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Arabidopsis Book

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https://www.readbyqxmd.com/read/27695390/using-phenomic-analysis-of-photosynthetic-function-for-abiotic-stress-response-gene-discovery
#1
Tepsuda Rungrat, Mariam Awlia, Tim Brown, Riyan Cheng, Xavier Sirault, Jiri Fajkus, Martin Trtilek, Bob Furbank, Murray Badger, Mark Tester, Barry J Pogson, Justin O Borevitz, Pip Wilson
Monitoring the photosynthetic performance of plants is a major key to understanding how plants adapt to their growth conditions. Stress tolerance traits have a high genetic complexity as plants are constantly, and unavoidably, exposed to numerous stress factors, which limits their growth rates in the natural environment. Arabidopsis thaliana, with its broad genetic diversity and wide climatic range, has been shown to successfully adapt to stressful conditions to ensure the completion of its life cycle. As a result, A...
2016: Arabidopsis Book
https://www.readbyqxmd.com/read/27489521/biotrophy-at-its-best-novel-findings-and-unsolved-mysteries-of-the-arabidopsis-powdery-mildew-pathosystem
#2
Hannah Kuhn, Mark Kwaaitaal, Stefan Kusch, Johanna Acevedo-Garcia, Hongpo Wu, Ralph Panstruga
It is generally accepted in plant-microbe interactions research that disease is the exception rather than a common outcome of pathogen attack. However, in nature, plants with symptoms that signify colonization by obligate biotrophic powdery mildew fungi are omnipresent. The pervasiveness of the disease and the fact that many economically important plants are prone to infection by powdery mildew fungi drives research on this interaction. The competence of powdery mildew fungi to establish and maintain true biotrophic relationships renders the interaction a paramount example of a pathogenic plant-microbe biotrophy...
2016: Arabidopsis Book
https://www.readbyqxmd.com/read/26380567/2-hydroxy-acids-in-plant-metabolism
#3
Veronica G Maurino, Martin K M Engqvist
Glycolate, malate, lactate, and 2-hydroxyglutarate are important 2-hydroxy acids (2HA) in plant metabolism. Most of them can be found as D- and L-stereoisomers. These 2HA play an integral role in plant primary metabolism, where they are involved in fundamental pathways such as photorespiration, tricarboxylic acid cycle, glyoxylate cycle, methylglyoxal pathway, and lysine catabolism. Recent molecular studies in Arabidopsis thaliana have helped elucidate the participation of these 2HA in in plant metabolism and physiology...
2015: Arabidopsis Book
https://www.readbyqxmd.com/read/26217168/a-journey-through-a-leaf-phenomics-analysis-of-leaf-growth-in-arabidopsis-thaliana
#4
Hannes Vanhaeren, Nathalie Gonzalez, Dirk Inzé
In Arabidopsis, leaves contribute to the largest part of the aboveground biomass. In these organs, light is captured and converted into chemical energy, which plants use to grow and complete their life cycle. Leaves emerge as a small pool of cells at the vegetative shoot apical meristem and develop into planar, complex organs through different interconnected cellular events. Over the last decade, numerous phenotyping techniques have been developed to visualize and quantify leaf size and growth, leading to the identification of numerous genes that contribute to the final size of leaves...
2015: Arabidopsis Book
https://www.readbyqxmd.com/read/26157354/photoperiodic-regulation-of-florigen-function-in-arabidopsis-thaliana
#5
Greg S Golembeski, Takato Imaizumi
One mechanism through which flowering in response to seasonal change is brought about is by sensing the fluctuation in day-length; the photoperiod. Flowering induction occurs through the production of the florigenic protein FLOWERING LOCUS T (FT) and its movement from the phloem companion cells in the leaf vasculature into the shoot apex, where meristematic reprogramming occurs. FT activation in response to photoperiod condition is accomplished largely through the activity of the transcription factor CONSTANS (CO)...
2015: Arabidopsis Book
https://www.readbyqxmd.com/read/26097438/co-immunoprecipitation-of-membrane-bound-receptors
#6
Julian R Avila, Jin Suk Lee, Keiko U Torii
The study of cell-surface receptor dynamics is critical for understanding how cells sense and respond to changing environments. Therefore, elucidating the mechanisms by which signals are perceived and communicated into the cell is necessary to understand immunity, development, and stress. Challenges in testing interactions of membrane-bound proteins include their dynamic nature, their abundance, and the complex dual environment (lipid/soluble) in which they reside. Co-Immunoprecipitation (Co-IP) of tagged membrane proteins is a widely used approach to test protein-protein interaction in vivo...
