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Trends in Genetics - Bridging the gap between genome analysis and precision breeding in potato

Trends in Genetics - Bridging the gap between genome analysis and precision breeding in potato | plant cell genetics | Scoop.it

Efficiency and precision in plant breeding can be enhanced by using diagnostic DNA-based markers for the selection of superior cultivars. This technique has been applied to many crops, including potatoes. The first generation of diagnostic DNA-based markers useful in potato breeding were enabled by several developments: genetic linkage maps based on DNA polymorphisms, linkage mapping of qualitative and quantitative agronomic traits, cloning and functional analysis of genes for pathogen resistance and genes controlling plant metabolism, and association genetics in collections of tetraploid varieties and advanced breeding clones. Although these have led to significant improvements in potato genetics, the prediction of most, if not all, natural variation in agronomic traits by diagnostic markers ultimately requires the identification of the causal genes and their allelic variants. This objective will be facilitated by new genomic tools, such as genomic resequencing and comparative profiling of the proteome, transcriptome, and metabolome in combination with phenotyping genetic materials relevant for variety development.

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Growing monstrous organisms: the construction of anti-GMO visual rhetoric through digital media

Growing monstrous organisms: the construction of anti-GMO visual rhetoric through digital media | plant cell genetics | Scoop.it
This paper explores the international controversy over genetically modified organisms (GMOs). We argue that the uncommonly high levels of opposition to genetically modified food in both the United States and in Europe can be attributed to the overwhelming success of the online visual campaign against GMOs. By exploiting the unique characteristics of the internet to create memetic images that can travel freely across linguistic and cultural borders, opponents of the technology have been able to refute rationalist claims about the safety of GMOs. In response to the single coherent narrative of scientific certainty, a diffuse set of challenges emerges. The risk of genetic engineering holds within it the potential for catastrophe, leaving the industries that produce and manufacture the technology in a perpetual state of crisis. Instead of a unified narrative of scientific certainty, each challenge presents a multiplicity of diffuse narratives that unsettle the public’s understanding of the risk presented by GMOs. We aim to augment traditional understandings of the way that publics may interact with the “public screen” by explicating one way in which dominance of the visual in mediated political discourse may privilege non-rational political decision making.
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Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Reconciling the evolutionary origin of bread wheat (Triticum aestivum) | plant cell genetics | Scoop.it
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.

Via Pierre-Marc Delaux, Loïc Lepiniec
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Italian horticultural and culinary records of summer squash (Cucurbita pepo, Cucurbitaceae) and emergence of the zucchini in 19th-century Milan

Italian horticultural and culinary records of summer squash (Cucurbita pepo, Cucurbitaceae) and emergence of the zucchini in 19th-century Milan | plant cell genetics | Scoop.it
The results indicate that Cucurbita fruits, both young and mature, entered Italian kitchens by the mid-16th century. A half-century later, round and elongate young fruits of C. pepo were addressed as separate cookery items and the latter had largely replaced the centuries-old culinary use of young, elongate bottle gourds, Lagenaria siceraria. Allusion to a particular, extant cultivar of the longest fruited C. pepo, the Cocozelle Group, dates to 1811 and derives from the environs of Naples. The Italian diminutive word zucchini arose by the beginning of the 19th century in Tuscany and referred to small, mature, desiccated bottle gourds used as containers to store tobacco. By the 1840s, the Tuscan word zucchini was appropriated to young, primarily elongate fruits of C. pepo. The Zucchini Group traces its origins to the environs of Milan, perhaps as early as 1850. The word zucchini and the horticultural product zucchini arose contemporaneously but independently. The results confirm that the Zucchini Group is the youngest of the four cultivar-groups of C. pepo subsp. pepo but it emerged approximately a half-century earlier than previously known.
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Science: Can Apulia's olive trees be saved? (2016)

Science: Can Apulia's olive trees be saved? (2016) | plant cell genetics | Scoop.it

On 21 October 2013, the Italian phytosanitary service notified the European Commission (EC) that the plant pathogen Xylella fastidiosa had been detected in olive trees near Gallipoli, a tourist destination in Italy's southern region of Apulia (1). This xylem-limited bacterium is spread by insect vectors and causes disease in crops such as grapevines, citrus, coffee, and almond; various ornamentals; and trees such as oaks, elms, and sycamores. Because of the risks of X. fastidiosa being introduced, established, and spread throughout Europe, this species is a regulated quarantine pest. Yet, X. fastidiosa has been left unchecked and has marched northward, leaving destruction in its wake (see the photo) (2). The establishment of X. fastidiosa in Italy has been an agricultural, environmental, political, and cultural disaster.

 

The threat of X. fastidiosa to European and Mediterranean agriculture, forests, and ecosystems goes beyond specific crops such as grapevines or citrus. The current host range of this bacterium includes more than 300 plant species (3). Most of these species support some degree of pathogen multiplication without expressing symptoms. Susceptible hosts infected with X. fastidiosa often show disease symptoms only after months or years, although epidemics can spread fast and be devastating.

 

A phylogenetic study has shown that the genotype in Italy was likely introduced via contaminated plant material from Costa Rica (3). Several X. fastidiosa-infected coffee plants from Costa Rica have been intercepted at European ports since 2014, supporting this hypothesis (4). As a response, the EC in February 2014 approved European Union (EU) emergency measures aimed at preventing the introduction and spread of X. fastidiosa. Since May 2015, the import of coffee plants from Costa Rica and Honduras into the EU has been forbidden. Limiting the introduction of insect vectors is considered an easier task, but this is not possible for X. fastidiosa because any xylem-sap-sucking insect species can be a potential vector. Europe has few sharpshooter leafhopper species, the most important group of vectors in the Americas. However, various endemic spittlebug species (froghoppers) are also potential vectors of X. fastidiosa (3).

