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Kevin Zelnio's moving personal account of leaving science

Kevin Zelnio's moving personal account of leaving science | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Today I end a 5-year run at Deep Sea News. I'm sad that I am unable to continuing committing to this great group, and indeed science and science communication more generally.
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I think you'll enjoy reading this very personal account of Kevin's sometimes frustrating experiences as a scientist and science writer. From unsupportive and obstructionist PhD advisors to money worries, stress, and the struggle to spend time with children, but finally a new start. Go Kevin!

 

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Plant Biology Teaching Resources (Higher Education)
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Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014)

Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

To test the efficacy of CRISPR/Cas9 in tomato, we chose to target a gene that, when function was disrupted, would result in a distinctive, immediately recognizable phenotype early in the plant tissue culture phase of Agrobacterium-mediated transformation. A CRISPR/Cas9 construct was designed to target neighboring sequences in the second exon of the tomato homolog of Arabidopsis ARGONAUTE7 (SlAGO7), because loss-of-function mutations are recessive and result in plants whose typical compound flat leaves become needle-like, or “wiry” (Fig. 1) (Lesley, 1928; Yifhar et al., 2012). SlAGO7 is required for the biogenesis of a class of small RNAs known as trans-acting short interfering RNAs (ta-siRNAs), which regulate organ polarity through post-transcriptional silencing of AUXIN RESPONSE FACTOR (ARF) genes (Husbands et al., 2009). Strong alleles of slago7 thus produce lower levels of ta-siRNAs and reduced ARF mRNA degradation, resulting in the first leaves of mutant plants having leaflets without petioles, and later formed leaves lacking laminae (Fig. 1C). These distinctive phenotypes allowed us to immediately identify first generation transformed (T0) plants in which both alleles of SlAGO7 might be mutated.


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Cell Host Microbes: Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life (2014)

Cell Host Microbes: Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life (2014) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.

 

Ralf Weßling, Petra Epple, Stefan Altmann,Yijian He, Li Yang, Stefan R. Henz, Nathan McDonald, Kristin Wiley, Kai Christian Bader, Christine Glaßer, M. Shahid Mukhtar, Sabine Haigis, Lila Ghamsari, Amber E. Stephens, Joseph R. Ecker, Marc Vidal, Jonathan D.G. Jones,Klaus F.X. Mayer, Emiel Ver Loren van Themaat, Detlef Weigel, Paul Schulze-Lefert, Jeffery L. Dangl, Ralph Panstruga, and Pascal Braun


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CP's curator insight, September 12, 1:04 AM

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HopBF1 is HopZ4...

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Keeping Up With The Plant Destroyers

Keeping Up With The Plant Destroyers | Plant Biology Teaching Resources (Higher Education) | Scoop.it

From PlantVilliage, a guest post by Sophien Kamoun, The Sainsbury Laboratory 

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Inside the Cell - National Institute of General Medical Sciences

Inside the Cell - National Institute of General Medical Sciences | Plant Biology Teaching Resources (Higher Education) | Scoop.it
This science education booklet explores the interior design of cells and vividly describes the processes that take place within its organelles and structures.
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Review (PLOS Genetics): Trans-kingdom Cross-Talk: Small RNAs on the Move

Review (PLOS Genetics): Trans-kingdom Cross-Talk: Small RNAs on the Move | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals."

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Special Issue: Functional-Structural Plant Modelling

Special Issue: Functional-Structural Plant Modelling | Plant Biology Teaching Resources (Higher Education) | Scoop.it

A number of research groups in various areas of plant biology as well as computer science and applied mathematics have addressed modelling the spatiotemporal dynamics of growth and development of plants. This has resulted in development of functional–structural plant models (FSPMs). In FSPMs, the plant structure is always explicitly represented in terms of a network of elementary units. In this respect, FSPMs are different from more abstract models in which a simplified representation of the plant structure is frequently used (e.g. spatial density of leaves, total biomass, etc.). This key feature makes it possible to build modular models and creates avenues for efficient exchange of model components and experimental data. They are being used to deal with the complex 3-D structure of plants and to simulate growth and development occurring at spatial scales from cells to forest areas, and temporal scales from seconds to decades and many plant generations. The plant types studied also cover a broad spectrum, from algae to trees. This special issue of Annals of Botany features selected papers on FSPM topics such as models of morphological development, models of physical and biological processes, integrated models predicting dynamics of plants and plant communities, modelling platforms, methods for acquiring the 3-D structures of plants using automated measurements, and practical applications for agronomic purposes.


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How do we save UK plant sciences?

How do we save UK plant sciences? | Plant Biology Teaching Resources (Higher Education) | Scoop.it

The UK Plant Sciences Federation is looking for suggestions from you! The concerns are not restricted to the UK (lack of student interest and teacher preparedness, lack of funding and job opportunities etc), so wherever you are please share your insights and solutions.

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Multiscale digital Arabidopsis predicts individual organ and whole-organism growth

Multiscale digital Arabidopsis predicts individual organ and whole-organism growth | Plant Biology Teaching Resources (Higher Education) | 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."

