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DEVELOPMENT, STEM CELLS AND REGENERATION IN PLANTS
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Frontiers | Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance | Microbial Symbioses

Frontiers | Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance | Microbial Symbioses | ROOTBOARD | Scoop.it

The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions.


Via Kemen Lab, Stéphane Hacquard, Christophe Jacquet
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Rescooped by ROOTSPROUT from Plant Biology Teaching Resources (Higher Education)
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Science: Making Hunger Yield

Science: Making Hunger Yield | ROOTBOARD | Scoop.it

Perspecitve article by Rob McClung, former ASPB president.

Summary:

"The human population reached 1 billion in the early 1800s, roughly 12,000 years after the dawn of agriculture. However, exponential growth in the ensuing 200 years resulted in the global population exceeding 7 billion, placing enormous demands on modern agriculture. Over the past half-century, the human population has doubled but food production has more than kept pace, and the fraction of people with insufficient food has declined dramatically, from 60% in 1960 to about 15% in 2010 (1), Nonetheless, ∼1 billion people remain chronically underfed and another ∼2 billion suffer from micronutrient deficiencies (1, 2). It is imperative, then, to accelerate increases in agricultural production."


Via Mary Williams
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Rescooped by ROOTSPROUT from Plant Biology Teaching Resources (Higher Education)
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Plant biologists FRET over stress

Plant biologists FRET over stress | ROOTBOARD | Scoop.it

Summary of a pair of papers that use FRET as a biosensor for ABA


Via Mary Williams
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Plants release chemical weapons and deploy insect armies in their defence

Plants release chemical weapons and deploy insect armies in their defence | ROOTBOARD | Scoop.it
Animals have an easy life. They can run, hide, or bite back when predators are on the prowl. Plants cannot. Instead they have evolved to deploy a range of defence mechanisms including chemical warfare and insect armies.

Via Mariaschnee
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Current Biology - Plant Development: From Biochemistry to Biophysics and Back

Nice summary of recent discoveries in root development. Some interesting mechanisms there! http://t.co/gcQjmLbpje
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Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis - Nishimura - 2014 - The Plant Journal - Wiley Online Library

Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis - Nishimura - 2014 - The Plant Journal - Wiley Online Library | ROOTBOARD | Scoop.it

Via PMG
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PMG's curator insight, January 25, 2:47 AM

5–(4–chlorophenyl)-4H-1,2,4–triazole-3–thiol (yucasin) as a potent inhibitor of IAA biosynthesis inYUC-expressing coleoptile tips. Enzymatic analysis of recombinant AtYUC1-His suggested that yucasin strongly inhibited YUC1-His activity against the substrate IPyA in a competitive manner. Phenotypic analysis of Arabidopsis YUC1 over-expression lines (35S::YUC1) demonstrated that yucasin acts in IAA biosynthesis catalyzed by YUC. In addition, 35S::YUC1 seedlings showed resistance to yucasin in terms of root growth. A loss-of-function mutant of TAA1, sav3–2, was hypersensitive to yucasin in terms of root growth and hypocotyl elongation of etiolated seedlings. Yucasin combined with the TAA1 inhibitor l–kynurenine acted additively in Arabidopsis seedlings, producing a phenotype similar to yucasin-treated sav3–2 seedlings, indicating the importance of IAA biosynthesis via the IPyA pathway in root growth and leaf vascular development. 

Rescooped by ROOTSPROUT from GEG-tech top picks: Genetic engineering and its applications
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Genotyping with CRISPR-Cas-derived RNA-guided endonucleases

Genotyping with CRISPR-Cas-derived RNA-guided endonucleases | ROOTBOARD | Scoop.it

Via BigField GEG-tech.com
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BigField GEG-tech.com's curator insight, January 27, 5:17 AM

Original use of CRISPR system to replace the old RFLP genotyping strategy.

