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National Academies Press free ebooks: Child Food Insecurity, & Massive Data Analysis

National Academies Press free ebooks: Child Food Insecurity, & Massive Data Analysis | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Two free ebooks from National Academies Press:

Frontiers in Massive Data Analysis: www.nap.edu/catalog.php?record_id=18374

and

Causes and Consequences of Child Food Insecurity and Hunger:

http://nap.edu/catalog.php?record_id=18504

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Plant Biology Teaching Resources (Higher Education)
Hooks and hot topics for university teachers and students
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Plant biologists FRET over stress

Plant biologists FRET over stress | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Summary of a pair of papers that use FRET as a biosensor for ABA

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Rescuing US biomedical research from its systemic flaws

Important Perspective from four heavy-hitters of US science (Bruce Alberts, Marc W. Kirschner, Shirley Tilghman, and Harold Varmus) = They call for a system that would " balance supply and demand in a sustainable fashion, adjust the pipeline that delivers new scientists, moderate the size of laboratories that are now difficult to fund, and restore an environment in which talented trainees and scientists can do their best work."

Mary Williams's insight:

One of their suggestions is to use more staff-level scientists in well-paid, permanent positions, rather than an endless stream of short-term postdocs. What do you think?

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Illuminating traffic control for cell–division planes

Illuminating traffic control for cell–division planes | Plant Biology Teaching Resources (Higher Education) | Scoop.it

From eLife,  an overview of plant cell divivision by Silke Robatzek

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Plant Cell: Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing

Plant Cell: Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing | Plant Biology Teaching Resources (Higher Education) | Scoop.it

" In conclusion, we provide a method for developing large-scale induced mutation resources with relatively small investments that is applicable to resource-poor organisms. Furthermore, our results demonstrate that large libraries of sequenced mutations can be readily generated, providing enhanced opportunities to study gene function and assess the effect of sequence and chromatin context on mutations. "

Mary Williams's insight:

Nice paper and resouce for genetic studies in rice and wheat

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Rescooped by Mary Williams from MycorWeb Plant-Microbe Interactions
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Central Cell–Derived Peptides Regulate Early Embryo Patterning in Flowering Plants

Central Cell–Derived Peptides Regulate Early Embryo Patterning in Flowering Plants | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Plant embryogenesis initiates with the establishment of an apical-basal axis; however, the molecular mechanisms accompanying this early event remain unclear. Here, we show that a small cysteine-rich peptide family is required for formation of the zygotic basal cell lineage and proembryo patterning in Arabidopsis. EMBRYO SURROUNDING FACTOR 1 (ESF1) peptides accumulate before fertilization in central cell gametes and thereafter in embryo-surrounding endosperm cells. Biochemical and structural analyses revealed cleavage of ESF1 propeptides to form biologically active mature peptides. Further, these peptides act in a non–cell-autonomous manner and synergistically with the receptor-like kinase SHORT SUSPENSOR to promote suspensor elongation through the YODA mitogen-activated protein kinase pathway. Our findings demonstrate that the second female gamete and its sexually derived endosperm regulate early embryonic patterning in flowering plants.


Via Francis Martin
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PNAS: Sugar demand, not auxin, is the initial regulator of apical dominance

PNAS: Sugar demand, not auxin, is the initial regulator of apical dominance | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"We have revealed that apical dominance is predominantly controlled by the shoot tip’s intense demand for sugars, which limits sugar availability to the axillary buds. These findings overturn a long-standing hypothesis on apical dominance and encourage us to reevaluate the relationship between hormones and sugars in this and other aspects of plant development."

By Michael G. Mason, John J. Ross, Benjamin A. Babst, Brittany N. Wienclaw, and Christine A. Beveridge

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3 April 2014 - Great British bioscience pioneers – Professor Ottoline Leyser - BBSRC

3 April 2014 - Great British bioscience pioneers – Professor Ottoline Leyser - BBSRC | Plant Biology Teaching Resources (Higher Education) | Scoop.it
In the fourth in a series of articles on Great British bioscience pioneers, Professor Ottoline Leyser at the University of Cambridge highlights advances in the understanding of plant developmental biology.
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NY Times: Eight (No, Nine!) Problems With Big Data

NY Times: Eight (No, Nine!) Problems With Big Data | Plant Biology Teaching Resources (Higher Education) | Scoop.it
It’s a valuable tool for analysis, but don’t believe all the hype.
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Low crown root number enhances nitrogen acquisition from low nitrogen soils in maize (Zea mays L.).

