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PLOS Pathogens: Mining Herbaria for Plant Pathogen Genomes: Back to the Future (2014)

PLOS Pathogens: Mining Herbaria for Plant Pathogen Genomes: Back to the Future (2014) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Since the dawn of agriculture, plant pathogens and pests have been a scourge of humanity. Yet we have come a long way since the Romans attempted to mitigate the effects of plant disease by worshipping and honoring the god Robigus. Books in the Middle Ages by Islamic and European scholars described various plant diseases and even proposed particular disease management strategies. Surprisingly, the causes of plant diseases remained a matter of debate over a long period. It took Henri-Louis Duhamel du Monceau's elegant demonstration in his 1728 “Explication Physique” paper that a “contagious” fungus was responsible for a saffron crocus disease to usher in an era of documented scientific inquiry. Confusion and debate about the exact nature of the causal agents of plant diseases continued until the 19th century, which not only saw the first detailed analyses of plant pathogens but also provided much-needed insight into the mechanisms of plant disease. An example of this is Anton de Bary's demonstration that a “fungus” is a cause, not a consequence, of plant disease. This coming of age of plant pathology was timely. In the 19th century, severe plant disease epidemics hit Europe and caused economic and social upheaval. These epidemics were not only widely covered in the press but also recognized as serious political issues by governments. Many of the diseases, including late blight of potato, powdery and downy mildew of grapevine, as well as phylloxera, were due to exotic introductions from the Americas and elsewhere. These and subsequent epidemics motivated scientific investigations into crop breeding and plant disease management that developed into modern plant pathology science over the 20th century.


Nowadays, our understanding of plant pathogens and the diseases they cause greatly benefits from molecular genetics and genomics. All aspects of plant pathology, from population biology and epidemiology to mechanistic research, are impacted. The polymerase chain reaction (PCR) first enabled access to plant pathogen DNA sequences from historical specimens deposited in herbaria. Historical records in combination with herbarium specimens have turned out to provide powerful tools for understanding the course of past plant epidemics. Recently, thanks to new developments in DNA sequencing technology, it has become possible to reconstruct the genomes of plant pathogens in herbaria. In this article, we first summarize how whole genome analysis of ancient DNA has been recently used to reconstruct the 19th-century potato-blight epidemic that rapidly spread throughout Europe and triggered the Irish potato famine. We then discuss the exciting prospects offered by the emergence of the discipline of ancient plant pathogen genomics.


Via Kamoun Lab @ TSL
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Good overview for students - very accessible and interesting!

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Freddy Monteiro's comment, April 25, 2014 4:21 AM
This is a great source of teaching materials for potato late blight. Congrats on the work behind it.
Plant Biology Teaching Resources (Higher Education)
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Profile in SEB Bulletin

Profile in SEB Bulletin | Plant Biology Teaching Resources (Higher Education) | Scoop.it

The Society of Experimental Biology (SEB) wrote up a profile of me in my role as Editor of Teaching Tools in Plant Biology. The original is here http://www.sebiology.org/publications/Bulletin/SEB_Bulletin.html

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Endogenous Arabidopsis messenger RNAs transported to distant tissues

Endogenous Arabidopsis messenger RNAs transported to distant tissues | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Endogenous Arabidopsis messenger RNAs transported to distant tissues
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Nature: Primary transcripts of microRNAs encode regulatory peptides (!)

Nature: Primary transcripts of microRNAs encode regulatory peptides (!) | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Primary transcripts of microRNAs encode regulatory peptides

See also the News&Views from which this figure is taken

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14378.html

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Biodiversity Heritage Library: Antique Seed Catalogs and Heirloom Gardening

Biodiversity Heritage Library: Antique Seed Catalogs and Heirloom Gardening | Plant Biology Teaching Resources (Higher Education) | Scoop.it

It's gardening week at Biodiversity Heritage Library, and they're featuring their collection of antique and historical seed catalogues. Maybe the prose is a bit over the top, but the drawings are stunning.

