Plant Gene Seeker -PGS
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Plant Gene Seeker -PGS
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Curated by Andres Zurita
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Role of NINJA in root jasmonate signaling

Andres Zurita's insight:

Plant growth, the basis of agricultural production, is compromised when plants defend themselves against herbivores.Wound-induced growth reduction is coordinated between organs by hormones termed “jasmonates.” We developed a sensitive assay that marks tissues where wounding activates jasmonate function in seedlings. This assay showed that a key repressor of jasmonate responses is active mainly in roots where it permits normal growth. A deeper understanding of cell-size control is crucial in successfully engineering plants that display reduced growth restriction under stress.

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A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis

A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in CELLULASE3/GLYCOSYLHYDROLASE9B3 and LEUCINE RICH EXTENSIN2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development.

 

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Scientists develop 200 GM crops, await govt nod for trials - Times of India (2013)

Scientists develop 200 GM crops, await govt nod for trials - Times of India (2013) | Plant Gene Seeker -PGS | Scoop.it

Do you think only 'Monsanto' (or any multi-national seed company) has the capacity to develop transgenic crops? The answer is a clear 'no'. Indian scientists, working with public sector research institutions and universities, too have developed many genetically engineered varieties which, in fact, could not move beyond lab or 'restricted' trials... 

Indian scientists have over the years developed more than 200 genetically modified (GM) varieties of as many as 15 crops including cotton, brinjal, castor, groundnut, mustard, papaya, potato, rice, rubber, sugarcane, wheat and tomato. These varieties... have all the traits — resistance to insect, fungal, drought and virus — which may bring them in the league of Bt cotton by increasing productivity and export earnings. 

Indigenous transgenic varieties include a high salt-tolerant rice which can grow in salty water near coast. This variety is developed using genes of mangrove. Similarly, Indian scientists have developed a tomato variety having shelf life of over 50 days. The farmers will, however, reap the benefit of these findings only when government allows the scientists to go for extensive field trials and eventually for commercial production... 

 

A green signal to commercial production of such crops will affect the Indian farmers due to monopolistic control of seed business by multi-national companies (MNCs). "The solution to this problem is to encourage competition among the GM seed companies and even more importantly to have mission-mode programmes for the development of genetically modified seeds in the public sector", said N K Singh, professor at National Research Centre on Plant Biotechnology... "The Seed Act and the Monopoly and Restrictive Trade Practices Act should be used effectively to ensure competition and control of seed prices in addition to the bio-safety". 

It is true that the MNCs are far ahead in the development of GM crop varieties due to heavy investment and focused attempts by the companies. But, Indian research data show that the public sector transgenic crops can compete if allowed to grow. Expressing his confidence over what the Indian scientists have developed over the years, Asis Datta, former vice-chancellor of Jawaharlal Nehru University, said, "GM crop is going to be an essential part of our life today or tomorrow. If we don't realize it now, it will only push the country back. It will be difficult to recover later due to intense global competition"... 


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CONICYT lanza concurso para apoyar retorno de graduados de doctorado en el extranjero | PAI

CONICYT lanza concurso para apoyar retorno de graduados de doctorado en el extranjero | PAI | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Iniciativa busca apoyar el retorno e inserción en el país de investigadores que hayan estudiado y se hayan graduado en el extranjero. Además tiene un componente de estímulo a la inserción en regiones distintas a la Metropolitana.

 

A través del Programa de Atracción e Inserción de Capital Humano Avanzado (PAI), CONICYT lanzó su Concurso Nacional de Apoyo al Retorno de Investigadores desde el Extranjero 2013, con el objetivo de incentivar y facilitar el retorno de los investigadores chilenos -o extranjeros con residencia definitiva-, que hayan obtenido su doctorado en el extranjero a partir del día 1 de enero de 2011, y se encuentren, al momento de postular, viviendo en el extranjero.

