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On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE

On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE | plant cell genetics | Scoop.it

A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

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Transgenic cotton: High hopes and farming reality

Transgenic cotton: High hopes and farming reality | plant cell genetics | Scoop.it
Veettil et al. never imply that GM cotton is a panacea to pesticide overuse, and they conclude both that transgenic seeds must be an element within a broader agricultural development strategy and that many Bt cotton farmers continue to overuse chemical pesticides. However, their comparisons between Bt and non-Bt cotton farmers miss important social dynamics driving farmer pesticide use: namely, the consequences of continued pesticide spraying even when Bt cotton obviates that need, and the risk that this poses to the largely young, poor, and female farm labouring population. Bt cotton is here to stay in India (and globally), and its impacts should be measured in practice, not as a comparison to the few, unrepresentative non-Bt planting holdouts. There is every reason to believe both that Bt cotton has helped reduce the quantity and overall toxicity of cotton agriculture, and that this profession, in practice, remains a precarious one.
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An Evolutionary Framework for Carpel Developmental Control Genes

An Evolutionary Framework for Carpel Developmental Control Genes | plant cell genetics | Scoop.it
Carpels are the female reproductive organs of flowering plants (angiosperms), enclose the ovules, and develop into fruits. The presence of carpels unites angiosperms, and they are suggested to be the most important autapomorphy of the angiosperms, e.g., they prevent inbreeding and allow efficient seed dispersal. Many transcriptional regulators and coregulators essential for carpel development are encoded by diverse gene families and well characterized in Arabidopsis thaliana. Among these regulators are AGAMOUS (AG), ETTIN (ETT), LEUNIG (LUG), SEUSS (SEU), SHORT INTERNODE/STYLISH (SHI/STY), and SEPALLATA1, 2, 3, 4 (SEP1, 2, 3, 4). However, the timing of the origin and their subsequent molecular evolution of these carpel developmental regulators are largely unknown. Here, we have sampled homologs of these carpel developmental regulators from the sequenced genomes of a wide taxonomic sampling of the land plants, such as Physcomitrella patens, Selaginella moellendorfii, Picea abies, and several angiosperms. Careful phylogenetic analyses were carried out that provide a phylogenetic background for the different gene families and provide minimal estimates for the ages of these developmental regulators. Our analyses and published work show that LUG-, SEU-, and SHI/STY-like genes were already present in the Most Recent Common Ancestor (MRCA) of all land plants, AG- and SEP-like genes were present in the MRCA of seed plants and their origin may coincide with the ξ Whole Genome Duplication. Our work shows that the carpel development regulatory network was, in part, recruited from preexisting network components that were present in the MRCA of angiosperms and modified to regulate gynoecium development.
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identification of a novel betalain-related cytochrome P450-type gene, CYP76AD6, which catalyzes the first step in the betalain biosynthetic- Planta Medica / Abstract

Betalains are tyrosine-derived red-violet and yellow pigments found in plants only of the Caryophyllales order, which hold both scientific and economic values. Their pH in-dependence and high stability make them a natural pigment of choice for food industries. Their strong antioxidant activities have prompted research into their potential health-promoting properties and led to commercialization of a variety of betalain-based dietary supplements. While the biosynthetic process of many natural colorants is well understood, many questions remain open with regards to biosynthesis of betalains. Transcriptome analysis of the betalain-producing plants red beet (Beta vulgaris) and four o'clocks (Mirabilis jalapa) led us to the identification of a novel betalain-related cytochrome P450-type gene, CYP76AD6, which catalyzes the first step in the betalain biosynthetic pathway, namely the 3-hydroxylation of tyrosine to form l-3,4-dihydroxyphenylalanine (L-DOPA) [1]. L-DOPA formation in red beet was found to be redundantly catalyzed by CYP76AD6 together with a known betalain-related enzyme, CYP76AD1. Gene silencing assays and recombinant expression in Nicotiana benthamiana and yeast cells revealed that while CYP76AD1 catalyzes both L-DOPA formation and its subsequent conversion to cyclo-DOPA, CYP76AD6 uniquely exhibits only tyrosine hydroxylase activity. The new findings enabled us to engineer stable betalain production through heterologous expression of three genes taking part in the fully decoded betalain biosynthetic pathway, namely CYP76AD1 and DOPA 4, 5-dioxygenase (BvDODA1) from red beet, and cyclo-DOPA-5-O-glucosyltransferase from four o'clocks (cDOPA5GT). High-quantity betalain production was achieved in a number of plant species, including tobacco (135 mg/kg fresh weight, leaf tissue) tomato (200 mg/kg, fruit) and eggplant (120 mg/kg, fruit). These betalain-producing transgenic plants offer an exceptional opportunity to study for example the health-promoting properties of betalains.

