Journal Club 2017

Monday, September 11, 2017
Mind the gap!

The PSGSC is very excited to kick off another semester of Journal Club, which will meet every Monday at noon to discuss scientific articles, popular press pieces, and topics of general interest. How can plant germplasm conservationists decide which genetic resources to preserve when future ecological and agricultural challenges are so unpredictable? Please join us this Monday to discuss a proposed solution to this problem in the article “A gap analysis methodology for collecting crop genepools: A case study with Phaseolus beans” by Julian Ramirez-Villegas and Colin Khoury.

Landraces, “obsolete” cultivars, and crop wild relatives are an invaluable source of genetic diversity for crop improvement efforts. Throughout history, plants of ostensibly little agricultural value have proven key in addressing new crop production challenges. However, there are significant economic, political, and technical challenges associated with the collection and maintenance of plant genetic resources. It is therefore imperative that ex situ plant collections be obtained with intention and maintained in a way that preserves genetic diversity efficiently. Gap analysis, a method commonly used in the context of wildlife conservation, is a potential model for guiding curation of plant germplasm collections. In this week’s article, gap analysis is implemented to identify taxonomic, geographic, and environmental gaps in a collection of wild Phaseolus (bean). This method is useful for prioritizing collection locations and quantifying the importance of maintaining specific accessions in a collection. Click here to access the article by Ramirez-Villegas et al.

Coffee and cookies will be provided to address any sampling gaps in your lunch!

Monday, April 10, 2017
Breeding “native” plants: Do ornamental plant breeders have a place in the native landscaping movement?

Join us Monday where Charlene Grahn will lead a discussion on the role of modern plant breeding in aesthetic native landscaping. Aesthetic landscaping using exotic ornamental plants has been shown to negatively affect the biodiversity of urban and suburban ecosystems at multiple trophic levels. Conservation groups have proposed the incorporation of native plant species in aesthetic landscaping installations as a solution to improve the ecological health of these environments. However, adoption of this practice is limited by the necessity for cost-effective production and marketability of plant material. It also relies upon production and distribution systems that limit genetic diversity within the plant populations being sold to consumers.

The review article by Wilde et al. discusses the potential of modern ornamental breeding techniques to address the barriers to adoption of native landscaping, and the problems these methods might raise in terms of altering plant ecological function. Click here to access the article by Wilde et al. The article by McKay et al. provides background information on considering the genetic structure of populations in plant conservation efforts when using plants that are not of local origin. Click here to access the article by McKay et al.

Coffee and cookies will serve the ecological function of increasing biodiversity of the plant scientist population within the journal club ecosystem!

Monday, April 3, 2017
Alternative energy: The Entner-Doudoroff pathway in plants

Join us this Monday where Eduardo D. Munaiz will lead a discussion on alternative plant glucose degradation pathways and their implications for plant physiology and evolutionary history.

The Entner–Doudoroff (ED) pathway is a glycolytic pathway of prokaryotic origin utilized by both cyanobacteria and plants that has been overshadowed in plant metabolic research by the more widespread Embden–Meyerhof–Parnas (EMP) and oxidative pentose phosphate (OPP) pathways. In Chen et al. (2016) the origins of the ED pathway are traced back through vascular and nonvascular plant lineage to discover the bacterial origin of this plant metabolic process. An experiment is also conducted to detect evidence of the ED pathway in barley. Click here to access the article by Chen et al.

Please feel free to digest the coffee and cookies provided at journal club using the metabolic pathways of your choice!

Monday, March 13, 2017
What’s that noise? “Measurements and the replication crisis”

Join us this Monday where Sarah Turner will lead a discussion on interpreting experimental data collected in noisy research settings. What exactly is the replication crisis? How do error and sample sizes influence effect sizes? What cautionary steps can we take to reduce error and avoid logical fallacies in research?

Research questions and insights are driven by the ability to detect a signal in the presence of noise. As a result, it is tempting to assume that measurement error reduces effect sizes, i.e. a significant effect under noisy conditions would be all the more significant in the absence of random variation. In their recent article, Loken and Gelman describe this reasoning in the context of a relatable scenario: “if you learned that a friend had run a mile in 5 minutes, you would be respectful; if you learned she had done it while carrying a heavy backpack, you would be awed. The obvious inference is that she would have been even faster without the backpack.”

Although the above logic seems intuitive, Loken and Gelman advocate against this reasoning in scientific research, citing it as a contributing factor to the replication crisis in science. They explain how significance in noisy research settings can be overestimated, especially when sample sizes are small, leading to overstated effects that misinform future studies.
Click here to access the article by Loken and Gelman.

Coffee and cookies will be provided to encourage a larger sample size at journal club!

Monday, February 27, 2017
Real bat pollinators manipulate artificial plant populations: Integrating in silico population genetics with animal behavior

Join us this Monday where Andrew Maule will lead a discussion on studying the cognition-mediated evolution of floral nectar rewards driven by Commissari’s long-tongued bat.

