Plant Gene Seeker -PGS
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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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Resources for academic writing and publishing


I led a workshop on academic writing and publishing last week, and this is a list of resources I gave to the participants. It's not an exhaustive list, so if you have any favorites let me know and I'll add them!


Links and resources


General writing resources


Strunk, W. Jr. (1999).The Elements of Style. http://www.bartleby.com/141/


 


Guidelines and lessons for good scientific writing


Cargill, M., and O’Connor, P. (2011). Writing Scientific Research Articles: Strategy and Steps. Wiley. http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1444356216.html


Doumont, J., ed. (2010). English Communication for Scientists. Cambridge, MA: NPG Education. http://www.nature.com/wls/ebooks/english-communication-for-scientists-14053993/contents (Free ebook - very useful)


Duke University Graduate School. Scientific Writing Resource.  https://cgi.duke.edu/web/sciwriting/index.php Short, online course for graduate students with examples and worksheets


Editorial (2010). Scientific writing 101. Nat Struct Mol Biol. 17: 139-139. http://www.nature.com/nsmb/journal/v17/n2/full/nsmb0210-139.html


European Association of Science Editors. EASE Toolkit for Authors. http://www.ease.org.uk/publications/ease-toolkit-authors


Nature Scitable Effective Writing. http://www.nature.com/scitable/topicpage/effective-writing-13815989


Nature Scitable Scientific Papers. http://www.nature.com/scitable/topicpage/scientific-papers-13815490


Lichtfouse, E. (2013). Scientific Writing for Impact Factor Journals. Nova Scientific Publishers, Inc. (New York).


Moreira, A., and Haahtela, T. (2011). How to write a scientific paper--and win the game scientists play! Rev. Port. Pneumol. 17:146-149. doi: 10.1016/j.rppneu.2011.03.007. http://www.elsevier.pt/en/linkresolver/320/how-to-write-scientific-paper-and-win/90020266


Plaxco, K.W. (2010). The art of writing science. Protein Science 19: 2261 – 2266. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009394/pdf/pro0019-2261.pdf


Rogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer. http://www.springer.com/medicine/book/978-3-642-39445-4 https://moodle.swarthmore.edu/pluginfile.php/179173/mod_resource/content/1/Good%20versus%20poor%20scientific%20writing%20from%20Silvia%20Rogers.pdf


Writing Center University of Wisconsin. (2014) The Writers Handbook: Reverse Outlines. http://writing.wisc.edu/Handbook/ReverseOutlines.html


 


Guidance from journals


J Exp Bot: http://www.oxfordjournals.org/our_journals/exbotj/for_authors/


Nature: http://www.nature.com/authors/author_resources/how_write.html


Plant Cell: http://www.plantcell.org/site/misc/ifora.xhtml


 


Figures preparation and ethical issues


Blatt, M. and Martin, C. (2013). Manipulation and Misconduct in the Handling of Image Data. Plant Physiology. 163: 3-4. http://www.plantphysiol.org/content/163/1/3.short


Cromey, D.W. (2010). Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci. Eng. Ethics 16: 639–667


Rossner, M., and Yamada, K.M. (2004). What’s in a picture? The temptation of image manipulation. J. Cell Biol 166: 11–15. http://jcb.rupress.org/content/166/1/11.short


 


Peer Review Guidelines and Policies, Post-publication peer review


Bastian, H. (2014) A Stronger Post-Publication Culture Is Needed for Better Science. PLoS Med 11(12): e1001772. doi:10.1371/journal.pmed.1001772


F1000Research: http://blog.f1000research.com/2014/07/08/what-is-post-publication-peer-review/


F1000: http://journal.frontiersin.org/Journal/10.3389/fncom.2012.00063/full


Mole. (2007). Rebuffs and rebuttals I: how rejected is rejected? J Cell Sci. 120: 1143-1144. http://hwmaint.jcs.biologists.org/cgi/reprint/120/7/1143


Nature: http://www.nature.com/authors/policies/peer_review.html


Office of Research Integrity. (US Dept of Health and Human Services) The Lab. http://ori.hhs.gov/THELAB


Office of Research Integrity. Research Clinic Case Book. http://ori.hhs.gov/rcr-casebook-stories-about-researchers-worth-discussing