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F1000Research Article: The culture of scientific research by Catherine Joynson & Ottoline Leyser

F1000Research Article: The culture of scientific research by Catherine Joynson & Ottoline Leyser | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"We found that scientists are motivated in their work to find out more about the world and to benefit society, and that they believe collaboration, multidisciplinarity, openness and creativity are important for the production of high quality science. However, in some cases, our findings suggest, the culture of research in higher education institutions does not support or encourage these goals or activities. For example, high levels of competition and perceptions about how scientists are assessed for jobs and funding are reportedly contributing to a loss of creativity in science, less collaboration and poor research practices. The project led to suggestions for action for funding bodies, research institutions, publishers and editors, professional bodies and individual researchers. "

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MH's curator insight, March 23, 4:23 AM

Sur les effets pervers de la concurrence entre laboratoires

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Adapting texts - an example from Mary Kingsley

Adapting texts - an example from Mary Kingsley | Plant Biology Teaching Resources (Higher Education) | Scoop.it

This is interesting - a teacher of 11-year olds describes how he has gently adapted a piece of Victorian-era writing to be accessible to his students. https://readingforlearning.wordpress.com/2015/03/17/a-hippo-banquet/

I can't help but think that this essay would be a good starting point when assigning university students the task of adapting a piece of scientific writing for the public. How do you keep the meaning and tone but make the text accessible?

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Video: Tuta absoluta on the rampage in Africa

Video: Tuta absoluta on the rampage in Africa | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Watch a new video illustrating the devastating impacts that Tuta absoluta (tomato leafminer) is having on tomato yields, and what this means for farmers who rely on these crops for sustenance and income.

This Invasive Alien Species is rapidly moving down the African continent, having already decimated crops in Egypt, Ethiopia, Kenya and northern Tanzania. Growers are at their wits end as to how best they can control this pest and many have abandoned tomato growing altogether. The race is on to prevent its spread further south with various interventions planned to mitigate its impact in areas where it is already present."

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How do plants remember - Professor Caroline Dean - YouTube

Professor Caroline Dean OBE FRS, winner of a BBSRC Excellence in Bioscience Award and the 2015 FEBS/EMBO Women in Science award, discusses the focus of her c...
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The Promises and Perils of Synthetic Biology

The Promises and Perils of Synthetic Biology | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Synbio was going to save the world. Now it’s being used to make vanilla flavoring.
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Definitely worth reading - good for classroom discussions too. Is a flavor molecule different if it's extracted from a plant, an engineered yeast or algae, or made entirely synthetically? How does the drop in oil prices affect biofuels research? What's the role of government in funding alternative energy sources? Is "synbio" a scary term for consumers, and if so what would be a better alternative?

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Chemists Know - (Parody of "Let It Go" from Frozen) - University of California Irvine - YouTube

What a brilliant video - makes me want to be a chemist :)


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The Ubiquitin Receptors DA1, DAR1, and DAR2 Redundantly Regulate Endoreduplication by Modulating the Stability of TCP14/15 in Arabidopsis

The Ubiquitin Receptors DA1, DAR1, and DAR2 Redundantly Regulate Endoreduplication by Modulating the Stability of TCP14/15 in Arabidopsis | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Here, we show that DA1 and its close family members DAR1 and DAR2 are redundantly required for endoreduplication during leaf development. DA1, DAR1, and DAR2 physically interact with the transcription factors TCP14 and TCP15, which repress endoreduplication by directly regulating the expression of cell-cycle genes. We also show that DA1, DAR1, and DAR2 modulate the stability of TCP14 and TCP15 proteins in Arabidopsis thaliana.
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Do you know an outstanding undergraduate science teacher? (Maybe you?)

Do you know an outstanding undergraduate science teacher? (Maybe you?) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

The Society for College Science Teachers soliticits nominations (including self-nominations) for the Outstanding Undergraduate Science Teacher Award. Application deadline is June 1. See website for more information http://www.scst.org/grants/ousta


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Rescooped by Mary Williams from GMOs & Sustainable agriculture
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Nature Biotechnology: Engineering insect-free cereals (2015)

Nature Biotechnology: Engineering insect-free cereals (2015) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

A cluster of three rice lectin receptor kinases confers resistance to planthopper insects.