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Plasticity of the Arabidopsis Root System under Nutrient Deficiencies

Plasticity of the Arabidopsis Root System under Nutrient Deficiencies | Plant Gene Seeker -PGS | Scoop.it
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Plant roots show a particularly high variation in their morphological response to different nutrient deficiencies. Although such changes often determine the nutrient efficiency or stress tolerance of plants, it is surprising that a comprehensive and comparative analysis of root morphological responses to different nutrient deficiencies has not yet been conducted. Since one reason for this is an inherent difficulty in obtaining nutrient-deficient conditions in agar culture, we first identified conditions appropriate for producing nutrient-deficient plants on agar plates. Based on a careful selection of agar specifically for each nutrient being considered, we grew Arabidopsis (Arabidopsis thaliana) plants at four levels of deficiency for 12 nutrients and quantified seven root traits. In combination with measurements of biomass and elemental concentrations, we observed that the nutritional status and type of nutrient determined the extent and type of changes in root system architecture (RSA). The independent regulation of individual root traits further pointed to a differential sensitivity of root tissues to nutrient limitations. To capture the variation in RSA under different nutrient supplies, we used principal component analysis and developed a root plasticity chart representing the overall modulations in RSA under a given treatment. This systematic comparison of RSA responses to nutrient deficiencies provides a comprehensive view of the overall changes in root plasticity induced by the deficiency of single nutrients and provides a solid basis for the identification of nutrient-sensitive steps in the root developmental program.


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De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana


Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, August 20, 2013 12:12 AM
Abstract (provisional)Background

Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits.

Results

Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis.

Conclusions

Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of agave biology and their improvement for bioenergy development.

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De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana


Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, August 20, 2013 12:12 AM
Abstract (provisional)Background

Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits.

Results

Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis.

Conclusions

Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of agave biology and their improvement for bioenergy development.

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Global calcium transducer P-type Ca2+-ATPases open new avenues for agriculture by regulating stress signalling

Global calcium transducer P-type Ca2+-ATPases open new avenues for agriculture by regulating stress signalling | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Food security is in danger under the continuous growing threat of various stresses including climate change and global warming, which ultimately leads to a reduction in crop yields. Calcium plays a very important role in many signal transduction pathways including stress signalling. Different extracellular stimuli trigger increases in cytosolic calcium, which is detrimental to plants. To cope with such stresses, plants need to develop efficient efflux mechanisms to maintain ionic homeostasis. The Ca2+-ATPases are members of the P-type ATPase superfamily, which perform many fundamental processes in organisms by actively transporting ions across cellular membranes. In recent years, many studies have revealed that, as well as efflux mechanisms, Ca2+-ATPases also play critical roles in sensing calcium fluctuations and relaying downstream signals by activating definitive targets, thus modulating corresponding metabolic pathways. As calcium-activated calmodulin (CaM) is reported to play vital roles in stress tolerance, the presence of a unique CaM-binding site in type IIB Ca2+-ATPases indicates their potential role in biotic as well as abiotic stress tolerance. The key roles of Ca2+-ATPases in transport systems and stress signalling in cellular homeostasis are addressed in this review. A complete understanding of plant defence mechanisms under stress will allow bioengineering of improved crop plants, which will be crucial for food security currently observed worldwide in the context of global climate changes. Overall, this article covers classification, evolution, structural aspects of Ca2+-ATPases, and their emerging roles in plant stress signalling.

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Bringing light into the discussion about GMOs? – A rather long reading list

[updated 21 July, 2013]  

 

These days I received an apparently easy request: “Do you have any recommendations for reading about the debate on GMOs? I think there is a lot of heat, but too little light in the discussion; I trust you can send me some…” To which I answered carelessly: “Sure, I will look into it, select a few references and post them…” 

 

I thought I’d have a quick look into my collection of bookmarks and references and post some of the links to satisfy the request. Obviously there would be too many individual studies and crop-specific or country-specific reports, but focusing only (i) on what was published in recent years, (ii) on sources where all this information was already aggregated (literature reviews, meta-analyses, authoritative statements, FAQs, etc.), and (iii) on academic or publicly funded sources should produce a fairly concise list, I thought. 

