Journal Club 2018

Monday, December 3rd, 2018
Sustainability and organic production: How information influences consumer’s expectation and preference for yogurt

It has been widely demonstrated that before purchasing or tasting a food product, consumers form expectations about the product based on its intrinsic quality (e.g. color, freshness) and associated information (e.g. brand name, health claim, local origin). These expectations, in turn, can affect consumer willingness to pay, flavor perception, and liking. Laureati et al. investigate this phenomenon by measuring blind, expected, and informed taste perception of organic and conventional yogurt. Led by Solveig Hanson, this week we’ll discuss the results of the study, their implications for flavor-focused plant breeding, and the strengths and limitations of this experimental design with regard to both internal validity and generalizability to a broader consumer population. Click here to access the article by Laureati et al. (2013).

Monday, November 26th, 2018
“Cover crops reduce nitrate leaching in agroecosystems”

Kate Ivancic will present Cover Crops Reduce Nitrate Leaching in Agroecosystems: A Global Meta-Analysis by Thapa et al. (2018). This paper presents a meta-analysis of cover crop leaching studies while accounting for climate, planting date, shoot biomass, cover crop species, management, and soil C and type. This analysis is wide enough in breadth to serve useful for crop breeders, while also providing applied cover crop management specifics useful for crop advisors and producers. When thinking about the goal of cover crops to reduced nitrate leaching in our agroecosystems, nitrate leaching measurements often have large variance due to spatial heterogeneity and measurement precision difficulty. This meta-analysis is a useful tool, helping readers to boil down the general trends across the literature and apply findings to their own systems. Click here to access the article by Thapa et al. (2018).

Monday, November 19th, 2018
France’s decade-old effort to slash pesticide use failed

A recent feature article in Science Magazine discusses France’s commitment to decreasing pesticide use, and a little on how they plan to do so. Join us for journal club to talk about the feasibility of these plans, and which ideas you think might be great, and which ideas are duds. Click here to access the Science article.

Since this article has a ~pest management~ theme, we also have *free* 2018 Wisconsin pest management guides for anyone who attends!

Monday, November 5th, 2018
Infusion of collaborative inquiry throughout a biology curriculum increases student learning: A four-year study of “Teams and Streams”

Join us at journal club this Monday where Katt Wigg will introduce the article: Infusion of collaborative inquiry throughout a biology curriculum increases student learning: A four-year study of “Teams and Streams” by Luckie et al. (2004). Students who take ownership for their learning by using techniques and procedures they’ve learned in lab to answer novel questions through experimentation perform better on measures of grad school readiness. How could plant science pedagogy be adapted to encourage inquiry-based learning? This will be a great journal club for anyone interested in learning, teaching, pedagogy, etc. Click here to access the article by Luckie et al. (2004).

Monday, October 29th, 2018
Special Journal Club: Professor Maria Finchk

Join us next Monday for a special journal club featuring visiting professor Maria Finchk from the University of Kassel in Germany. Professor Finchk has been doing research on the effects of diversification strategies on plant pathogens since 1986. Her academic interests are to understand population genetic and population ecological processes in plant-pathogen co-evolution. Of specific interest are the interrelations of the different levels of diversity from the microbial diversity of the rhizosphere, phyllosphere and endosphere up to intra-and interspecific diversity of plants and landscape aspects. A specific focus is on approaches to breeding for diversity and the effects of the agricultural system as a whole and specifically aspects of plant nutrition on host-pathogen interactions.

At journal club, she will present some of her latest work regarding effective population size in wheat as well as root system evolution and yield stability over 11 generations of selection of differentially bred (organic, conventional, baking, high yielding, hybrid, CCPs) wheat varieties. Click here to access the article by Bertholdsson et al. (2016). We’re very excited to welcome Professor Finchk to Journal Club!