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Efficient and Heritable Targeted Mutagenesis in Mosses Using the CRISPR/Cas9 System

Targeted genome modification by RNA-guided nucleases derived from the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has seen rapid development in many organisms, including several plant species. In the present study, we succeeded in introducing the CRISPR/Cas9 system into the non-model organism Scopelophila cataractae, a moss that exhibits heavy metal tolerance, and the model organism Physcomitrella patens. Utilizing the process by which moss plants regenerate from protoplasts, we conducted targeted mutagenesis by expression of single-chain guide RNA (sgRNA) and Cas9 in protoplasts. Using this method, the acquisition rate of strains exhibiting phenotypic changes associated with the target genes was approximately 45–69%, and strains with phenotypic changes exhibited various insertion and deletion mutations. In addition, we report that our method is capable of multiplex targeted mutagenesis (two independent genes) and also permits the efficient introduction of large deletions (∼3 kbp). These results demonstrate that the CRISPR/Cas9 system can be used to accelerate investigations of bryology and land plant evolution.
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Draft genome of the living fossil Ginkgo biloba

Draft genome of the living fossil Ginkgo biloba | plant cell genetics | Scoop.it
Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution.
Findings

The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways.
Conclusions

The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.
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Neighbor Detection Induces Organ-specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-specific Growth

Neighbor Detection Induces Organ-specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-specific Growth | plant cell genetics | Scoop.it

In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana. PIFs initiate transcriptional reprogramming in both organs within 15 minutes, comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. We show that cotyledon-derived auxin is both necessary and sufficient to initiate hypocotyl growth, but we also provide evidence for the functional importance of the local PIF-induced response. With time, the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between different developmentally regulated growth processes and responses to the environment in different organs.

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Seeds of doubt: Mendel’s choice of Hieracium to study inheritance, a case of right plant, wrong trait

Seeds of doubt: Mendel’s choice of Hieracium to study inheritance, a case of right plant, wrong trait | plant cell genetics | Scoop.it
Seeds of doubt: Mendel’s choice of Hieracium to study inheritance, a case of right plant, wrong trait
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Origin and function of stomata in the moss Physcomitrella patens

Origin and function of stomata in the moss Physcomitrella patens | plant cell genetics | Scoop.it
Stomata are microscopic valves on plant surfaces that originated over 400 million years (Myr) ago and facilitated the greening of Earth's continents by permitting efficient shoot–atmosphere gas exchange and plant hydration1. However, the core genetic machinery regulating stomatal development in non-vascular land plants is poorly understood2,​3,​4 and their function has remained a matter of debate for a century5. Here, we show that genes encoding the two basic helix–loop–helix proteins PpSMF1 (SPEECH, MUTE and FAMA-like) and PpSCREAM1 (SCRM1) in the moss Physcomitrella patens are orthologous to transcriptional regulators of stomatal development in the flowering plant Arabidopsis thaliana and essential for stomata formation in moss. Targeted P. patens knockout mutants lacking either PpSMF1 or PpSCRM1 develop gametophytes indistinguishable from wild-type plants but mutant sporophytes lack stomata. Protein–protein interaction assays reveal heterodimerization between PpSMF1 and PpSCRM1, which, together with moss–angiosperm gene complementations6, suggests deep functional conservation of the heterodimeric SMF1 and SCRM1 unit is required to activate transcription for moss stomatal development, as in A. thaliana7. Moreover, stomata-less sporophytes of ΔPpSMF1 and ΔPpSCRM1 mutants exhibited delayed dehiscence, implying stomata might have promoted dehiscence in the first complex land-plant sporophytes.
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A hypergravity environment increases chloroplast size, photosynthesis, and plant growth in the moss Physcomitrella patens