 

While not unmanageable, the list has become quite long. To get a rough idea of the current state of knowledge, it may be sufficient to peruse the first 1-2 (starred *) references under each heading, and to have a quick look at the abstracts and summaries of some of the others. (Given the controversy surrounding this topic I did not want to suggest just one or two sources, but show a bit the width of the scientific consensus, and to offer some titbits of related information.) ... 

 

http://ajstein.tumblr.com/post/40504136918/
 

 


Via Alexander J. Stein
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Jennifer Mach's comment, March 30, 2013 9:05 AM
I admit I haven't read this list... but for future reference, I'll definitely have a look.
Karen Ashby's curator insight, April 5, 2016 4:26 AM

Conflicted about how your view on GM ties in with a career in Biotech? Look no further

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Cactus helps solve prickly problem

Cactus helps solve prickly problem | Plant Gene Seeker -PGS | Scoop.it
Arrays of tiny copper spikes can clean oil from water, mimicking the way cacti pull water out of desert air.

Via Meristemi
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How significant to plant N nutrition is the direct consumption of soil microbes by roots? New Phytologist

How significant to plant N nutrition is the direct consumption of soil microbes by roots? New Phytologist | Plant Gene Seeker -PGS | Scoop.it
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SummaryThe high degree to which plant roots compete with soil microbes for organic forms of nitrogen (N) is becoming increasingly apparent. This has culminated in the finding that plants may consume soil microbes as a source of N, but the functional significance of this process remains unknown.We used 15N- and 14C-labelled cultures of soil bacteria to measure rates of acquisition of microbes by sterile wheat roots and plants growing in soil. We compared these rates with acquisition of 15N delivered as nitrate, amino acid monomer (l-alanine) and short peptide (l-tetraalanine), and the rate of decomposition of [14C] microbes by indigenous soil microbiota.Acquisition of microbe 15N by both sterile roots and roots growing in soil was one to two orders of magnitude slower than acquisition of all other forms of 15N. Decomposition of microbes was fast enough to account for all 15N recovered, but approximately equal recovery of microbe 14C suggests that microbes entered roots intact.Uptake of soil microbes by wheat (Triticum aestivum) roots appears to take place in soil. If wheat is typical, the importance of this process to terrestrial N cycling is probably minor in comparison with fluxes of other forms of soil inorganic and organic N.

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Properties of the halophyte microbiome and their implications for plant salt tolerance - Functional Plant Biology

Functional Plant Biology is an international journal of plant function publishing high quality research papers in all areas of plant physiology, applied agricultural research and pure molecular biology...
Andres Zurita's insight:

Saline habitats cover a wide area of our planet and halophytes (plants growing naturally in saline soils) are increasingly used for human benefits. Beside their genetic and physiological adaptations to salt, complex ecological processes affect the salinity tolerance of halophytes. Hence, prokaryotes and fungi inhabiting roots and leaves can contribute significantly to plant performance. Members of the two prokaryotic domains Bacteria and Archaea, as well as of the fungal kingdom are known to be able to adapt to a range of changes in external osmolarity. Shifts in the microbial community composition with increasing soil salinity have been suggested and research in functional interactions between plants and micro-organisms contributing to salt stress tolerance is gaining interest. Among others, microbial biosynthesis of polymers, exopolysaccharides, phytohormones and phytohormones-degrading enzymes could be involved.

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Improving Photosynthesis

Improving Photosynthesis | Plant Gene Seeker -PGS | Scoop.it
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Photosynthesis is the basis of plant growth, and improving photosynthesis can contribute toward greater food security in the coming decades as world population increases. Multiple targets have been identified that could be manipulated to increase crop photosynthesis. The most important target is Rubisco because it catalyses both carboxylation and oxygenation reactions and the majority of responses of photosynthesis to light, CO2, and temperature are reflected in its kinetic properties. Oxygenase activity can be reduced either by concentrating CO2 around Rubisco or by modifying the kinetic properties of Rubisco. The C4 photosynthetic pathway is a CO2-concentrating mechanism that generally enables C4 plants to achieve greater efficiency in their use of light, nitrogen, and water than C3 plants. To capitalize on these advantages, attempts have been made to engineer the C4 pathway into C3 rice (Oryza sativa). A simpler approach is to transfer bicarbonate transporters from cyanobacteria into chloroplasts and prevent CO2 leakage. Recent technological breakthroughs now allow higher plant Rubisco to be engineered and assembled successfully in planta. Novel amino acid sequences can be introduced that have been impossible to reach via normal evolution, potentially enlarging the range of kinetic properties and breaking free from the constraints associated with covariation that have been observed between certain kinetic parameters. Capturing the promise of improved photosynthesis in greater yield potential will require continued efforts to improve carbon allocation within the plant as well as to maintain grain quality and resistance to disease and lodging.

