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Plant Gene Seeker -PGS
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Curated by Andres Zurita
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¿Por qué la quinua podría jugar un papel clave en la seguridad alimentaria de A. Latina?

¿Por qué la quinua podría jugar un papel clave en la seguridad alimentaria de A. Latina? | Plant Gene Seeker -PGS | Scoop.it
La quinua, un alimento típicamente andino y muy vinculado a las comunidades andinas que durante siglos la han cuidado con esmero, se ha convertido en producto estrella para la ONU, organismo que le dedicó el año 2013.
Andres Zurita's insight:

Sus virtudes son enormes pues se adapta a las condiciones climáticas más diversas, es resistente, fácil de cultivar y con un bajo coste de producción. Por si todo ello fuera poco, tiene bajo impacto ambiental, contribuye a la biodiversidad (hay más de 3.000 variedades) y protege los ecosistemas, según documentos publicados por la Organización de Naciones Unidas para la Agricultura y la Alimentación (FAO).

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Sergio Escanilla's curator insight, December 9, 2013 8:04 AM

"Quinua" est le principal component de la substance laquelle Archibald a decouvert et elle pouvais éradiquer la faim dans le monde

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Transcriptome profiling of cytokinin and auxin regulation in tomato root

Transcriptome profiling of cytokinin and auxin regulation in tomato root | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Tomato is a model and economically important crop plant with little information available about gene expression in roots. Currently, there have only been a few studies that examine hormonal responses in tomato roots and none at a genome-wide level. This study examined the transcriptome atlas of tomato root regions (root tip, lateral roots, and whole roots) and the transcriptional regulation of each root region in response to the plant hormones cytokinin and auxin using Illumina RNA sequencing. More than 165 million 1×54 base pair reads were mapped onto the Solanum lycopersicum reference genome and differential expression patterns in each root region in response to each hormone were assessed. Many novel cytokinin- and auxin-induced and -repressed genes were identified as significantly differentially expressed and the expression levels of several were confirmed by qPCR. A number of these regulated genes represent tomato orthologues of cytokinin- or auxin-regulated genes identified in other species, including CKXs, type-A RRs, Aux/IAAs, and ARFs. Additionally, the data confirm some of the hormone regulation studies for recently examined genes in tomato such as SlIAAs and SlGH3s. Moreover, genes expressed abundantly in each root region were identified which provide a spatial distribution of many classes of genes, including plant defence, secondary metabolite production, and general metabolism across the root. Overall this study presents the first global expression patterns of hormone-regulated transcripts in tomato roots, which will be functionally relevant for future studies directed towards tomato root growth and development.

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Local auxin biosynthesis regulation by PLETHORA transcription factors controls phyllotaxis in Arabidopsis

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Lateral organ distribution at the shoot apical meristem defines specific and robust phyllotaxis patterns that have intrigued biologists and mathematicians for centuries. In silico studies have revealed that this self-organizing process can be recapitulated by modeling the polar transport of the phytohormone auxin. Phyllotactic patterns change between species and developmental stages, but the processes behind these variations have remained unknown. Here we use regional complementation experiments to reveal that phyllotactic switches in Arabidopsis shoots can be mediated by PLETHORA-dependent control of local auxin biosynthesis.

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Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

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The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.


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Free eBook from FAO: Save and grow - A new paradigm of agriculture (2011)

Free eBook from FAO: Save and grow - A new paradigm of agriculture (2011) | Plant Gene Seeker -PGS | Scoop.it
Sustainable crop production intensification can be summed up in the words save and grow. Sustainable intensification means a productive agriculture that conserves and enhances natural resources

 

Here's a link to the full free ebook (PDF format): http://www.fao.org/docrep/014/i2215e/i2215e.pdf.


Via Mary Williams, Biswapriya Biswavas Misra
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Mary Williams's curator insight, December 28, 2012 7:54 AM

You could assign this book in an undergraduate course as an introduction to the challenges of agricultural intensification, and opportunities such as genetic improvements and irrigation. It's full of information but also highly readable, and includes references.

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New research & maps provide a detailed look at how the brain organizes visual information

New research & maps provide a detailed look at how the brain organizes visual information | Plant Gene Seeker -PGS | Scoop.it

How does our brain organize the visual information that our eyes capture? Researchers at the University of California, Berkeley, used computational models of brain imaging data to answer this question and arrived at what they call “continuous semantic space” – a notion which serves as the basis for the first interactive maps showing how the brain categorizes what we see.The data on which the maps are based was collected while the subjects watched movie clips. Brain activity was recorded via functional Magnetic Resonance Imaging (fMRI), a type of MRI that measures brain activity by detecting related changes in blood flow. In order to find the correlations in the data collected, the researchers used a type of analysis known as regularized linear regression...


