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Plant Biology Teaching Resources (Higher Education)
Hooks and hot topics for university teachers and students
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The Seeds That Sowed a Revolution

The Seeds That Sowed a Revolution | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"By the time the Beagle left the Galapagos, Darwin had amassed a spectacular collection of Galapagos plants. It is fortunate that he took such trouble. Most popular narratives of Darwin and the Galapagos concentrate on the far more celebrated finches or the giant tortoises. Yet when he finally published On the Origin of Species almost 25 years later, Darwin made no mention of these creatures. In his discussion of the Galapagos, he dwelt almost exclusively on the islands’ plants."

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JExpBot: Characteristics of a root hair-less line of Arabidopsis thaliana under physiological stresses

JExpBot: Characteristics of a root hair-less line of Arabidopsis thaliana under physiological stresses | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Otherwise normal plants lacking root hairs show significant disadvantages in mineral assimilation and water uptake .


"The present results suggest that root hairs play significant roles in the absorption of water and several minerals, secretion of acid phosphatase(s) and organic acids, and in penetration of the primary roots into gels. "



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Plant Cell: Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis

Plant Cell: Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via comparison of gene coexpression networks, implemented as an R package called machine learning–based differential network analysis (mlDNA) and apply this method to reanalyze a set of abiotic stress expression data in Arabidopsis thaliana. "

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Plant Phys: Phylogenetics identifies new cytokinin receptor subfamily

Plant Phys: Phylogenetics identifies new cytokinin receptor subfamily | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"To shed light on the origin and evolution of two-component signaling members in plants, we conducted a comprehensive domain-based phylogenetic study across the relevant kingdoms including charophyceae algae, the group of green algae giving rise to land plants. Surprisingly, we identified a novel subfamily of cytokinin receptors with members only from the early diverging land plants... Finally, the analysis provided hints that one additional group of RRs, the type-C RRs, might be degenerated receptors and thus evolutionary of a different origin than bona fide response regulators."

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The Arabidopsis Book: Genetic and Epigenetic Mechanisms Underlying Vernalization

The Arabidopsis Book: Genetic and Epigenetic Mechanisms Underlying Vernalization | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Dong-Hwan Kim and Sibum Sung (2014) Genetic and Epigenetic Mechanisms Underlying Vernalization. The Arabidopsis Book: Vol. , No. , pp. null. doi: http://dx.doi.org/10.1199/tab.0171
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PNAS: DNA-binding specificities of plant transcription factors and their potential to define target genes

PNAS: DNA-binding specificities of plant transcription factors and their potential to define target genes | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"We described the high-throughput identification of DNA-binding
specificities of 63 plant transcription factors (TFs) and their relevance
as cis-regulatory elements in vivo. Almost half of the TFs
recognized secondary motifs partially or completely differing
from their corresponding primary ones. Analysis of coregulated
genes, transcriptomic data, and chromatin hypersensitive regions
revealed the biological relevance of more than 80% of the
binding sites identified. Our combined analysis allows the prediction
of the function of a particular TF as activator or repressor
through a particular DNA sequence."

Mary Williams's insight:

There is something very pretty about the way these data are presented

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EMBO Workshop: Intercellular communication in plant development and disease 24–29 August 2014 | Bischoffsheim, France

EMBO Workshop: Intercellular communication in plant development and disease 24–29 August 2014 | Bischoffsheim, France | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Plants are sessile organisms that need to respond to changing environments during development. As a result they have evolved unique signalling mechanisms through plasmodesmata that allow rapid communication between different parts of the plant. Communication through plasmodesmata involves the trafficking of informational macromolecules such as transcription factors, gene transcripts, and small RNAs. Moreover, viral pathogens exploit these cell wall channels for intercellular and systemic spread, which often results in serious crop diseases. The EMBO workshop will bring together scientists working on plasmodesmata structure and regulation, plant development, defense signaling, gene silencing, and virus movement.


Via Kamoun Lab @ TSL, Francis Martin
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PLOS Computational Biology: A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses

PLOS Computational Biology: A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Computational models and functional studies using the plant Arabidopsis thaliana have led to competing models for how the PIN-FORMED1 (PIN1) auxin transporter polarizes in the cell to create both the maxima required for organ initiation and the narrow streams required for vein patterning. Here we identify a previously uncharacterized PIN protein most closely related to PIN1 that is present in all flowering plants but lost in the Brassicaceae, including Arabidopsis. .........This model reveals a minimal framework of necessary functions involved in auxin-transport-mediated patterning in the shoot and demonstrates that work outside of Arabidopsis is essential to understanding how auxin-transport mediates patterning in most flowering plants."

