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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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Xylem development – from the cradle to the grave - New Phytologist

Xylem development – from the cradle to the grave - New Phytologist | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The development and growth of plants, as well as their successful adaptation to a variety of environments, is highly dependent on the conduction of water, nutrients and other important molecules throughout the plant body. Xylem is a specialized vascular tissue that serves as a conduit of water and minerals and provides mechanical support for upright growth. Wood, also known as secondary xylem, constitutes the major part of mature woody stems and roots. In the past two decades, a number of key factors including hormones, signal transducers and (post)transcriptional regulators have been shown to control xylem formation. We outline the main mechanisms shown to be essential for xylem development in various plant species, with an emphasis on Arabidopsis thaliana, as well as several tree species where xylem has a long history of investigation. We also summarize the processes which have been shown to be instrumental during xylem maturation. This includes mechanisms of cell wall formation and cell death which collectively complete xylem cell fate.

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Friends or Foes: New Insights in Jasmonate and Ethylene Co-Actions

Friends or Foes: New Insights in Jasmonate and Ethylene Co-Actions | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

One strategy for sessile plants to adapt to their surrounding environment involves the modulation of their various internal phytohormone signaling and distributions when the plants sense environmental change. There are currently dozens of identified phytohormones in plant cells and they act in concert to regulate plant growth, development, metabolism and defense. It has been determined that phytohormones often act together to achieve certain physiological functions. Thus, the study of hormone–hormone interactions is becoming a competitive research field for deciphering the underlying regulatory mechanisms. Among phytohormones, jasmonate and ethylene present a fascinating case of synergism and antagonism. They are commonly recognized as defense hormones that act synergistically. Plants impaired in jasmonate and/or ethylene signaling are susceptible to infections by necrotrophic fungi, suggesting that these two hormones are both required for defense. Moreover, jasmonate and ethylene also act antagonistically, such as in the regulation of apical hook development and wounding responses. Here, we highlight the recent breakthroughs in the understanding of jasmonate–ethylene co-actions and point out the potential power of studying protein–protein interactions for systematically exploring signal cross-talk.

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Special issue on the impacts of climate change on food safety

Andres Zurita's insight:

Climate change is a current global concern and, despite continuing controversy about the magnitude of its effects, has affected the food production systems and supply chain (IPCC, 2014a and IPCC, 2014b). Climate change has an impact not only on crop production or food security (Fischer et al., 2005 and Gregory et al., 2005), but also on food safety, incidence and prevalence of foodborne diseases (Bezirtzoglou et al., 2011, Lal et al., 2012, Miraglia et al., 2009 and Tirado et al., 2010).

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Agriculture & Food Security | Full text | Genetically modified crops: the truth unveiled

Andres Zurita's insight:

What has long been suspected is true: genetically modified (GM) crops do have real benefits for the environment and for the economic well-being of farmers. A meta-analysis of peer-reviewed journal articles and other literature not published in journals reveals that the adoption of GM crops reduces pesticide input and increases crop yields and farmers’ income. The results confirm earlier and smaller studies and therefore are not unexpected. But they are particularly welcome for significantly informing the public debate on GM crops.

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Tonoplast CBL–CIPK calcium signaling network regulates magnesium homeostasis in Arabidopsis

Tonoplast CBL–CIPK calcium signaling network regulates magnesium homeostasis in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Plant growth requires a balanced supply of mineral nutrients. However, the availability of minerals varies constantly in the environment. How do plants adapt to low or high levels of minerals in the soil? The answer to this question holds the key to sustainable crop production. Mg is an essential macronutrient for plants, but high levels of Mg2+ can become toxic. This study uncovered a regulatory mechanism, consisting of two calcineurin B-like (CBL) Ca sensors partnering with four CBL-interacting protein kinases (CIPKs) forming a CBL–CIPK network that allows plant cells to sequester the extra Mg2+ into vacuoles, thereby protecting plant cells from high-Mg toxicity. To our knowledge, this report is the first that describes such a signaling mechanism for regulation of Mg homeostasis.

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Plant salt tolerance: adaptations in halophytes

Plant salt tolerance: adaptations in halophytes | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Background 

Most of the water on Earth is seawater, each kilogram of which contains about 35 g of salts, and yet most plants cannot grow in this solution; less than 0·2 % of species can develop and reproduce with repeated exposure to seawater. These ‘extremophiles’ are called halophytes.

Scope 

Improved knowledge of halophytes is of importance to understanding our natural world and to enable the use of some of these fascinating plants in land re-vegetation, as forages for livestock, and to develop salt-tolerant crops. In this Preface to a Special Issue on halophytes and saline adaptations, the evolution of salt tolerance in halophytes, their life-history traits and progress in understanding the molecular, biochemical and physiological mechanisms contributing to salt tolerance are summarized. In particular, cellular processes that underpin the ability of halophytes to tolerate high tissue concentrations of Na+ and Cl−, including regulation of membrane transport, their ability to synthesize compatible solutes and to deal with reactive oxygen species, are highlighted. Interacting stress factors in addition to salinity, such as heavy metals and flooding, are also topics gaining increased attention in the search to understand the biology of halophytes.

Conclusions 

Halophytes will play increasingly important roles as models for understanding plant salt tolerance, as genetic resources contributing towards the goal of improvement of salt tolerance in some crops, for re-vegetation of saline lands, and as ‘niche crops’ in their own right for landscapes with saline soils.

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Severe drought stress is affecting selected primary metabolites, polyphenols, and volatile metabolites in grapevine leaves (Vitis vinifera cv. Pinot noir)

Severe drought stress is affecting selected primary metabolites, polyphenols, and volatile metabolites in grapevine leaves (Vitis vinifera cv. Pinot noir) | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Extreme weather conditions with prolonged dry periods and high temperatures as well as heavy rain events can severely influence grapevine physiology and grape quality. The present study evaluates the effects of severe drought stress on selected primary metabolites, polyphenols and volatile metabolites in grapevine leaves. Among the 11 primary metabolites, 13 polyphenols and 95 volatiles which were analyzed, a significant discrimination between control and stressed plants of 7 primary metabolites, 11 polyphenols and 46 volatile metabolites was observed. As single parameters are usually not specific enough for the discrimination of control and stressed plants, an unsupervised (PCA) and a supervised (PLS-DA) multivariate approach were applied to combine results from different metabolic groups. In a first step a selection of five metabolites, namely citric acid, glyceric acid, ribose, phenylacetaldehyde and 2-methylbutanal were used to establish a calibration model using PLS regression to predict the leaf water potential. The model was strong enough to assign a high number of plants correctly with a correlation of 0.83. The PLS-DA provides an interesting approach to combine data sets and to provide tools for the specific evaluation of physiological plant stresses.

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Introduced and invasive cactus species: a global review

Andres Zurita's insight:

Understanding which species are introduced and become invasive, and why, are central questions in invasion science. Comparative studies on model taxa have provided important insights, but much more needs to be done to unravel the context dependencies of these findings. The cactus family (Cactaceae), one of the most popular horticultural plant groups, is an interesting case study. Hundreds of cactus species have been introduced outside their native ranges; a few of them are among the most damaging invasive plant species in the world. We reviewed the drivers of introductions and invasions in the family and seek insights that can be used to minimize future risks. We compiled a list of species in the family and determined which have been recorded as invasive. We also mapped current global distributions and modelled the potential global distributions based on distribution data of known invasive taxa. Finally, we identified whether invasiveness is phylogenetically clustered for cacti and whether particular traits are correlated with invasiveness. Only 57 of the 1922 cactus species recognized in this treatment have been recorded as invasive. There are three invasion hotspots: South Africa (35 invasive species recorded), Australia (26 species) and Spain (24 species). However, there are large areas of the world with climates suitable for cacti that are at risk of future invasion—in particular, parts of China, eastern Asia and central Africa. The invasive taxa represent an interesting subset of the total species pool. There is a significant phylogenetic signal: invasive species occur in 2 of the 3 major phylogenetic clades and in 13 of the 130 genera. This phylogenetic signal is not driven by human preference, i.e. horticultural trade, but all invasive species are from 5 of the 12 cactus growth forms. Finally, invasive species tend to have significantly larger native ranges than non-invasive species, and none of the invasive species are of conservation concern in their native range. These results suggest fairly robust correlates of invasiveness that can be used for proactive management and risk assessments.

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Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as “junk” DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

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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.


Via Christophe Jacquet, Fenglin Deng
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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


Via Mary Williams
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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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The Soil Microbiome Influences Grapevine-Associated Microbiota

The Soil Microbiome Influences Grapevine-Associated Microbiota | Plant Gene Seeker -PGS | Scoop.it

mBio

Open Access

Andres Zurita's insight:

Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g., Rhizobiaceae and Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.

 
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The Draft Genome of Hop (Humulus lupulus), an Essence for Brewing

The Draft Genome of Hop (Humulus lupulus), an Essence for Brewing | Plant Gene Seeker -PGS | Scoop.it

Plant & Cell Physiology

Andres Zurita's insight:

The female flower of hop (Humulus lupulus var. lupulus) is an essential ingredient that gives characteristic aroma, bitterness and durability/stability to beer. However, the molecular genetic basis for identifying DNA markers in hop for breeding and to study its domestication has been poorly established. Here, we provide draft genomes for two hop cultivars [cv. Saazer (SZ) and cv. Shinshu Wase (SW)] and a Japanese wild hop [H. lupulus var. cordifolius; also known as Karahanasou (KR)]. Sequencing and de novo assembly of genomic DNA from heterozygous SW plants generated scaffolds with a total size of 2.05 Gb, corresponding to approximately 80% of the estimated genome size of hop (2.57 Gb). The scaffolds contained 41,228 putative protein-encoding genes. The genome sequences for SZ and KR were constructed by aligning their short sequence reads to the SW reference genome and then replacing the nucleotides at single nucleotide polymorphism (SNP) sites. De novoRNA sequencing (RNA-Seq) analysis of SW revealed the developmental regulation of genes involved in specialized metabolic processes that impact taste and flavor in beer. Application of a novel bioinformatics tool, phylogenetic comparative RNA-Seq (PCP-Seq), which is based on read depth of genomic DNAs and RNAs, enabled the identification of genes related to the biosynthesis of aromas and flavors that are enriched in SW compared to KR. Our results not only suggest the significance of historical human selection process for enhancing aroma and bitterness biosyntheses in hop cultivars, but also serve as crucial information for breeding varieties with high quality and yield.

 
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Iron- and Ferritin-Dependent Reactive Oxygen Species Distribution: Impact on Arabidopsis Root System Architecture

Iron- and Ferritin-Dependent Reactive Oxygen Species Distribution: Impact on Arabidopsis Root System Architecture | Plant Gene Seeker -PGS | Scoop.it

Molecular Plant

Andres Zurita's insight:

Iron (Fe) homeostasis is integrated with the production of reactive oxygen species (ROS), and distribution at the root tip participates in the control of root growth. Excess Fe increases ferritin abundance, enabling the storage of Fe, which contributes to protection of plants against Fe-induced oxidative stress. AtFer1 and AtFer3 are the two ferritin genes expressed in the meristematic zone, pericycle and endodermis of the Arabidopsis thaliana root, and it is in these regions that we observe Fe stained dots. This staining disappears in the triple fer1-3-4 ferritin mutant. Fe excess decreases primary root length in the same way in wild-type and in fer1-3-4 mutant. In contrast, the Fe-mediated decrease of lateral root (LR) length and density is enhanced in fer1-3-4 plants due to a defect in LR emergence. We observe that this interaction between excess Fe, ferritin, and root system architecture (RSA) is in part mediated by the H2O2/O2·− balance between the root cell proliferation and differentiation zones regulated by the UPB1 transcription factor. Meristem size is also decreased in response to Fe excess in ferritin mutant plants, implicating cell cycle arrest mediated by the ROS-activated SMR5/SMR7 cyclin-dependent kinase inhibitors pathway in the interaction between Fe and RSA.

 
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The genome of melon (Cucumis melo L.)

The genome of melon (Cucumis melo L.) | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site–leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

 
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Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple

Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple | Plant Gene Seeker -PGS | Scoop.it
Fruit crops: Determining dwarfism in apples
Dwarfing revolutionized apple cultivation, but its genetic basis is poorly understood. Researchers led by Toshi Foster at the New Zealand Institute for Plant and Food Research have now analysed the basis of dwarfing and discovered two interacting genetic regions account for the reduced growth produced by most ‘dwarfing’ apple rootstocks. To distinguish genetic from environmental effects, the team analysed a large, standardized population of apple trees grown on both dwarfing and more vigorous rootstocks. Their results confirmed one previously identified dwarfing gene, Dw1, and uncovered a second, Dw2. Unlike Dw1, Dw2 alone does not cause dwarfing, suggesting it may act as an enhancer of Dw1. Foster's team found markers of Dw1 and Dw2 in most modern dwarfing apple rootstocks, implying all such rootstocks derive from a single origin. The study provides crucial information for future apple rootstock breeding.
Andres Zurita's insight:

The apple dwarfing rootstock ‘Malling9’ (‘M9’) has been used worldwide both to reduce scion vigour and as a genetic source for breeding new rootstocks. Progeny of ‘M9’ segregate for rootstock-induced dwarfing of the scion, indicating that this trait is controlled by one or more genetic factors. A quantitative trait locus (QTL) analysis of a rootstock population derived from the cross between ‘M9’ × ‘Robusta5’ (non-dwarfing) and grafted with ‘Braeburn’ scions identified a major QTL (Dw1) on linkage group (LG) 5, which exhibits a significant influence on dwarfing of the scion. A smaller-effect QTL affecting dwarfing (Dw2) was identified on LG11, and four minor-effect QTLs were found on LG6, LG9, LG10 and LG12. Phenotypic analysis indicates that the combination of Dw1 and Dw2 has the strongest influence on rootstock-induced dwarfing, and that Dw1 has a stronger effect than Dw2. Genetic markers linked to Dw1 and Dw2 were screened over 41 rootstock accessions that confer a range of effects on scion growth. The majority of the dwarfing and semi-dwarfing rootstock accessions screened carried marker alleles linked to Dw1 and Dw2. This suggests that most apple dwarfing rootstocks have been derived from the same genetic source.

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Functional characterization and developmental expression profiling of gibberellin signalling components in Vitis vinifera

Functional characterization and developmental expression profiling of gibberellin signalling components in Vitis vinifera | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Gibberellins (GAs) regulate numerous developmental processes in grapevine (Vitis vinifera) such as rachis elongation, fruit set, and fruitlet abscission. The ability of GA to promote berry enlargement has led to its indispensable use in the sternospermocarpic (‘seedless’) table grape industry worldwide. However, apart from VvGAI1 (VvDELLA1), which regulates internode elongation and fruitfulness, but not berry size of seeded cultivars, little was known about GA signalling in grapevine. We have identified and characterized two additional DELLAs (VvDELLA2 and VvDELLA3), two GA receptors (VvGID1a and VvGID1b), and two GA-specific F-box proteins (VvSLY1a and VvSLY1b), in cv. Thompson seedless. With the exception of VvDELLA3-VvGID1b, all VvDELLAs interacted with the VvGID1s in a GA-dependent manner in yeast two-hybrid assays. Additionally, expression of these grape genes in corresponding Arabidopsis mutants confirmed their functions in planta. Spatiotemporal analysis of VvDELLAs showed that both VvDELLA1 and VvDELLA2 are abundant in most tissues, except in developing fruit where VvDELLA2 is uniquely expressed at high levels, suggesting a key role in fruit development. Our results further suggest that differential organ responses to exogenous GA depend on the levels of VvDELLA proteins and endogenous bioactive GAs. Understanding this interaction will allow better manipulation of GA signalling in grapevine.

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Suppression of soil nitrification by plants

Suppression of soil nitrification by plants | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:
Highlights

• Modern agricultural systems have become high-nitrifying.


• Nitrification control is critical to improve NUE in agricultural systems.

• Release of nitrification inhibitors from plant roots is termed BNI function.• BNI-enabled food and feed crops can reduce nitrification and N2O emissions.• Next-generation production systems need to be low-nitrifying and low-N2O emitting.
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Shoot and root branch growth angle control—the wonderfulness of lateralness

Shoot and root branch growth angle control—the wonderfulness of lateralness | Plant Gene Seeker -PGS | Scoop.it
The overall shape of plants, the space they occupy above and below ground, is determined principally by the number, length, and angle of their lateral branches. The function of these shoot and root branches is to hold leaves and other organs to the sun, and below ground, to provide anchorage and facilitate the uptake of water and nutrients. While in some respects lateral roots and shoots can be considered mere iterations of the primary root-shoot axis, in others there are fundamental differences in their biology, perhaps most conspicuously in the regulation their angle of growth. Here we discuss recent advances in the understanding of the control of branch growth angle, one of the most important but least understood components of the wonderful diversity of plant form observed throughout nature.
Andres Zurita's insight:
Highlights

 • Gravitropic setpoint angles are growth angles that are maintained relative to gravity.

• Non-vertical branch growth is an important adaptive trait that is poorly understood.• Auxin is central to the gravity-dependent, non-vertical growth of lateral branches.• Non-vertical GSAs arise via balancing gravitropic and antigravitropic components.
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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, 10:49 AM

Großartige Literatursammlung für wissenschaftliches Schreiben. 

Bibhya Sharma's curator insight, February 3, 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


Via Mary Williams, Christophe Jacquet
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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

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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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