In developing nations, low soil nitrogen (N) availability is a primary limitation to crop production and food security, while in rich nations, intensive N fertilization is a primary economic, energy, and environmental cost to crop production. It has been proposed that genetic variation for root architectural and anatomical traits enhancing exploitation of deep soil strata could be deployed to develop crops with greater N acquisition. Here we provide evidence that maize (Zea mays L.) genotypes with few crown roots (crown root number: CN) have greater N acquisition from low N soils. Maize genotypes differed in their CN response to N limitation in greenhouse mesocosms and in the field. Low CN genotypes had 45% greater rooting depth in low N soils than high CN genotypes. Deep injection of 15N-labeled nitrate showed that low CN genotypes acquired more N from deep soil strata than high CN genotypes, resulting in greater photosynthesis and total nitrogen content. Under low N, low CN genotypes had greater biomass than high CN genotypes at flowering (85% in the field study in the US and 25% in South Africa). In the field in the US, 1.8x variation in CN was associated with 1.8x variation in yield reduction by N limitation. To our knowledge, this is the first report of the utility of CN for nutrient acquisition. Our results indicate that CN deserves consideration as a potential trait for genetic improvement of nitrogen acquisition from low N soils.


Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, April 5, 11:51 AM

Very interesting.

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Isopentenyltransferase-1 (IPT1) knockout in Physcomitrella together with phylogenetic analyses of IPTs provide insights into evolution of plant cytokinin biosynthesis


Via PMG, Jean-Pierre Zryd
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PMG's curator insight, April 3, 5:17 PM

chloroplast-bound IPT1 was almost exclusively responsible for the A37 prenylation of tRNA in Physcomitrella. Ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS)-based cytokinin profiling demonstrated that the total amount of all free cytokinins in tissue was almost unaffected. However, the knockout plants showed increased levels of the N 6-isopentenyladenine (iP)- andtrans-zeatin (tZ)-type cytokinins, considered to provide active forms, while cis-zeatin (cZ)-type cytokinins were reduced. The data provide evidence for an additional and unexpected tRNA-independent cytokinin biosynthetic pathway in moss. Comprehensive phylogenetic analysis indicates a diversification of tRNA-IPT-like genes in bryophytes probably related to additional functions.

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Where Do Ph.D. Scientists Work? | Science Careers

Where Do Ph.D. Scientists Work? | Science Careers | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Follow this link to the full report about where PhD scientists find work, broken down by gender and ethnic background


http://www.air.org/sites/default/files/downloads/report/STEM%20nonacademic%20careers%20April14.pdf

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Q&A with Alice Roberts, President of the Association for Science Education (UK)

Q&A with Alice Roberts, President of the Association for Science Education (UK) | Plant Biology Teaching Resources (Higher Education) | Scoop.it
We speak to the new president of the Association for Science Education


This quote is particularly good, "Distilling ideas to make them accessible, and weaving narrative into science, is not the same thing as “dumbing down”."

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NASA news: Satellite Shows High Productivity from U.S. Corn Belt

NASA news: Satellite Shows High Productivity from U.S. Corn Belt | Plant Biology Teaching Resources (Higher Education) | Scoop.it
During the U.S. Midwest's growing season, the region boasts more photosynthetic activity than any other spot on Earth.
Mary Williams's insight:

This is a summary of a new paper in PNAS that shows "that chlorophyll fluorescence data can be used as a unique benchmark to improve our global models, thus providing more reliable projections of agricultural productivity and climate impact on crop yields."


www.pnas.org/content/early/2014/03/24/1320008111.abstract

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Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns | Plant Biology Teaching Resources (Higher Education) | Scoop.it

What's going in in that understory?

Wonderful evolutionary story here

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Where Will a Biology PhD Take You?

Where Will a Biology PhD Take You? | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Based primarily on the 2012 NIH Workforce report this infographic represents current workforce sizes and annual fluxes before and after a PhD in the b...
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Plant Cell: What is Stress? Dose-Response Effects in Commonly Used In Vitro Stress Assays

Plant Cell: What is Stress? Dose-Response Effects in Commonly Used In Vitro Stress Assays | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"We found that the commonly used stress-inducing agents mannitol, sorbitol, NaCl and H2O2 impact shoot growth in a highly specific and dose-dependent way. Therefore, shoot growth is a sensitive, relevant and easily measured phenotype to assess stress tolerance over a wide range of stress levels."

Mary Williams's insight:

Often students use Arabidopsis seedlings in the teaching lab to learn about plant physiology. This paper shows that shoot growth is sensitive parameter to quantify even mild stress.

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Rescooped by Mary Williams from Plant-Microbe Symbioses
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Botany: Special issue: The microbiota of plants

In this Special Issue, we have tried to capture the diversity of plant–microbe research that is on-going, and that might not normally be marketed under the banner of “plant microbiome research”. Nevertheless, it belongs under this banner and we highlight some of this research here, including a variety of plant “habitats” such as roots, leaves, and floral parts, as well as a variety of microbes, from bacteria and arbuscular mycorrhizal fungi to dark septate fungi. Of course, the field is broader than what we are able present in a single issue, but we hope that it inspires researchers of overlooked aspects of plant microbiota research to get in on the game, and contribute to a more complete picture of this complex “ecosystem”.