Monday, December 10th, 2018
Lab Girl Journal Club

The last week of journal club this semester will be held on Monday where we will be discussing Lab Girl, a memoir by geobiologist, Hope Jahren. The book has been read by several council members and we felt it would be a great topic for journal club discussion. Please check this book out between now and then. It is a fairly quick read, not too dense (it made for great bedtime reading), but if you need something quick, check out the talks below. More details to come!

Monday, October 22nd, 2018
Population structure and gene flow of the tropical seagrass, Syringodium filiforme, in the Florida Keys and subtropical Atlantic region

Journal club will meet this Monday where Bridget will share a journal article titled Population structure and gene flow of the tropical seagrass, Syringodium filiforme, in the Florida Keys and subtropical Atlantic region.

Insights into the population dynamics of different species aids development of effective conservation strategies. In this study by Bijak et al., the researchers use species-specific microsatellite markers to examine genetic diversity and structure in tropical seagrass. They found patterns of gene flow and genetic diversity within and among populations consistent with expectations of early-successional species, patterns which are likely driven by ocean hydrology and historic continent arrangements. The common name of Syringodium filiform is manatee grass. Click here to access a video of a baby manatee. Click here to access the actual article by Bijak et al.

Monday, October 15th, 2018
Expense Reports Workshop

Expense reports. We all have to write them. Most of us have also messed them up more than a few times. Join us for a special journal club this Monday to learn how to do expense reports right.

Ellen and Amy have graciously agreed to give a graduate student e-reimbursement training. The online reimbursement system is upgrading and so there are new rules to consider. They’ll walk us through a sample expense report that you can keep in your files for future reference, review Expense Report changes and answer other travel related question. Please bring your laptop this week!

Monday, October 1st, 2018
A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitos

Join us next Monday for a special journal club with students from Nanjing Agricultural University in China! We’ll discuss a recent article published in Nature Biotech A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitos.

Gene drive technologies promise the ability to selectively alter natural populations, however, their use is complicated by a number of technical, ecological and ethical dilemmas. In this paper, the authors report successful disruption of the sex determination pathway in the human malaria vector A. gambiae by targeting the alternatively spliced gene doublesex. They also report rapid spread of a gene drive construct targeting this same sequence in a population of caged mosquitoes, which lead to complete population collapse. In contrast to simulation studies, they did not find evidence for selection of resistant alleles. Click here to access the article by Kyrou et al. (2018). And click here to access a related NPR article. 

Monday, September 24th, 2018
Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles

Join us this Monday when Charlene Grahn will lead a discussion on Asian ladybeetles! The Asian ladybeetle (Harmonia axyridis) will soon make its way into our homes as nighttime temperatures begin to drop. You likely know of these insects as the invasive orange ladybugs that leave unpleasant stains on your walls and curtains every fall, or the biological pest control reducing aphid populations in your greenhouse or field. You may have also been curious about why their spot patterns are so variable; the polymorphic nature of these spots has earned this species its status as one of the best model organisms for studying biological invasion genetics!

In the following article, the authors explore genetic mechanisms responsible for this dramatic variation in spot patterns using a genome-wide association study, linkage mapping, and gene expression analysis. Click here for access. By the end of Journal Club next Monday, you will be able to inform each Asian ladybeetle invading your home this fall of which alleles it possesses at its h locus! Your friends and family will surely be impressed as you assess the genetic diversity of the H. axyridis exoskeleton population they’ve accumulated on their windowsill!

Monday, September 17th, 2018
Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security

Next Monday we will discuss Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security by the folks at CIMMYT. From the authors: “Numerous publications have emphasized the importance of pre-breeding and gene bank use but seldom have made an effort practically. The present research elaborates the exhaustive efforts taken by SeeD (starting with 400,000 initial segregating pre-breeding lines) to bring in the untapped diversity of wheat exotics in gene bank into PBLs (pre-breeding lines)….the use of high-density genotyping, in combination with multi-location phenotyping for a set of agronomic and stress tolerance traits, enabled the quantification of significant and positive genomic contributions from exotic wheat germplasm to progenies of their three-way crosses with pairs of elite wheat lines.” Click here to access the article by Singh et al. (2018).