Science: http://www.sciencemag.org/site/feature/contribinfo/review.xhtml


PLOS ONE: www.plosone.org/static/reviewerGuidelines


Provenzale, J.M. and Stanley, R.J. (2006). A Systematic Guide to Reviewing a Manuscript. J. Nuclear Med.Techn.. 34: 92-99. http://tech.snmjournals.org/content/34/2/92.full.pdf+html


Times Higher Education: http://www.timeshighereducation.co.uk/news/can-post-publication-peer-review-endure/2016895.article


 


Readability


RavenBlog (2010). Ultimate list of online content readability tests. http://blog.raventools.com/ultimate-list-of-online-content-readability-tests/


 


Communicating more broadly


Kuehne, L.M., et al. (2014). Practical science communication strategies for graduate students. Conservation Biology. 28: 1225–1235. .DOI: 10.1111/cobi.12305


Osterrieder, A. (2013). The value and use of social media as communication tool in the plant sciences. Plant Methods. 9: 26. http://www.plantmethods.com/content/9/1/26


 



Via Mary Williams
Andres Zurita's insight:
Outstanding source of fine material! Thanks Mary!
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AckerbauHalle's curator insight, February 3, 2015 10:49 AM

Großartige Literatursammlung für wissenschaftliches Schreiben. 

Bibhya Sharma's curator insight, February 3, 2015 8:58 PM

Very helpful for teachers and researchers. 

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PRL1 modulates root stem cell niche activity and meristem size through WOX5 and PLTs in Arabidopsis

PRL1 modulates root stem cell niche activity and meristem size through WOX5 and PLTs in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The stem cell niche in the root meristem maintains pluripotent stem cells to ensure a constant supply of cells for root growth. Despite extensive progress, the molecular mechanisms through which root stem cell fates and stem cell niche activity are determined remain largely unknown. In Arabidopsis thaliana, the Pleiotropic Regulatory Locus 1 (PRL1) encodes a WD40-repeat protein subunit of the spliceosome-activating Nineteen Complex (NTC) that plays a role in multiple stress, hormone and developmental signaling pathways. Here, we show that PRL1 is involved in the control of root meristem size and root stem cell niche activity. PRL1 is strongly expressed in the root meristem and its loss of function mutation results in disorganization of the quiescent center (QC), premature stem cell differentiation, aberrant cell division, and reduced root meristem size. Our genetic studies indicate that PRL1 is required for confined expression of the homeodomain transcription factor WOX5 in the QC and acts upstream of the transcription factor PLETHORA (PLT) in modulating stem cell niche activity and root meristem size. These findings define a role for PRL1 as an important determinant of PLT signaling that modulates maintenance of the stem cell niche and root meristem size.

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The Plant Cell Reviews Dynamic Aspects of Plant Hormone Signaling and Crosstalk

The Plant Cell Reviews Dynamic Aspects of Plant Hormone Signaling and Crosstalk | Plant Gene Seeker -PGS | Scoop.it

The Roles of ROS and ABA in Systemic Acquired Acclimation

Ron Mittler and Eduardo Blumwald

Plant Cell 2015 tpc.114.133090; First Published on January 20, 2015; doi:10.1105/tpc.114.133090 OPEN

http://www.plantcell.org/content/early/2015/01/20/tpc.114.133090.abstract

 

SCFTIR1/AFB-Based Auxin Perception: Mechanism and Role in Plant Growth and Development

Mohammad Salehin, Rammyani Bagchi, and Mark Estelle

Plant Cell 2015 tpc.114.133744; First Published on January 20, 2015; doi:10.1105/tpc.114.133744

http://www.plantcell.org/content/early/2015/01/20/tpc.114.133744.abstract

 

The PB1 Domain in Auxin Response Factor and Aux/IAA Proteins: A Versatile Protein Interaction Module in the Auxin Response

Tom J. Guilfoyle

Plant Cell 2015 tpc.114.132753; First Published on January 20, 2015; doi:10.1105/tpc.114.132753 OPEN

http://www.plantcell.org/content/early/2015/01/20/tpc.114.132753.abstract

 

PIN-Dependent Auxin Transport: Action, Regulation, and Evolution

Maciek Adamowski and Jiří Friml

Plant Cell 2015 tpc.114.134874; First Published on January 20, 2015; doi:10.1105/tpc.114.134874

http://www.plantcell.org/content/early/2015/01/20/tpc.114.134874.abstract

 