2015: Arabidopsis Book
https://www.readbyqxmd.com/read/26078728/vascular-cambium-development
#7
Kaisa Nieminen, Tiina Blomster, Ykä Helariutta, Ari Pekka Mähönen
Secondary phloem and xylem tissues are produced through the activity of vascular cambium, the cylindrical secondary meristem which arises among the primary plant tissues. Most dicotyledonous species undergo secondary development, among them Arabidopsis. Despite its small size and herbaceous nature, Arabidopsis displays prominent secondary growth in several organs, including the root, hypocotyl and shoot. Together with the vast genetic resources and molecular research methods available for it, this has made Arabidopsis a versatile and accessible model organism for studying cambial development and wood formation...
2015: Arabidopsis Book
https://www.readbyqxmd.com/read/26019693/microtubules-in-plants
#8
Takashi Hashimoto
Microtubules (MTs) are highly conserved polar polymers that are key elements of the eukaryotic cytoskeleton and are essential for various cell functions. αβ-tubulin, a heterodimer containing one structural GTP and one hydrolysable and exchangeable GTP, is the building block of MTs and is formed by the sequential action of several molecular chaperones. GTP hydrolysis in the MT lattice is mechanistically coupled with MT growth, thus giving MTs a metastable and dynamic nature. MTs adopt several distinct higher-order organizations that function in cell division and cell morphogenesis...
2015: Arabidopsis Book
https://www.readbyqxmd.com/read/26019692/mechanism-of-cytoplasmic-mrna-translation
#9
Karen S Browning, Julia Bailey-Serres
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems...
2015: Arabidopsis Book
https://www.readbyqxmd.com/read/24465174/cellulose-synthesis-and-its-regulation
#10
Shundai Li, Logan Bashline, Lei Lei, Ying Gu
Cellulose, the most abundant biopolymer synthesized on land, is made of linear chains of ß (1-4) linked D-glucose. As a major structural component of the cell wall, cellulose is important not only for industrial use but also for plant growth and development. Cellulose microfibrils are tethered by other cell wall polysaccharides such as hemicellulose, pectin, and lignin. In higher plants, cellulose is synthesized by plasma membrane-localized rosette cellulose synthase complexes. Despite the recent advances using a combination of molecular genetics, live cell imaging, and spectroscopic tools, many aspects of the cellulose synthesis remain a mystery...
January 13, 2014: Arabidopsis Book
https://www.readbyqxmd.com/read/24465173/cytokinins
#11
Joseph J Kieber, G Eric Schaller
Cytokinins are N (6) substituted adenine derivatives that affect many aspects of plant growth and development, including cell division, shoot initiation and growth, leaf senescence, apical dominance, sink/source relationships, nutrient uptake, phyllotaxis, and vascular, gametophyte, and embryonic development, as well as the response to biotic and abiotic factors. Molecular genetic studies in Arabidopsis have helped elucidate the mechanisms underlying the function of this phytohormone in plants. Here, we review our current understanding of cytokinin biosynthesis and signaling in Arabidopsis, the latter of which is similar to bacterial two-component phosphorelays...
January 2, 2014: Arabidopsis Book
https://www.readbyqxmd.com/read/25505853/composition-roles-and-regulation-of-cullin-based-ubiquitin-e3-ligases
#12
Christina M Choi, William M Gray, Sutton Mooney, Hanjo Hellmann
Due to their sessile nature, plants depend on flexible regulatory systems that allow them to adequately regulate developmental and physiological processes in context with environmental cues. The ubiquitin proteasome pathway, which targets a great number of proteins for degradation, is cellular tool that provides the necessary flexibility to accomplish this task. Ubiquitin E3 ligases provide the needed specificity to the pathway by selectively binding to particular substrates and facilitating their ubiquitylation...
2014: Arabidopsis Book
https://www.readbyqxmd.com/read/25320573/the-ubiquitination-machinery-of-the-ubiquitin-system
#13
Judy Callis
The protein ubiquitin is a covalent modifier of proteins, including itself. The ubiquitin system encompasses the enzymes required for catalysing attachment of ubiquitin to substrates as well as proteins that bind to ubiquitinated proteins leading them to their final fate. Also included are activities that remove ubiquitin independent of, or in concert with, proteolysis of the substrate, either by the proteasome or proteases in the vacuole. In addition to ubiquitin encoded by a family of fusion proteins, there are proteins with ubiquitin-like domains, likely forming ubiquitin's β-grasp fold, but incapable of covalent modification...
2014: Arabidopsis Book
https://www.readbyqxmd.com/read/24982600/root-hairs
#14
Claire Grierson, Erik Nielsen, Tijs Ketelaarc, John Schiefelbein
Roots hairs are cylindrical extensions of root epidermal cells that are important for acquisition of nutrients, microbe interactions, and plant anchorage. The molecular mechanisms involved in the specification, differentiation, and physiology of root hairs in Arabidopsis are reviewed here. Root hair specification in Arabidopsis is determined by position-dependent signaling and molecular feedback loops causing differential accumulation of a WD-bHLH-Myb transcriptional complex. The initiation of root hairs is dependent on the RHD6 bHLH gene family and auxin to define the site of outgrowth...
