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Plant Small RNA

Plant Small RNA
Biogenesis, Regulation and Application

by Praveen Guleria,Vineet Kumar

  • Publisher : Academic Press
  • Release : 2020-02-19
  • Pages : 635
  • ISBN : 012817336X
  • Language : En, Es, Fr & De
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Plant Small RNA: Biogenesis, Regulation and Application describes the biosynthesis of small RNA in plant systems. With an emphasis on the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival, this books presents the basics and most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. In addition, it emphasizes the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival. Final sections cover the most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. Presents foundational information about small RNA biology and regulation in plants Includes small RNA pathway advances Describes the application and scope of small RNA technology for agricultural stability

Non Coding RNAs in Plants

Non Coding RNAs in Plants
A Book

by Volker A. Erdmann,Jan Barciszewski

  • Publisher : Springer Science & Business Media
  • Release : 2011-07-20
  • Pages : 510
  • ISBN : 9783642194542
  • Language : En, Es, Fr & De
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In the most recent years, each of the RNA silencing pathways of plants have appeared to generate ncRNAs with dedicated functions, specialized biological activities and specific functional scopes. RNA silencing plays a crucial role in coordinating the expression, stability, protection and inheritance of eukaryotic genomes. It compromises several mechanisms, that invariably depend on core small non coding RNAs and that achieve dedicated sequence-specific functions. RNA silencing has been recognized to carry critical developmental, stress-response and bodyguard functions be coordinating the expression, protection, stability and inheritance of virtually all eukaryotic genomes. Thus, the ncRNAs encompass a wide set of mechanisms that achieve specialized functions.

Bioinformatics Tools to Classify and Characterize Plant Small RNAs

Bioinformatics Tools to Classify and Characterize Plant Small RNAs
A Book

by Reza Hammond

  • Publisher : Unknown Publisher
  • Release : 2019
  • Pages : 140
  • ISBN : 9781687974853
  • Language : En, Es, Fr & De
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Small RNAs (sRNAs) in plants are a highly abundant class of noncoding RNAs that regulate silencing processes, mostly on the basis of sequence complementarity. There are several classes of small RNA that differ in both their biogenesis and mode of silencing. With the advent of next generation sequencing technologies, sRNA presence can be quantified at a relatively low cost and in a short amount of time. Due to the large amount of data however, there are many challenges associated with the classification of individual sRNAs in these datasets. It is for this reason that I have developed several tools to assist in the classification of sRNAs. The first of these tools is miRador, a novel micro RNA (miRNA) prediction tool that I designed to predict miRNAs from a set of sRNA libraries. This tool utilizes a newly established set of criteria for annotating plant miRNAs which enable it to predict miRNAs with a high level of accuracy. sPARTA is a miRNA target prediction and validation tool which utilizes Parallel Analysis of RNA Ends (PARE) sequencing libraries to validate target cleavage facilitated by a miRNA. Utilizing sPARTA in conjunction with miRador allows for the prediction and validation of novel miRNAs for a variety of plant species. In this dissertation, I utilize this pipeline on maize sRNA data to predict four novel miRNAs. I also present a clustering script that makes use of the Meyers Lab database systems to quickly cluster a variety of sequencing data. Using this approach, I attempted to characterize 24-nt phasiRNA producing loci for two separate projects, presented as case studies. In the first case study, we identify that 24-nt phasiRNAs in maize may be required for robust fertility at higher growth temperatures. In the second case study, we identify that asparagus generates inverted repeat-derived phasiRNAs from mRNAs lacking a miR2275 target site. Taken together, these tools improve scientists ability to characterize various classes of small RNAs, and their effects on their encoding genomes.