 

Insect pests reduce yields of crops worldwide through direct damage and because they spread devastating viral diseases. In Asia, the brown planthopper (BPH) decimates rice (Oryza sativa) crops, causing the loss of billions of dollars annually1. In this issue, Liu et al.2 report the cloning of a rice genetic locus that confers broad-spectrum resistance to BPH and at least one other planthopper species (white back planthopper). Introducing this locus into plant genomes is likely to provide an effective means of combating insect pests of rice and of other cereals such as maize.

 

In modern rice agriculture, BPH damage is controlled through breeding and the application of vast amounts of chemical pesticides1. Pesticides are not a sustainable approach, however, owing to high costs, harmful environmental effects and rapid development of resistant insects. Breeding programs have identified more than 20 genetic loci in cultivated or wild rice species that confer BPH resistance1. However, these Bph loci are usually only effective against specific BPH biotypes, and newly evolved BPH populations have rapidly overcome several Bph resistance loci deployed in the field..

 

Of the >20 identified Bph loci, only Bph14 and Bph26 have been cloned. Both of these loci encode coiled-coil, nucleotide-binding and leucine-rich repeat proteins3, 4, the main class of plant intracellular immune receptors5. Bph3 is a resistance locus that was first pinpointed genetically in the Sri Lankan rice indica cultivar Rathu Heenati. Notably, unlike most other Bph loci, including Bph14 and Bph26, Bph3 confers broad-spectrum resistance to many BPH biotypes as well as to the white back planthopper1, 2. The success of Bph3 as a resistance locus might be linked to the fact that it acts against BPH at an early stage of the feeding cycle, before the insect can deploy its arsenal of virulence proteins that circumvent plant defenses.

 

Despite the huge potential of Bph3 for rice agriculture, its molecular identity has been unknown. Liu et al.2 now identify Bph3 through map-based cloning in a cross between the resistant indica cultivar Rathu Heenati and the susceptible japonica cultivar 02428. Bph3 maps to a 79-kb genomic region that contains a cluster of three lectin receptor kinases, OsLecRK1–3 (ref. 2) (Fig. 1). The authors find that single-nucleotide polymorphisms in these genes are associated with BPH resistance in different cultivated rice accessions. They also show that ectopic expression of the OsLecRK1–3 gene cluster in the susceptible japonica Kitaake cultivar confers BPH resistance.

 

See Liu et al. Nature Biotechnology http://www.nature.com/nbt/journal/v33/n3/full/nbt.3069.html


Via Kamoun Lab @ TSL, Francis Martin, Christophe Jacquet
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Bringing light into the discussion about GMOs? – A rather long reading list

[updated 08 March, 2015]  

 

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.
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COLD1 Confers Chilling Tolerance in Rice: Cell

COLD1 Confers Chilling Tolerance in Rice: Cell | Plant Biology Teaching Resources (Higher Education) | Scoop.it
QTL COLD1 regulates G-protein signaling to confer chilling tolerance in rice
•SNP2 in COLD1jap/ind enhances its ability to activate G-protein α GTPase
•COLD1 interacts with G protein to activate the Ca2+ channel for temperature sensing
•The SNP2-containing allele is selected during japonica rice domestication
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Learning from nature's best : Nature : Nature Publishing Group

Learning from nature's best : Nature : Nature Publishing Group | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Materials researchers are taking cues from specific plants and animals that make substances that could endow humans with superhero powers.
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Cute and cool look at bio-inspired designs

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Are you fresh as a daisy in French? Can you spill the beans in Spanish? Do plant metaphors transcend language?

Are you fresh as a daisy in French? Can you spill the beans in Spanish? Do plant metaphors transcend language? | Plant Biology Teaching Resources (Higher Education) | Scoop.it

“A voice like a peat bog”


I came across this expression over the weekend, and although I’m still not sure what it means, it made me wonder about other plant-based similes and metaphors. I did a little searching and found that at least in English, plant metaphors are pretty common (see link).