Via Lauren Moss
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Pedro Barbosa's curator insight, December 28, 2012 7:53 AM

Excellent articple about neuroscience - visual mapping.

Understanding our minds is important on all types of management tasks;)

 

Pedro Barbosa | www.pbarbosa.com | www.harvardtrends.com

Beth Kanter's curator insight, December 30, 2012 4:10 PM

Good points to make about why going visual is important

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The Drunken Botanist

A book trailer for Amy Stewart's new book, THE DRUNKEN BOTANIST: The Plants That Create the World's Great Drinks. Coming March 2013 from Algonquin Books.

Via Eve Emshwiller, diana buja, Mary Williams
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Eve Emshwiller's curator insight, December 22, 2012 1:00 PM

Funny video, less than 3 minutes.  Now, do I use it in teaching ethnobotany, or intro botany, or both?

Marybeth Shea's comment, January 1, 2013 9:14 PM
Both!
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Plant Physiol: Proteome analysis shoot- and root-specific targets of cytokinin action ...

Plant Physiol: Proteome analysis shoot- and root-specific targets of cytokinin action ... | Plant Gene Seeker -PGS | Scoop.it

"Here, we show that the Arabidopsis proteome responds with strong tissue- and time-specificity to aromatic CK 6-benzylaminopurine (BAP) and that fast posttranscriptional and/or posttranslational regulation of protein abundance is involved in the contrasting shoot and root proteome response to BAP. In the shoot, BAP upregulates the abundance of proteins involved in abscisic acid (ABA) biosynthesis and the ABA response, whereas in the root, BAP rapidly and strongly upregulates the majority of proteins in the ethylene biosynthetic pathway."

 

Nice!


Via Mary Williams, ROOTSPROUT
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Parental contributions to the transcriptome of early plant embryos | Current Comments

Parental contributions to the transcriptome of early plant embryos | Current Comments | Plant Gene Seeker -PGS | Scoop.it

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, December 26, 2012 1:51 PM

In plants and animals, embryo development becomes ultimately controlled by zygotic genes, but the timing of zygotic genome activation (ZGA) varies greatly between organisms[1,2]. We recently showed that the transcriptome of young Arabidopsis embryos is dominated by maternal transcripts with a progressive ZGA under the maternal control of epigenetic pathways [3]. In contrast, another study reported that both parental genomes contribute equally to the transcriptome of young embryos, suggesting that ZGA occurs immediately after fertilization[4]. How to explain such dramatic differences?We propose that the discrepancies between these two studies likely reflect genuine biological differences between the two experiments, paving the road towards exciting discoveries on ZGA mechanisms in plants.

In animals, early stages of embryo development are associated with extensive epigenetic reprogramming to coordinate zygotic genome activation (ZGA) [2]. ZGA is typically delayed, although to a varying extent depending on the species, with a gradual loss of the maternal dominance and increase of zygotic influence [1,2]. In flowering plants, maternal effects on seed development have been recognized, yet are difficult to investigate because of the intricate relationships between the embryo, the embryo-nourishing endosperm, and the maternal seed coat [5]. To understand the interaction of parental genomes following fertilization, allele-specific assays were used to distinguish paternal and maternal contributions for selected loci or at the genome-wide level in dissected embryos (reviewed in [1]), with surprisingly different results. Yet, the diversity of species (Arabidopsis, maize, tobacco) and developmental stages analyzed made it difficult to draw general conclusions. In fact, the observed differences may reflect yet undiscovered biological factors controlling ZGA in flowering plants.

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Improving Freezing Tolerance of ‘Chambourcin’ Grapevines with Exogenous Abscisic Acid

Improving Freezing Tolerance of ‘Chambourcin’ Grapevines with Exogenous Abscisic Acid | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The purpose of this study was to develop a protocol to increase freezing tolerance of field-grown ‘Chambourcin’ grapevines (Vitis spp.) using exogenous abscisic acid (ABA). The specific objectives were to determine the optimum concentration and timing for ABA foliar application in ‘Chambourcin’ and to evaluate morphological and physiological changes that lead to increased freezing tolerance in response to foliar ABA application. ‘Chambourcin’ grapevines were treated with a foliar ABA application of concentrations of 0, 100, 200, 300, 400, 500, 600, 700, and 800 mg·L−1 at 50% fruit set stage to evaluate ABA phytotoxicity under field conditions and identify the optimum concentration. In a subsequent experiment, ‘Chambourcin’ grapevines were treated with 400 and 600 mg·L−1 of ABA at different stages of development corresponding to 50% fruit set, 21 days after 50% fruit set, 50% veraison, 20, 30, 40, and 55 days postveraison. ABA concentrations of 700 and 800 mg·L−1 were phytotoxic and caused significant damage to leaves and flowers. Optimum concentrations of ABA did not affect yield components or basic fruit chemical composition, yet it promoted anthocyanin accumulation at harvest. Furthermore, ABA advanced bud dormancy, decreased bud water content, and eventually increased freezing tolerance under simulated freezing tests. The increased freezing tolerance of ABA-treated vines was confirmed by bud injury assessment after a natural freezing event in Jan. 2011. It was also determined that ABA was most effective when applied with an optimum concentration of 400 mg·L−1 20 to 30 days postveraison. It is concluded that exogenous ABA enhanced dormancy and increased freezing tolerance; thus, it has the potential to protect grape cultivars from freezing injury.

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Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice

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Grain size and shape are important components determining rice grain yield, and they are controlled by quantitative trait loci (QTLs). Here, we report the cloning and functional characterization of a major grain length QTL, qGL3, which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of theqgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties, due to its favorable effect on grain length, filling, and weight.

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Responses of root architecture development to low phosphorus availability: a review

Andres Zurita's insight:

Phosphorus (P) is an essential element for plant growth and development but it is often a limiting nutrient in soils. Hence, P acquisition from soil by plant roots is a subject of considerable interest in agriculture, ecology and plant root biology. Root architecture, with its shape and structured development, can be considered as an evolutionary response to scarcity of resources.

Scope This review discusses the significance of root architecture development in response to low P availability and its beneficial effects on alleviation of P stress. It also focuses on recent progress in unravelling cellular, physiological and molecular mechanisms in root developmental adaptation to P starvation. The progress in a more detailed understanding of these mechanisms might be used for developing strategies that build upon the observed explorative behaviour of plant roots.

Conclusions The role of root architecture in alleviation of P stress is well documented. However, this paper describes how plants adjust their root architecture to low-P conditions through inhibition of primary root growth, promotion of lateral root growth, enhancement of root hair development and cluster root formation, which all promote P acquisition by plants. The mechanisms for activating alterations in root architecture in response to P deprivation depend on changes in the localized P concentration, and transport of or sensitivity to growth regulators such as sugars, auxins, ethylene, cytokinins, nitric oxide (NO), reactive oxygen species (ROS) and abscisic acid (ABA). In the process, many genes are activated, which in turn trigger changes in molecular, physiological and cellular processes. As a result, root architecture is modified, allowing plants to adapt effectively to the low-P environment. This review provides a framework for understanding how P deficiency alters root architecture, with a focus on integrated physiological and molecular signalling.

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PLOS ONE: Effects of Feeding Bt Maize to Sows during Gestation and Lactation on Maternal and Offspring Immunity and Fate of Transgenic Material

PLOS ONE: Effects of Feeding Bt Maize to Sows during Gestation and Lactation on Maternal and Offspring Immunity and Fate of Transgenic Material | 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.
Andres Zurita's insight:

Treatment differences observed following feeding of Bt maize to sows did not indicate inflammation or allergy and are unlikely to be of major importance. These results provide additional data for Bt maize safety assessment.

 
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Oxford Journals | Life Sciences | Journal of Experimental Botany | Interdrought Collection

Oxford Journals | Life Sciences | Journal of Experimental Botany | Interdrought Collection | Plant Gene Seeker -PGS | Scoop.it
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A series of interesting papers in drought effects and mitigation.

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Arabidopsis aux1rcr1 mutation alters AUXIN RESISTANT1 targeting and prevents expression of the auxin reporter DR5:GUS in the root apex

Arabidopsis aux1rcr1 mutation alters AUXIN RESISTANT1 targeting and prevents expression of the auxin reporter DR5:GUS in the root apex | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Multilevel interactions of the plant hormones ethylene and auxin coordinately and synergistically regulate many aspects of plant growth and development. This study isolated the AUXIN RESISTANT1 (AUX1) alleleaux1rcr1 (RCR1 for REVERSING CTR1-10 ROOT1) that suppressed the root growth inhibition conferred by the constitutive ethylene-responseconstitutive triple response1-10 (ctr1-10) allele. The aux1rcr1 mutation resulted from an L126F substitution at loop 2 of the plasma membrane-associated auxin influx carrier protein AUX1. aux1rcr1 and the T-DNA insertion mutant aux1-T were both defective in auxin transport and many aspects of the auxin response. Unexpectedly, expression of the auxin-response reporter DR5:GUS in the root apex was substantially prevented by the aux1rcr1 but not the aux1-T mutation, even in the presence of the wild-type AUX1 allele. Following treatment with the synthetic auxin 1-naphthaleneacetic acid (NAA), DR5:GUS expression in aux1rcr1 and aux1-Toccurred mainly in the root apex and mature zone. NAA-induced DR5:GUSexpression in the root apex was markedly prevented by ethylene in genotypes with aux1rcr1 but not in aux1-T genotypes and the wild type. The effect of aux1rcr1 on DR5:GUS expression seemed to be associated with AUX1-expressing domains. Green fluorescence protein-fused aux1rcr1 was localized in the cytoplasm and probably not to the plasma membrane, indicating important roles of the Lys126 residue at loop 2 in AUX1 targeting. The possible effects of aux1rcr1 on DR5:GUS expression are discussed.


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Root hydrotropism: An update

Andres Zurita's insight:

While water shortage remains the single-most important factor influencing world agriculture, there are very few studies on how plants grow in response to water potential, i.e., hydrotropism. Terrestrial plant roots dwell in the soil, and their ability to grow and explore underground requires many sensors for stimuli such as gravity, humidity gradients, light, mechanical stimulations, temperature, and oxygen. To date, extremely limited information is available on the components of such sensors; however, all of these stimuli are sensed in the root cap. Directional growth of roots is controlled by gravity, which is fixed in direction and intensity. However, other environmental factors, such as water potential gradients, which fluctuate in time, space, direction, and intensity, can act as a signal for modifying the direction of root growth accordingly. Hydrotropism may help roots to obtain water from the soil and at the same time may participate in the establishment of the root system. Current genetic analysis of hydrotropism in Arabidopsis has offered new players, mainly AHR1, NHR1, MIZ1, and MIZ2, which seem to modulate how root caps sense and choose to respond hydrotropically as opposed to other tropic responses. Here we review the mechanism(s) by which these genes and the plant hormones abscisic acid and cytokinins coordinate hydrotropism to counteract the tropic responses to gravitational field, light or touch stimuli. The biological consequence of hydrotropism is also discussed in relation to water stress avoidance.

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The Impact of Global Change Factors on Redox Signaling Underpinning Stress Tolerance

Andres Zurita's insight:

Reduction/oxidation (redox) metabolism and associated signaling are key components of cross tolerance to biotic and abiotic stresses in plants. Climate change factors such as predicted increases in temperature and the availability of atmospheric carbon dioxide (CO2) and ozone (O3) will have a profound effect on oxidative signaling in plants, particularly in relation to photosynthetic metabolism and environmental stress responses. Redox signaling is responsive to myriad environmental signals through influences on metabolism and the triggered activation of the suite of oxidative burst-generating enzymes, whose function is to enhance the oxidation state of the apoplast/cell wall environment. Like reactive oxygen species (ROS), the abundance of low molecular antioxidants such as ascorbate, glutathione, tocopherols and carotenoids, and antioxidant enzymes is modified by environmental triggers. Oxidants and antioxidants do not operate in isolated linear redox signaling pathways. Rather, they are part of a much larger stress signaling network that integrates information from many pathways including hormones and sugars to regulate plant growth and defense responses. Here, we explore the likely responses of oxidants and antioxidants to global change factors and discuss how they might modify gene expression, influencing overall plant fitness through altered stress responses.


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Trends in Plant Science - Structure and function of abscisic acid receptors

RT @TiPSc_news: Structure and function of abscisic acid receptors
http://t.co/zqPYoozC

Via ROOTSPROUT
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ScienceDirect.com - New Biotechnology - Bred for Europe but grown in America: the case of GM sugar beet

ScienceDirect.com - New Biotechnology - Bred for Europe but grown in America: the case of GM sugar beet | Plant Gene Seeker -PGS | Scoop.it

In 2007, a genetically modified herbicide tolerant (GMHT) sugar beet (Beta vulgaris L.) tolerant against glyphosate, a commonly used broad spectrum herbicide, was commercialised in the USA and Canada. The speed of uptake of GMHT sugar beet by farmers has no precedent. While it took the hitherto most successful GM crop in the USA 15 years to reach an adoption rate of 95%, GMHT sugar beet achieved this figure after only 2 years. This paper traces the history of GMHT sugar beet which started at the European continent and describes the economic and environmental impact of its introduction in the USA. The results suggest that the rapid adoption is economically sound with adopter rents averaging $257/ha. Moreover the adoption has a high potential to reduce the environmental impact of sugar beet production. Will these experiences bring GMHT sugar beet back to its roots in Europe?


Via Jean-Pierre Zryd
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Why China's Explosive Economic Growth Could Trigger a Global Food Crisis

Why China's Explosive Economic Growth Could Trigger a Global Food Crisis | Plant Gene Seeker -PGS | Scoop.it
Rising demand and disappearing arable land could lead China to import more food and produce a spike in global prices.

Via CIMMYT, Int.
Andres Zurita's insight:

There's another serious issue that is water depletion for sustaining agriculture growth...

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At Year's End, News of a Global Health Success

At Year's End, News of a Global Health Success | Plant Gene Seeker -PGS | Scoop.it
The stunning drop in global child mortality is proof that poor countries are not doomed to eternal misery. Here's how it happened.

Via Seth Dixon, diana buja, Luigi Guarino
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diana buja's curator insight, December 27, 2012 3:44 AM
Seth Dixon, Ph.D.'s insight:

Global health has substantially improved in the last two decades.  This article explores the improvements in global health that have been made this year, and the attached interactive feature allows users to explore the changes in global health risks.  Click here for the Guardian's version of this same data and interactive.  

 

100 Pound Loans's comment, December 27, 2012 4:05 AM
Hi, Great to see a new list of top travel blogs. With over 8000 uniques per month, I feel mine should be in there somewhere. Could you take a look at http://www.honeymoonpackagesindia.org.in/ ? Thanks
Matt Evan Dobbie's curator insight, December 27, 2012 8:24 PM

Child mortality info

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PLOS ONE: The Vineyard Yeast Microbiome, a Mixed Model Microbial Map

PLOS ONE: The Vineyard Yeast Microbiome, a Mixed Model Microbial Map | Plant Gene Seeker -PGS | Scoop.it

Vineyards harbour a wide variety of microorganisms that play a pivotal role in pre- and post-harvest grape quality and will contribute significantly to the final aromatic properties of wine. The aim of the current study was to investigate the spatial distribution of microbial communities within and between individual vineyard management units. For the first time in such a study, we applied the Theory of Sampling (TOS) to sample gapes from adjacent and well established commercial vineyards within the same terroir unit and from several sampling points within each individual vineyard. Cultivation-based and molecular data sets were generated to capture the spatial heterogeneity in microbial populations within and between vineyards and analysed with novel mixed-model networks, which combine sample correlations and microbial community distribution probabilities. The data demonstrate that farming systems have a significant impact on fungal diversity but more importantly that there is significant species heterogeneity between samples in the same vineyard. Cultivation-based methods confirmed that while the same oxidative yeast species dominated in all vineyards, the least treated vineyard displayed significantly higher species richness, including many yeasts with biocontrol potential. The cultivatable yeast population was not fully representative of the more complex populations seen with molecular methods, and only the molecular data allowed discrimination amongst farming practices with multivariate and network analysis methods. Importantly, yeast species distribution is subject to significant intra-vineyard spatial fluctuations and the frequently reported heterogeneity of tank samples of grapes harvested from single vineyards at the same stage of ripeness might therefore, at least in part, be due to the differing microbiota in different sections of the vineyard.


Via Jean-Pierre Zryd
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Crop yields stall in China, India - SciDev.Net

Crop yields stall in China, India - SciDev.Net | Plant Gene Seeker -PGS | Scoop.it
Crop yields of staples like rice, wheat, maize and soybean are stagnant in China and India.
Andres Zurita's insight:

China and India, the world's two most populous countries, are beset by stagnation in the production of staples like rice, wheat, soybean and maize (corn), says a new study on crop yield growth.

Based on statistics from around the world during the 1951– 2008 period, the study 'Recent patterns of crop yield growth and stagnation', says that for some crops in China and India the spatial extent of yield stagnation is more than half the cropped area.

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El salmón transgénico, a punto de ver la luz después de 23 años de exámenes

El salmón transgénico, a punto de ver la luz después de 23 años de exámenes | Plant Gene Seeker -PGS | Scoop.it
EEUU concluye que el primer animal modificado para consumo no daña la salud ni el medio ambiente. Gracias a la biotecnología, crece el doble de rápido que los ejemplares salvajes

Via Isabel Etayo
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New form of cell division found (Dec. 17, 2012)

New form of cell division found (Dec. 17, 2012) | Plant Gene Seeker -PGS | Scoop.it
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Researchers at the University of Wisconsin Carbone Cancer Center have discovered a new form of cell division in human cells.

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