RNA-Based Technologies for Functional Genomics in Plants

RNA-Based Technologies for Functional Genomics in Plants
A Book

by Guiliang Tang,Sachin Teotia,Xiaoqing Tang,Deepali Singh

  • Publisher : Springer Nature
  • Release : 2021-05-13
  • Pages : 428
  • ISBN : 3030649946
  • Language : En, Es, Fr & De
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This book offers a unique and comprehensive overview of key RNA-based technologies, as well as their development and applications for the functional genomics of plant coding and non-coding genes. It focuses on the latest as well as classical RNA-based techniques used for studies on small RNAs, long non-coding RNAs and protein-coding genes. These techniques chiefly focus on target mimics (TMs) and short tandem target mimics (STTMs) for small RNAs, and artificial microRNAs (amiRNAs), RNA interference (RNAi) and CRISPR/Cas for genes. Furthermore, the book discusses the latest trends in the field and various modifications of the above-mentioned approaches, and explores how these RNA-based technologies have been developed, applied and validated as essential technologies in plant functional genomics. RNA-based technologies, their mechanisms of action, their advantages and disadvantages, and insights into the further development and applications of these technologies in plants are discussed. These techniques will enable the users to functionally characterize genes and small RNAs through silencing, overexpression and editing. Gathering contributions by globally respected experts, the book will appeal to students, teachers and scientists in academia and industry who are interested in horticulture, genetics, pathology, entomology, physiology, molecular genetics and breeding, in vitro culture & genetic engineering, and functional genomics.

Gating of Small RNA Mobility in Plant Stem Cell Niches

Gating of Small RNA Mobility in Plant Stem Cell Niches
A Book

by Simon Klesen

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Plant Gene Silencing

Plant Gene Silencing
Mechanisms and Applications

by Tamas Dalmay

  • Publisher : CABI
  • Release : 2017-05-29
  • Pages : 223
  • ISBN : 1780647670
  • Language : En, Es, Fr & De
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Plant gene silencing is a crucially important phenomenon in gene expression and epigenetics. This book describes the way small RNA is produced and acts to silence genes, its likely origins in defence against viruses, and also its potential to improve plants. Plant gene silencing can be used to improve industrial traits, make plants more nutritious or more valuable to consumers, to remove allergens, and to improve resistance to weeds and pathogens.

Regulation of Gene Expression by Small RNAs

Regulation of Gene Expression by Small RNAs
A Book

by Rajesh K. Gaur,John J. Rossi

  • Publisher : CRC Press
  • Release : 2009-04-27
  • Pages : 440
  • ISBN : 1420008706
  • Language : En, Es, Fr & De
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New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p

Identification of Small RNA Producing Genes in the Moss Physcomitrella Patens

Identification of Small RNA Producing Genes in the Moss Physcomitrella Patens
A Book