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Integration of epigenetic and genetic controls of seed size by cytokinin in Arabidopsis

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The development of seeds in flowering plants is placed under complex interactions between maternal tissues, the embryo, and the endosperm. The endosperm plays a major role in the regulation of seed size. In Arabidopsis thaliana, endosperm size depends on the coordination of the genetic pathway HAIKU (IKU) with epigenetic controls comprising genome dosage, DNA methylation, and trimethylated lysine 27 on histone H3 (H3K27me3) deposition. However, the effectors that integrate these pathways have remained unknown. Here, we identify a target of the IKU pathway, the cytokinin oxidase CKX2, that affects cytokinin signaling. CKX2 expression is activated by the IKU transcription factor WRKY10 directly and promotes endosperm growth. CKX2 expression also depends on H3K27me3 deposition, which fluctuates in response to maternal genome dosage imbalance and DNA demethylation of male gametes. Hence, the control of endosperm growth by CKX2 integrates genetic and epigenetic regulations. In angiosperms, cytokinins are highly active in endosperm, and we propose that IKU effectors coordinate environmental and physiological factors, resulting in modulation of seed size.

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Soybeans, Poverty and Inequality in the Brazilian Amazon - Weinhold &al (2013) - World Development

Soybeans, Poverty and Inequality in the Brazilian Amazon - Weinhold &al (2013) - World Development | Plant Gene Seeker -PGS | Scoop.it

Using a mixed-method approach of econometric and ethnographic field research, this article examines the social and economic costs and benefits of increases in soybean production in the Brazilian Amazon. Statistical analysis suggests that increased soy production both reduces poverty indicators and raises median rural incomes, but is also associated with increased measures of inequality.

 

Since the 1960s, Brazil’s national and regional governments have invested large sums in the development of soybean production… Soybean products are currently one of Brazil’s most valuable agricultural exports, and a key component of the nation’s continued economic development… Observers, however, remain divided about the social and environmental effects of this development. On one side many researchers fear that the large scale of this plantation crop will both increase deforestation and displace small farmers, increasing inequality and poverty… Other researchers, however, argue that most new soybean production takes place on land converted from pasture, rather than from forest, and that the growth of supporting enterprises that accompany large soybean production creates jobs and reduces poverty…

 

While all interlocutors are aware that any decisions concerning Brazil’s economic and developmental future and its land use involve trade-offs between economic, social, political, and environmental outcomes, the debate at all levels of society can be extremely impassioned. These arguments are often played out in public forums both in the areas most directly affected by soybean expansion as well as at the governmental level and in the national and international media, and this domestic political debate has had real consequences in the pattern of Brazilian agricultural expansion.

 

Thus an understanding of the economic consequences of particular agricultural land use patterns is incomplete without a complementary understanding of how that land use pattern impacts the political discourse. This article contributes to this debate by focussing on the socio-economic impacts of soy cultivation in the Amazon… This article thus presents new empirical evidence on the relationship between soy expansion and poverty.