A hypergravity environment increases chloroplast size, photosynthesis, and plant growth in the moss Physcomitrella patens | plant cell genetics | Scoop.it
The physiological and anatomical responses of bryophytes to altered gravity conditions will provide crucial information for estimating how plant physiological traits have evolved to adapt to significant increases in the effects of gravity in land plant history. We quantified changes in plant growth and photosynthesis in the model plant of mosses, Physcomitrella patens, grown under a hypergravity environment for 25 days or 8 weeks using a custom-built centrifuge equipped with a lighting system. This is the first study to examine the response of bryophytes to hypergravity conditions. Canopy-based plant growth was significantly increased at 10×g, and was strongly affected by increases in plant numbers. Rhizoid lengths for individual gametophores were significantly increased at 10×g. Chloroplast diameters (major axis) and thicknesses (minor axis) in the leaves of P. patens were also increased at 10×g. The area-based photosynthesis rate of P. patens was also enhanced at 10×g. Increases in shoot numbers and chloroplast sizes may elevate the area-based photosynthesis rate under hypergravity conditions. We observed a decrease in leaf cell wall thickness under hypergravity conditions, which is in contrast to previous findings obtained using angiosperms. Since mosses including P. patens live in dense populations, an increase in canopy-based plant numbers may be effective to enhance the toughness of the population, and, thus, represents an effective adaptation strategy to a hypergravity environment for P. patens.
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Integration of Phytochrome and Cryptochrome Signals Determines Plant Growth during Competition for Light

Integration of Phytochrome and Cryptochrome Signals Determines Plant Growth during Competition for Light | plant cell genetics | Scoop.it
Highlights

•Blue light depletion combined with low R:FR mimics vegetation shade
•Low blue light perception enhances the low R:FR response through PIFs and COP1
•Low blue light perception counteracts a low R:FR-induced negative feedback loop

Summary

Plants in dense vegetation perceive their neighbors primarily through changes in light quality. Initially, the ratio between red (R) and far-red (FR) light decreases due to reflection of FR by plant tissue well before shading occurs. Perception of low R:FR by the phytochrome photoreceptors induces the shade avoidance response [ 1 ], of which accelerated elongation growth of leaf-bearing organs is an important feature. Low R:FR-induced phytochrome inactivation leads to the accumulation and activation of the transcription factors PHYTOCHROME-INTERACTING FACTORs (PIFs) 4, 5, and 7 and subsequent expression of their growth-mediating targets [ 2, 3 ]. When true shading occurs, transmitted light is especially depleted in red and blue (B) wavelengths, due to absorption by chlorophyll [ 4 ]. Although the reduction of blue wavelengths alone does not occur in nature, long-term exposure to low B light induces a shade avoidance-like response that is dependent on the cryptochrome photoreceptors and the transcription factors PIF4 and PIF5 [ 5–7 ]. We show in Arabidopsis thaliana that low B in combination with low R:FR enhances petiole elongation similar to vegetation shade, providing functional context for a low B response in plant competition. Low B potentiates the low R:FR response through PIF4, PIF5, and PIF7, and it involves increased PIF5 abundance and transcriptional changes. Low B attenuates a low R:FR-induced negative feedback loop through reduced gene expression of negative regulators and reduced HFR1 levels. The enhanced response to combined phytochrome and cryptochrome inactivation shows how multiple light cues can be integrated to fine-tune the plant’s response to a changing environment.
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Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits

Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits | plant cell genetics | Scoop.it
Young sunflower plants track the Sun from east to west during the day and then reorient during the night to face east in anticipation of dawn. In contrast, mature plants cease movement with their flower heads facing east. We show that circadian regulation of directional growth pathways accounts for both phenomena and leads to increased vegetative biomass and enhanced pollinator visits to flowers. Solar tracking movements are driven by antiphasic patterns of elongation on the east and west sides of the stem. Genes implicated in control of phototropic growth, but not clock genes, are differentially expressed on the opposite sides of solar tracking stems. Thus, interactions between environmental response pathways and the internal circadian oscillator coordinate physiological processes with predictable changes in the environment to influence growth and reproduction.
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Effect of bearing position on phenolics profiles in the skins of four cultivars of grapevine (Vitis vinifera L.)

Effect of bearing position on phenolics profiles in the skins of four cultivars of grapevine (Vitis vinifera L.) | plant cell genetics | Scoop.it
The fan-shaped trellis training system, resulting in grapevines (Vitis vinifera L.) with more than two trunks, has been widely used in northern China. The fruiting zone of grapevines trained to the fan-shaped trellis system is distributed from the top to the bottom of the canopy. The phenolics profiles of the skins of ‘Cabernet Sauvignon’, ‘Merlot’, ‘Chardonnay’, and ‘Italian Riesling’ grape berries were analysed to measure the effect of differences in bearing position on the phenolic compound and anthocyanin compositions of grape berries.The results showed that the upper bearing position significantly increased the concentrations of most phenolic compounds in grape berry skins. Among the non-anthocyanin and anthocyanin phenolic compounds identified in this study, the upper bearing position promoted the accumulation of delphinidin-, cyanidin-, and petunidin-glucosides in the skin of the two red grape cultivars. However, lowering the bearing position was associated with greater methylation of anthocyanins, and the flow of photosynthate towards the biosynthesis of kaempferol. These results were correlated with micrometeorological alterations in the canopy at the different bearing positions. The findings of this study suggest that higher bearing positions can increase the accumulation of phenolic compounds in grape berry skins in four different grapevine cultivars.
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Down the Rabbit Hole–Carrots, Genetics and Art

Down the Rabbit Hole–Carrots, Genetics and Art | plant cell genetics | Scoop.it
The large, unbranched cultivated carrot (Daucus carota subspecies sativus) is a popular vegetable with high sugar and dietary provitamin A carotenoid contents. The orange-coloured one is best known, but there are also white, yellow, red, and purple varieties. By contrast, the wild carrot Daucus carota subspecies carota (commonly referred to as Queen Anne's Lace) is a weedy plant that does not accumulate any detectable levels of carotenoid pigments in roots i. When visiting the museums of his native country in the late 1950s, the Dutch agronomer Otto Banga started to ponder the question on the origin of the modern carrot. He observed that paintings from the Dutch Golden Century (∼17th century) show an enormous diversity of carrots: white, red, yellow, and orange versions (Figure 1A). However, he noticed the orange carrot featuring more prominently on pictures that were painted later in the 17th century. He concluded that the orange carrot as we currently know it, appeared in the late 16th to early 17th century, and that it was likely first cultivated in The Netherlands [1]. Here, in view of the recent carrot genome assembly [2], we noncomprehensively discuss the origin of the carrot, explain how art can help in our understanding of its development, and elaborate upon some of the molecular mechanisms and underlying genetic network responsible for the observed colour differences.
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What is this thing called organic? – How organic farming is codified in regulations