 

Trade is an important pathway in the introduction of plant pests and pathogens (5), and X. fastidiosa-infected plant material has likely been introduced via European ports on a regular basis. Given that biological and environmental conditions in Europe support X. fastidiosainfection, the question arises why the pathogen has not been reported previously. One possible explanation is that limited surveillance efforts missed previous introductions. Monitoring was one component of the EU emergency measures. After the French authorities started a systematic monitoring program for X. fastidiosa in 2014, they found 250 distinct infected areas in Corsica and several in the French Riviera. However, no disease epidemic has yet been noted in France, and the genotype of X. fastidiosa differs from that found in Italy.


Via Kamoun Lab @ TSL, Luigi Guarino
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The sticky materiality of neo-liberal neonatures: GMOs and the agrarian question - Carroll (2016) - New Political Economy

The sticky materiality of neo-liberal neonatures: GMOs and the agrarian question - Carroll (2016) - New Political Economy | plant cell genetics | Scoop.it
This article uses Marxist theories of agrarian capitalism to explore the political economy of genetically modified organisms (GMO) agriculture. It argues that the successes and failures of GMO agriculture have been partly circumscribed by the structural requirements of the capitalist system, as well as by the materiality of GMO crops themselves. Successful innovations have been able to mitigate the material barriers to accumulation found in agricultural production, and thus appeal directly to farmers as comparatively profitable capital inputs. In this way, they cohere with David Goodman’s notion of appropriationism, where manufactured capital inputs (such as pesticides, machinery and fertilisers) replace ‘natural’ inputs (such as manure or draft animals), reducing labour time and biological contingency, and thus creating a competitive advantage for those farmers who adopt the new technology (at least temporarily). Conversely, innovations that are geared at consumers rather than farmers have largely failed due to their status as value-added products (whose value is subjective and market-driven) rather than capital goods. The article uses contrasting case studies of herbicide-tolerant soybeans, beta-keratin[sic!]-enhanced rice and slow-ripening tomatoes to demonstrate how and why the structural imperatives of global capitalism have enabled the success of some, and the failure of other innovations. 

The late-twentieth-century rise of biotechnology – and GMOs (genetically modified organisms) in particular – garnered tremendous popular, activist, scholarly and corporate attention. Evaluations of GMO technologies ranged from apocalyptic to utopian, but few doubted that GMOs would significantly transform our food system… However, two decades since the commercial release of the first GMO food… GMOs have been neither a global panacea nor a pandemic. Their modest, if not underwhelming, performance may be what needs accounting. This is not to say there have been no successes, particularly early on in the late 1990s. Two transgenic events – tolerance to herbicides and resistance to pests – have been remarkably implemented, capturing substantial control over some of the world’s most significant crops… From the perspective of… corporations… these innovations have been cash cows, enabling near-monopoly control over not only transgenic seed sales, but also often other agricultural inputs, such as herbicides. But these innovations – among them Roundup Ready soybeans and canola and Bt corn and cotton – are virtually the only commercially successful GMOs. Moreover, all of these innovations were already commercially available in the late 1990s. In the meantime, no further innovations of significance have emerged, while many have faltered, such as Bt potatoes, Roundup Ready wheat and perhaps most notably, beta-keratin[sic!]-enhanced ‘Golden Rice’… 

No single factor accounts for either the early success or subsequent setbacks of the GMO food economy. To understand the contemporary context, we have to examine its juridico-political, economic, biophysical and cultural dimensions. However, this article focuses on the material, in particular the economic, considering from a Marxist perspective how the logic of capital has both enabled and constrained the development of the GMO food economy, and how the biophysicality of GMO crops has been manifested as both an opportunity and a challenge to capital. It locates GMOs within the historical context of agrarian capitalism, linking with earlier debates over the problems that agriculture poses to capital as a site of profitable accumulation, showing how both the successes and failures of GMO agriculture can be understood in the wider context of agrarian capitalism, and the problems (and opportunities) that agriculture’s unique spatial, temporal and biophysical demands pose to capital. 

I argue that technologies that can temporarily overcome or reduce these barriers to accumulation hold the potential to be highly profitable and thus successful, while those that do not directly alter the conditions of production will likely be ignored by industry. This dialectic can, therefore, help explain both the successes and failures of GMO agriculture to date, and demonstrate the extent to which corporate profitability rather than social utility has driven GMO innovation thus far. The trajectory of GMO technological innovation has been heavily structured by the logic of capital, a condition that accounts for the lack of success in innovations not targeted at reducing the temporal, spatial and biophysical constraints to capital within the production process. For example, herbicide tolerance and pest resistance are both innovations that affect production by changing the ways farmers address the problems posed by weeds and pests. Innovations geared at consumers (such as nutrient enhancement or slower ripening), which yield value-added end products but make no difference in the actual production process, have largely failed. 

