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Widespread adoption of Bt cotton and insecticide decrease promotes biocontrol services

Widespread adoption of Bt cotton and insecticide decrease promotes biocontrol services | plant cell genetics | Scoop.it
Over the past 16 years, vast plantings of transgenic crops producing insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) have helped to control several major insect pests and reduce the need for insecticide sprays.
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Rothamsted Research is granted permission by Defra to carry out field trial with GM wheat plants - Rothamsted (2017) 

Rothamsted Research is granted permission by Defra to carry out field trial with GM wheat plants - Rothamsted (2017)  | plant cell genetics | Scoop.it

Rothamsted Research... submitted an application... for permission to carry out GM field trials on the Rothamsted Farm between 2017 and 2019. The risk assessment was reviewed by the independent Advisory Committee on Releases to the Environment (ACRE), and a 48-day public consultation was carried out... ACRE is satisfied that all scientific issues raised by the public with respect to this application have been addressed... Scientists... developed wheat plants that can carry out photosynthesis more efficiently i.e. convert light energy into plant biomass more efficiently. This trait has the potential to result in higher yielding plants. The purpose of the proposed trial is to evaluate the performance of the engineered plants in the field. 


Ensuring food security is a major challenge given the projected need to increase world food production by... 70% by 2050. Wheat is one of the major grain crops worldwide and provides approximately one-fifth of the total calories consumed globally. However, wheat yields have reached a plateau in recent years and predictions are that yield gains will not reach the level required to feed the 9 billion population... Traditional breeding and agronomic approaches have maximised light capture and allocation to the grain. A promising but as yet-unexploited route to increase wheat yields is to improve the efficiency by which energy in the form of light is converted to wheat biomass... 

“The efficiency of the process of photosynthesis integrated over the season is the major determinant of crop yield. However, to date photosynthesis has not been used to select for high yielding crops in conventional breeding programmes and represents an unexploited opportunity. But there is now evidence that improving the efficiency of photosynthesis by genetic modification is one of the promising approaches to achieve higher wheat yield potential... In this project we have genetically modified wheat plants to increase the efficiency of the conversion of energy from sunlight into biomass. We have shown that these plants carry out photosynthesis more efficiently in glasshouse conditions”... 

During the field trial, we will measure the photosynthetic efficiency of the plants in the field and we will determine total aboveground plant biomass and grain yield on an area basis at full maturity. We will also measure the number of wheat ears on an area basis and the grain number and weight per ear. From these data we will estimate the harvest index, which is the proportion of biomass allocated to the grain”...  

“This trial will be a significant step forward as we will be able to assess in ‘real environmental conditions’ the potential of these plants to produce more using the same resources and land area as their non-GM counterparts. These field trials are the only way to assess the viability of a solution that can bring economic benefits to farmers, returns to the UK tax payer from the long-term investment in this research, benefits to the UK economy as a whole and the environment in general”...  


http://www.rothamsted.ac.uk/news-views/rothamsted-research-granted-permission-defra-carry-out-field-trial-with-gm-wheat-plants



Via Alexander J. Stein
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Annual Review of Food Science and Technology

Annual Review of Food Science and Technology | plant cell genetics | Scoop.it
The color of food is often associated with the flavor, safety, and nutritional value of the product. Synthetic food colorants have been used because of their high stability and low cost. However, consumer perception and demand have driven the replacement ...
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Characterization Of Phytochrome Interacting Factors From The Moss Physcomitrella Patens Illustrates Conservation Of Phytochrome Signaling Modules In Land Plants

Across the plant kingdom, phytochrome (PHY) photoreceptors play an important role during adaptive and developmental responses to light. In Arabidopsis thaliana, light-activated PHYs accumulate in the nucleus, where they regulate downstream signaling components, such as phytochrome interacting factors (PIFs). PIFs are transcription factors that act as repressors of photomorphogenesis; their inhibition by PHYs leads to substantial changes in gene expression. The nuclear function of PHYs, however, has so far been investigated in only a few non-seed plants. Here, we have identified putative target genes of PHY signaling in the moss Physcomitrella patens and found light-regulated genes that are putative orthologs of PIF-controlled genes in A. thaliana. Phylogenetic analyses revealed that an ancestral PIF-like gene was already present in streptophyte algae, i.e., before the water-to-land-transition of plants. The PIF homologs in the genome of P. patens resemble A. thaliana PIFs in their protein domain structure, molecular properties, and physiological effects, albeit with notable differences in the motif-dependent PHY interaction. Our results suggest that P. patens PIFs are involved in PHY signaling. The PHY-PIF signaling node that relays light signals to target genes has been largely conserved during land plant evolution, with evidence of lineage-specific diversification.
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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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mlo-based resistance: An apparently universal “weapon” to defeat powdery mildew disease | Molecular Plant-Microbe Interactions