 

http://geg-tech.com

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Growth Secret of the World’s Tallest Trees Uncovered

Growth Secret of the World’s Tallest Trees Uncovered | ROOTBOARD | Scoop.it
California’s giant sequoias only thrive atop granite with a particular chemical composition

Via Wildforests
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Cell - Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors

Cell - Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors | ROOTBOARD | Scoop.it

HighlightsCrystal structures of auxin response transcription factors and an ARF-DNA complexARF DNA-binding domains constitute a dimerization domainDNA-binding domain dimerization generates cooperative binding to complex DNA motifsDifferent binding site spacing requirements generate specificity among ARFsSummary

Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.


Via Suayib Üstün, Christophe Jacquet
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Rescooped by ROOTSPROUT from Plant Breeding and Genetics
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USDA considering allowing genetically altered seed for 2,4-D

A proposal by Dow AgroSciences to eliminate restrictions on the use of corn and soybean seeds that are genetically altered to resist 2,4-D has caused a lively debate.

Via CIMMYT, Int., Valerio Hoyos-Villegas
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Rescooped by ROOTSPROUT from Emerging Research in Plant Cell Biology
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Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery | ROOTBOARD | Scoop.it

Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled. A reference annotation-based transcript assembly was also generated, identifying 438 unannotated loci that were differentially expressed under Pi starvation. Several genes also showed induction of unannotated splice isoforms under Pi starvation. Among these, PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi starvation–induced isoform, which was associated with increased translation activity. In addition, microRNA (miRNA) expression profiles after long-term Pi starvation in roots and shoots were assessed, identifying 20 miRNA families that were not previously associated with Pi starvation, such as miR6250. In this article, we present a comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress, revealing a large number of potential key regulators of Pi homeostasis in plants.


Via Jennifer Mach
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Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis : Nature Genetics : Nature Publishing Group

Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis : Nature Genetics : Nature Publishing Group | ROOTBOARD | Scoop.it

With the increased availability of high-resolution sequence information, genome-wide association (GWA) studies have become feasible in a number of species1, 2, 3, 4, 5, 6, 7, 8. The vast majority of these studies are conducted in human populations, where it is difficult to provide strong evidence for the functional involvement of unknown genes that are identified using GWA. Here we used the model organism Arabidopsis thaliana to combine high-throughput confocal microscopy imaging of traits at the cellular level, GWA and expression analyses to identify genomic regions that are associated with developmental cell–type traits. We identify and characterize a new F-box gene, KUK, that regulates meristem and cell length. We further show that polymorphisms in the coding sequence are the major causes of KUK allele–dependent natural variation in root development. This work demonstrates the feasibility of GWA using cellular traits to identify causal genes for basic biological processes such as development


Via Christophe Jacquet
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Photon-plasmon nanowire laser offers new opportunities in light manipulation

Photon-plasmon nanowire laser offers new opportunities in light manipulation | ROOTBOARD | Scoop.it
Recently, researchers have been developing a new type of laser that combines photons and plasmons (electron density oscillations) into a single radiation-emitting device with unique properties.
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Rescooped by ROOTSPROUT from Plant and Seed Biology
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Editorial overview: Growing the future: synthetic biology in plants


Via Loïc Lepiniec
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Programmed Cell Death Controlled by ANAC033/SOMBRERO Determines Root Cap Organ Size in Arabidopsis

Programmed Cell Death Controlled by ANAC033/SOMBRERO Determines Root Cap Organ Size in Arabidopsis | ROOTBOARD | Scoop.it

SummaryBackground

The root cap is a plant organ that ensheathes the meristematic stem cells at the root tip. Unlike other plant organs, the root cap shows a rapid cellular turnover, balancing constant cell generation by specific stem cells with the disposal of differentiated cells at the root cap edge. This cellular turnover is critical for the maintenance of root cap size and its position around the growing root tip, but how this is achieved and controlled in the model plant Arabidopsis thaliana remains subject to contradictory hypotheses.

Results

Here, we show that a highly organized cell death program is the final step of lateral root cap differentiation and that preparation for cell death is transcriptionally controlled by ANAC033/SOMBRERO. Precise timing of cell death is critical for the elimination of root cap cells before they fully enter the root elongation zone, which in turn is important in order to allow optimal root growth. Root cap cell death is followed by a rapid cell-autonomous corpse clearance and DNA fragmentation dependent on the S1-P1 type nuclease BFN1.