Mary Williams's insight:

Nice work demonstrating again the need for many models to understand plant biology. I love Arabidopsis but you can't build a chair with only one leg.....

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Cell - Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors

Cell - Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). "

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Teaching Tools. Plant-Water Relations (1): Uptake and Transport

Teaching Tools. Plant-Water Relations (1): Uptake and Transport | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"Vascular plants evolved structures that enable them to transport water long distances with little input of energy, but the hollow tracheary elements are just one of many adaptations that enable plants to cope with a very dry atmosphere. This lecture examines the physical laws that govern water uptake and transport, the biological properties of cells and plant tissues that facilitate it, and the strategies that enable plants to survive in diverse environments. Written with Mel Oliver and Steve Pallardy"

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Requires subscription to Plant Cell or ASPB membership

http://my.aspb.org/?page=Membership
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Nature Methods : Kick the bar chart habit

Nature Methods : Kick the bar chart habit | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Bar charts are too frequently used to communicate data that they cannot represent well. We strongly encourage the use of more appropriate plots to display statistical samples.
Mary Williams's insight:

Great! Why box plots are better than bar graphs, AND a simple tool that allows you to generate them. Pass on to your students when you are talking about how to present data! Free from Nature Methods.

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Super collection of inquiry-based plant activities from Inquire Botany

Super collection of inquiry-based plant activities from Inquire Botany | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"INQUIRE is helping to reinvigorate inquiry-based science education throughout Europe. Run by botanic gardens in 11 countries, INQUIRE teacher training courses are demonstrating how IBSE can inspire students in science and help address biodiversity and climate change"

 

 

Mary Williams's insight:

Great collection of inquiry-based plant activities on topics from seed dispersal to biodiversity!

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Plant Cell: Geminivirus Vectors Deliver Reagents for Plant Genome Engineering (2014)

Plant Cell: Geminivirus Vectors Deliver Reagents for Plant Genome Engineering (2014) | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Jennifer Mach commentary http://www.plantcell.org/content/early/2014/01/16/tpc.114.122606.full.pdf+html

 

Baltes et al. article http://www.plantcell.org/content/early/2014/01/16/tpc.113.119792.abstract


Via Kamoun Lab @ TSL
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For all you systems biologists....

For all you systems biologists.... | Plant Biology Teaching Resources (Higher Education) | Scoop.it
Mary Williams's insight:

"Now in the further development of science, we want more than just a formula. First we have an observation, then we have numbers that we measure, then we have a law which summarizes all the numbers. But the real glory of science is that we can find a way of thinking such that the law is evident."
Richard Feynman 1963

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Frontiers in Plant Systems Biology | Protein intrinsic disorder in plants

Frontiers in Plant Systems Biology | Protein intrinsic disorder in plants | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"In contrast to the classical dogma, intrinsic disorder is an important feature for many proteins to function. In general, protein disorder allows interaction versatility and adds complexity to the interactomes.... In plants, the predominance of intrinsic disorder in proteins involved in responses to environmental conditions could be explained as a requirement of these processes to be more complex due to the special characteristics of these sessile organism."

Mary Williams's insight:

Fascinating stuff - I find the model that disordered protein domains are capable of more diverse interactions very interesting and exciting.


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Plant Phys Update: Plant Water Uptake in Drying Soils

Plant Phys Update: Plant Water Uptake in Drying Soils | Plant Biology Teaching Resources (Higher Education) | Scoop.it
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"Over the last decade, investigations on root water uptake have evolved towards a deeper integration of the soil and roots compartments properties, with the aim to improve our understanding of water acquisition from drying soils. ...Recent results have led to the description of root system architectures that could contribute to deep water extraction or to water saving strategies. ....However, modeling studies highlight the role of soil hydraulics in the control of water uptake in drying soil and calls for integrative soil-plant systems approaches."

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Plant Cell (Review): Phototropism Growing towards an Understanding of Plant Movement

Plant Cell (Review): Phototropism Growing towards an Understanding of Plant Movement | Plant Biology Teaching Resources (Higher Education) | Scoop.it
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PNAS: Variation in MPK12 affects water use efficiency in Arabidopsis and reveals a pleiotropic link between guard cell size and ABA response

PNAS: Variation in MPK12 affects water use efficiency in Arabidopsis and reveals a pleiotropic link between guard cell size and ABA response | Plant Biology Teaching Resources (Higher Education) | Scoop.it

"We identify a molecular variant that drives variation in water use efficiency between two natural genotypes of Arabidopsis thaliana. We show that two alleles, distinguished by a single substitution in a signaling protein, cause whole-plant differences in plant water relations via inducible and constitutive mechanisms."