The article begins with an historical overview of the agrarian question, discussing how Marxists have dealt with the problems agriculture poses to capital accumulation and how capital has sought to overcome these problems. Section II theorises the conditions under which GMO agriculture has been successful, considering how GMOs fit a wider tendency within agricultural capitalism to mitigate spatial, temporal and biophysical barriers to the reduction of labour and production time (and thus to added surplus value) through capital inputs, or what Goodman et al. (1987) have termed ‘appropriationism’. However, at stake in GMO agriculture is not simply the way biophysical inputs are replaced with synthetic industrial inputs, but how property rights are managed throughout the commodity chain with patents and technology use agreements (TUAs), ensuring the extraction of rents for patent holders, a logic of accumulation that Pechlaner (2010) has termed ‘expropriationism’. Through both of these logics, capital is able to subsume elements of the production process, extracting greater surplus value than under an unsubsumed system of production… My analysis builds on these earlier accounts by arguing and demonstrating that the logic of capital works to both enable and constrain the trajectory of GMO development. Appropriationism and expropriationism are thus significant in understanding not only how and why certain innovations have met with success, but also why so many others have failed. This demonstrates that although capitalism’s competitive logic may promote innovation, in biotechnology and elsewhere, it is only certain innovations – and by no means the most socially useful – that can ever be profitably pursued… 

Section III turns to a theorisation of the barriers to accumulation posed by both the logic of capital and the materiality of GMOs. It considers how consumption-oriented innovations have failed to provide an impetus for capital to invest and have thus been ignored, despite great potential benefits to the public. Just as the logic of capital has enabled the development of certain innovations, it has hindered the development of others. The section also considers a separate set of constraints: the ecological and biophysical barriers to accumulation that are in part a consequence of the inherent dynamism and complexity of the life sciences… Ultimately, the argument advanced here is not meant to dismiss GMOs as a failed technology. Their failures are overdetermined by the structural contours of global capitalism, among other factors. Today’s GMO food economy emerged in the context of the particular political economic configuration of neo-liberal globalisation, and its real-world manifestations cannot be detached from this context. However, a different political economic context, driven by motives other than profit and capital accumulation, would enable a different, and perhaps more hopeful, GMO food economy. The story of GMO agriculture is today only a recent iteration of the story of capitalist agriculture. The future of GMO agriculture holds the potential for a wholly different narrative… 

The story of GMOs – their successes and failures – is only the latest chapter in the story of agricultural capitalism. The path of their development has been significantly conditioned by the materiality of agricultural capitalism. GMOs have been successful because they help overcome barriers to accumulation inherent to the biophysicality of agriculture. In this way, their commercial success has paralleled earlier appropriationist technologies, including machinery and chemical inputs. As on-farm labour and production are replaced with off-farm, industrial labour and production, the barriers to accumulation posed by agriculture’s inherent materiality are diminished. However, GMOs, like hybrid seeds before them, differ from other appropriationist technologies. Their liveliness and in particular their reproducibility present both new challenges and new opportunities. There are challenges of maintaining control, not just of the reproductive capacities of the seeds, but of how ownership rights can be preserved for patent holders beyond the first generation of the plants. This challenge has necessitated a stringent IPR regime, which has substantially empowered biotechnology firms, and been termed expropriationism. 

This paper has demonstrated how the dual accumulation strategy of appropriationism and expropriationism has made certain GMOs profitable for capital and inescapable for (most) farmers. The converse of this process has been the failure of numerous innovations that do not cohere with the industrial logic inherent to successful GMOs. Biotechnology multinationals have eschewed innovations that address consumer health, nutrition or aesthetic considerations because of the uncertainty of any success in these innovations. Without any structural impetus for farmers to adopt transgenic crops that do not inherently improve the production process, there is no guarantee that such crops would even be planted, let alone sold for a premium in grocery stores. In this way, the logic of agricultural capitalism has significantly narrowed the spectrum of GMO development. 

However, if the current situation is the result of a particular set of material constraints inherent to the logic of capital, this does not render it inevitable. A categorical rejection of GMOs without consideration of the contingency of their location within capitalist political economies only serves to further entrench and naturalise the hegemony of capitalism. A critical reformulation of the global food economy must start with a decoupling of the biotech baby from the capitalist bathwater. 



Via Alexander J. Stein
Jean-Pierre Zryd's insight:
Excellent analysis of the complicity between capitalism and the anti - biotech crowd in the  (almost) killing of #GMO
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Alexander J. Stein's curator insight, August 6, 9:11 AM
“From the perspective of… corporations… these innovations have been cash cows, enabling near-monopoly control over not only transgenic seed sales, but also often other agricultural inputs, such as herbicides.” >> It’s only a monopoly if a buyer has no other option but to buy from one supplier. However, there is more than just one seed provider (and depending on the country, the global companies can be in competition with local providers, too), and farmers have the option to choose not only between different GM seeds but also to buy non-GM, for which there are even more companies and providers. Moreover, even if GM seeds from one company should dominate a market, it’s only a temporary phenomenon – which only lasts until the patent on the seed technology expires (as it in 2015 e.g. for Monsanto’s first-generation Roundup Ready soybean). Regarding agricultural inputs (herbicides), the patent on Roundup already expired in 2000… 

“corporate profitability rather than social utility has driven GMO innovation thus far” >> The reason that so far only crops that “directly alter the conditions of production” have been successful is to some extent also because social forces (activists) have blocked, hampered and opposed progress of social-utility GMOs… 

“at stake in GMO agriculture is… how property rights are managed… ensuring the extraction of rents for patent holders… termed ‘expropriationism’… Capital is able to subsume elements of the production process, extracting greater surplus value than under an unsubsumed system of production…” >> Studies showed that the gains of cultivating GM crops are shared (even if to varying degrees) by patent holders, farmers and consumers, with everybody being better off… 

“although capitalism’s competitive logic may promote innovation, in biotechnology and elsewhere, it is only certain innovations – and by no means the most socially useful – that can ever be profitably pursued” >> There’s also the (albeit smaller) public and philanthropic sectors that promote (socially useful) innovations – which (as in the case of Golden Rice) are not hampered by capital but amongst others by social forces (such as activists, incl. anti-capitalists) 

“the dual accumulation strategy of appropriationism and expropriationism has made certain GMOs profitable for capital and inescapable for (most) farmers” >> But it made GMOs not only profitable for capital but also for (most) farmers… 

“Biotechnology multinationals have eschewed innovations that address consumer health… because of the uncertainty of any success in these innovations. Without any structural impetus for farmers to adopt transgenic crops that do not inherently improve the production process, there is no guarantee that such crops would even be planted, let alone sold for a premium in grocery stores.” >> This seems far-fetched: Organic farming does not improve the production process (rather the contrary, and it does not even address consumer health etc.) and yet organic food is sold for a premium in grocery stores. Ditto for heirloom varieties or humane eggs… (And some multinationals can make some consumers pay a premium for their products, even if these do not address any issues at all, simply by slapping their logo on it…) The problem here is probably more one of lacking purchasing power (poverty) by those who could benefit from such innovations… 

“A critical reformulation of the global food economy must start with a decoupling of the biotech baby from the capitalist bathwater.” >> Indeed, biotechnology per se is not capitalist and opposing GMOs as such out of related political reasons is misguided and futile.
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Growing Out of Stress: The Role of Cell- and Organ-scale Growth Control in Plant Water-stress Responses

Growing Out of Stress: The Role of Cell- and Organ-scale Growth Control in Plant Water-stress Responses | plant cell genetics | Scoop.it
Water is the most limiting resource on land for plant growth, and its uptake by plants is affected by many abiotic stresses such as salinity, cold, heat and drought. While much research has focused on exploring the molecular mechanisms underlying the cellular signaling events governing water-stress responses, it is also important to consider the role organismal structure plays as a context for such responses. The regulation of growth in plants occurs at two spatial scales: the cell and the organ. In this review, we focus on how the regulation of growth at these different spatial scales enables plants to acclimate to water-deficit stress. The cell wall is discussed with respect to how the physical properties of this structure affect water loss and how regulatory mechanisms that affect wall extensibility maintain growth under water deficit. At a higher spatial scale, the architecture of the root system represents a highly dynamic physical network that facilitates access of the plant to a heterogeneous distribution of water in soil. We discuss the role differential growth plays in shaping the structure of this system and the physiological implications of such changes.
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Allowing pseudoscience into EU risk assessment processes is eroding public trust in science experts and in science as a whole: The bigger picture

Unfortunately Europe, in the application of its legislation relating to chemicals, is in danger of falling back into the medieval approach. The most recent example is the advocacy group- [1], media- and NGO- [2] driven move to have glyphosate banned, despite solid evidence and multiple expert assessments [3], [4] and [5] that this herbicide is without risk to consumers and is the herbicide with the least negative environmental and health impact. The “public” is being misled by pseudoscientists to believe that the compound is highly dangerous to humans and the environment, a claim that runs counter to the evidence and to expert (critical) assessment of that evidence. The media are rife with quotes from poorly informed and often scientifically less well-informed politicians and others who had analysed their water, urine, beer, and vegetables and reported trace amounts of glyphosate, four-thousand-fold below potentially harmful levels for humans [6]. Under this onslaught of misinformation, decision-makers may prefer to disregard evidence-based data that contradict a precautionary viewpoint.
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Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles

Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles | plant cell genetics | Scoop.it
Recent advances in single-cell analysis have revealed the stochasticity and nongenetic heterogeneity inherent to cellular processes. However, our knowledge of the actual cellular behaviors in a living multicellular organism is still limited. By using a single-cell bioluminescence imaging technique on duckweed, Lemna gibba , we demonstrate that, under constant conditions, cells in the intact plant work as individual circadian clocks that oscillate with their own frequencies and respond independently to external stimuli. Quantitative analysis uncovered the heterogeneity and instability of cellular clocks and partial synchronization between neighboring cells. Furthermore, we found that cellular clocks in the plant body under light-dark cycles showed a centrifugal phase pattern in which the effect of cell-to-cell heterogeneity in period lengths was almost masked. The inherent heterogeneity in the properties of cellular clocks observed under constant conditions is corrected under light-dark cycles to coordinate the daily rhythms of the plant body. These findings provide a novel perspective of spatiotemporal architectures in the plant circadian system.
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Nature News: Bacterial tricks for turning plants into zombies (2014)

Nature News: Bacterial tricks for turning plants into zombies  (2014) | plant cell genetics | Scoop.it

Many parasites commandeer the bodies of their hosts in order to spread. Examples of this include horsehair worms that reach water by forcing their cricket hosts to drown themselves, and liver flukes that drive infected ants to climb blades of grass, where cows can eat the insects, and so the flukes. But parasites can turn plants into zombies, too — and a team of scientists from the John Innes Centre in Norwich, UK, has now discovered how they do it.


When plants are infected by parasitic bacteria called phytoplasmas, their flowers turn into leafy shoots, their petals turn green and they develop a mass of shoots called ‘witches’ brooms’. This transformation sterilizes the plant, while attracting the sap-sucking insects that carry the bacteria to new hosts. “The plant appears alive, but it’s only there for the good of the pathogen,” says plant pathologist Saskia Hogenhout from the John Innes Centre in Norwich, UK. “In an evolutionary sense, the plant is dead and will not produce offspring.” “Many might baulk at the concept of a zombie plant because the idea of plants behaving is strange,” says David Hughes, a parasitologist at Pennsylvania State University in University Park. “But they do, and since they do, why wouldn't parasites have evolved to take over their behaviour, as they do for ants and crickets?”


Via Kamoun Lab @ TSL
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Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley | plant cell genetics | Scoop.it
The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture1. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.
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Copper-induced structural conversion templates prion protein oligomerization and neurotoxicity

Copper-induced structural conversion templates prion protein oligomerization and neurotoxicity | plant cell genetics | Scoop.it
Prion protein (PrP) misfolding and oligomerization are key pathogenic events in prion disease. Copper exposure has been linked to prion pathogenesis; however, its mechanistic basis is unknown. We resolve, with single-molecule precision, the molecular mechanism of Cu2+-induced misfolding of PrP under physiological conditions. We also demonstrate that misfolded PrPs serve as seeds for templated formation of aggregates, which mediate inflammation and degeneration of neuronal tissue. Using a single-molecule fluorescence assay, we demonstrate that Cu2+ induces PrP monomers to misfold before oligomer assembly; the disordered amino-terminal region mediates this structural change. Single-molecule force spectroscopy measurements show that the misfolded monomers have a 900-fold higher binding affinity compared to the native isoform, which promotes their oligomerization. Real-time quaking-induced conversion demonstrates that misfolded PrPs serve as seeds that template amyloid formation. Finally, organotypic slice cultures show that misfolded PrPs mediate inflammation and degeneration of neuronal tissue. Our study establishes a direct link, at the molecular level, between copper exposure and PrP neurotoxicity.
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CRISPR-Cas9 mediated efficient directed mutagenesis and RAD51-dependent and -independent gene targeting in the moss Physcomitrella patens

CRISPR-Cas9 mediated efficient directed mutagenesis and RAD51-dependent and -independent gene targeting in the moss Physcomitrella patens | plant cell genetics | Scoop.it
The ability to address the CRISPR-Cas9 nuclease complex to any target DNA using customizable single guide RNAs has now permitted genome engineering in many species. Here, we report its first successful use in a non-vascular plant, the moss Physcomitrella patens. Single guide RNAs (sgRNAs) were designed to target an endogenous reporter gene, PpAPT, whose inactivation confers resistance to 2-fluoroadenine. Transformation of moss protoplasts with these sgRNAs and the Cas9 coding sequence from Streptococcus pyogenes triggered mutagenesis at the PpAPT target in about 2% of the regenerated plants. Mainly deletions were observed, most of them resulting from alternative end joining (alt-EJ)-driven repair. We further demonstrate that, in the presence of a donor DNA sharing sequence homology with the PpAPT gene, most transgene integration events occur by homology-driven repair (HDR) at the target locus, but also that Cas9-induced double-strand breaks are repaired with almost equal frequencies by mutagenic illegitimate recombination. Finally, we establish that a significant fraction of HDR-mediated gene targeting events (30%) is still possible in the absence of PpRAD51 protein, indicating that CRISPR-induced HDR is only partially mediated by the classical homologous recombination (HR) pathway.
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Evolutionary Conservation of Xylan Biosynthetic Genes in Selaginella moellendorffii and Physcomitrella patens

Evolutionary Conservation of Xylan Biosynthetic Genes in Selaginella moellendorffii and Physcomitrella patens | plant cell genetics | Scoop.it
Xylan is a major cross-linking hemicellulose in secondary walls of vascular tissues, and the recruitment of xylan as a secondary wall component was suggested to be a pivotal event for the evolution of vascular tissues. To decipher the evolution of xylan structure and xylan biosynthetic genes, we analyzed xylan substitution patterns and characterized genes mediating methylation of glucuronic acid (GlcA) side chains in xylan of the model seedless vascular plant, Selaginella moellendorffii, and investigated GT43 genes from S. moellendorffii and the model non-vascular plant, Physcomitrella patens, for their roles in xylan biosynthesis. Using nuclear magentic resonance spectroscopy, we have demonstrated that S. moellendorffii xylan consists of β-1,4-linked xylosyl residues subsituted solely with methylated GlcA residues and that xylans from both S. moellendorffii and P. patens are acetylated at O-2 and O-3. To investigate genes responsible for GlcA methylation of xylan, we identified two DUF579 genes in the S. moellendorffii genome and showed that one of them, SmGXM, encodes a glucuronoxylan methyltransferase capable of adding the methyl group onto the GlcA side chain of xylooligomers. Furthermore, we revealed that the two GT43 genes in S. moellendorffii, SmGT43A and SmGT43B, are functional orthologs of the Arabidopsis xylan backbone biosynthetic genes IRX9 and IRX14, respectively, indicating the evolutionary conservation of the involvement of two functionally non-redundant groups of GT43 genes in xylan backbone biosynthesis between seedless and seed vascular plants. Among the five GT43 genes in P. patens, PpGT43A was found to be a functional ortholog of Arabidopsis IRX9, suggesting that the recruitment of GT43 genes in xylan backbone biosynthesis occurred when non-vascular plants appeared on land.
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Highly efficient gene tagging in the bryophyte Physcomitrella patens using the tobacco (Nicotiana tabacum) Tnt1 retrotransposon - Vives - 2016 - New Phytologist - Wiley Online Library

Highly efficient gene tagging in the bryophyte Physcomitrella patens using the tobacco (Nicotiana tabacum) Tnt1 retrotransposon - Vives - 2016 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
Because of its highly efficient homologous recombination, the moss Physcomitrella patens is a model organism particularly suited for reverse genetics, but this inherent characteristic limits forward genetic approaches.
Here, we show that the tobacco (Nicotiana tabacum) retrotransposon Tnt1 efficiently transposes in P. patens, being the first retrotransposon from a vascular plant reported to transpose in a bryophyte. Tnt1 has a remarkable preference for insertion into genic regions, which makes it particularly suited for gene mutation.
In order to stabilize Tnt1 insertions and make it easier to select for insertional mutants, we have developed a two-component system where a mini-Tnt1 with a retrotransposition selectable marker can only transpose when Tnt1 proteins are co-expressed from a separate expression unit.
We present a new tool with which to produce insertional mutants in P. patens in a rapid and straightforward manner that complements the existing molecular and genetic toolkit for this model species.
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Survey and Risk Assessment of Apis mellifera (Hymenoptera: Apidae) Exposure to Neonicotinoid Pesticides in Urban, Rural, and Agricultural Settings

Survey and Risk Assessment of Apis mellifera (Hymenoptera: Apidae) Exposure to Neonicotinoid Pesticides in Urban, Rural, and Agricultural Settings | plant cell genetics | Scoop.it
A comparative assessment of apiaries in urban, rural, and agricultural areas was undertaken in 2013 and 2014 to examine potential honey bee colony exposure to neonicotinoid insecticides from pollen foraging. Apiaries ranged in size from one to hundreds of honey bee colonies, and included those operated by commercial, sideline (semicommercial), and hobbyist beekeepers. Residues in and on wax and beebread (stored pollen in the hive) were evaluated for the nitro-substituted neonicotinoid insecticides imidacloprid and its olefin metabolite and the active ingredients clothianidin, thiamethoxam, and dinotefuran. Beebread and comb wax collected from hives in agricultural landscapes were more likely to have detectable residues of thiamethoxam and clothianidin than that collected from hives in rural or urban areas (∼50% of samples vs. <10%). The maximum neonicotinoid residue detected in either wax or beebread was 3.9 ppb imidacloprid. A probabilistic risk assessment was conducted on the residues recovered from beebread in apiaries located in commercial, urban, and rural landscapes. The calculated risk quotient based on a dietary no observable adverse effect concentration (NOAEC) suggested low potential for negative effects on bee behavior or colony health.
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Towards a multidimensional root trait framework: a tree root review - Weemstra - 2016 - New Phytologist - Wiley Online Library

Towards a multidimensional root trait framework: a tree root review - Weemstra - 2016 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
The search for a root economics spectrum (RES) has been sparked by recent interest in trait-based plant ecology. By analogy with the one-dimensional leaf economics spectrum (LES), fine-root traits are hypothesised to match leaf traits which are coordinated along one axis from resource acquisitive to conservative traits. However, our literature review and meta-level analysis reveal no consistent evidence of an RES mirroring an LES. Instead the RES appears to be multidimensional. We discuss three fundamental differences contributing to the discrepancy between these spectra. First, root traits are simultaneously constrained by various environmental drivers not necessarily related to resource uptake. Second, above- and belowground traits cannot be considered analogues, because they function differently and might not be related to resource uptake in a similar manner. Third, mycorrhizal interactions may offset selection for an RES. Understanding and explaining the belowground mechanisms and trade-offs that drive variation in root traits, resource acquisition and plant performance across species, thus requires a fundamentally different approach than applied aboveground. We therefore call for studies that can functionally incorporate the root traits involved in resource uptake, the complex soil environment and the various soil resource uptake mechanisms – particularly the mycorrhizal pathway – in a multidimensional root trait framework.
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Biofortified β-carotene rice improves vitamin A intake and reduces the prevalence of inadequacy among women and young children in a simulated analysis in Bangladesh, Indonesia, and the Philippines ...

Vitamin A deficiency continues to be a major public health problem affecting developing countries where people eat mostly rice as a staple food. In Asia, rice provides up to 80% of the total daily energy intake. 


We used existing data sets from Bangladesh, Indonesia, and the Philippines, where dietary intakes have been quantified at the individual level to 1) determine the rice and vitamin A intake in nonpregnant, nonlactating women of reproductive age and in nonbreastfed children 1-3 y old and 2) simulate the amount of change that could be achieved in the prevalence of inadequate intake of vitamin A if rice biofortified with β-carotene were consumed instead of the rice consumed at present. 


We considered a range of 4-20 parts per million (ppm) of β-carotene content and 10-70% substitution levels for the biofortified rice… the substitution of biofortified rice for white rice in the optimistic scenario (20 ppm and 70% substitution) decreased the prevalence of vitamin A inadequacy from baseline 78% in women and 71% in children in Bangladesh. In Indonesia and the Philippines, the prevalence of inadequacy fell by 55-60% in women and dropped by nearly 30% in children from baseline. 


The results of the simulation analysis were striking in that even low substitution levels and modest increases in the β-carotene of rice produced a meaningful decrease in the prevalence of inadequate intake of vitamin A. Increasing the substitution levels had a greater impact than increasing the β-carotene content by >12 ppm… 


In β-carotene rice, commonly known as golden rice because of its yellow hue, 2 genes naturally involved in carotene biosynthesis were inserted into the rice genome by using transgenics. This insertion restarts the carotenoid biosynthetic pathway that is normally inactive, leading to the production of β-carotene in the grain. The current amount of β-carotene in biofortified b-carotene rice is 35 parts per million (ppm), with an estimated bioconversion rate of 3.8:1 from β-carotene to vitamin A… 


Biofortified β-carotene rice can substantially increase vitamin A intake and consequently reduce the prevalence of inadequacy of this vitamin. Increasing vitamin A intake through biofortified rice at 8-12 ppm of β-carotene, in combination with programs that increase adoption of biofortified rice in a population, can be an effective method at reducing population prevalence of inadequate vitamin A intakes... However... increasing the β-carotene beyond 12 ppm has little added benefit; rather, public health programs will have the most impact by increasing the substitution of white rice by biofortified β-carotene rice. 


http://ajcn.nutrition.org/content/early/2016/08/10/ajcn.115.129270.abstract



Via Alexander J. Stein
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How to make a red flower: the combinatorial effect of pigments

How to make a red flower: the combinatorial effect of pigments | plant cell genetics | Scoop.it
Red flowers have evolved repeatedly across angiosperms and are frequently examined in an ecological context. However, less is known about the biochemical basis of red colouration in different taxa. In this study, we examine the spectral properties, anthocyanin composition and carotenoid expression of red flowers in the tomato family, Solanaceae, which have evolved independently multiple times across the group. Our study demonstrates that Solanaceae typically make red flowers either by the sole production of red anthocyanins or, more commonly, by the dual production of purple or blue anthocyanins and orange carotenoids. In using carotenoids to modify the effect of purple and/or blue anthocyanins, these Solanaceae species have converged on the same floral hue as those solely producing red anthocyanins, even when considering the visual system of pollinators. The use of blue anthocyanins in red flowers appears to differ from other groups, and suggests that the genetic changes underlying evolutionary shifts to red flowers may not be as predictable as previously suggested.
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Plant acoustics: in the search of a sound mechanism for sound signaling in plants

Plant acoustics: in the search of a sound mechanism for sound signaling in plants | plant cell genetics | Scoop.it
Being sessile, plants continuously deal with their dynamic and complex surroundings, identifying important cues and reacting with appropriate responses. Consequently, the sensitivity of plants has evolved to perceive a myriad of external stimuli, which ultimately ensures their successful survival. Research over past centuries has established that plants respond to environmental factors such as light, temperature, moisture, and mechanical perturbations (e.g. wind, rain, touch, etc.) by suitably modulating their growth and development. However, sound vibrations (SVs) as a stimulus have only started receiving attention relatively recently. SVs have been shown to increase the yields of several crops and strengthen plant immunity against pathogens. These vibrations can also prime the plants so as to make them more tolerant to impending drought. Plants can recognize the chewing sounds of insect larvae and the buzz of a pollinating bee, and respond accordingly. It is thus plausible that SVs may serve as a long-range stimulus that evokes ecologically relevant signaling mechanisms in plants. Studies have suggested that SVs increase the transcription of certain genes, soluble protein content, and support enhanced growth and development in plants. At the cellular level, SVs can change the secondary structure of plasma membrane proteins, affect microfilament rearrangements, produce Ca2+ signatures, cause increases in protein kinases, protective enzymes, peroxidases, antioxidant enzymes, amylase, H+-ATPase / K+ channel activities, and enhance levels of polyamines, soluble sugars and auxin. In this paper, we propose a signaling model to account for the molecular episodes that SVs induce within the cell, and in so doing we uncover a number of interesting questions that need to be addressed by future research in plant acoustics.
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Basidiomycete yeasts in the cortex of ascomycete macrolichens

Basidiomycete yeasts in the cortex of ascomycete macrolichens | plant cell genetics | Scoop.it
For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi.
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Current Biology: Pathogen Tactics to Manipulate Plant Cell Death (2016)

Current Biology: Pathogen Tactics to Manipulate Plant Cell Death (2016) | plant cell genetics | Scoop.it

Programmed cell death (PCD) is a conserved process among eukaryotes that serves a multitude of functional roles during an organism’s natural life cycle. PCD involves the tightly regulated process of cell death cued by specific spatiotemporal stimuli, which confer survival benefits. In eukaryotes, PCD is an essential process involved in senescence, aging, embryo development, cell differentiation, and immunity. In animal systems, morphologically distinct forms of PCD have been described (Figure 1) [1, 2]. Type I, or apoptotic cell death, is the best understood form of PCD and is defined by cell shrinkage, nuclear condensation and fragmentation, and eventual disintegration of the cell into apoptotic bodies that are digested by phagocytes. Type II cell death is an autophagic process that is induced during nutrient deprivation and chronic stress. Autophagic cell death is characterized by the rupture of the lysosome and subsequent release of toxic chemicals that degrade the cell contents. Unlike type I and type II, type III PCD is distinguished by the swelling of organelles and subsequent rupture of the plasma membrane. A programmed necrosis or necroptosis was initially believed to be an uncontrolled process of necrosis, but has been recently reclassified as type III form of cell death. Finally, pyroptosis is another recently categorized form of cell death that is mediated by caspase-1 activity. Morphologically, pyroptotic cells share characteristics of both apoptosis and necrosis [1]. Noteworthy, necroptosis and pyroptosis are pro-inflammatory forms of PCD activated by microbial infections and diverse environmental stimuli.

 

In plants, PCD is less rigorously classified (Figure 1). One difficulty in distinguishing the forms of PCD in plants and animals comes as a result of the different cellular morphology in plant cells — most notably the presence of the cell wall and chloroplasts. Unlike the plasma membrane, the degradation of the cell wall is not a universal feature of PCD in plants. Additionally, the formation of apoptotic bodies is not observed in plant cells, as there are no circulating phagocytes to engulf them [3]. Instead, plant cells committed to PCD release autolytic compounds stored in the vacuole that degrade cell contents. In these cases, the cell wall may develop perforations for the absorption and recycling of cellular components by neighboring cells. Although not as well characterized as the mitochondria, the chloroplasts have been shown to induce light-dependent PCD through singlet oxygen species (1O2) that may function in parallel to mitochondrial-mediated PCD at an early step in initiating the rupture of the vacuole [3].

 

A specialized form of plant cell death called hypersensitive response (HR) is initiated as a defense response to pathogen infection. HR shares morphological features and molecular mechanisms reminiscent of both pyroptosis and necroptosis [4]. Moreover, HR is unique in that it induces a signaling cascade to propagate immunity in neighboring cells as well as priming distal tissues for potential pathogen challenge, a phenomenon known as systemic acquired resistance [5]. Here we will briefly describe diverse plant disease resistance pathways, early molecular events during pathogen perception, and downstream signaling components. We will thoroughly discuss how pathogens have evolved strategies to circumvent and/or suppress diverse immune responses, in particular plant cell death. While many of these mechanisms involve indirect disabling of upstream immune responses to avoid cell death, direct manipulation of PCD regulators by pathogen effectors has not been extensively explored in the literature, and will be the focal point of this article.


Via Kamoun Lab @ TSL
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Rakesh Yashroy's curator insight, July 27, 10:06 PM
Good description of APOPTOSIS in animal and plant cells. Gram negative pathogens like Salmonella use their outer membrane vesicles to signal hijacking and apoptosis in defense macrophages in animal body @ http://s3.amazonaws.com/academia.edu.documents/33932139/1211.pdf?AWSAccessKeyId=AKIAJ56TQJRTWSMTNPEA&Expires=1469674971&Signature=0HXlHa3eNfInsWTE0YqGOgD6HTA%3D&response-content-disposition=inline%3B%20filename%3DYashRoy_R_C_2007_Mechanism_of_infection.pdf
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Factors associated with the farmer suicide crisis in India Bt cotton is unlikely to be an important factor

Socioeconomic factors, rather than mental health problems, are associated with farmer suicides, with increased indebtedness playing the predominant role. Available research suggests this has arisen to a greater extent recently, due to an agrarian crisis affecting the most vulnerable farmers. This has multiple manifestations, including a lack of agricultural investment and irrigation improvement, use of cash crops, the increased use of noninstitutional credit sources, and the reduction of trade barriers. Bt cotton is unlikely to be an important factor and no studies reported a significant burden of mental health problems.
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The Cultivar Series

The Cultivar Series | plant cell genetics | Scoop.it
This website showcases the work of Berlin based artist Uli Westphal. His works deal with the way humans perceive, depict and transform the natural world.

Via Saclay Plant Sciences
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The critical role of pre-publication peer review—a case study of glyphosate

This discussion considers the impact of inadequate peer review on an internationally important decision on the safety of a common pesticide. There have been hundreds of articles and essays and conferences on the importance and the problems of pre-publication review, but difficulties with the process are still with us.

Ideally, before publication, a research report submitted to a scientific journal is sent by the editor to one or more experts in the field for review. The author responds to the critiques and the editor(s) decide whether the revised paper is to be published. That ideal may fail if the pre-publication peer review has been less than thorough or the work has been sent to a journal with inadequate or no review. Unfortunately, such outlets do exist. When poor work finds its way into print, it is too often accepted as authoritative. The costs in time, knowledge, and social distress are substantial.

The consequences of insufficiently critiqued publication on an issue of worldwide concern can be expected to draw more attention to the problem: A useful example has been handed the scientific community in the recent Monograph 112 of the International Agency for Research on Cancer (IARC), declaring the herbicide glyphosate to be a category 2A, probable human carcinogen (IARC 2015). This is an internationally visible official decision, and it is founded on flawed publications. (Several of the papers used as authoritative by IARC in Monograph 112 were discussed years ago as examples of defective review (Dost 2008).)
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The shocking consequences of hybrid epigenomes

The shocking consequences of hybrid epigenomes | plant cell genetics | Scoop.it
DNA methylation is perhaps the best-known and best-studied chromatin modification. Occurring primarily at cytosine nucleotides in eukaryotic genomes, methylation is a reversible DNA modification that is linked with epialleles, which are genes that are identical in sequence but differ in methylation status and that are inherited between generations. A recent study by Rigal et al. [1] published in Proceedings of the National Academy of Sciences U S A reported the discovery of novel epialleles in hybrids that formed from crossing mutants that are defective in the maintenance of DNA methylation with wild-type plants, highlighting a potential mechanism by which natural epialleles arise.
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