It is an evolutionary paradox that flowers pollinated by birds and bats tend to have low-sugar nectar. Behavioral studies show that bats preferentially favor nectar as sweet as 60% sugar content, however most plants produce nectar that is 18-23% sugar. Given the tight coevolution of flowers and their pollinators, one would expect that pollinator preference would  drive plants to produce high-sugar nectar rewards. Join us to discuss an intriguing experiment that uses radio-tagged bats, computer-controlled artificial ‘flowers’, and evolving in silico ‘genomes’ to explain this evolutionary phenomenon by observing floral evolution in real time. Topics of discussion will include the theory of psychometrics and perception of rewards, and how proportional processing can explain this phenomenon of stabilizing selection. Click here to access the popular press article by Ed Yong. And click here to access the Science article by Nachev et al.

Assuming Weber’s Law, coffee and cookies of a sufficient quality and quantity to attract plant science graduate students will be provided!

Monday, February 20, 2017
Toxic fruits: The role of plant scientists in addressing public health concerns

Join us this Monday where Chris D’Angelo will lead a discussion on breeding for reduced toxicity and the plight of the Lychee fruit.

Every summer since the mid 1990s children in India have been dying from a brain disorder called hypoglycemic encephalopathy. What do all these deaths have in common? Lychee fruit. Unripe lychee fruits contain high levels of two compounds, hypoglycin A and MCPA, both of which can cause hypoglycemia in under-nourished individuals. The findings reported by Shrivastava et al. in the public health journal, The Lancet, garnered international attention as the story was picked up by mainstream media outlets two weeks ago. This week we will talk about the role that breeders can play in reducing toxicity in crop plants and the importance of interdisciplinary research in solving complex problems. Click here to access the article by Shrivastava et al. Click here to access the article by Das et al. And click here to access the article by Isenberg et. al.

Coffee and cookies will be ripe for the taking!

Monday, February 13, 2017
Miscanthus x giganteus as a potential bioenergy crop

Join us this Monday where Kate Ivancic will lead a discussion on using perennial grasses to produce biofuel on marginal soils.

Miscanthus x giganteus has potential to be one of the great bioenergy grasses of our time. Changing soil salinity levels around the world propose a challenge to plant productivity and reduce arable acreage for commodity speciality crops. This paper explores the potential for M. giganteus production on marginal lands by quantifying the morphological, physiological, and biochemical responses of M. giganteus to different soil salinity levels over time. Join us for a thrilling discussion of  M. giganteus and the use of perennial grasses as bioenergy crops and phytoremediators as we venture into a future of uncertain soil conditions! Click here to access the article by Stavridou et al.

Coffee and cookies will be provided to fuel our discussion!

Monday, January 30, 2017
Contemporary Strategies for Crop Domestication

Join us this Monday where Jamie Bugel will lead a discussion on strategies for contemporary domestication of new crops, including a pipeline strategy for identifying wild species that show potential for domestication and using genomic selection to increase domestication efficiency. What advantages might domestication of novel crop species have over breeding to enhance performance of existing crops? How much can we expect molecular breeding techniques to shorten the timeline of crop domestication? What specific agricultural problems can we solve with novel crop domestication, and how can we identify the best plant to solve a particular problem?

Over the past centuries traditional crop breeding and domestication methods have fed the world’s growing populations. As breeding techniques advance, breeders are able to use more varied tools to develop edible crops that can both feed our population and maintain the integrity of agricultural land. In journal club this week we will discuss one possible approach to developing new crops using domestication and touch on the domestication and breeding techniques of intermediate wheatgrass or Kernza™ and what has been accomplished thus far with this particular perennial crop. Click here to access the article by DeHaan et al. And click here to access the article by Zhang et al.

Coffee and cookies will be provided to decrease the attrition rate of Journal Club through the Graduate Student Time Management Pipeline.

Monday, January 23, 2017
Biological control of crop pests

Join us on Monday for the first meeting of Journal Club of 2017, where Charlene Grahn will lead a discussion on the potential of extrafloral nectar and volatile organic compounds as breeding targets for enhancing the biological control of crop pests. How might the efficacy of biological control methods be precisely quantified? Can substantial enhancement of biological control methods realistically be achieved through plant breeding? How would a widespread adoption of biological control methods change the agricultural landscape nationally and internationally?

Biological pest control has proven successful in some perennial cropping systems and greenhouse environments by exploiting tri-trophic interactions between a host plant, an herbivorous pest, and the pest’s natural enemy (i.e. a predator, parasitoid, or insecticidal pathogen). Plant-produced volatile organic compounds and nectar rewards function in these interactions to increase the apparency and attractiveness of plant hosts to the pest’s natural enemy. Plant breeding and agricultural management practices have unintentionally decreased the ability of many crops to engage in tritrophic interactions, however the potential for enhancing these interactions through plant breeding by exploiting variability in plant-produced volatile organic compounds and nectar reward production has been explored only minimally. In this opinion article, the authors discuss potential breeding strategies for enhancing the efficacy and feasibility of biological control methods as well as some obstacles and risks that such breeding efforts might entail. Please click here to access the article by Stenberg et al.

Coffee and cookies will be provided to enhance the apparency and attractiveness of Journal Club to plant science graduate students.