Mary Williams's insight:

Nice combination of methods and concepts, a good choice for students to read.

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Dr Laura Vickers's curator insight, February 8, 2014 3:50 AM

Good paper particularly for #brumbio398  

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Human and Plant Fungal Pathogens: The Role of Secondary Metabolites

Human and Plant Fungal Pathogens: The Role of Secondary Metabolites | Plant Biology Teaching Resources (Higher Education) | Scoop.it
by Daniel H. Scharf, Thorsten Heinekamp, Axel A. Brakhage

Via IPM Lab, Francis Martin
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Denialism: what is it and how should scientists respond? - Diethelm & McKee (2009) - Eur J Public Health

Denialism: what is it and how should scientists respond? - Diethelm & McKee (2009) - Eur J Public Health | Plant Biology Teaching Resources (Higher Education) | Scoop.it

HIV does not cause AIDS. The world was created in 4004 BCE. Smoking does not cause cancer. And if climate change is happening, it is nothing to do with man-made CO2 emissions... The consequences of policies based on views such as these can be fatal. Thabo Mbeki's denial that that HIV caused AIDS prevented thousands of HIV positive mothers in South Africa receiving anti-retrovirals so that they, unnecessarily, transmitted the disease to their children... 

 

It took many decades for the conclusions of authoritative reports... on the harmful effects of smoking to be accepted, while even now, despite clear evidence of rapid reductions in myocardial infarctions where bans have been implemented, there are some who deny that second-hand smoke is dangerous. In large part this was due to the efforts of the tobacco industry... The reports of the Intergovernmental Panel on Climate Change have suffered similar attacks from commentators with links to major oil companies.

 

All of these examples have one feature in common. There is an overwhelming consensus on the evidence among scientists yet there are also vocal commentators who reject this consensus, convincing many of the public, and often the media too, that the consensus is not based on ‘sound science’ or denying that there is a consensus by exhibiting individual dissenting voices as the ultimate authorities on the topic in question. Their goal is to convince that there are sufficient grounds to reject the case for taking action to tackle threats to health... 

 

Defining and recognizing denialism... the employment of rhetorical arguments to give the appearance of legitimate debate where there is none, an approach that has the ultimate goal of rejecting a proposition on which a scientific consensus exists. In this viewpoint, we argue that public health scientists should be aware of the features of denialism and be able to recognize and confront it. Denialism is a process that employs some or all of five characteristic elements in a concerted way.

 

The first is the identification of conspiracies. When the overwhelming body of scientific opinion believes that something is true, it is argued that this is not because those scientists have independently studied the evidence and reached the same conclusion. It is because they have engaged in a complex and secretive conspiracy. The peer review process is seen as a tool by which the conspirators suppress dissent, rather than as a means of weeding out papers and grant applications unsupported by evidence or lacking logical thought... 

 

The second is the use of fake experts. These are individuals who purport to be experts in a particular area but whose views are entirely inconsistent with established knowledge. They have been used extensively by the tobacco industry since 1974... In 1998, the American Petroleum Institute... recruitment of ‘scientists who share the industry's views of climate science [who can] help convince journalists, politicians and the public that the risk of global warming is too uncertain to justify controls on greenhouse gases’... the administration of President George W Bush was characterized by the promotion of those whose views were based on their religious beliefs or corporate affiliations... The use of fake experts is often complemented by denigration of established experts and researchers, with accusations and innuendo that seek to discredit their work and cast doubt on their motivations... 

 

The third characteristic is selectivity, drawing on isolated papers that challenge the dominant consensus or highlighting the flaws in the weakest papers among those that support it as a means of discrediting the entire field. An example of the former is the much-cited Lancet paper describing intestinal abnormalities in 12 children with autism, which merely suggested a possible link with immunization against measles, mumps and rubella. This has been used extensively by campaigners against immunization, even though 10 of the paper's 13 authors subsequently retracted the suggestion of an association... Denialists are usually not deterred by the extreme isolation of their theories, but rather see it as the indication of their intellectual courage against the dominant orthodoxy and the accompanying political correctness, often comparing themselves to Galileo.