Via Stéphane Hacquard, Jean-Michel Ané
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Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Plant phenology is known to depend on many different environmental variables, but soil microbial communities have rarely been acknowledged as possible drivers of flowering time. Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. Flowering time was sensitive to both microbes and the abiotic properties of different soils; varying soil microbiota also altered patterns of selection on flowering time. Thus, soil microbes potentially contribute to phenotypic plasticity of flowering time and to differential selection observed between habitats. We also describe a method to dissect the microbiome into single axes of variation that can help identify candidate organisms whose abundance in soil correlates with flowering time. This approach is broadly applicable to search for microbial community members that alter biological characteristics of interest.


Via Stéphane Hacquard, Francis Martin, Jean-Michel Ané
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Bacterial tricks for turning plants into zombies

Bacterial tricks for turning plants into zombies | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Microbe deploys proteins that manipulate both the plant it infects and the insects that spread it.
Mary Williams's insight:

Here's the article in PLOS Biology http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001835

And an article about the research in the local Norwich newspaper

http://www.edp24.co.uk/news/graphic_scientists_solve_mystery_of_the_zombie_plants_1_3533805

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JExpBot: Insights into evolution of plant cytokinin biosynthesis from Physcomitrella

JExpBot: Insights into evolution of plant cytokinin biosynthesis from Physcomitrella | Plant Biology Teaching Resources (Higher Education) | Scoop.it

It's always good to ask, "How does Physomitrella do this?"


"The moss Physcomitrella patens is part of an early divergent clade of land plants utilizing the plant hormone cytokinin for growth control. The rate-limiting step of cytokinin biosynthesis is mediated by isopentenyltransferases (IPTs), found in land plants either as adenylate-IPTs or as tRNA-IPTs. Although a dominant part of cytokinins in flowering plants are synthesized by adenylate-IPTs, the Physcomitrella genome only encodes homologues of tRNA-IPTs."

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Seeds for Needs: Climate-proofing agriculture by optimizing crop variety use - YouTube

s ehBioversity International scientist, Jacob van Etten (http://www.bioversityinternational.org/about-us/who-we-are/staff-bios/single-details-bios/van-etten-jaco...

Mary Williams's insight:

This is a nice short video that describes one approach to climate-proofing agriculture. There are lots of good ideas behind this project and it makes a good case study for students thinking about the diversity of farming methods as well as crops. 

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Interaction between Two Timing MicroRNAs Controls Trichome Distribution in Arabidopsis

Interaction between Two Timing MicroRNAs Controls Trichome Distribution in Arabidopsis | Plant Biology Teaching Resources (Higher Education) | Scoop.it

The miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) transcription factors function as an endogenous age cue in regulating plant phase transition and phase-dependent morphogenesis, but the control of SPL output remains poorly understood. InArabidopsis thaliana the spatial pattern of trichome is a hallmark of phase transition and governed by SPLs. Here, by dissecting the regulatory network controlling trichome formation on stem, we show that the miR171-targeted LOST MERISTEMS 1 (LOM1), LOM2 and LOM3, encoding GRAS family members previously known to maintain meristem cell polarity, are involved in regulating the SPL activity. Reduced LOM abundance by overexpression of miR171 led to decreased trichome density on stems and floral organs, and conversely, constitutive expression of the miR171-resistant LOM (rLOM) genes promoted trichome production, indicating that LOMs enhance trichome initiation at reproductive stage. Genetic analysis demonstrated LOMs shaping trichome distribution is dependent on SPLs, which positively regulate trichome repressor genes TRICHOMELESS 1 (TCL1) and TRIPTYCHON (TRY). Physical interaction between the N-terminus of LOMs and SPLs underpins the repression of SPL activity. Importantly, other growth and developmental events, such as flowering, are also modulated by LOM-SPL interaction, indicating a broad effect of the LOM-SPL interplay. Furthermore, we provide evidence that MIR171 gene expression is regulated by its targeted LOMs, forming a homeostatic feedback loop. Our data uncover an antagonistic interplay between the two timing miRNAs in controlling plant growth, phase transition and morphogenesis through direct interaction of their targets.


Via Jennifer Mach
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Jennifer Mach's curator insight, April 4, 9:56 AM

From the punctuation makes a difference files, glad these were "two timing microRNAs", not "two-timing microRNAs".

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Plant defensins in eLife

Plant defensins in eLife | Plant Biology Teaching Resources (Higher Education) | Scoop.it

This article in elife got a lot of silly press coverage this week ("tobacco plants cure cancer"), but it provides an interesting look at the structural interaction of a plant defensin with membrane phosphoinisitides.
These two review articles provide good background on these intersting peptides
http://www.sciencedirect.com/science/article/pii/S1749461312000346
http://www.sciencedirect.com/science/article/pii/S019697810900045X

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The arable ecosystem as battleground for emergence of new human pathogens

The arable ecosystem as battleground for emergence of new human pathogens | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.


Via Chris Upton + helpers
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Planta: Plant systems biology: insights, advances and challenges (review)

Planta: Plant systems biology: insights, advances and challenges  (review) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this  review, we discuss the basics of systems biology including the various ‘omics’ approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends."

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