by Ceyda Coruh

  • Publisher : Unknown Publisher
  • Release : 2014
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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In plants, a significant fraction of the genome is responsible for making regulatory small RNAs. These ubiquitous, endogenous small RNAs are currently categorized into two groups: microRNAs (miRNAs) and small interfering RNAs (siRNAs). They are produced by Dicer-Like (DCL) proteins and utilized by Argonaute (AGO) proteins to guide repressive regulation of target mRNAs and/or chromatin selected on the basis of small RNA-target complementarity at the transcriptional or post-transcriptional levels. 21 nt miRNAs and 24 nt heterochromatic siRNAs are the two major types of small RNAs found in angiosperms (flowering plants). The small RNA populations in angiosperms are dominated by 24 nt heterochromatic siRNAs which derive from intergenic, repetitive regions and mediate DNA methylation and repressive histone modifications to targeted loci in angiosperms. However, the existence and extent of heterochromatic siRNAs in other land plant lineages has been less clear. The failure to identify 24 nt heterochromatic siRNA accumulation by initial small RNA-seq attempts from several other species including gymnosperms (Dolgosheina et al. 2008), and the lycophyte Selaginella (Banks et al. 2011) has raised the question whether the heterochromatic siRNA pathway is angiosperm-specific. Previous work in Physcomitrella provides evidence that supports the hypothesis that the heterochromatic siRNA pathway is an ancestral trait that was present in the last common ancestor of bryophytes and all other subsequently diverged lineages of plants (Cho et al. 2008). However, comprehensive annotation of small RNA genes in the basal lineage Physcomitrella is still lacking and an investigation of small RNA populations in this model organism would shed more light on the evolution of regulatory small RNA pathways in land plants.With the advent of next-generation sequencing, small RNA-seq has become a good resource for producing enormous volumes of data on plant miRNA and siRNA expression. Therefore, we produced extensive small RNA-seq data (more than 108 mapped reads) to annotate small RNA genes in ten-day-old protonemata from wild-type Physcomitrella. ShortStack is a recently developed tool to analyze small RNA-seq data with respect to a reference genome and to provide a comprehensive annotation of de novo discovered small RNA genes. Utilizing ShortStack, we identified 16,024 distinct DCL-dependent small RNA producing loci and classified them into five different groupings based on the RNA secondary structure evaluation and the predominant small RNA size. These Physcomitrella small RNA producing loci is now available in our developing web server (plantsmallrnagenes.psu.edu).In order to investigate the features of heterochromatic siRNAs, we revisited the Physcomitrella genome to find functional orthologs of the heterochromatic siRNA genes. We identified candidate proteins that could potentially be involved in the accumulation of heterochromatic siRNAs and created mutants to perform genetic analysis. With the power of consistent biological replicates, differential expression analysis on small RNA-seq data revealed that the accumulation of siRNAs from 23-24 nt siRNA loci depends upon Physcomitrella homologs of DICER-LIKE 3 (DCL3), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), and the largest sub-unit of DNA-DEPENDENT RNA POLYMERASE IV (Pol IV), with the largest sub-unit of a Pol V homolog contributing to expression at a smaller subset of the loci. These data lead us to conclude that Physcomitrella utilizes a heterochromatic siRNA pathway fundamentally similar to that of flowering plants. In contrast to angiosperms, we identified a Physcomitrella-specific MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, but contains the 'catalytic core' (the PAZ domain and the twin RNAseIII domains) of the DCL proteins. We showed that Physcomitrella heterochromatic siRNAs are not solely composed of 24 nt siRNAs as seen in angiosperms, but rather contain equal mixtures of 23 and 24 nt siRNAs. Interestingly, Physcomitrella-specific mDCL is found to be specifically required for 23 nt siRNA accumulation from these loci. Overall, our data lead us to conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely but not completely identical between angiosperms and basal land plants, as represented by the bryophyte, Physcomitrella patens.Significant effort has been made in small RNA gene annotation, but this progress has been unevenly distributed, with MIRNA loci in particular receiving a disproportionate share of the attention. We believe that further efforts at comprehensive and consistent reference annotations of all types of small RNA producing genes, and improvements in the dissemination of such annotations, will greatly enhance the future of plant genomics. Our developing web server (plantsmallrnagenes.psu.edu), which currently hosts small RNA gene annotations of just two species, Amborella trichopoda and Physcomitrella patens, is intended to serve this purpose. In particular, we look forward to the day when researchers seeking to study small RNAs will be liberated from the need to "re-invent the wheel" by generating their own de novo annotations of small RNA-producing genes with each analysis.

Plant Hormones

Plant Hormones
Methods and Protocols

by Sean Cutler,Dario Bonetta

  • Publisher : Unknown Publisher
  • Release : 2009
  • Pages : 146
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Given the rapid increase in our understanding of plant hormone biology, this second edition of a comprehensive review could not have come at a better time. In its chapters, expert researchers explore the latest approaches to understanding plant hormone action.

Genome Research

Genome Research
A Book

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2009
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Dissertation Abstracts International

Dissertation Abstracts International
The sciences and engineering. B

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2008
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Plant Epigenetics

Plant Epigenetics
A Book

by Nikolaus Rajewsky,Stefan Jurga,Jan Barciszewski

  • Publisher : Springer
  • Release : 2017-04-27
  • Pages : 536
  • ISBN : 3319555200
  • Language : En, Es, Fr & De
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This book presents, in 26 chapters, the status quo in epigenomic profiling. It discusses how functional information can be indirectly inferred and describes the new approaches that promise functional answers, collectively referred to as epigenome editing. It highlights the latest important advances in our understanding of the functions of plant epigenomics and new technologies for the study of epigenomic marks and mechanisms in plants. Topics include the deposition or removal of chromatin modifications and histone variants, the role of epigenetics in development and response to environmental signals, natural variation and ecology, as well as applications for epigenetics in crop improvement. Discussing areas ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, it presents breakthroughs in our understanding of complex phenotypic phenomena.