Join us to harness the power of coffee and cookies to motivate your Monday afternoon.

Monday, September 9th, 2018
Whatever moves you, make it a priority

Join us for Journal Club on where Maddy Olberg will be leading a discussion on a Science Careers article entitled “I find my inspiration in the outdoors. Whatever moves you, make it a priority.”

Come kick off the semester with a lively and unconventional Journal Club discussion of what motivates us and the healthy need for work-life balance. As Wisconsin and UW-Madison’s own John Muir, put it, “Wildness is a necessity.” Us plant people generally find solace and inspiration in the outdoors. We can use that to better ourselves AND our work/research. So let’s talk about it! Click here to access the article.

Monday, April 30th, 2018
Initiating maize pre-breeding programs using genomic-selection to harness polygenic variation from landrace population

Join us for the last Journal club of the semester tomorrow where Keo Corak will present an article by Gorjanc et al. (2016) titled “Initiating maize pre-breeding programs using genomic-selection to harness polygenic variation from landrace populations.”

Harnessing genetic diversity in maize landrace populations is an appealing strategy to increase the genetic variance of elite breeding populations. In this study, the authors use stochastic simulation to model different strategies for the initiation of pre-breeding programs with landrace populations. Analysis of several design factors, including genetic parameters of the founding population and logistical aspects of breeding, allow the study authors to develop decision-support trees that will be immediately valuable to programs interested in developing their own pre-breeding germplasm. Click here to access the article by Gorjanc et al. (2016).

Monday, April 23rd, 2018
From Teosinte to Maize: The Catastrophic Sexual Transmutation

Join your fellow grad students this Monday for the penultimate journal club of the semester! Brett Burdo will present “From Teosinte to Maize: The Catastrophic Sexual Transmutation” by Hugh H. Iltis. Come learn about a now catastrophically debunked theory of maize evolution. Click here to access the article by Iltis.

Monday, April 16th, 2018
A Y-encoded Suppressor of Feminization Arose via Lineage-specific Duplication of a Cytokinin Response Regulator in Kiwifruit

Join us at journal club this Monday for a discussion on the genetic basis of dioecy led by Andrew Maule. Dioecy, although the exception in the plant kingdom, has evolved independently in distinct lineages. For dioecious plants with heterogametic males carrying both X and Y chromosomes, one theoretical model describes a requirement for two mutations: a recessive mutation for male sterility, and a tightly-linked dominant gain-of-function female suppression factor, SuF. Despite independent origins, similar evolutionary tools are likely implicated in most cases of gain-of-function dominant SuF: genome duplication events followed by subfunctionalization of cis-regulatory sequences in cytokinin response regulator pathways.

Akagi et al. set out to fine map and functionally characterize the genetic basis of a suppressor of feminization in the genus Actinidia, which contains many dioecious species. Mapping the sex phenotype in an F1 interspecific cross, the authors were able to plot the phenotype to a 61-gene, 0.49Mb non-recombining region of the Y-chromosome. Subsequent transcriptome analysis on early development floral buds revealed two differentially expressed genes from the 61-gene region, with only one highly correlated with maleness. This gene, dubbed “Shy Girl”, or SyGl, encodes a type-C cytokinin response regulator. To functionally assess this gene, the authors transformed Arabidopsis thaliana and Nicotiana tabacum with transgenic SyGl under the control of its native promoter. They were able to suppress carpel development and maintain male fertility in both cases. Additionally, they were able to partially restore gynoecia development in male kiwifruit through exogenous application of synthetic cytokinin, adding further support to SyGl as a cytokinin response regulator.

In the end, the authors make a strong case for the genetic basis of female sterility in male kiwifruit individuals and support a paleopolyploid-derived genome duplication driving the evolution of this trait. Although they did not find SyGl to confer dioecy in other distinct plant lineages, they did postulate that other dioecious plants likely use a similar evolutionary toolkit to derive sex-determinism.  While they did not characterize the gene responsible for male infertility, they did lay the framework for uncovering the genetic basis of this trait in Actinidia. Click here to access the article by Akagi et al. (2018).