 

However, we seek not only to measure the impact of the introduction of soy production on socio-economic outcomes, but also to better understand the political impact of this new development and the sources of some of the bitter local debates that surround the issue. In the process we attempt to reconcile the results of the statistical work with the political debate on the ground; to the extent that we find robust evidence that soy production does not increase poverty… how can we explain the continuing strong local political resistance to soy cultivation on the grounds of its socio-economic impact? Thus we combine an econometric analysis of the data with qualitative fieldwork to identify how the economic impacts of soy link to the continued political debates over its impact…

 

The need for such work is particularly important given the numerous criticisms of the soybean industry made by many researchers, activists, and local populations. The main emphasis here has been on the argument that the large scale of this plantation displaces small farmers, increasing inequality and poverty and, in turn, pushes such individuals to claim new land, often through deforestation…

 

The basic premise of this argument is that large-scale mechanized agriculture uses less labor per hectare than small-scale farming techniques… However others have argued that this kind of reasoning misses the dynamic argument that, in the long run, large scale mechanized agriculture increases overall productivity and avoids vicious cycles of rural poverty and population growth associated with low productivity smallholdings and deforestation.

 

In addition, wealth generated by large-scale soybean farms adds not only to both regional economies and government revenues but also to the growth of supporting enterprises that, in turn, creates jobs and reduces poverty all over the nation. It can also be argued that the associated increased investment in infrastructure also contributes to general, local welfare. It has also been suggested that the expansion of agriculture, the use of modern technology and the resulting productivity gains, result in the diversification of local economies…

 

The important point for the current article is that although there is a widespread belief among the public and NGOs about the negative effects of soy, empirical analysis is lacking on both sides of the debate. Here we make use of a large panel data set on agricultural and economic variables to address the question of the socio-economic impact of soy. We further complement and augment our econometric analysis with ethnographic fieldwork in a region which has recently undergone a large increase in soy production, interviewing local residents, policy makers, and other relevant actors about their views on the impact of soy cultivation. These qualitative findings shed light on why and how changing local land use patterns shape perceptions and drive significant political debates in ways that may seem at odds with the statistical results…

 

Given the relatively robust econometric finding of significant economic growth effects of soy, the existence of relatively strong local political resistance… in some areas raises some interesting questions… from both an econometric as well as a policy perspective, it would be useful to better understand the source of the beliefs and political debates surrounding the soy boom in the Amazon. To that end, in parallel with our quantitative research, we conducted qualitative fieldwork in areas of soy production in the Brazilian Amazon…

 

Differences are noted and often commented on by members of both groups in the region. More than physical distinctions, individuals tend to emphasize the cultural differences that exist in the working and social practices of the two groups. One focus is on the distinctions between homes and living styles. While local populations tend to have smaller houses and spend more time sitting outside them in their surrounding grounds, immigrants from the south bring a particular style of large house, with surrounding verandas that provide privacy from the outside. Members of older local populations portray themselves as very sociable in comparison to the more recent arrivals from Brazil’s southern states. However people from the South tend to portray such sociability as a form of laziness that they contrast with their own work ethic…

 

As our quantitative analysis shows the rise of median incomes and local GDP associated with soybean production and, most importantly, a lowering of poverty levels, it also supports the view that increased soy production increases inequality. This result is consistent with our qualitative observations that soybean production in Legal Amazonia is mostly controlled by wealthy landowners on large farms. Thus, even as all levels of local populations benefit economically from the growth of soybean production, large landowners accrue, or are perceived to accrue, relatively more gains… it appears that it is local perceptions of this growing inequality that fuel much of the long term opposition to the increase in large-scale soy farming… the emphasis on inequality is linked to other social and political factors, and in particular the fact that most large-scale farmers are immigrants to the region.. these tensions help to explain some of the continued animosity felt toward soybean cultivation even as its appears to have the effect of lowering poverty levels…

 

In this article we have provided both quantitative and qualitative evidence rejecting the hypothesis that the introduction of soy into the Amazon has increased poverty. On the contrary, our evidence is suggestive of poverty reducing effects, and strongly indicative of positive income gains. We… find that increases in soy cultivation are associated with strong increases in rural median household income and rural and urban GDP per capita. Both the quantitative evidence as well as ethnographic fieldwork also point to an association between increased soy production and inequality… to ethnic differences between large soy farmers and local populations that raise long standing prejudices and tensions… A significant portion of the negative publicity and local beliefs about soy held by a subset of the population can be traced to this perceived (and actual) unequal gains of soy expansion between different ethnic groups with historical rivalries…

 

http://dx.doi.org/10.1016/j.worlddev.2012.11.016


Via Alexander J. Stein
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Alexander J. Stein's curator insight, September 15, 2013 7:55 PM

An interesting article, not least because of its contribution to the ongoing discussion on how smallholder farming and large-scale agriculture can contribute to poverty alleviation. It is well worth to be read in its entirety. (Unfortunately it is behind a pay-wall.) 