The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development

G. Eric Schaller, Anthony Bishopp, and Joseph J. Kieber

Plant Cell 2015 tpc.114.133595; First Published on January 20, 2015; doi:10.1105/tpc.114.133595

http://www.plantcell.org/content/early/2015/01/20/tpc.114.133595.abstract


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Spatial and temporal variation in plant hydraulic traits and their relevance for climate change impacts on vegetation

Spatial and temporal variation in plant hydraulic traits and their relevance for climate change impacts on vegetation | Plant Gene Seeker -PGS | Scoop.it

Anderegg - 2014 - New Phytologist - Wiley Online Library

Open Minireview

Andres Zurita's insight:

Plant hydraulics mediate terrestrial woody plant productivity, influencing global water, carbon, and biogeochemical cycles, as well as ecosystem vulnerability to drought and climate change. While inter-specific differences in hydraulic traits are widely documented, intra-specific hydraulic variability is less well known and is important for predicting climate change impacts. Here, I present a conceptual framework for this intra-specific hydraulic trait variability, reviewing the mechanisms that drive variability and the consequences for vegetation response to climate change. I performed a meta-analysis on published studies (n = 33) of intra-specific variation in a prominent hydraulic trait – water potential at which 50% stem conductivity is lost (P50) – and compared this variation to inter-specific variability within genera and plant functional types used by a dynamic global vegetation model. I found that intra-specific variability is of ecologically relevant magnitudes, equivalent to c. 33% of the inter-specific variability within a genus, and is larger in angiosperms than gymnosperms, although the limited number of studies highlights that more research is greatly needed. Furthermore, plant functional types were poorly situated to capture key differences in hydraulic traits across species, indicating a need to approach prediction of drought impacts from a trait-based, rather than functional type-based perspective.

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The origin and evolution of maize in the Southwestern United States

The origin and evolution of maize in the Southwestern United States | Plant Gene Seeker -PGS | Scoop.it

Nature Plants

Andres Zurita's insight:

The origin of maize (Zea maysmays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal1,2,3,4 or highland5,6 routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized7. To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.

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Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants

Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants | Plant Gene Seeker -PGS | Scoop.it

PLOS Biology

Andres Zurita's insight:

Inorganic arsenic is a carcinogen, and its ingestion through foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content 1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit both its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1-encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots, causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Furthermore, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic-containing food such as rice.

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The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway

The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway | Plant Gene Seeker -PGS | Scoop.it
Alan Lloyd and colleagues identify a MYB gene in beet that acts as a key regulator of the betalain red pigmentation pathway. They further show that this gene resides at the classical Y pigmentation locus and shares homology with MYB genes that encode positive regulators of the anthocyanin pigmentation pathway in other species.
Andres Zurita's insight:

Nearly all flowering plants produce red/violet anthocyanin pigments. Caryophyllales is the only order containing families that replace anthocyanins with unrelated red and yellow betalain pigments1, 2. Close biological correlation of pigmentation patterns suggested that betalains might be regulated by a conserved anthocyanin-regulating transcription factor complex consisting of a MYB, a bHLH and a WD repeat–containing protein (the MBW complex)3. Here we show that a previously uncharacterized anthocyanin MYB-like protein, Beta vulgaris MYB1 (BvMYB1), regulates the betalain pathway in beets. Silencing BvMYB1 downregulates betalain biosynthetic genes and pigmentation, and overexpressing BvMYB1 upregulates them. However, unlike anthocyanin MYBs, BvMYB1 will not interact with bHLH members of heterologous anthocyanin MBW complexes because of identified nonconserved residues. BvMYB1 resides at the historic beet pigment-patterning locus, Y, required for red-fleshed beets4. We show that Y and y express different levels of BvMYB1 transcripts. The co-option of a transcription factor regulating anthocyanin biosynthesis would be an important evolutionary event allowing betalains to largely functionally replace anthocyanins.

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How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity

How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity | Plant Gene Seeker -PGS | Scoop.it

Tree Physiology

Andres Zurita's insight:

Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and ‘improved’ trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity.

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How is water-use efficiency of terrestrial ecosystems distributed and changing on Earth?