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Sprinter and sprummer: scrap the four seasons (in Australia at least)

Sprinter and sprummer: scrap the four seasons (in Australia at least) | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Spring starts on the first day of September, right? Not if Dr Tim Entwisle, director of the Royal Botanic Gardens in Melbourne and the author of 'Sprinter and Sprummer', has anything to do with it. Here he argues we should scrap the European approach and adopt a five season model.
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Can Plants Grow on Mars and the Moon: A Growth Experiment on Mars and Moon Soil Simulants

Can Plants Grow on Mars and the Moon: A Growth Experiment on Mars and Moon Soil Simulants | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Science fair project anyone? My first thought was, "How to you make Martian soil?" and the answer is, you can BUY growth substrates that simulate Martian / moon soils. How about that.

http://www.orbitec.com/store/simulant.html


The only concern I have is about the first sentence of the abstract - "WHEN humans will settle on the moon or Mars they will have to eat there". Personally, I'd rather we put our energy into keeping earth habitable, thank you!

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Plant Tissue Culture Media Preparation - YouTube

Here's a video for new students starting plant tissue culture - how to prepare the media, step-by-step


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Feeding the future: Roslyn Gleadow

Feeding the future: Roslyn Gleadow | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Ros Gleadow explores how rising carbon dioxide emissions affect the nutritional value of food crops in developing countries.
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Four minute video showing Ros's research on how [CO2] affects cyanide production in cassava

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Plant genetic engineering, climate change and food security - Ortiz &al (2014) - CGIAR [pdf]

This paper exploreswhether crop genetic engineering can contribute to addressing food security, as well as enhancing human nutrition and farming under a changing climate.


The review is based on peer-refereed literature, using results to determine the potential of this gene technology. It also provides a brief summary of issues surrounding this genetic enhancement approach to plant breeding, and the impacts on farming, livelihoods, and the environment achieved so far.


The genetic engineering pipeline looks promising, particularly for adapting more nutritious, input-efficient crops in the development of the world’s farming systems... 


Although the technologies demonstrate potential to reduce crop losses, food waste, and enhance nutritional quality... farmers’ surveys reveal that increased yields are among the benefits for growing transgenic crops. Such a finding results from yield increases because of reduced losses from insect pests and weeds. In most developing countries, crop yields are low and yield gaps are large because of low input use, poor soil health, and pests and diseases.


Genetic engineering has a lot promise in increasing overall adaptive capacity of agriculture but emphasis on good agricultural practices, including maintenance of soil, water, and genetic resources and increasing irrigation and fertilizers remains critical to increasing production...

 

Given that current trends in yield increase are insufficient to double food production by 2050 and keep up with population and shifting consumption patterns, new approaches to the problem are needed. Transgenic cultivars could be a piece of that puzzle, building on success stories such as that of WEMA, but it is crucial that safety concerns are adequately addressed.


Further research should benchmark conventional approaches to crop improvement, compare them with likely yield increases available from transgenic approaches, and explicitly address climate impacts to ascertain the true potential of transgenic technologies in adapting to and mitigating climate change in the long term.

 

https://www.results.waterandfood.org/bitstream/handle/10568/41934/CCAFS%20WP%2072.pdf



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Autophagy as initiator or executioner of cell death: Trends in Plant Science

Autophagy as initiator or executioner of cell death: Trends in Plant Science | Plant Biology Teaching Resources (Higher Education) | Scoop.it

•Autophagy can suppress, initiate, or execute cell death depending on the biological context.

•Autophagy is an initiator of localized, hypersensitive response-associated cell death upon pathogen infection.

•Autophagy executes ‘formative’ vacuolar cell death and prevents ‘destructive’ necrosis in terminally differentiated cells.

•Homeostatic and anti-aging functions of autophagy complicate the dissection of its distinct roles in cell death.

Autophagy plays multiple, often antagonistic roles in plants. In particular, cytoprotective functions of autophagy are well balanced by cell death functions to compensate for the absence of apoptosis culminating in phagocytic clearance of dead cells. If autophagy is indeed required for plant programmed cell death (PCD), then what place does it occupy in the PCD pathways? Recent studies have examined the effects of impaired autophagy on pathogen-induced hypersensitive response (HR) and developmental PCD. While HR death was efficiently suppressed, inhibition of autophagy induced a switch from vacuolar PCD essential for development to necrosis. We therefore propose a dual role for autophagy in plant PCD: as an effector of HR PCD lying upstream of the ‘point-of-no-return’, and also as a downstream mechanism for clearance of terminally differentiated cells during developmental PCD.


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Epigenetic Regulation in Plant Responses to the Environment (Baulcombe and Dean)

Epigenetic Regulation in Plant Responses to the Environment (Baulcombe and Dean) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications."

Mary Williams's insight:

Free from Cold Spring Harbor Perspectives in Biology - good for your teaching!