 

What is also interesting is that the study confirms that absolute poverty (or income growth) only matters to some extent for people's overal satisfaction and contentment and that inequality (or income distribution) is also an important determinant of social welfare and social peace. 

 

I found it a bit surprising, though, that the authors did not mention that most soybeans in Brazil are genetically modified and that this is probably one of the motivations why there was a "demonstration organized by Greenpeace against soybean farming" or that this may have been a driver behind the "publicity generating tactics of confrontation used by the international environmental NGO Greenpeace". Therefore, while the authors very nicely analyse the cultural differences between ethnic groups and their historical rivalries, perhaps they could have done more to elaborate on the influence of such global interest groups and their role in social conflicts. 

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Cell - The Regulation of Cell Size

Cell - The Regulation of Cell Size | Plant Gene Seeker -PGS | Scoop.it
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An adult animal consists of cells of vastly different size and activity, but the regulation of cell size remains poorly understood. Recent studies uncovering some of the signaling pathways important for size/growth control, together with the identification of diseases resulting from aberrations in these pathways, have renewed interest in this field. This Review will discuss our current understanding of how a cell sets its size, how it can adapt its size to a changing environment, and how these processes are relevant to human disease.

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Lateral root formation and growth of Arabidopsis is redundantly regulated by cytokinin metabolism and signalling genes

Lateral root formation and growth of Arabidopsis is redundantly regulated by cytokinin metabolism and signalling genes | Plant Gene Seeker -PGS | Scoop.it
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The plant root system is important for the uptake of water and nutrients and the anchoring of plants in the soil. Lateral roots (LRs) contribute considerably to root system architecture. Their post-embryonic formation is regulated by hormones and environmental cues. The hormone cytokinin influences LR formation and growth in Arabidopsis thaliana on different levels by disturbing cell division activity and pattern formation. This includes inhibition of the first formative cell division of pericycle founder cells and inhibition of the outgrowth of young LR primordia. Mutant analysis revealed that the cytokinin biosynthesis genes IPT3 and IPT5 and all three cytokinin receptor genes (AHK2, AHK3, and CRE1/AHK4) act redundantly during LR initiation. Mutation of AHK2 and AHK3 caused increased auxin sensitivity of LR formation, corroborating the functional relevance of auxin–cytokinin interaction during LR formation. In contrast, LR development of cytokinin receptor mutants in response to other hormones was mostly similar to that of the wild type, which is consistent with separate response pathways. A noticeable exception was an increased sensitivity of LR elongation to brassinolide in ahk2 ahk3 mutants indicating antagonistic action of cytokinin and brassinosteroid. It is proposed that the multilevel redundancy of the cytokinin system in modulating LR formation reflects its role in mediating environmental cues.

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Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture

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Significance

Species display a range of plastic phenotypes that presumably have evolved as a result of adaptation to heterogeneous environments. We asked whether the genetic mechanisms that underlie adaptation across populations also determine the response of an individual plant to environmental cues in Arabidopsis. Using an integrative root phenotyping approach, genes that underlie natural variation in root architecture across populations were shown to control plasticity responses within an individual. Together, our results uncover a genetic mechanism underlying the phenotypic plasticity of an individual and phenotypic diversity across natural variants.