Conclusions

Based on these results, we propose a novel concept in plant development that recognizes programmed cell death as a mechanism for maintaining organ size and tissue homeostasis in the Arabidopsis root cap.


Via Christophe Jacquet
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Rescooped by ROOTSPROUT from plant cell genetics
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Drought-tolerant varieties begin global march

Drought-tolerant varieties begin global march | ROOTBOARD | Scoop.it

175.2 million hectares of biotech crops were grown globally in 2013. In the United States, the first commercialized drought-tolerant maize (MON87460) expressing Bacillus subtilis cold shock protein B (cspB) was planted by 2,000 farmers over 50,000 hectares. Indonesia also approved drought-tolerant sugarcane expressing choline dehydrogenase (betA), which accumulates membrane-protectant glycine betaine. Other drought-resistant varieties of sugarcane, maize, wheat and rice are also in field trials in Argentina, Brazil, India, Egypt, South Africa, Kenya and Uganda. Brazil continues to lead the world in annual growth (10%) of transgenic acreage.


Via Jean-Pierre Zryd
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Rescooped by ROOTSPROUT from Plant Genetics, NGS and Bioinformatics
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Opportunities in plant synthetic biology

Opportunities in plant synthetic biology | ROOTBOARD | Scoop.it

Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.


Via Ali Taheri
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CurrOpinPlantBiol: DNA assembly for plant biology: techniques and tools

CurrOpinPlantBiol: DNA assembly for plant biology: techniques and tools | ROOTBOARD | Scoop.it

Via Mary Williams
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Eight types of stem cells in the life cycle of the moss Physcomitrella patens

Eight types of stem cells in the life cycle of the moss Physcomitrella patens | ROOTBOARD | Scoop.it

Stem cells self-renew and produce cells that differentiate to become the source of the plant body. The moss Physcomitrella patens forms eight types of stem cells during its life cycle and serves as a useful model in which to explore the evolution of such cells. The common ancestor of land plants is inferred to have been haplontic and to have formed stem cells only in the gametophyte generation. A single stem cell would have been maintained in the ancestral gametophyte meristem, as occurs in extant basal land plants. During land plant evolution, stem cells diverged in the gametophyte generation to form different types of body parts, including the protonema and rhizoid filaments, leafy-shoot and thalloid gametophores, and gametangia formed in moss. A simplex meristem with a single stem cell was acquired in the sporophyte generation early in land plant evolution. Subsequently, sporophyte stem cells became multiple in the meristem and were elaborated further in seed plant lineages, although the evolutionary origin of niche cells, which maintain stem cells is unknown. Comparisons of gene regulatory networks are expected to give insights into the general mechanisms of stem cell formation and maintenance in land plants and provide information about their evolution. P. patens develops at least seven types of simplex meristem in the gametophyte and at least one type in the sporophyte generation and is a good material for regulatory network comparisons. In this review, we summarize recently revealed molecular mechanisms of stem cell initiation and maintenance in the moss.


Via Jean-Pierre Zryd
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Rescooped by ROOTSPROUT from Plants&Bacteria
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Genome-wide prediction of highly specific guide RNA spacers for the CRISPR-Cas9 mediated genome editing in model plants and major crops

Genome-wide prediction of highly specific guide RNA spacers for the CRISPR-Cas9 mediated genome editing in model plants and major crops | ROOTBOARD | Scoop.it

Scooped from: Molecular Plant, 2013

Authors: Kabin Xie, Jianwei Zhang and Yinong Yang

 

Genome-wide prediction of highly specific guide RNA (gRNA) spacer sequences  in eight model plants and agricultural crop species, including 

Arabidopsis thaliana, Medicago truncatula, Glycine max (soybean), Solanum lycopersicum (tomato), Brachypodium distachyon, Oryza sativa (rice), Sorghum bicolor and Zea mays (maize).

 

CRISPR-PLANT Database - http://www.genome.arizona.edu/crispr "enables the plant research community to access genome-wide predictions of specific gRNAs, and facilitate the application of CRISPR-Cas9 mediated genome editing in model plants and major agricultural crops".