Highlights • The meaning of organic agriculture is highly debated. • Regulations define organic mostly in terms of ‘natural’ vs. ‘synthetic’ inputs. • Environmental best practices are not well represented in regulations. Abstract Organic farming is one of the fastest growing sectors of world agriculture. Although it represents only 1% of world agricultural area, organic is one of the most recognized food labels and most people in developed countries consume some amount of organic food today. There is a wide range of interpretations of what organic means by different actors in the sector. Here we examine eight different organic regulations from across the world to understand how they have codified the large diversity of ideas inherent in organic agriculture. Our analysis shows that organic practices and regulations do not differ substantially between countries – across the board organic regulations define organic mainly in terms of 'natural' vs. 'artificial' substances that are allowed (or not) as inputs. This interpretation of organic as “chemical-free” farming, largely void of broader environmental principles, does not fully incorporate the original ideas of organic theoreticians who conceived it as a holistic farming system aimed primarily at improving soil health, thereby leading to improved animal, human, and societal health. This narrow focus of organic regulations can be explained by the interest of organic consumers who predominantly buy organic because they believe it is healthier and more nutritious due to the absence of harmful substances. Organic regulations need to place more emphasis on environmental best practices in order to ensure that organic agriculture can contribute to sustainability objectives.
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Occurrence of brassinosteroids in non-flowering land plants, liverwort, moss, lycophyte and fern

Occurrence of brassinosteroids in non-flowering land plants, liverwort, moss, lycophyte and fern | plant cell genetics | Scoop.it
Endogenous brassinosteroids (BRs) in non-flowering land plants were analyzed. BRs were found in a liverwort (Marchantia polymorpha), a moss (Physcomitrella patens), lycophytes (Selaginella moellendorffii and S. uncinata) and 13 fern species. A biologically active BR, castasterone (CS), was identified in most of these non-flowering plants but another biologically active BR, brassinolide, was not. It may be distinctive that levels of CS in non-flowering plants were orders of magnitude lower than those in flowering plants. 22-Hydroxycampesterol and its metabolites were identified in most of the non-flowering plants suggesting that the biosynthesis of BRs via 22-hydroxylation of campesterol occurs as in flowering plants. Phylogenetic analyses indicated that M. polymorpha, P. patens and S. moellendorffii have cytochrome P450s in the CYP85 clans which harbors BR biosynthesis enzymes, although the P450 profiles are simpler as compared with Arabidopsis and rice. Furthermore, these basal land plants were found to have multiple P450s in the CYP72 clan which harbors enzymes to catabolize BRs. These findings indicate that green plants were able to synthesize and inactivate BRs from the land-transition stage.
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Publication bias and the canonization of false facts

Publication bias and the canonization of false facts | plant cell genetics | Scoop.it

Publication bias and the canonization of false facts | Publication bias, in which positive results are preferentially reported by authors and published by journals, can restrict the visibility of evidence against false claims and allow such claims to be canonized inappropriately as facts.

Science is facing a “replication crisis” in which many experimental findings cannot be replicated and are likely to be false. Does this imply that many scientific facts are false as well? To find out, we explore the process by which a claim becomes fact. We model the community’s confidence in a claim as a Markov process with successive published results shifting the degree of belief. Publication bias in favor of positive findings influences the distribution of published results. We find that unless a sufficient fraction of negative results are published, false claims frequently can become canonized as fact. Data-dredging, p-hacking, and similar behaviors exacerbate the problem. Should negative results become easier to publish as a claim approaches acceptance as a fact, however, true and false claims would be more readily distinguished. To the degree that the model reflects the real world, there may be serious concerns about the validity of purported facts in some disciplines.

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Open-source tools accelerate plant breeding in developing countries

Open-source tools accelerate plant breeding in developing countries | plant cell genetics | Scoop.it
Crop breeders in developing countries can now access free tools to accelerate the breeding of improved crops varieties, thanks to a collaboration between the GOBII project at Cornell University and the Boyce Thompson Institut...
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Moss-Produced, Glycosylation-Optimized Human Factor H for Therapeutic Application in Complement Disorders