Abstract

Phenotypic plasticity is presumed to be involved in adaptive change toward species diversification. We thus examined how candidate genes underlying natural variation across populations might also mediate plasticity within an individual. Our implementation of an integrative “plasticity space” approach revealed that the root plasticity of a single Arabidopsis accession exposed to distinct environments broadly recapitulates the natural variation “space.” Genome-wide association mapping identified the known gene PHOSPHATE 1(PHO1) and other genes such as Root System Architecture 1 (RSA1) associated with differences in root allometry, a highly plastic trait capturing the distribution of lateral roots along the primary axis. The response of mutants in the Columbia-0 background suggests their involvement in signaling key modulators of root development including auxin, abscisic acid, and nitrate. Moreover, genotype-by-environment interactions for the PHO1 and RSA1 genes in Columbia-0 phenocopy the root allometry of other natural variants. This finding supports a role for plasticity responses in phenotypic evolution in natural environments.

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Mary Williams's comment, August 27, 2013 10:35 AM
I got so excited I recooped this without acknowledging you - sorry! Nice paper, I like it!
Andres Zurita's comment, August 27, 2013 12:43 PM
Thanks Mary! I also forget to acknowledge some great tips from scoopers... Cheers
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How will crops fare under climate change? Depends on how you ask

How will crops fare under climate change? Depends on how you ask | Plant Gene Seeker -PGS | Scoop.it
The damage scientists expect climate change to do to crop yields can differ greatly depending on which type of model was used to make those projections, according to new research.
Andres Zurita's insight:

The report in the journal Global Change Biology is one of the first to compare the agricultural projections generated by empirical models -- which rely largely on field observations -- to those by mechanistic models, which draw on an understanding of how crop growth and development are affected by the environment. Building on similar studies from ecology, the researchers found yet more evidence that empirical models may show greater losses as a result of climate change, while mechanistic models may be overly optimistic.

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Changes in the taste and textural attributes of apples in response to climate change : Scientific Reports

Changes in the taste and textural attributes of apples in response to climate change : Scientific Reports | Plant Gene Seeker -PGS | Scoop.it
The effects of climate change on the taste and textural attributes of foods remain largely unknown, despite much public interest.
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The effects of climate change on the taste and textural attributes of foods remain largely unknown, despite much public interest. On the basis of 30–40 years of records, we provide evidence that the taste and textural attributes of apples have changed as a result of recent global warming. Decreases in both acid concentration, fruit firmness and watercore development were observed regardless of the maturity index used for harvest date (e.g., calendar date, number of days after full bloom, peel colour and starch concentration), whereas in some cases the soluble-solids concentration increased; all such changes may have resulted from earlier blooming and higher temperatures during the maturation period. These results suggest that the qualities of apples in the market are undergoing long-term changes.

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Not all droughts are created equal: translating meteorological drought into woody plant mortality

Not all droughts are created equal: translating meteorological drought into woody plant mortality | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Widespread drought-induced mortality of woody plants has recently occurred worldwide, is likely to be exacerbated by future climate change and holds large ecological consequences. Yet despite decades of research on plant–water relations, the pathways through which drought causes plant mortality are poorly understood. Recent work on the physiology of tree mortality has begun to reveal how physiological dysfunction induced by water stress leads to plant death; however, we are still far from being able to predict tree mortality using easily observed or modeled meteorological variables. In this review, we contend that, in order to fully understand when and where plants will exceed mortality thresholds when drought occurs, we must understand the entire path by which precipitation deficit is translated into physiological dysfunction and lasting physiological damage. In temperate ecosystems with seasonal climate patterns, precipitation characteristics such as seasonality, timing, form (snow versus rain) and intensity interact with edaphic characteristics to determine when and how much water is actually available to plants as soil moisture. Plant and community characteristics then mediate how quickly water is used and seasonally varying plant physiology determines whether the resulting soil moisture deficit is physiologically damaging. Recent research suggests that drought seasonality and timing matter for how an ecosystem experiences drought. But, mortality studies that bridge the gaps between climatology, hydrology, plant ecology and plant physiology are rare. Drawing upon a broad hydrological and ecological perspective, we highlight key and underappreciated processes that may mediate drought-induced tree mortality and propose steps to better include these components in current research.