 


Via Freddy Monteiro
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The ERECTA receptor kinase regulates Arabidopsis shoot apical meristem size, phyllotaxy and floral meristem identity

The ERECTA receptor kinase regulates Arabidopsis shoot apical meristem size, phyllotaxy and floral meristem identity | ROOTBOARD | Scoop.it

Via PMG
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PMG's curator insight, February 7, 10:50 PM

ERECTA (ER) pathway as a second receptor kinase signaling pathway that regulates WUS expression, and therefore shoot apical and floral meristem size, independently of the CLV pathway. We demonstrate that reduction in class III HD-ZIP and ER function together leads to a significant increase in WUS expression, resulting in extremely enlarged shoot meristems and a switch from spiral to whorled vegetative phyllotaxy. We further show that strong upregulation of WUS in the inflorescence meristem leads to ectopic expression of the AGAMOUS homeotic gene to a level that switches cell fate from floral meristem founder cell to carpel founder cell, suggesting an indirect role for ER in regulating floral meristem identity. This work illustrates the delicate balance between stem cell specification and differentiation in the meristem and shows that a shift in this balance leads to abnormal phyllotaxy and to altered reproductive cell fate.

Rescooped by ROOTSPROUT from Plant roots and rhizosphere
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Review: Root growth movements: Waving and skewing

Review: Root growth movements: Waving and skewing | ROOTBOARD | Scoop.it

Roots anchor a plant in the soil, acquire nutrition and respond to environmental cues. Roots perform these functions using intricate movements and a variety of pathways have been implicated in mediating their growth patterns. These include endogenous genetic factors, perception of multiple environmental stimuli, signaling pathways interacting with hormonal dynamics and cellular processes of rapid cell elongation. In this review we attempt to consolidate our understanding of two specific types of root movements, waving and skewing, that arise on the surface of growth media, and how they are regulated by various genes and factors. These include crucial factors that are part of a complex nexus of processes including polar auxin transport and cytoskeletal dynamics. This knowledge can be extrapolated in the future for engineering plants with root architecture better suited for different soil and growth conditions such as abiotic stresses or even extended spaceflight. Technological innovations and interdisciplinary approaches promise to allow the tracking of root movements on a much finer scale, thus helping to expedite the discovery of more nodes in the regulation of root waving and skewing and movement in general.


Via Christophe Jacquet
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The shifting paradigms of auxin biosynthesis

The shifting paradigms of auxin biosynthesis | ROOTBOARD | Scoop.it

Auxins are an important group of hormones found in all land plants and several soil-dwelling microbes. Although auxin was the first phytohormone identified, its biosynthesis remained unclear until recently. In the past few years, our understanding of auxin biosynthesis has improved dramatically, to the stage where many believe there is a single predominant pathway in Arabidopsis (Arabidopsis thaliana L.). However, there is still uncertainty over the applicability of these findings to other plant species. Indeed, it appears that in certain organs of some species, other pathways can operate. Here we review the key advances that have led to our current understanding of auxin biosynthesis and its many proposed pathways.


Via Christophe Jacquet
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Christophe Jacquet's curator insight, December 31, 2013 6:08 AM

Highlights•

We summarize the long and complex history of auxin biosynthesis in plants.

At least five pathways have been proposed, including four from tryptophan.

Tryptophan can be converted to auxin via a single intermediate, indole-3-pyruvic acid.

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Why seedlings always grow towards the light

Why seedlings always grow towards the light | ROOTBOARD | Scoop.it
Scientists have discovered how cells in the stems of seedlings use blue light to grow towards the light. During earlier research the discovery was made that the cells in the seedling stems responded to blue light used in the microscope.

Via R K Upadhyay
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María Serrano's curator insight, June 24, 12:29 PM
Explicación del crecimiento de las plántulas hacia la luz
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RNA controls splicing during gene expression, further evidence of 'RNA world' origin in modern life

RNA controls splicing during gene expression, further evidence of 'RNA world' origin in modern life | ROOTBOARD | Scoop.it
RNA is the key functional component of spliceosomes, molecular machines that control how genes are expressed, report scientists from the University of Chicago online, Nov. 6 in Nature.
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