Genetic defects in complement regulatory proteins can lead to severe renal diseases, including atypical hemolytic uremic syndrome and C3 glomerulopathies, and age-related macular degeneration. The majority of the mutations found in patients with these diseases affect the glycoprotein complement factor H, the main regulator of the alternative pathway of complement activation. Therapeutic options are limited, and novel treatments, specifically those targeting alternative pathway activation, are highly desirable. Substitution with biologically active factor H could potentially treat a variety of diseases that involve increased alternative pathway activation, but no therapeutic factor H is commercially available. We recently reported the expression of full-length recombinant factor H in moss (Physcomitrella patens). Here, we present the production of an improved moss-derived recombinant human factor H devoid of potentially immunogenic plant–specific sugar residues on protein N-glycans, yielding approximately 1 mg purified moss–derived human factor H per liter of initial P. patens culture after a multistep purification process. This glycosylation-optimized factor H showed full in vitro complement regulatory activity similar to that of plasma-derived factor H and efficiently blocked LPS-induced alternative pathway activation and hemolysis induced by sera from patients with atypical hemolytic uremic syndrome. Furthermore, injection of moss-derived factor H reduced C3 deposition and increased serum C3 levels in a murine model of C3 glomerulopathy. Thus, we consider moss-produced recombinant human factor H a promising pharmaceutical product for therapeutic intervention in patients suffering from complement dysregulation.
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Scientific Opinion on an application by DOW AgroSciences LLC (EFSA‐GMO‐NL‐2010‐89) for placing on the market the genetically modified herbicide‐tolerant maize DAS‐40278‐9 for food and feed uses, im...

Maize DAS-40278-9 was developed by direct Whiskers-mediated transformation to express the aryloxyalkanoate dioxygenase-1 (AAD-1) protein, conferring tolerance to 2,4-dichlorophenoxyacetic acid (2,4-D) and aryloxyphenoxypropionate (AOPP) herbicides. The molecular characterisation of maize DAS-40278-9 did not raise safety issues. The agronomic, phenotypic and compositional characteristics of maize DAS-40278-9 tested under field conditions revealed no differences between maize DAS-40278-9 and its non-genetically modified (GM) comparator that would give rise to food and feed or environmental safety concerns. There were no concerns regarding the potential toxicity and allergenicity of the newly expressed protein AAD-1, and no evidence that the genetic modification might significantly change the overall allergenicity of maize DAS-40278-9. The nutritional characteristics of maize DAS-40278-9 are not expected to differ from those of non-GM maize varieties and no post-market monitoring of food/feed is considered necessary. Maize DAS-40278-9 is as nutritious as its non-GM comparator and other non-GM commercial varieties. There are no indications of an increased likelihood of establishment and spread of occasional feral maize DAS-40278-9 plants, unless these plants are exposed to the intended herbicides. However, this will not result in different environmental impacts compared to conventional maize. Considering the scope of the application, interactions with the biotic and abiotic environment were not considered an issue. Risks associated with the unlikely but theoretically possible horizontal gene transfer from maize DAS-40278-9 to bacteria were not identified. The post-market environmental monitoring plan and reporting intervals are in line with the scope of the application. In conclusion, the EFSA GMO Panel considers that the information available for maize DAS-40278-9 addresses the scientific comments raised by the Member States and that maize DAS-40278-9, as described in this application, is as safe as the non-GM comparator and non-GM maize reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.
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Withdrawal of maize protection by herbicides and insecticides increases mycotoxins contamination near maximum thresholds

