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Plant Biology Teaching Resources (Higher Education)
Hooks and hot topics for university teachers and students
Curated by Mary Williams
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BMC Biology | Article collections | Beyond Mendel: modeling in biology

BMC Biology | Article collections | Beyond Mendel: modeling in biology | Plant Biology Teaching Resources (Higher Education) | Scoop.it

I just found this - useful collection of article about modeling in biology. The 2010 article by Lander, "The edges of understanding" would be a good way to start a discussion about the hows and whys of biologica modeling with your students.

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BRASSINOSTEROID INSENSITIVE2 Interacts with ABSCISIC ACID INSENSITIVE5 to Mediate the Antagonism of Brassinosteroids to Abscisic Acid during Seed Germination in Arabidopsis

BRASSINOSTEROID INSENSITIVE2 Interacts with ABSCISIC ACID INSENSITIVE5 to Mediate the Antagonism of Brassinosteroids to Abscisic Acid during Seed Germination in Arabidopsis | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Seed germination and postgerminative growth are regulated by a delicate hormonal balance. Abscisic acid (ABA) represses Arabidopsis thaliana seed germination and postgerminative growth, while brassinosteroids (BRs) antagonize ABA-mediated inhibition and promote these processes. However, the molecular mechanism underlying BR-repressed ABA signaling remains largely unknown. Here, we show that the Glycogen Synthase Kinase 3-like kinase BRASSINOSTEROID INSENSITIVE2 (BIN2), a critical repressor of BR signaling, positively regulates ABA responses during seed germination and postgerminative growth. Mechanistic investigation revealed that BIN2 physically interacts with ABSCISIC ACID INSENSITIVE5 (ABI5), a bZIP transcription factor. Further genetic analysis demonstrated that the ABA-hypersensitive phenotype of BIN2-overexpressing plants requires ABI5. BIN2 was found to phosphorylate and stabilize ABI5 in the presence of ABA, while application of epibrassinolide (the active form of BRs) inhibited the regulation of ABI5 by BIN2. Consistently, the ABA-induced accumulation of ABI5 was affected in BIN2-related mutants. Moreover, mutations of the BIN2 phosphorylation sites on ABI5 made the mutant protein respond to ABA improperly. Additionally, the expression of several ABI5 regulons was positively modulated by BIN2. These results provide evidence that BIN2 phosphorylates and stabilizes ABI5 to mediate ABA response during seed germination, while BRs repress the BIN2-ABI5 cascade to antagonize ABA-mediated inhibition.

Via Christophe Jacquet
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A Lego animation of the Hounsfield Facility at the University of Nottingham - YouTube

This stop frame animation uses a lego model to show the workings of the new Hounsfield Facility at the Sutton Bonnington campus of the University of Nottingh...
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Plant phenotyping facilities are cool too!

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Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Our analysis suggests that a small number of maize transposable element families may contribute to the response of nearby genes to abiotic stress by providing stress-responsive enhancer-like functions. The specific insertions of transposable elements are" often polymorphic within a species. Our data demonstrate that allelic variation for insertions of the transposable elements associated with stress-responsive expression can contribute to variation in the regulation of nearby genes. Thus novel insertions of transposable elements provide a potential mechanism for genes to acquire cis-regulatory influences that could contribute to heritable variation for stress response."

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An Arabidopsis gene regulatory network for secondary cell wall synthesis : Nature

An Arabidopsis gene regulatory network for secondary cell wall synthesis : Nature | Plant Biology Teaching Resources (Higher Education) | Scoop.it
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Best of Plants 2014: From Phenotype to Genotype and Back Again, great strides in plant breeding tools

Best of Plants 2014: From Phenotype to Genotype and Back Again, great strides in plant breeding tools | Plant Biology Teaching Resources (Higher Education) | Scoop.it


2014 saw numerous advances in plant breeding technologies. Genetic diversity can be sourced from the broader gene pool of crop relatives, induced, or engineered. The rapidly growing body of genomic information and tools facilitate the molecular identification of genetic variation, high-throughput phenotyping platforms allow precise characterization of its effects, and modeling approaches are helping to predict optimal genotypes for success in different environments.  Through these rapid advances we are moving toward two important outcomes; the development of plants whose genomes are optimized for their environment (in terms of water and nutrient availability, presence of pathogens or herbivores etc), and their development by way of methods that don’t cause them get stuck in an endless regulatory process.