How is water-use efficiency of terrestrial ecosystems distributed and changing on Earth? | Plant Gene Seeker -PGS | Scoop.it

Scientific Reports

Open Access

Andres Zurita's insight:

A better understanding of ecosystem water-use efficiency (WUE) will help us improve ecosystem management for mitigation as well as adaption to global hydrological change. Here, long-term flux tower observations of productivity and evapotranspiration allow us to detect a consistent latitudinal trend in WUE, rising from the subtropics to the northern high-latitudes. The trend peaks at approximately 51°N, and then declines toward higher latitudes. These ground-based observations are consistent with global-scale estimates of WUE. Global analysis of WUE reveals existence of strong regional variations that correspond to global climate patterns. The latitudinal trends of global WUE for Earth's major plant functional types reveal two peaks in the Northern Hemisphere not detected by ground-based measurements. One peak is located at 20° ~ 30°N and the other extends a little farther north than 51°N. Finally, long-term spatiotemporal trend analysis using satellite-based remote sensing data reveals that land-cover and land-use change in recent years has led to a decline in global WUE. Our study provides a new framework for global research on the interactions between carbon and water cycles as well as responses to natural and human impacts.

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PlantStars: Highly influential articles in Plant Sciences

PlantStars: Highly influential articles in Plant Sciences | Plant Gene Seeker -PGS | Scoop.it
Highly influential articles in Plant SciencesWelcome!   We would like to draw your attention to the “top mentioned”, “highly cited”, and “most downloaded” articles from select Springer and BioMed Central journals in Plant Sciences.  


Open access articles are freely available online on a permanent basis and all other articles have been made freely available until January 31, 2015. Enjoy - and spread the word!
Andres Zurita's insight:

Nice source of  plant references.

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Molecular basis of angiosperm tree architecture - New Phytologist

Molecular basis of angiosperm tree architecture - New Phytologist | Plant Gene Seeker -PGS | Scoop.it

New Phytologist

Tansley review

 

Free

Andres Zurita's insight:

The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science.

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Polyols in grape berry: transport and metabolic adjustments as a physiological strategy for water-deficit stress tolerance in grapevine

Polyols in grape berry: transport and metabolic adjustments as a physiological strategy for water-deficit stress tolerance in grapevine | Plant Gene Seeker -PGS | Scoop.it

Journal of Experimental Botany

Andres Zurita's insight:

Polyols are important metabolites that often function as carbon and energy sources and/or osmoprotective solutes in some plants. In grapevine, and in the grape berry in particular, the molecular aspects of polyol transport and metabolism and their physiological relevance are virtually unknown to date. Here, the biochemical function of a grapevine fruit mesocarp polyol transporter (VvPLT1) was characterized after its heterologous expression in yeast. This H+-dependent plasma membrane carrier transports mannitol (K m=5.4mM) and sorbitol (K m=9.5mM) over a broad range of polyols and monosaccharides. Water-deficit stress triggered an increase in the expression of VvPLT1 at the fully mature stage, allowing increased polyol uptake into pulp cells. Plant polyol dehydrogenases are oxireductases that reversibly oxidize polyols into monosaccharides. Mannitol catabolism in grape cells (K m=30.1mM mannitol) and mature berry mesocarps (K m=79mM) was, like sorbitol dehydrogenase activity, strongly inhibited (50–75%) by water-deficit stress. Simultaneously, fructose reduction into polyols via mannitol and sorbitol dehydrogenases was stimulated, contributing to their higher intracellular concentrations in water-deficit stress. Accordingly, the concentrations of mannitol, sorbitol, galactinol, myo-inositol, and dulcitol were significantly higher in berry mesocarps from water-deficit-stressed Tempranillo grapevines. Metabolomic profiling of the berry pulp by GC-TOF-MS also revealed many other changes in its composition induced by water deficit. The impact of polyols on grape berry composition and plant response to water deficit stress, via modifications in polyol transport and metabolism, was analysed by integrating metabolomics with transcriptional analysis and biochemical approaches.

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Strigolactones are involved in phosphate- and nitrate-deficiency-induced root development and auxin transport in rice

Strigolactones are involved in phosphate- and nitrate-deficiency-induced root development and auxin transport in rice | Plant Gene Seeker -PGS | Scoop.it

Journal of Experimental Botany

Andres Zurita's insight:

Strigolactones (SLs) or their derivatives have recently been defined as novel phytohormones that regulate root development. However, it remains unclear whether SLs mediate root growth in response to phosphorus (P) and nitrogen (N) deficiency. In this study, the responses of root development in rice (Oryza sativa L.) to different levels of phosphate and nitrate supply were investigated using wild type (WT) and mutants defective in SL synthesis (d10 and d27) or insensitive to SL (d3). Reduced concentration of either phosphate or nitrate led to increased seminal root length and decreased lateral root density in WT. Limitation of either P or N stimulated SL production and enhanced expression of D10, D17, and D27and suppressed expression of D3 and D14 in WT roots. Mutation of D10, D27, or D3 caused loss of sensitivity of root response to P and N deficiency. Application of the SL analogue GR24 restored seminal root length and lateral root density in WT and d10 and d27 mutants but not in the d3 mutant, suggesting that SLs were induced by nutrient-limiting conditions and led to changes in rice root growth via D3. Moreover, P or N deficiency or GR24 application reduced the transport of radiolabelled indole-3-acetic acid and the activity of DR5::GUS auxin reporter in WT and d10 and d27 mutants. These findings highlight the role of SLs in regulating rice root development under phosphate and nitrate limitation. The mechanisms underlying this regulatory role involve D3 and modulation of auxin transport from shoots to roots.

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Digging deeper: high-resolution genome-scale data yields new insights into root biology

Digging deeper: high-resolution genome-scale data yields new insights into root biology | Plant Gene Seeker -PGS | Scoop.it

Highlights•

Cell-type specific hormone signaling is important for the high-resolution salt stress response in the root.

Computational modeling of cell-type specific data illustrates the complexity of these networks.

Mutants that lack morphological phenotypes often have molecular phenotypes that are revealed with cell-type specific data.

High-resolution analysis of auxin responses identifies a bipartite auxin response along the longitudinal axis of the root.

New advances allowing simultaneous root growth and cellular imaging identify novel regulators of root growth and development.

Development in multicellular organisms is the result of designated cellular programs occurring at specific points in time and space. The root is an excellent model to address how spatio-temporal complexity impacts organ development. High-resolution ‘omic’ approaches have delineated the transcriptional, proteomic, metabolomic, and small RNA profiles of multiple cell types in the Arabidopsis root. Similar approaches have shed light on root cell-type specific transcriptional programs in rice and soybean. These data are being used to identify specific spatio-temporal mechanisms of root development, dissect regulatory networks that control cell identity, and understand hormone responses in the root. Computational modeling of these data combined with new advances in imaging technologies is generating new biological insights into root growth and development.


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Wise words from a tree physiologist

Wise words from a tree physiologist | Plant Gene Seeker -PGS | Scoop.it

Really enjoyed reading the biographies of Dennis Hoagland and William Chander, who collaborated on studies of mineral nutrition of plants. This quote from Chandler is abridged from a speech he gave during the second world war, but it's just as appropriate now.

 

http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/chandler-william-h.pdf

http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/hoagland-dennis-r.pdf


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Genomic selection in hybrid breeding

Genomic selection in hybrid breeding | Plant Gene Seeker -PGS | Scoop.it

Plant Breeding

Wiley Online Library

Open

Andres Zurita's insight:

While hybrid breeding is widely applied in outbreeding species, for many self-pollinating crop plants, it has only recently been established. This may have had its reason in the limitations of methods available for hybrid performance prediction, in particular when established heterotic pools were absent. Genomic selection has been suggested as a promising approach to resolve these limitations. In our review, we briefly introduce the principles of genomic selection as an extension of marker-assisted selection using genome-wide high-density molecular marker data and discuss the advantages and limitations of currently used algorithms. Including the outcome from a recent extended approach to hybrid wheat as a timely example, we summarize current progress in empirical studies on the application of genomic selection for prediction of hybrid performance. Here, we put emphasis on the factors affecting the accuracy of prediction, pointing in particular to the relevance of relatedness, genotype x environment interaction and experimental design. Finally, we discuss future research needs and potential applications.

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Identification of the transporter responsible for sucrose accumulation in sugar beet taproots

Identification of the transporter responsible for sucrose accumulation in sugar beet taproots | Plant Gene Seeker -PGS | Scoop.it
Nature Plants, Published online: 8 January 2015; | doi:10.1038/nplants.2014.1
Andres Zurita's insight:

Sugar beet provides around one third of the sugar consumed worldwide and serves as a significant source of bioenergy in the form of ethanol. Sucrose accounts for up to 18% of plant fresh weight in sugar beet. Most of the sucrose is concentrated in the taproot, where it accumulates in the vacuoles. Despite 30 years of intensive research, the transporter that facilitates taproot sucrose accumulation has escaped identification. Here, we combine proteomic analyses of the taproot vacuolar membrane, the tonoplast, with electrophysiological analyses to show that the transporter BvTST2.1 is responsible for vacuolar sucrose uptake in sugar beet taproots. We show that BvTST2.1 is a sucrose-specific transporter, and present evidence to suggest that it operates as a proton antiporter, coupling the import of sucrose into the vacuole to the export of protons. BvTST2.1 exhibits a high amino acid sequence similarity to members of the tonoplast monosaccharide transporter family in Arabidopsis, prompting us to rename this group of proteins ‘tonoplast sugar transporters’. The identification of BvTST2.1 could help to increase sugar yields from sugar beet and other sugar-storing plants in future breeding programs.