Withdrawal of maize protection by herbicides and insecticides increases mycotoxins contamination near maximum thresholds | plant cell genetics | Scoop.it
Environmental and economic issues affect decision-making for whether or not to control small infestations of pests and pathogens in crops. Even where no crop yield loss is expected, other risks may be evident, such as the slow accumulation of pathogen inocula. The prevalence of toxins, arising from biotic interactions with fungal diseases, can alter crop quality rather than quantity. Thus, farmer decisions for whether to tolerate pest infestation must take into account several direct and immediate and/or delayed potential risks. Published scientific evidence on the co-occurrence of risk factors resulting from the presence of different pests and pathogens are largely absent, and this has stifled the adoption of integrated pest management. Here, we tested how the withdrawal of herbicide and insecticide protection in maize, alone and in combination, might induce higher prevalence of up to 23 mycotoxins in the crop at harvest. The experiment was conducted over 4 years in 29 fields in the south west of France. The test involved a comparison of paired samples collected from treated and untreated plots. All nine major mycotoxins that were observed in more than 4 % of the samples showed highly variable concentrations both between fields and years. The overall trend following the cessation of pesticide protection, however, is for higher levels of mycotoxins and up to a six-fold increased in nivalenol mean concentration (to 202.3 μg kg−1 of maize seeds) compared to its treated control. Overall mycotoxin concentrations approached 55–67 % of their maximum acceptable rate, a situation of reduced security margin that could lead to economic penalties and market restrictions. We found that the removal of herbicides had a greater impact than that of insecticides on the prevalence of mycotoxins, which differs from the expectation stated in the literature. This finding is further reinforced by the observation that certain species of weeds harbor several species of Fusarium. This means that weeds not only play a role as crop competitors but also as reservoirs of inoculum in the field. Our findings illustrate the importance of sanitary evaluation when the implementation of new cropping systems will alter the distribution and occurrence of pests and pathogens.
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Frontiers | Proteomic studies of the abiotic stresses response in model moss – Physcomitrella patens | Plant Proteomics

Frontiers | Proteomic studies of the abiotic stresses response in model moss – Physcomitrella patens | Plant Proteomics | plant cell genetics | Scoop.it
Moss species Physcomitrella patens has been used as a model system in plant science for several years, because it has a short life cycle and is easy to be handled. With the completion of its genome sequencing, more and more proteomic analyses were conducted to study the mechanisms of P. patens abiotic stress resistance. It can be concluded from these studies that abiotic stresses could lead to the repression of photosynthesis and enhancement of respiration in P. patens, although different stresses could also result in specific responses. Comparative analysis showed that the responses to drought and salinity were very similar to that of abscisic acid, while the response to cold was quite different from these three. Based on previous studies, it is proposed that sub-proteomic studies on organelles or protein modifications, as well as functional characterization of those candidate proteins identified from proteomic studies will help us to further understand the mechanisms of abiotic stress resistance in P. patens.
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Frontiers | The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation | Plant Proteomics

Frontiers | The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation | Plant Proteomics | plant cell genetics | Scoop.it
Plant protoplasts are widely used for genetic manipulation and functional studies in transient expression systems. However, little is known about the molecular pathways involved in a cell response to the combined stress factors resulted from protoplast generation. Plants often face more than one type of stress at a time, and how plants respond to combined stress factors is therefore of great interest. Here, we used protoplasts of the moss Physcomitrella patens as a model to study the effects of short-term stress on the chloroplast proteome. Using label-free comparative quantitative proteomic analysis (SWATH-MS), we quantified 479 chloroplast proteins, 219 of which showed a more than 1.4-fold change in abundance in protoplasts. We additionally quantified 1451 chloroplast proteins using emPAI. We observed degradation of a significant portion of the chloroplast proteome following the first hour of stress imposed by the protoplast isolation process. Electron-transport chain (ETC) components underwent the heaviest degradation, resulting in the decline of photosynthetic activity. We also compared the proteome changes to those in the transcriptional level of nuclear-encoded chloroplast genes. Globally, the levels of the quantified proteins and their corresponding mRNAs showed limited correlation. Genes involved in the biosynthesis of chlorophyll and components of the outer chloroplast membrane showed decreases in both transcript and protein abundance. However, proteins like dehydroascorbate reductase 1 and 2-cys peroxiredoxin B responsible for ROS detoxification increased in abundance. Further, genes such as thylakoid ascorbate peroxidase were induced at the transcriptional level but down-regulated at the proteomic level. Together, our results demonstrate that the initial chloroplast reaction to stress is due changes at the proteomic level.
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Phytochrome B integrates light and temperature signals in Arabidopsis

Phytochrome B integrates light and temperature signals in Arabidopsis | plant cell genetics | Scoop.it
Combining heat and light responses

Plants integrate a variety of environmental signals to regulate growth patterns. Legris et al. and Jung et al. analyzed how the quality of light is interpreted through ambient temperature to regulate transcription and growth (see the Perspective by Halliday and Davis). The phytochromes responsible for reading the ratio of red to far-red light were also responsive to the small shifts in temperature that occur when dusk falls or when shade from neighboring plants cools the soil.