mlo-based resistance: An apparently universal “weapon” to defeat powdery mildew disease | Molecular Plant-Microbe Interactions | plant cell genetics | Scoop.it
Loss-of-function mutations of the appropriate Mildew resistance locus o (Mlo) gene(s) are an apparently reliable “weapon” to protect plants from infection by powdery mildew fungi, as they confer durable broad-spectrum resistance. Originally detected as a natural mutation in an Ethiopian barley landrace, this so-called mlo-based resistance has been successfully employed in European barley agriculture for more than four decades. More recently, mlo-mediated resistance was discovered to be inducible in virtually every plant species of economical or scientific relevance. By now, mlo resistance has been found (as natural mutants) or generated (by induced mutagenesis, gene silencing, and targeted or non-targeted gene knock-out) in a broad range of monocotyledonous and dicotyledonous plant species. Here, we review features of mlo resistance in barley, discuss approaches to identify the appropriate Mlo gene targets to induce mlo-based resistance, and consider the issue of pleiotropic effects often associated with mlo-mediated immunity, which can harm plant yield and quality. We portray mlo-based resistance as an apparently universal and effective “weapon” to defeat powdery mildew disease in a multitude of plant species.

Via Christophe Jacquet, Agriculture Nouvelle
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Evolutionary origin of phytochrome responses and signaling in land plants

Phytochromes comprise one of the major photoreceptor families in plants, and they regulate many aspects of plant growth and development throughout the plant life cycle. A canonical land plant phytochrome originated in the common ancestor of streptophytes. Phytochromes have diversified in seed plants and some basal land plants due to lineage-specific gene duplications that occurred during the course of land plant evolution. Molecular genetic analyses using Arabidopsis thaliana suggested that there are two types of phytochromes in angiosperms, light-labile type I and light-stable type II, which have different signaling mechanisms and which regulate distinct responses. In basal land plants, little is known about molecular mechanisms of phytochrome signaling, although R/FR photoreversible physiological responses and the distribution of phytochrome genes are relatively well documented. Recent advances in molecular genetics using the moss Physcomitrella patens and the liverwort, Marchantia polymorpha, revealed that basal land plants show FR-induced responses and that the establishment of phytochrome-mediated transcriptional regulation dates back to at least the common ancestor of land plants. In this review we summarize our knowledge concerning functions of land plant phytochromes, especially in basal land plants, and discuss sub-/neofunctionalization of phytochrome signaling during the course of land plant evolution.
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A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens

A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens | plant cell genetics | Scoop.it
Both land plants and metazoa have the capacity to reprogram differentiated cells to stem cells. Here we show that the moss Physcomitrella patens Cold-Shock Domain Protein 1 (PpCSP1) regulates reprogramming of differentiated leaf cells to chloronema apical stem cells and shares conserved domains with the induced pluripotent stem cell factor Lin28 in mammals. PpCSP1 accumulates in the reprogramming cells and is maintained throughout the reprogramming process and in the resultant stem cells. Expression of PpCSP1 is negatively regulated by its 3′-untranslated region (3′-UTR). Removal of the 3′-UTR stabilizes PpCSP1 transcripts, results in accumulation of PpCSP1 protein and enhances reprogramming. A quadruple deletion mutant of PpCSP1 and three closely related PpCSP genes exhibits attenuated reprogramming indicating that the PpCSP genes function redundantly in cellular reprogramming. Taken together, these data demonstrate a positive role of PpCSP1 in reprogramming, which is similar to the function of mammalian Lin28.
Introduction

Stem cells can self-renew and produce cells to be differentiated during development1,2,3,4. On the other hand, differentiated cells can change their cell fate to stem cells under certain conditions in both land plants and metazoa3,4. In flowering plants, differentiated cells can form undifferentiated cell masses called callus. With the addition of the appropriate phytohormones they can regenerate shoot and root meristems including stem cells, as was first shown with carrot in 1958 (ref. 5). Several genes have been shown to be involved in the formation of callus or regeneration of stem cells in Arabidopsis thaliana (Arabidopsis). Overexpression of a plant-specific AP2/ERF transcription factor ENHANCER OF SHOOT REGENERATION 1 (ESR1)/DORNROESCHEN (DRN) promotes the formation of shoot meristems from callus6. Induction of another AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) enhances callus formation without exogenous hormones7. In bryophytes, differentiated cells have a remarkable ability of being reprogrammed into stem cells without callus formation. In the moss Physcomitrella patens (Physcomitrella), wounding can induce the transition from differentiated leaf cells into proliferating chloronema stem cells without any exogenous phytohormones8,9. To understand the molecular mechanisms underlying this reprogramming, transcriptome analysis was performed during the reprogramming10 and several factors were identified as playing a role in the process. For instance, Cyclin-Dependent Kinase A (CDKA) activation is essential for cell cycle re-entry during reprogramming9. WUSCHEL-related homeobox 13-like (WOX13L) genes are required for the initiation of tip growth during stem cell formation11.
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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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