 Just a few of many hundreds of articles published in 2014 highlighting some of these advances:


Reinventing the Green Revolution by Harnessing Crop Mutant Resources (http://www.plantphysiol.org/content/166/4/1682.full)

MSH1-Induced Non-Genetic Variation Provides a Source of Phenotypic Diversity in Sorghum bicolor  (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0108407)

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice (http://www.nature.com/ncomms/2014/141008/ncomms6087/full/ncomms6087.html)

Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping (http://www.plantphysiol.org/content/165/2/506)

Field high-throughput phenotyping: the new crop breeding frontier (http://www.cell.com/trends/plant-science/abstract/S1360-1385%2813%2900199-4)

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding (http://nar.oxfordjournals.org/content/early/2014/11/26/nar.gku1195.full)

Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU (http://onlinelibrary.wiley.com/doi/10.1111/tpj.12413/abstract)

Evolution of physiological responses to salt stress in hexaploid wheat (http://www.pnas.org/content/111/32/11882.abstract)

Microbial genome-enabled insights into plant–microorganism interactions  (http://www.nature.com/nrg/journal/v15/n12/abs/nrg3748.html)

Are we ready for back-to-nature crop breeding? (www.cell.com/trends/plant-science/abstract/S1360-1385(14)00290-8)

TraitCapture: genomic and environment modelling of plant phenomic data (http://www.sciencedirect.com/science/article/pii/S1369526614000181)

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To Raise Science Scores, Colleges Look Beyond the Lecture

To Raise Science Scores, Colleges Look Beyond the Lecture | Plant Biology Teaching Resources (Higher Education) | Scoop.it
A small but growing number of universities have adopted a more engaging, demanding form of the standard introductory courses, and research suggests the new style works better.
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Molecular Gastronomy: A New Emerging Scientific Discipline

Molecular Gastronomy: A New Emerging Scientific Discipline | Plant Biology Teaching Resources (Higher Education) | Scoop.it

You can impress your friends and relatives with your knowledge of food chemistry after reading this 53 page article (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855180/), or the much shorter version here on the Chemical Blog (http://www.thechemicalblog.co.uk/the-chemistry-of-a-christmas-dinner)

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Reaching Students: What Research Says About Effective Instruction in Undergraduate Science and Engineering

Reaching Students: What Research Says About Effective Instruction in Undergraduate Science and Engineering | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Reaching Students:
What Research Says About Effective Instruction in Undergraduate Science and Engineering (2014)
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Free ebook, from National Academies Press

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PNAS: Local plant names reveal that enslaved Africans recognized substantial parts of the New World flora

PNAS: Local plant names reveal that enslaved Africans recognized substantial parts of the New World flora | Plant Biology Teaching Resources (Higher Education) | Scoop.it

What an interesting study! PNAS publishes it under the categories of Ethnobotany and Folk Taxonomy.
One of the important messages it conveys is that "Most of the Africans who arrived in the Americas were already skilled farmers and came from cultures considerably practiced in using local flora and fauna" and it "reveals the frequency with which enslaved Africans recognized familiar taxa but also show their detailed botanical knowledge."

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Current Opinion in Biotechnology: Engineering the plant rhizosphere

Current Opinion in Biotechnology: Engineering the plant rhizosphere | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Plant natural products are low molecular weight compounds playing important roles in plant survival under biotic and abiotic stresses. In the rhizosphere, several groups of plant natural products function as semiochemicals that mediate the interactions of plants with other plants, animals and microorganisms. The knowledge on the biosynthesis and transport of these signaling molecules is increasing fast. This enables us to consider to optimize plant performance by changing the production of these signaling molecules or their exudation into the rhizosphere. Here we discuss recent advances in the understanding and metabolic engineering of these rhizosphere semiochemicals.


Via Stéphane Hacquard
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What happened 15 Dec 1994?

What happened 15 Dec 1994? | Plant Biology Teaching Resources (Higher Education) | Scoop.it
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Why start from scratch when you can recycle and adapt?

Why start from scratch when you can recycle and adapt? | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Leaf development is such a fascinating topic, because it reveals the molecular processes the are involved in pattern formation. Interestingly, several genes and small molecules (e.g., auxin) are used repeatedly during the initiation and elaboration of leaves. A pair of papers out in Plant Cell highlights this thrifty genetic strategy.
In the first, we see how the development of the ligule in a maize leaf involves the redeployment of several genes that are involved in leaf initiation, a process that occurs much earlier in the developmental pathway.


Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation (www.plantcell.org/…/early/2014/12/16/tpc.114.132688.abstract).
In the second, we see the KNOX1 / GA module that is so important in leaf developmental patterning also contributes to the environtmental responsiveness of leaf shape (heterophylly), as found in aquatic plants such as Rorippa aquatica.
Regulation of the KNOX-GA Gene Module Induces Heterophyllic Alteration in North American Lake Cress (http://www.plantcell.org/…/20…/12/16/tpc.114.130229.abstract).
These studies also reinforce our understanding of process of evolution; why start from scratch when you can just tweak something that aleady works in another context?


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Lake District phytophthora ramorum tree felling gets underway

Lake District phytophthora ramorum tree felling gets underway | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Lake District phytophthora ramorum tree felling gets underway - from Horticulture Week

Via Niklaus Grunwald
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Genome Editing with CRISPR-Cas9 - YouTube

This animation depicts the CRISPR-Cas9 method for genome editing – a powerful new technology with many applications in biomedical research, including the pot...
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Identification of the transporter responsible for sucrose accumulation in sugar beet taproots

Identification of the transporter responsible for sucrose accumulation in sugar beet taproots | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Nature Plants, Published online: 8 January 2015; | doi:10.1038/nplants.2014.1

Via Andres Zurita
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Andres Zurita's curator insight, January 8, 2015 7:36 AM

Sugar beet provides around one third of the sugar consumed worldwide and serves as a significant source of bioenergy in the form of ethanol. Sucrose accounts for up to 18% of plant fresh weight in sugar beet. Most of the sucrose is concentrated in the taproot, where it accumulates in the vacuoles. Despite 30 years of intensive research, the transporter that facilitates taproot sucrose accumulation has escaped identification. Here, we combine proteomic analyses of the taproot vacuolar membrane, the tonoplast, with electrophysiological analyses to show that the transporter BvTST2.1 is responsible for vacuolar sucrose uptake in sugar beet taproots. We show that BvTST2.1 is a sucrose-specific transporter, and present evidence to suggest that it operates as a proton antiporter, coupling the import of sucrose into the vacuole to the export of protons. BvTST2.1 exhibits a high amino acid sequence similarity to members of the tonoplast monosaccharide transporter family in Arabidopsis, prompting us to rename this group of proteins ‘tonoplast sugar transporters’. The identification of BvTST2.1 could help to increase sugar yields from sugar beet and other sugar-storing plants in future breeding programs.

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Insights into the origin and evolution of plant hormone signaling machinery

Insights into the origin and evolution of plant hormone signaling machinery | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Our multi-species genome-wide analysis reveals: i) AUX, CK and SL signaling pathways originated in charophyte lineages; ii) ABA, JA, and SA signaling pathways arose in the last common ancestor of land plants; iii) the GA signaling evolved after the divergence of bryophytes from land plants; iv) the canonical BR signaling originated before the emergence of angiosperms but likely after the split of gymnosperms and angiosperms; v) the origin of the canonical ETH signaling pathway postdates shortly the emergence of angiosperms. Our findings might have important implications in understanding the molecular mechanisms underlying the emergence of land plants"

Mary Williams's insight:

This is a pretty fabulous paper - I'm sure it'll find many uses, not the least being the one-page figure that summarizes all of the hormone signaling pathways. The figure shown here examines the presence or absence of signaling gene homologs in green algal species.

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Science Graphic of the Week: Scientists Discover the First Protein That Can Edit Other Proteins | WIRED

Science Graphic of the Week: Scientists Discover the First Protein That Can Edit Other Proteins | WIRED | Plant Biology Teaching Resources (Higher Education) | Scoop.it
A new graphic shows how that DNA isn't the only thing in charge of handing out code for proteins.
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Best of Plants 2014: Headline makers

Best of Plants 2014: Headline makers | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Gruber Genetics Prize awarded to Professor David Baulcombe and others for Pioneering Discoveries of microRNAs and small interfering RNAs . http://www.plantsci.cam.ac.uk/news/2014-06-17