Monday April 2nd, 2018
Evidence for a mental health crisis in graduate education

Hope you all had a lovely and relaxing spring break. Ease back in to classes by joining your peers at Journal Club tomorrow. Kevin Coe will present a Nature article about mental health concerns among graduate students.

The authors of this article surveyed over 2,000 graduate students and found that the graduate student community has a considerable prevalence of individuals with anxiety and depression. Taken overall, the authors found that graduate students are more than six times likely to experience depression and anxiety than members of the general population. These results provide evidence of a mental health crisis in academia that must be addressed. Click here to access the article by Evans et al (2018).

Monday March 19th, 2018
Experience teaches plants to learn faster and forget slower in environments where it matters and Learning by Association in Plants

Next Journal Club will meet Monday where Lily Hislop will lead us in discussion of the articles “Experience teaches plants to learn faster and forget slower in environments where it matters” and “Learning by Association in Plants.”

The authors of these articles explore plants’ ability to “learn” and adapt to stimuli. They explore the question of how and where plants process information. The authors ultimately conclude that associated learning is a trait shared by animals and plants. Click here to listen to a recent feature on this topic on Radiolab.

Monday March 12th, 2018
Gamification of farmer-participatory priority setting in plant breeding: Design and validation of “AgroDuos”

Next Journal Club will meet Monday where Charlene Grahn will lead us in a discussion of the attached article: “Gamification of farmer-participatory priority setting in plant breeding: Design and validation of ‘AgroDuos.'” Please join us to discuss the benefits and drawbacks of this novel PPB method as well as the utility of gamification for enhancing all forms of citizen science!

Participatory plant breeding (PPB) enables breeders to efficiently allocate resources toward breeding goals that most matter to farmers while enhancing adoption of new varieties. However, PPB efforts are often limited by the need for involvement of skilled academic staff and funding for extrinsic incentives for participants. The authors of this paper discuss the creation, implementation, and efficacy of AgroDuos, a card game-like tool that leverages gamification principles to address these barriers to PPB efforts while producing statistically robust results.

Monday, March 5th, 2018
Many shades of gray: The context-dependent performance of organic agriculture

Journal Club will meet this Monday where Jamie Bugel will lead us in adiscussion about the context-dependent performance of organic agriculture.

A recent paper (attached) by Verena Seufert and Navin Ramankutty will guide ourconversation. In this review, the authors discuss the complex nature of what makes different farming practices sustainable or not. The review focuses on organic and conventional agriculture and what environments and social systems might make one practice more desirable than another. Overall, the authors state, understanding these complexities can help to inform policies to promote the most sustainable way to grow food for a growing population. Click here to access the article by Seufert and Ramankutty (2017).

Monday, February 26th, 2018
Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Grey skies and grey sidewalks and grey slush piles got you down? Join us at Journal Club next week where Maddy Olberg will lead us in a spring-y discussion about Flower Power and the use of Petunia as a model species. Click here to access the article by Bombarely et al. (2016). And click here to access the comment by van der Krol and Immink (2016).

Monday, February 19th, 2018
Soil microbiomes to suppress aboveground insect pests

Join us at Journal Club next Monday where Lindsay Chamberlain will discuss a recent opinion piece in Cell: “Steering Soil Microbiomes to Suppress Aboveground Insect Pests.” Click here to access the article by Pineda et al.

Monday, February 5th, 2018
Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing

Join us this Monday for the first journal club of the semester! We will discuss a recent article titled “Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing.” Visiting students from Nanjing Agriculture University will be joining our group so this should be a great opportunity to hear some new perspectives.

Our discussion this week will focus on mostly on the impact and significance of this article and less on the nitty-gritty details. So please come even if you didn’t have time to wade through everything; your insights and ideas will be valuable regardless! Click here to access the article by Rodriguez-Leal et al. And click here to access a short opinion piece on the topic.