Science, this issue p. 897, p. 886; see also p. 832
Abstract

Ambient temperature regulates many aspects of plant growth and development, but its sensors are unknown. Here, we demonstrate that the phytochrome B (phyB) photoreceptor participates in temperature perception through its temperature-dependent reversion from the active Pfr state to the inactive Pr state. Increased rates of thermal reversion upon exposing Arabidopsis seedlings to warm environments reduce both the abundance of the biologically active Pfr-Pfr dimer pool of phyB and the size of the associated nuclear bodies, even in daylight. Mathematical analysis of stem growth for seedlings expressing wild-type phyB or thermally stable variants under various combinations of light and temperature revealed that phyB is physiologically responsive to both signals. We therefore propose that in addition to its photoreceptor functions, phyB is a temperature sensor in plants.
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Phototropic solar tracking in sunflower plants: an integrative perspective

Phototropic solar tracking in sunflower plants: an integrative perspective | plant cell genetics | Scoop.it
Background One of the best-known plant movements, phototropic solar tracking in sunflower (Helianthus annuus), has not yet been fully characterized. Two questions are still a matter of debate. (1) Is the adaptive significance solely an optimization of photosynthesis via the exposure of the leaves to the sun? (2) Is shade avoidance involved in this process? In this study, these concepts are discussed from a historical perspective and novel insights are provided.

Scope and Methods Results from the primary literature on heliotropic growth movements led to the conclusion that these responses cease before anthesis, so that the flowering heads point to the East. Based on observations on 10-week-old plants, the diurnal East–West oscillations of the upper fifth of the growing stem and leaves in relation to the position of the sun (inclusive of nocturnal re-orientation) were documented, and photon fluence rates on the leaf surfaces on clear, cloudy and rainy days were determined. In addition, the light–response curve of net CO2 assimilation was determined on the upper leaves of the same batch of plants, and evidence for the occurrence of shade-avoidance responses in growing sunflower plants is summarized.

Conclusions. Only elongating, vegetative sunflower shoots and the upper leaves perform phototropic solar tracking. Photon fluence response and CO2 assimilation measurements cast doubt on the ‘photosynthesis-optimization hypothesis’ as the sole explanation for the evolution of these plant movements. We suggest that the shade-avoidance response, which maximizes light-driven CO2 assimilation, plays a major role in solar tracking populations of competing sunflower plants, and an integrative scheme of these growth movements is provided.
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Evaluating the Economic and Environmental Impacts of a Global GMO Ban

Evaluating the Economic and Environmental Impacts of a Global GMO Ban | plant cell genetics | Scoop.it
The objective of this research is to assess the global economic and greenhouse gas emission impacts of banning GMO crops. This is done by modeling two counterfactual scenarios and evaluating them apart and in combination using a well-know Computable General Equilibrium (CGE) model, GTAP-BIO. The first scenario models the impact of a global GMO ban. The second scenario models the impact of increased GMO penetration. The focus is on the price and welfare impacts, and land use change greenhouse gas (GHG) emissions associated with GMO technologies. Much of the prior work on the economic impacts of GMO technology has relied on a combination of partial equilibrium analysis and econometric techniques. However, CGE modelling is a way of analyzing economy-wide impacts that take into account the linkages in the global economy. Here the goal is to contribute to the literature on the benefits of GMO technology by estimating the impacts on price, supply and welfare. Food price impacts range from an increase of 0.27% to 2.2%, depending on the region. Total welfare losses associated with loss of GMO technology total up to $9.75 billion. The loss of GMO traits as an intensification technology has not only economic impacts, but also environmental ones. The full environmental analysis of GMO is not undertaken here. Rather we model the land use change owing to the loss of GMO traits and calculate the associated increase in GHG emissions. We predict a substantial increase in GHG emissions if GMO technology is banned.
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