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♥ princess leia ♥'s curator insight, September 15, 10:26 AM

Our environment affects everything 

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Journal of Visualized Experiments (JOVE) Cell Specific Analysis of Arabidopsis Leaves using Fluorescently Activated Cell Sorting (FACS)

Journal of Visualized Experiments (JOVE) Cell Specific Analysis of Arabidopsis Leaves using Fluorescently Activated Cell Sorting (FACS) | Plant Biology Teaching Resources (Higher Education) | Scoop.it
A method for producing Arabidopsis leaf protoplasts that are compatible with fluorescence activated cell sorting (FACS),...
Mary Williams's insight:

Great video here!

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"Hungry, hungry humans" New series by Grist author Nathanael Johnson

"Hungry, hungry humans" New series by Grist author Nathanael Johnson | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"As global population grows, are we ever going to run out of food? There are lots of people who say we need to work very hard to make farming more efficient to feed the word. Then there are others who say, no, the real problem is more equitably dividing the food up, and efficient farming techniques actually make the inequality worse. Finally, there are people who say that growing more, and sharing it better, doesn’t matter as long as keep making babies. Here we sort through the sweeping claims and look beyond the rhetoric to understand how to make food systems green and fair."

Mary Williams's insight:

I like his articles because they are clear, well-researched and accessible. Good resources for students!

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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Science, "The coffee genome provides insight into the convergent evolution of caffeine biosynthesis"
"With more than 2.25 billion cups consumed every day, coffee is one of the most important crops on Earth, cultivated across more than 11 million hectares"

And one of the most important contributors to the efforts of scientists, too!

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Eva’s endeavours: a professional path in plant science inspired by Norman Borlaug

“…I wanted to contribute in a similar way” – Eva Weltzien   Learning about the work of Nobel laureate, Norman Borlaug, in high school inspired Eva Weltzien to become a plant breeder so she too could contribute to improving the living conditions in the developing world. Today, Eva is a Principal Scientist in sorghum breeding and genetic resources at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Mali. “Not only did Norman Borlaug revolutionise agriculture by breeding high-yielding wheat varieties, he then selflessly distributed these to the countries in the world that most needed them, saving hundreds of millions from starvation,” Eva recollects passionately, as she speaks about her scientific hero. “I remember being inspired when he won his Nobel Prize in [...]
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NY Times: Biologist Climbs High to Prove Hypothesis About Plants

NY Times: Biologist Climbs High to Prove Hypothesis About Plants | Plant Biology Teaching Resources (Higher Education) | Scoop.it
A 20-year quest to prove a longstanding hypothesis about how nutrients are transported may come to an end thanks to tiny needles that probe leaves 40 feet up an oak tree.
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Breakthrough in the understanding of plant growth and development

Breakthrough in the understanding of plant growth and development | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Plants grow through cell division, cell elongation and differentiation of cells within tissues. These processes provide the structure of the plant. At the same time, plants can react very quickly to stimuli: the shoot bends towards light, and roots respond to gravity. “For the first time, we begin to understand how those quick responses can combine with the processes that preserve the structure of the plant, in an interplay between the hormone auxin and regulatory proteins”, says Professor Ben Scheres of Wageningen University. The breakthrough was published in the prestigious journal Nature.
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A comprehensive analysis of root morphological changes and nitrogen allocation in maize in response to low-nitrogen stress

A comprehensive analysis of root morphological changes and nitrogen allocation in maize in response to low-nitrogen stress | Plant Biology Teaching Resources (Higher Education) | Scoop.it

The plasticity of root architecture is crucial for plants to acclimate unfavorable environments including low nitrogen (LN) stress. How maize roots coordinate the growth of axile roots and lateral roots (LRs), as well as longitudinal and radial cell behaviours in response to LN stress remains unclear. Maize plants were cultivated hydroponically under control (4 mM nitrate) and LN (40 μM) conditions. Temporal and spatial samples were taken to analyse changes in the morphology, anatomical structure, and carbon/nitrogen (C/N) ratio in the axile and lateral roots. LN stress increased axile root elongation, reduced the number of crown roots, and decreased LR density and length. LN extended cell elongation zones and increased the mature cell length in the roots. LN reduced the cell diameter and total area of vessels and increased the amount of aerenchyma, but the number of cell layers in the crown root cortex was unchanged. The C/N ratio was higher in axile roots than in LRs. Maize roots acclimate to LN by optimizing the anatomical structure and N allocation. As a result axile root elongation is favored to efficiently find available N in the soil.


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From Apathy to Apogee

From Apathy to Apogee | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Hardly anyone believed George Rédei’s research mattered — until it changed everything.
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In search of biological control agents for Himalayan balsam - YouTube

I think this is a great story - here's a video from 2009 showing an expedition to find natural enemies of the invasive plant Himalayan balsam, and today the rust fungus (after years of study and testing) is being released in an effort to combat it.

http://www.cabi.org/news-and-media/2014/cabi-releases-rust-fungus-to-control-invasive-weed-himalayan-balsam/


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Issues in Ecology | Ecological Society of America

Issues in Ecology | Ecological Society of America | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Mary Williams's insight:

I just stumbled across one of these and wanted to share the link - published by the Ecological Society of America, and written for the general public / high school / university undergraduates. Topics include biofuels, nitrogen in the environment, climate change.

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