...

Abstract	Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas phaseoli pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. In this work, we direct methylation to the TAL20 effector binding element within the MeSWEET10a promoter using a synthetic zinc-finger DNA binding domain fused to a component of the RNA-directed DNA methylation pathway. We demonstrate that this methylation prevents TAL20 binding, blocks transcriptional activation of MeSWEET10a in vivo and that these plants display decreased CBB symptoms while maintaining normal growth and development. This work therefore presents an epigenome editing approach useful for crop improvement.
MeSH term(s)	Manihot/genetics ; Epigenome ; Xanthomonas/genetics ; Disease Resistance/genetics ; Transcription Factors/metabolism ; Plant Diseases/genetics ; Plant Diseases/microbiology
Chemical Substances	Transcription Factors
Language	English
Publishing date	2023-01-05
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	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-35675-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Small RNAs and Arabidopsis. A fast forward look.

Carrington, James C

Plant physiology

2005 Volume 138, Issue 2, Page(s) 565–566

MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/physiology ; Biological Evolution ; MicroRNAs/physiology ; RNA, Plant/genetics ; RNA, Plant/physiology ; RNA, Small Interfering/physiology ; Signal Transduction
Chemical Substances	MicroRNAs ; RNA, Plant ; RNA, Small Interfering
Language	English
Publishing date	2005-06
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1104/pp.104.900156
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Full text

In stock of ZB MED Bonn / Germany

Z 1193: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design.

Fahlgren, Noah / Hill, Steven T / Carrington, James C / Carbonell, Alberto

Bioinformatics (Oxford, England)

2016 Volume 32, Issue 1, Page(s) 157–158

Abstract: Summary: The Plant Small RNA Maker Site (P-SAMS) is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in ... ...

Abstract	Summary: The Plant Small RNA Maker Site (P-SAMS) is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants. P-SAMS includes two applications, P-SAMS amiRNA Designer and P-SAMS syn-tasiRNA Designer. The navigation through both applications is wizard-assisted, and the job runtime is relatively short. Both applications output the sequence of designed small RNA(s), and the sequence of the two oligonucleotides required for cloning into 'B/c' compatible vectors. Availability and implementation: The P-SAMS website is available at http://p-sams.carringtonlab.org. Contact: acarbonell@ibmcp.upv.es or nfahlgren@danforthcenter.org.
MeSH term(s)	Computational Biology ; Internet ; MicroRNAs/genetics ; Plants/genetics ; RNA, Plant/genetics ; RNA, Small Interfering/genetics ; Software
Chemical Substances	MicroRNAs ; RNA, Plant ; RNA, Small Interfering
Language	English
Publishing date	2016-01-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btv534
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Full text

In stock of ZB MED Cologne/Königswinter

Zs.A 2374: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: miRNA Target Prediction in Plants.

Fahlgren, Noah / Carrington, James C

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

2010 Volume 592, Page(s) 51–57

Abstract: In plants, miRNA bind to target RNAs with a high degree of complementarity. In this chapter, a simple method for computationally predicting plant miRNA targets, using a position-dependent scoring system, is described. ...

Abstract	In plants, miRNA bind to target RNAs with a high degree of complementarity. In this chapter, a simple method for computationally predicting plant miRNA targets, using a position-dependent scoring system, is described.
MeSH term(s)	Computational Biology/methods ; Databases, Genetic ; Genes, Plant/genetics ; MicroRNAs/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2010
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-60327-005-2_4
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design

Fahlgren, Noah / Hill, Steven T / Carrington, James C / Carbonell, Alberto

Bioinformatics. 2016 Jan. 01, v. 32, no. 1

2016

Abstract: Summary: The Plant Small RNAMaker Site (P-SAMS) is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants. ...

Abstract	Summary: The Plant Small RNAMaker Site (P-SAMS) is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants. P-SAMS includes two applications, P-SAMS amiRNA Designer and P-SAMS syn-tasiRNA Designer. The navigation through both applications is wizard-assisted, and the job runtime is relatively short. Both applications output the sequence of designed small RNA(s), and the sequence of the two oligonucleotides required for cloning into ‘B/c’ compatible vectors. Availability and implementation: The P-SAMS website is available at http://p-sams.carringtonlab.org. Contact: acarbonell@ibmcp.upv.es or nfahlgren@danforthcenter.org
Keywords	Internet ; automation ; bioinformatics ; gene silencing ; microRNA ; oligonucleotides ; small interfering RNA ; world wide web
Language	English
Dates of publication	2016-0101
Size	p. 157-158.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1468345-3
ISSN	1460-2059 ; 1367-4811 ; 1367-4803
ISSN (online)	1460-2059 ; 1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btv534
Database	NAL-Catalogue (AGRICOLA)

Order via subito

To top

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito