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Rescooped by jesus vicente from DNA and RNA research
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At Tiny Scales, a Giant Burst on Tree of Life

At Tiny Scales, a Giant Burst on Tree of Life | jvc | Scoop.it

A new technique for finding and characterizing microbes has boosted the number of known bacteria by almost 50 percent, revealing a hidden world all around us.


Via Integrated DNA Technologies
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Rescooped by jesus vicente from Healthy trees, healthy future: Phytophthora systems biology
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Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis | jvc | Scoop.it

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.


Via Stéphane Hacquard, Francis Martin, Nari Williams
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Rescooped by jesus vicente from Plant and Seed Biology
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New Negatives in Plant Science

New Negatives in Plant Science | jvc | Scoop.it
New Negatives in Plant Science is an open access, peer reviewed, online journal that will publish hypothesis-driven, scientifically sound studies...

Via Loïc Lepiniec
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Rescooped by jesus vicente from Plant and Seed Biology
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Multiscale digital Arabidopsis predicts individual organ and whole-organism growth

Multiscale digital Arabidopsis predicts individual organ and whole-organism growth | jvc | Scoop.it

How do you model a plant? By modeling pieces and assembling them in a meaningful way. Here's a multiscale model that works. From the abstract:

"Our model brings together gene dynamics, carbon partitioning, organ growth, shoot architecture, and development in response to environmental signals. It predicted the biomass of each leaf in independent data, demonstrated flexible control of photosynthesis across photoperiods, and predicted the pleiotropic phenotype of a developmentally misregulated transgenic line. Systems biology, crop science, and ecology might thus be linked productively in a community-based approach to modeling."


Via Mary Williams, Loïc Lepiniec
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Rescooped by jesus vicente from Plant and Seed Biology
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Hacked photosynthesis could boost crop yields

Hacked photosynthesis could boost crop yields | jvc | Scoop.it
Algal enzyme can speed up rate at which plants make food.

Via Loïc Lepiniec
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Rescooped by jesus vicente from Healthy trees, healthy future: Phytophthora systems biology
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Ten Simple Rules for Better Figures

Ten Simple Rules for Better Figures | jvc | Scoop.it

Scientific visualization is classically defined as the process of graphically displaying scientific data. However, this process is far from direct or automatic. There are so many different ways to represent the same data: scatter plots, linear plots, bar plots, and pie charts, to name just a few. Furthermore, the same data, using the same type of plot, may be perceived very differently depending on who is looking at the figure. A more accurate definition for scientific visualization would be a graphical interface between people and data. In this short article, we do not pretend to explain everything about this interface; rather, see [1], [2] for introductory work. Instead we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.


Via Niklaus Grunwald, Nari Williams
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Nari Williams's curator insight, September 17, 2014 5:52 AM

At the end of the day, as scientists it is our data that carries the message. How we present it therefore makes the world of difference. Here is one article to tag and refer to when presenting data in any format and to any audience.

Rescooped by jesus vicente from Plant and Seed Biology
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PLOS Collections : "The promise of plant translational research"

PLOS Collections : "The promise of plant translational research" | jvc | Scoop.it

A collection of articles, essays, perspectives and editorials on "The Promise of Plant Translational Research" - great collection to share with your students!


Via Mary Williams, Loïc Lepiniec
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Rescooped by jesus vicente from Plant and Seed Biology
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Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains | jvc | Scoop.it

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently~11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.


Via Francis Martin, Loïc Lepiniec
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Rescooped by jesus vicente from Plant and Seed Biology
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After Long Delays, Radical Nanopore Sequencer Finally in Labs | MIT Technology Review

After Long Delays, Radical Nanopore Sequencer Finally in Labs | MIT Technology Review | jvc | Scoop.it
A DNA sequencer the size of a cell phone could change where, and how, gene research occurs.

Via Loïc Lepiniec
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