2014: Arabidopsis Book
https://www.readbyqxmd.com/read/24955076/auxin-biosynthesis
#15
Yunde Zhao
lndole-3-acetic acid (IAA), the most important natural auxin in plants, is mainly synthesized from the amino acid tryptophan (Trp). Recent genetic and biochemical studies in Arabidopsis have unambiguously established the first complete Trp-dependent auxin biosynthesis pathway. The first chemical step of auxin biosynthesis is the removal of the amino group from Trp by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) family of transaminases to generate indole-3-pyruvate (IPA). IPA then undergoes oxidative decarboxylation catalyzed by the YUCCA (YUC) family of flavin monooxygenases to produce IAA...
2014: Arabidopsis Book
https://www.readbyqxmd.com/read/24653667/genetic-and-epigenetic-mechanisms-underlying-vernalization
#16
Dong-Hwan Kim, Sibum Sung
Plants have evolved a number of monitoring systems to sense their surroundings and to coordinate their growth and development accordingly. Vernalization is one example, in which flowering is promoted after plants have been exposed to a long-term cold temperature (i.e. winter). Vernalization results in the repression of floral repressor genes that inhibit the floral transition in many plant species. Here, we describe recent advances in our understanding of the vernalization-mediated promotion of flowering in Arabidopsis and other flowering plants...
2014: Arabidopsis Book
https://www.readbyqxmd.com/read/24653666/protocols-chromatin-immunoprecipitation-from-arabidopsis-tissues
#17
Nobutoshi Yamaguchi, Cara M Winter, Miin-Feng Wu, Chang Seob Kwon, Dilusha A William, Doris Wagner
The ability of proteins to associate with genomic DNA in the context of chromatin is critical for many nuclear processes including transcription, replication, recombination, and DNA repair. Chromatin immunoprecipication (ChIP) is a practical and useful technique for characterizing protein / DNA association in vivo. The procedure generally includes six steps: (1) crosslinking the protein to the DNA; (2) isolating the chromatin; (3) chromatin fragmentation; (4) imunoprecipitation with antibodies against the protein of interest; (5) DNA recovery; and (6) PCR identification of factor associated DNA sequences...
2014: Arabidopsis Book
https://www.readbyqxmd.com/read/24465172/apoplastic-diffusion-barriers-in-arabidopsis
#18
Christiane Nawrath, Lukas Schreiber, Rochus Benni Franke, Niko Geldner, José J Reina-Pinto, Ljerka Kunst
During the development of Arabidopsis and other land plants, diffusion barriers are formed in the apoplast of specialized tissues within a variety of plant organs. While the cuticle of the epidermis is the primary diffusion barrier in the shoot, the Casparian strips and suberin lamellae of the endodermis and the periderm represent the diffusion barriers in the root. Different classes of molecules contribute to the formation of extracellular diffusion barriers in an organ- and tissue-specific manner. Cutin and wax are the major components of the cuticle, lignin forms the early Casparian strip, and suberin is deposited in the stage II endodermis and the periderm...
December 27, 2013: Arabidopsis Book
https://www.readbyqxmd.com/read/24273463/abscisic-acid-synthesis-and-response
#19
Ruth Finkelstein
Abscisic acid (ABA) is one of the "classical" plant hormones, i.e. discovered at least 50 years ago, that regulates many aspects of plant growth and development. This chapter reviews our current understanding of ABA synthesis, metabolism, transport, and signal transduction, emphasizing knowledge gained from studies of Arabidopsis. A combination of genetic, molecular and biochemical studies has identified nearly all of the enzymes involved in ABA metabolism, almost 200 loci regulating ABA response, and thousands of genes regulated by ABA in various contexts...
2013: Arabidopsis Book
https://www.readbyqxmd.com/read/23908601/translational-regulation-of-cytoplasmic-mrnas
#20
Bijoyita Roy, Albrecht G von Arnim
Translation of the coding potential of a messenger RNA into a protein molecule is a fundamental process in all living cells and consumes a large fraction of metabolites and energy resources in growing cells. Moreover, translation has emerged as an important control point in the regulation of gene expression. At the level of gene regulation, translational control is utilized to support the specific life histories of plants, in particular their responses to the abiotic environment and to metabolites. This review summarizes the diversity of translational control mechanisms in the plant cytoplasm, focusing on specific cases where mechanisms of translational control have evolved to complement or eclipse other levels of gene regulation...
2013: Arabidopsis Book
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