Annual Plant Reviews, Molecular Aspects of Plant Disease Resistance

Annual Plant Reviews, Molecular Aspects of Plant Disease Resistance
A Book

by Jane Parker

  • Publisher : John Wiley & Sons
  • Release : 2009-01-28
  • Pages : 400
  • ISBN : 1444301454
  • Language : En, Es, Fr & De
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Annual Plant Reviews, Volume 34 Molecular Aspects of Plant Disease Resistance Edited by Jane Parker In recent years, our understanding of the mechanisms involved in plant resistance to disease has seen major advances. This important new volume in Wiley-Blackwell’s Annual Plant Reviews provides cutting edge reviews on major aspects of plant immunity from many of the world's leading researchers in the area. Coverage includes: • Establishment of disease by microbial pathogens • Genomic approaches to understanding host-pathogen interactions • Local and systemic resistance signalling • Activities of small bioactive molecules • Plant-insect ecology This exciting volume is essential reading for all those studying plant-pathogen interactions including plant and agricultural scientists, molecular biologists, geneticists and microbiologists. Libraries in all universities and research establishments where biological and agricultural sciences are studied and taught should have copies of this important volume on their shelves. About the Editor Dr Jane Parker is a Group Leader in the Department of Plant-Microbe Interactions at The Max-Planck Institute of Plant Breeding Research, Cologne and Associate Professor at The Institute of Genetics, University of Cologne, Germany. Also Available Annual Plant Reviews, Volume 33 Intracellular Signaling in Plants Edited by Zhenbiao Yang Print: 9781405160025 Annual Plant Reviews, Volume 32 Cell Cycle Control and Plant Development Edited by Dirk Inzé Print: 9781405150439 Online: 9780470988923 Annual Plant Reviews, Volume 31 Plant Mitochondria Edited by David Logan Print: 9781405149396 Online: 9780470986592 Annual Plant Reviews, Volume 30 Light and Plant Development Edited by Garry C. Whitelam and Karen J. Halliday Print: 9781405145381 Online: 9780470988893

Proceedings

Proceedings
Biological sciences

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2006
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Annual Review of Plant Physiology and Plant Molecular Biology

Annual Review of Plant Physiology and Plant Molecular Biology
A Book

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2000
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Adaptive Immunity, Gene Silencing and Viral Silencing Suppressor Proteins Play a Role in the Bipartite Begomovirus-plant Interaction

Adaptive Immunity, Gene Silencing and Viral Silencing Suppressor Proteins Play a Role in the Bipartite Begomovirus-plant Interaction
A Book

by Charles Hagen

  • Publisher : Unknown Publisher
  • Release : 2007
  • Pages : 384
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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PLANT PROTOPLASTS

PLANT PROTOPLASTS
A Book

by Fowke,Constabel

  • Publisher : Boca Raton, Fla. : CRC Press
  • Release : 1985-10-04
  • Pages : 245
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Protoplast isolation and culture; Regeneration of plants; Protoplasts for studies of cell organelles; Protoplast fusion, Plant protoplasts and the cell cycle; Isolated protoplasts as laboratory tools in the study of cell wall deposition; Cytodifferentiation; The use of protoplasts for studies on membrane transport in plants; Protoplasts in virology; Plant protoplasts and genetic variation; Plant mutant isolation via protoplasts; Hybridization by somatic cell fusion; Plant protoplast transformation by Agrobacterium in relation to plant biotechnology.

Plant Virology

Plant Virology
A Book

by Richard Ellis Ford Matthews

  • Publisher : Unknown Publisher
  • Release : 1991
  • Pages : 835
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Containing material new to previous editions, including information on the application and results of gene manipulation techniques, this volume covers all aspects of plant virology from the molecular to the ecological.

In Vivo Analysis of Mutants of a Plant Virus Satellite RNA.

In Vivo Analysis of Mutants of a Plant Virus Satellite RNA.
A Book

by Catherine Alice Chay

  • Publisher : Unknown Publisher
  • Release : 1992
  • Pages : 260
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Proceedings of the National Academy of Sciences of the United States of America

Proceedings of the National Academy of Sciences of the United States of America
A Book

by National Academy of Sciences (U.S.)

  • Publisher : Unknown Publisher
  • Release : 2007
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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