 
Most Promising Innovator. Professor Cathie Martin and Dr Eugenio Butelli from the John Innes Centre were named BBSRC’s “Most Promising Innovator 2014” for their development of tomatoes enriched beneficial nutrients such as anthocyanins. https://www.jic.ac.uk/news/2014/03/most-promising-innovator-award/

 

Norman Borlaug statue placed into U.S. Capitol’s Statuary Hall. http://iowaborlaugstatue.org/


Dr. Sanjaya Rajaram, World Food Prize Laureate (2014), “for his scientific research that led to a prodigious increase in world wheat production – by more than 200 million tons – building upon the successes of the Green Revolution.”  http://www.worldfoodprize.org/en/laureates/2014__rajaram/

 

Irish teens Ciara Judge, Sophie Healy-Thow and Émer Hick won Google Science Fair top prize for the project investigating the effects of bacteria on seed germination and ultimately crop yields. http://phys.org/news/2014-09-irish-teens-idea-bacteria-crop.html

 

Dance your PhD contest won by plant scientist Uma Nagendra, a PhD student at the University of Georgia (US), with her dance interpretation of the effects of hurricanes on soil pathogens. http://news.sciencemag.org/people-events/2014/11/dance-your-ph-d-winner-announced


Mary Williams's insight:

Any others? Send me a link and I can add other 2014 plant headliners!

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Introduction to the Herbarium of the Royal Botanic Garden Edinburgh - YouTube

See behind the scenes of the Herbarium of the Royal Botanic Garden Edinburgh and the 3 million specimens it holds. Curators and researchers show how the coll...
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Plant Cell: The Root Hair “Infectome” of Medicago truncatula Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection

Plant Cell: The Root Hair “Infectome” of Medicago truncatula Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection | Plant Biology Teaching Resources (Higher Education) | Scoop.it
The Root Hair “Infectome” of Medicago truncatula Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection
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Published "OPEN" - no subscription required

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Life in a World without Microbes

Life in a World without Microbes | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Our discussion begins by considering life without the human gut microbiome, follows with a hypothetical scenario of a world without Bacteria and Archaea, and concludes with the implications of a world without all microbes, including microbial eukaryotes and viruses. We do not include the organelles, such as mitochondria and chloroplasts, as microbes in our discussion, simply because most eukaryotic life would cease instantly in their absence."


Mary Williams's insight:

Good short read. What was the first process you thought of that would stop without microbes? I thought of nitrogen fixation. The authors argue that to some extent the Haber-Bosch process could substitute for the missing microbes, but not optimally.

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Secret of long life lies underground (Morales - 2014 - New Phytologist)

Secret of long life lies underground (Morales - 2014 - New Phytologist) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"This tuber contains high amounts of vitamin E, which may protect lipids from free radical attack and lower the levels of lipid peroxidation. This, together with the capacity to grow slowly, but continuously, presumably helps to prevent senescence at the organism level. Reduced growth and high longevity (compared with other herbs) make this geophyte unique within the tree of life, and at least partially explain the evolutionary success of B. pyrenaica from the Tertiary to date. This success involves surviving changes in climatic conditions, presumably by being somewhat protected underground. The present study further supports the notion that this plant species shows negative senescence and that its mortality may be explained by factors different from ageing."
(Thanks to Christophe Jacquet for alerting me to the paper)

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Frontiers | Danger signals – damaged-self recognition across the tree of life | Plant-Microbe Interaction

Frontiers | Danger signals – damaged-self recognition across the tree of life | Plant-Microbe Interaction | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Multicellular organisms suffer injury and serve as hosts for microorganisms. Therefore, they require mechanisms to detect injury and to distinguish the self from the non-self and the harmless non-self (microbial mutualists and commensals) from the detrimental non-self (pathogens). Danger signals are 'damage-associated molecular patterns' (DAMPs) that are released from the disrupted host tissue or exposed on stressed cells."

Mary Williams's insight:

This is a nice overview of how plants perceive damage, and how damage responess affect responses to pathogens and herbivores. One of the interesting things about this review is the effort made to compare and contrast plant responses to those of animals, which makes it particularly useful if you're teaching students who are very intersted in animal immunological responses.

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Twelve days of Dr M - YouTube

By popular demand Dr M's dead cert Christmas hit is an eXtreme botanical twist on an old favourite with brand new botanical lyrics lovingly crafted by a host...
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A botanical twist on a traditional song

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