 
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No effects of Bacillus thuringiensis maize on nontarget organisms in the field in southern Europe: a meta-analysis of 26 arthropod taxa - Online First - Springer

No effects of Bacillus thuringiensis maize on nontarget organisms in the field in southern Europe: a meta-analysis of 26 arthropod taxa - Online First - Springer | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Maize with the insecticidal properties of the entomopathogenic bacterium Bacillus thuringiensisBerliner, known as Bt maize, has been sown in Europe since 1998. For several years, EU and Spanish regulations have required laboratory and field trials to assess risks of genetically modified crops for nontarget organisms prior to their authorization. Thirteen field trials were conducted in Spain to measure the effects of Bt maize on a broad range of arthropod taxa; no effects were found in accordance with most literature records. However, statistical analyses of single trials rarely have the statistical power to detect low effect sizes if they do not have a sufficient sample size. When sample size is low, meta-analysis may improve statistical power by combining several trials and assuming a common measure of effect size. Here we perform a meta-analysis of the results of 13 independent field trials conducted in Spain in which effects of single or stacked Bt traits on several arthropod taxa were measured with no significant results. Since the taxa included in each single trial were not the same for all trials, for the meta-analysis we selected only those taxa recorded in a minimum of six trials, resulting finally in 7, 7, and 12 taxa analyzed in visual counts, pitfall traps and yellow sticky traps, respectively. In comparison with single trial analysis, meta-analysis dramatically increased the detectability of treatment effects for most of the taxa regardless of the sampling technique; of the 26 taxa analyzed, only three showed poorer detectability in the meta-analysis than the best recorded in the 13 single trials. This finding reinforces the conclusion that Bt maize has no effect on the most common herbivore, predatory and parasitoid arthropods found in the maize ecosystems of southern Europe.

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PLOS ONE: Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development

PLOS ONE: Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development | Plant Gene Seeker -PGS | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Science Special Issue Once and Future Climate Change

Andres Zurita's insight:

Anthropogenic climate change is now a part of our reality. Even the most optimistic estimates of the effects of contemporary fossil fuel use suggest that mean global temperature will rise by a minimum of 2°C before the end of this century and that CO2 emissions will affect climate for tens of thousands of years. A key goal of current research is to predict how these changes will affect global ecosystems and the human population that depends on them. This special section ofScience focuses on the current state of knowledge about the effects of climate change on natural systems, with particular emphasis on how knowledge of the past is helping us to understand potential biological impacts and improve predictive power.

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Photosynthesis of Root Chloroplasts Developed in Arabidopsis Lines Overexpressing GOLDEN2-LIKE Transcription Factors

Photosynthesis of Root Chloroplasts Developed in Arabidopsis Lines Overexpressing GOLDEN2-LIKE Transcription Factors | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

In plants, genes involved in photosynthesis are encoded separately in nuclei and plastids, and tight cooperation between these two genomes is therefore required for the development of functional chloroplasts. Golden2-like (GLK) transcription factors are involved in chloroplast development, directly targeting photosynthesis-associated nuclear genes for up-regulation. Although overexpression of GLKs leads to chloroplast development in non-photosynthetic organs, the mechanisms of coordination between the nuclear gene expression influenced by GLKs and the photosynthetic processes inside chloroplasts are largely unknown. To elucidate the impact of GLK-induced expression of photosynthesis-associated nuclear genes on the construction of photosynthetic systems, chloroplast morphology and photosynthetic characteristics in greenish roots of Arabidopsis thaliana lines overexpressing GLKs were compared with those in wild-type roots and leaves. Overexpression of GLKs caused up-regulation of not only their direct targets but also non-target nuclear and plastid genes, leading to global induction of chloroplast biogenesis in the root. Large antennae relative to reaction centers were observed in wild-type roots and were further enhanced by GLK overexpression due to the increased expression of target genes associated with peripheral light-harvesting antennae. Photochemical efficiency was lower in the root chloroplasts than in leaf chloroplasts, suggesting that the imbalance in the photosynthetic machinery decreases the efficiency of light utilization in root chloroplasts. Despite the low photochemical efficiency, root photosynthesis contributed to carbon assimilation in Arabidopsis. Moreover, GLK overexpression increased CO2 fixation and promoted phototrophic performance of the root, showing the potential of root photosynthesis to improve effective carbon utilization in plants.


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