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Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses

Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses | Plant Gene Seeker -PGS | Scoop.it

New Phytologist

Tansley Insight

OPEN ACCESS

Andres Zurita's insight:

For survival, plants have to efficiently adjust their phenotype to environmental challenges, finely coordinating their responses to balance growth and defence. Such phenotypic plasticity can be modulated by their associated microbiota. The widespread mycorrhizal symbioses modify plant responses to external stimuli, generally improving the resilience of the symbiotic system to environmental stresses. Phytohormones, central regulators of plant development and immunity, are instrumental in orchestrating plant responses to the fluctuating environment, but also in the regulation of mycorrhizal symbioses. Exciting advances in the molecular regulation of phytohormone signalling are providing mechanistic insights into how plants coordinate their responses to environmental cues and mycorrhizal functioning. Here, we summarize how these mechanisms permit the fine-tuning of the symbiosis according to the ever-changing environment.

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An Arabidopsis gene regulatory network for secondary cell wall synthesis

An Arabidopsis gene regulatory network for secondary cell wall synthesis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein–DNA network between Arabidopsis thalianatranscription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

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The genome sequence of the orchid Phalaenopsis equestris

The genome sequence of the orchid Phalaenopsis equestris | Plant Gene Seeker -PGS | Scoop.it

Nature Genetics

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Andres Zurita's insight:

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

 
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Salinity tolerance in soybean is modulated by natural variation in GmSALT3

Salinity tolerance in soybean is modulated by natural variation in GmSALT3 | Plant Gene Seeker -PGS | Scoop.it

The Plant Journal - Wiley Online Library

OPEN ACCESS

Andres Zurita's insight:

The identification of genes that improve the salt tolerance of crops is essential for the effective utilization of saline soils for agriculture. Here, we use fine mapping in a soybean (Glycine max (L.) Merr.) population derived from the commercial cultivars Tiefeng 8 and 85–140 to identify GmSALT3 (salt tolerance-associated gene on chromosome 3), a dominant gene associated with limiting the accumulation of sodium ions (Na+) in shoots and a substantial enhancement in salt tolerance in soybean. GmSALT3 encodes a protein from the cation/H+ exchanger family that we localized to the endoplasmic reticulum and which is preferentially expressed in the salt-tolerant parent Tiefeng 8 within root cells associated with phloem and xylem. We identified in the salt-sensitive parent, 85–140, a 3.78-kb copia retrotransposon insertion in exon 3 of Gmsalt3 that truncates the transcript. By sequencing 31 soybean landraces and 22 wild soybean (Glycine soja) a total of nine haplotypes including two salt-tolerant haplotypes and seven salt-sensitive haplotypes were identified. By analysing the distribution of haplotypes among 172 Chinese soybean landraces and 57 wild soybean we found that haplotype 1 (H1, found in Tiefeng 8) was strongly associated with salt tolerance and is likely to be the ancestral allele. Alleles H2–H6, H8 and H9, which do not confer salinity tolerance, were acquired more recently. H1, unlike other alleles, has a wide geographical range including saline areas, which indicates it is maintained when required but its potent stress tolerance can be lost during natural selection and domestication. GmSALT3 is a gene associated with salt tolerance with great potential for soybean improvement.

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The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions

The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions | Plant Gene Seeker -PGS | Scoop.it

Cheeseman - 2014 - New Phytologist - Wiley Online Library

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Andres Zurita's insight:

The effective development of salt tolerant crops requires an understanding that the evolution of halophytes, glycophytes and our major grain crops has involved significantly different processes. Halophytes (and other edaphic endemics) generally arose through colonization of habitats in severe disequilibrium by pre-adapted individuals, rather than by gradual adaptation from populations of ‘glycophytes’. Glycophytes, by contrast, occur in low sodium ecosystems, where sodium was and is the major limiting nutrient in herbivore diets, suggesting that their evolution reflects the fact that low sodium individuals experienced lower herbivory and had higher fitness. For domestication/evolution of crop plants, the selective pressure was human imposed and involved humans co-opting functions of defense and reproductive security. Unintended consequences of this included loss of tolerance to various stresses and loss of the genetic variability needed to correct that. Understanding, combining and manipulating all three modes of evolution are now critical to the development of salt tolerant crops, particularly those that will offer food security in countries with few economic resources and limited infrastructure. Such efforts will require exploiting the genetic structures of recently evolved halophytes, the genetic variability of model plants, and endemic halophytes and ‘minor’ crops that already exist.

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SPINDLY, ERECTA, and Its Ligand STOMAGEN Have a Role in Redox-Mediated Cortex Proliferation in the Arabidopsis Root

SPINDLY, ERECTA, and Its Ligand STOMAGEN Have a Role in Redox-Mediated Cortex Proliferation in the Arabidopsis Root | Plant Gene Seeker -PGS | Scoop.it

MOLECULAR PLANT

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Andres Zurita's insight:

Reactive oxygen species (ROS) are harmful to all living organisms and therefore they must be removed to ensure normal growth and development. ROS are also signaling molecules, but so far little is known about the mechanisms of ROS perception and developmental response in plants. We here report that hydrogen peroxide induces cortex proliferation in the Arabidopsis root and that SPINDLY (SPY), an O-linked glucosamine acetyltransferase, regulates cortex proliferation by maintaining cellular redox homeostasis. We also found that mutation in the leucine-rich receptor kinase ERECTA and its putative peptide ligand STOMAGEN block the effect of hydrogen peroxide on root cortex proliferation. However, ERECTA and STOMAGEN are expressed in the vascular tissue, whereas extra cortex cells are produced from the endodermis, suggesting the involvement of intercellular signaling. SPY appears to act downstream of ERECTA, because the spy mutation still caused cortex proliferation in the erecta mutant background. We therefore have not only gained insight into the mechanism by which SPY regulates root development but also uncovered a novel pathway for ROS signaling in plants. The importance of redox-mediated cortex proliferation as a protective mechanism against oxidative stress is also discussed.

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Producción sostenible de alimentos: hechos y cifras

Producción sostenible de alimentos: hechos y cifras | Plant Gene Seeker -PGS | Scoop.it
La agricultura debe alimentar a más gente y más sosteniblemente. Zareen Bharucha analiza diversos enfoques científicos.
Andres Zurita's insight:
De un vistazo 

El deterioro del suelo, el cambio climático y la disponibilidad de agua y energía son todos retos de la agricultura

La CyT ha hecho contribuciones para aumentar la producción de alimentos, pero aún son necesarias nuevas estrategias

La agricultura sostenible se puede beneficiar del enfoque de 'sistema' y de la participación campesina

- See more at: http://www.scidev.net/america-latina/agricultura/especial/producci-n-sostenible-de-alimentos-hechos-y-cifras.html#sthash.QhalJT4u.dpuf

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ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1) is required for cell production, patterning, and morphogenesis in root development

ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1) is required for cell production, patterning, and morphogenesis in root development | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1/SDG27), a known regulator of flower development, encodes a H3K4histone methyltransferase that maintains a number of genes in an active state. In this study, the role of ATX1 in root development was evaluated. The loss-of-function mutant atx1-1 was impaired in primary root growth. The data suggest that ATX1 controls root growth by regulating cell cycle duration, cell production, and the transition from cell proliferation in the root apical meristem (RAM) to cell elongation. In atx1-1, the quiescent centre (QC) cells were irregular in shape and more expanded than those of the wild type. This feature, together with the atypical distribution of T-divisions, the presence of oblique divisions, and the abnormal cell patterning in the RAM, suggests a lack of coordination between cell division and cell growth in the mutant. The expression domain of QC-specific markers was expanded both in the primary RAM and in the developing lateral root primordia of atx1-1 plants. These abnormalities were independent of auxin-response gradients. ATX1 was also found to be required for lateral root initiation, morphogenesis, and emergence. The time from lateral root initiation to emergence was significantly extended in the atx1-1 mutant. Overall, these data suggest that ATX1 is involved in the timing of root development, stem cell niche maintenance, and cell patterning during primary and lateral root development. Thus, ATX1 emerges as an important player in root system architecture.

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