 

The fourth is the creation of impossible expectations of what research can deliver. For example, those denying the reality of climate change point to the absence of accurate temperature records from before the invention of the thermometer. Others use the intrinsic uncertainty of mathematical models to reject them entirely as a means of understanding a phenomenon... 

 

The fifth is the use of misrepresentation and logical fallacies... Logical fallacies include the use of red herrings, or deliberate attempts to change the argument and straw men, where the opposing argument is misrepresented to make it easier to refute... Other fallacies used by denialists are false analogy, exemplified by the argument against evolution that, as the universe and a watch are both extremely complex, the universe must have been created by the equivalent of a watchmaker and the excluded middle fallacy (either passive smoking causes a wide range of specified diseases or causes none at all, so doubt about an association with one disease, such as breast cancer, is regarded as sufficient to reject an association with any disease).

 

Responding to denialism: Denialists are driven by a range of motivations. For some it is greed, lured by the corporate largesse of the oil and tobacco industries. For others it is ideology or faith, causing them to reject anything incompatible with their fundamental beliefs. Finally there is eccentricity and idiosyncrasy, sometimes encouraged by the celebrity status conferred on the maverick by the media... it is important to recognize denialism when confronted with it.

 

The normal academic response to an opposing argument is to engage with it... However, this requires that both parties obey certain ground rules, such as a willingness to look at the evidence as a whole, to reject deliberate distortions and to accept principles of logic. A meaningful discourse is impossible when one party rejects these rules. Yet it would be wrong to prevent the denialists having a voice. Instead, we argue, it is necessary to shift the debate from the subject under consideration, instead exposing to public scrutiny the tactics they employ and identifying them publicly for what they are...

 

http://dx.doi.org/10.1093/eurpub/ckn139


Via Alexander J. Stein
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Mary Williams's comment, February 2, 2014 6:59 AM
Interesting article, I hadn't seen it before, thanks for sharing!
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Garden Professors | Science-based gardening information

Garden Professors | Science-based gardening information | Plant Biology Teaching Resources (Higher Education) | Scoop.it

I just stumbled on this blog which might be of interest to some of you. Four US-based plant science / horticulture professors post on wide-ranging topics about plant science for gardeners. Enjoy!

And if you use facebook, they have a pretty active page:

https://www.facebook.com/TheGardenProfessors

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Australian Scientists Awarded For Method Of Identifying Water Efficient Crops

Australian Scientists Awarded For Method Of Identifying Water Efficient Crops | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Distinguished ANU Professor Graham Farquhar AO and CSIRO Fellow Dr Richard Richards have won a coveted international science prize for their ground-breaking research into more water efficient wheat.

They will receive the 2014 UK-based Rank Prize in human and animal nutrition and crop husbandry.


Via CIMMYT, Int., AckerbauHalle
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Five fabulous photobiology reviews from The Plant Cell

Five fabulous photobiology reviews from The Plant Cell | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Five fabulous photobiology reviews from The Plant Cell!

And an overview by Nan Eckardt

www.plantcell.org/content/early/2014/01/29/tpc.114.123026.full.pdf

PIFs: Systems Integrators in Plant Development
Mathematical Models Light Up Plant Signaling
Phototropism: Growing towards an Understanding of Plant Movement
The UV-B Photoreceptor UVR8: From Structure to Physiology
Multiple Layers of Posttranslational Regulation Refine Circadian Clock Activity in Arabidopsis

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SAPS: Animation - Transport in Xylem and Phloem - YouTube

This animation covers plant transport, demonstrating how water travels through the plant, and how sugars are distributed around the plant. ...

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Read about this animation and other teaching resources in the SAPS newsletter https://www.youtube.com/watch?v=LQ03xIkLLQU

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Developmental Cell - Auxin-Callose-Mediated Plasmodesmal Gating Is Essential for Tropic Auxin Gradient Formation and Signaling

Developmental Cell - Auxin-Callose-Mediated Plasmodesmal Gating Is Essential for Tropic Auxin Gradient Formation and Signaling | Plant Biology Teaching Resources (Higher Education) | Scoop.it

Via PMG
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PMG's curator insight, January 28, 2014 10:38 PM

 operation of an auxin-GSL8 feedback circuit that regulates the level of plasmodesmal-localized callose in order to locally downregulate symplasmic permeability during hypocotyl tropic response. This system likely involves a plasmodesmal switch that would prevent the dissipation of a forming gradient by auxin diffusion through the symplasm. This regulatory system may represent a mechanism by which auxin could also regulate symplasmic delivery of a wide range of signaling agents.