For example,
“They were like two peas in a pod and their love blossomed until through the grapevine she learned of trouble and decided to get to the root of the problem.”


I'm curious though, are there plant metaphors that span many languages? Can you be "fresh as a daisy" in French? Is there a "thorny problem" in Thai? Can you "spill the beans" in Spanish?

Here's an extensive list in English from Garden Digest to help you green up your next writing task. http://www.gardendigest.com/cliche.htm I'd be happy to get a link to a similar list in other languages!

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A whole bunch of TED Talks about eating insects (or "land shrimp")

A whole bunch of TED Talks about eating insects (or "land shrimp") | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Well, their carbon footprint is a lot lower than that of mammals, but there's a lot of cultural baggage to overcome....


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Plant Nutrition-Opoly?

Plant Nutrition-Opoly? | Plant Biology Teaching Resources (Higher Education) | Scoop.it

I worked too late last night and then dreamed I was playing Plant Nutrition-Opoly.....


Designing and playing games is a terrific way for students to learn. What would the Railroads be - ion transporters? What events would be described on the Chance cards - Mycorrhizal symbiosis, win $10?

For an introductory class, students could redesign the board using plant taxa... orchids for the high-rent squares?


What other games can be modified for teaching? I've seen Top Trumps (http://en.wikipedia.org/wiki/Top_Trumps) adapted which is great game for students to design themselves. Here's a link to a Cambridge University  "Meet the algae" Top Trumps card set http://www.plantsci.cam.ac.uk/meetthealgae/pdfs/top-trumps.pdf/view

and here's a link to a Top Trumps game called "Journey to the Centre of the Earth - The First 23 cm"  from Rothamsted http://www.rothamsted.ac.uk/Content/JourneyCentreEarth/TopTrumps.pdf.


Have you designed a game to teach plant science, or asked your students to demonstrate their understanding by designing a game?

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Tansley Review: Adaptation in flower form: a comparative evodevo approach (good for teaching)

Adaptation in flower form: a comparative evodevo approach
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The Altmetric System

The Altmetric System | Plant Biology Teaching Resources (Higher Education) | Scoop.it
In the budding field of article-level metrics, Altmetric has been leading the way in measuring the attention and impact of research papers beyond the archaic method of counting citations. Founder Euan Adie sheds light on the inadequacy of journal-level metrics, the future relationship between academia and Twitter, and the work that goes on behind the scenes at Altmetric
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Punctual Transcriptional Regulation by the Rice Circadian Clock under Fluctuating Field Conditions (Plant Cell)

Punctual Transcriptional Regulation by the Rice Circadian Clock under Fluctuating Field Conditions (Plant Cell) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Using hundreds of samples of field-grown rice (Oryza sativa) leaves, we developed a statistical model for the expression of circadian clock-related genes integrating diurnally entrained circadian clock with phase setting by light, both responses to light and temperature gated by the circadian clock. We show that expression of individual genes was strongly affected by temperature. However, internal time estimated from expression of multiple genes, which may reflect transcriptional regulation of downstream genes, is punctual to 22 min and not affected by weather, daylength, or plant developmental age in the field. Thus, we demonstrated that the circadian clock is a regulatory network of multiple genes that retains accurate physical time of day by integrating the perturbations on individual genes under fluctuating environments in the field.

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Preparing Solutions - Parts 1 - 3: Calculating Molar or % Concentrations and diluting stock solutions

Three useful videos for students starting out in the lab.
Part 1 - Calculating molar concentrations (https://www.youtube.com/watch?v=vOwdQRBENJQ)
Part 2 - Calculating % concentrations (https://www.youtube.com/watch?v=pVNpFP2Wmlc)
Part 3 - Dilutions from stock solutions (https://www.youtube.com/watch?v=vHx4nqRdpMg)
From University of Glasgow


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Popped Secret: The Mysterious Origin of Corn — HHMI BioInteractive Video - YouTube

Where did corn come from? Genetic and archeological data point to what may seem like an unlikely ancestor. Discover the secret of corn in this HHMI BioInteractive video.

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